();
-
- /** Default location (endpoint) of a Moby registry. */
- public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
-
- /** Default namespace used by the contacted Moby registry. */
- public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
-
- /**
- * The META-INF resource file that will be checked to determine what
- * default class should be instantiated in order to create a Central Implementation
- * when getDefaultCentral() is called.
- */
- public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
- /** The class to use for getDefaultCentral if all else fails */
- public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
- private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
-
- /**
- * Thread local that gives each thread its own
- * DocumentBuilderFactory (since it is not thread-safe). Code taken
- * from Apache's JaxpUtils.
- */
- public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
- protected synchronized Object initialValue() {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware (true);
- return dbf;
- }
- };
-
-
- /*************************************************************************
- * Default constructor. It connects to a default Moby registry
- * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
- * (as defined int {@link #DEFAULT_NAMESPACE}).
- *************************************************************************/
- public CentralImpl()
- throws MobyException {
- this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
- }
-
- /*************************************************************************
- * Constructor allowing to specify which Moby Registry to use.
- *
- * @throws MobyException if 'endpoint' is not a valid URL, or if no
- * DOM parser is available
- *************************************************************************/
- public CentralImpl (String endpoint)
- throws MobyException {
- this (endpoint, DEFAULT_NAMESPACE);
- }
-
- /*************************************************************************
- * Constructor allowing to specify which Moby Registry and what
- * namespace to use. If any of the parameters is null, its default
- * value is used instead.
- *
- * @throws MobyException if 'endpoint' is not a valid URL, or if no
- * DOM parser was found
- *************************************************************************/
- public CentralImpl (String endpoint, String namespace)
- throws MobyException {
-
- if (endpoint == null || "".equals (endpoint.trim()))
- endpoint = DEFAULT_ENDPOINT;
- if (namespace == null || "".equals (namespace.trim()))
- namespace = DEFAULT_NAMESPACE;
-
- try {
- this.endpoint = new URL (endpoint);
- } catch (MalformedURLException e) {
- throw new MobyException ("Bad URL: " + endpoint);
- }
- this.uri = namespace;
-
- cache = new Hashtable();
- useCache = true;
- }
-
- /*************************************************************************
- * Loads a DOM Document from an InputStream. Uses thread-safe
- * mechanism.
- *************************************************************************/
- public static Document loadDocument (InputStream input)
- throws MobyException {
- try {
- DocumentBuilderFactory dbf
- = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
- DocumentBuilder db = dbf.newDocumentBuilder();
- return (db.parse (input));
- } catch (Exception e) {
- throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
- }
- }
-
- /*************************************************************************
- * Call 'method' with 'parameters' and return its result.
- *************************************************************************/
- protected Object doCall (String method, Object[] parameters)
- throws MobyException {
-
- Call call = null;
- try {
- Service service = new Service();
- call = (Call) service.createCall();
- call.setTargetEndpointAddress (endpoint);
- call.setTimeout (new Integer (0));
-
- call.setSOAPActionURI (uri + "#" + method);
-
- if (debug) {
- System.err.println ("METHOD CALL: " + method);
- System.err.println ("------------");
- if (parameters.length > 0)
- System.err.println (parameters[0] + "\n");
- System.err.println ("------------\n");
-
- Object result = call.invoke (uri, method, parameters);
-
- System.err.println ("METHOD RETURN:");
- System.err.println ("------------");
- if (result != null)
- System.err.println (result + "\n");
- System.err.println ("------------\n");
-
- return resultToString (result);
-
- } else {
- return resultToString (call.invoke (uri, method, parameters));
- }
-
- } catch (AxisFault e) {
- throw new MobyException
- (formatFault (e,
- endpoint.toString(),
- (call == null ? null : call.getOperationName())),
- e);
-// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
-
- } catch (Exception e) {
- throw new MobyException (e.toString(), e);
-// e.printStackTrace();
- }
- }
-
-
- /**************************************************************************
- * Parse the given XML sniplet to find tag 'success'. If it has value '1'
- * look further for tag 'id' and return it back (or return an empty string
- * if ID is not there). Otherwise raise an exception with the 'culprit'
- * and with the message from the tag 'message'.
- *
- * The return value is a two-element long array. The first element
- * is the ID (given by BioMobe registry), and the second element
- * is RDF corresponding with the registered object (BioMoby
- * returns this only for service instances, so for other objects
- * this will be null).
- *
- * This is how the XML is supposed to look:
- *
- *
- *
- *
- *
- *
- *
- * Success takes the value "1" to indicate success, "0" to
- * indicate failure, and "-1" to indicate "Pending Curation".
- *************************************************************************/
- protected String[] checkRegistration (String xml, Object culprit)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String id = "", success = "0", message = "", rdf = "";
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
- Element root = document.getDocumentElement();
-
- NodeList children = root.getChildNodes();
- for (int i = 0; i < children.getLength(); i++) {
- if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
- continue;
- Element elem = (Element)children.item (i);
- if (elem.getNodeName().equals ("id")) {
- if (elem.getFirstChild() != null)
- id = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals("success")) {
- if (elem.getFirstChild() != null)
- success = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals ("message")) {
- if (elem.getFirstChild() != null)
- message = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals ("RDF")) {
- if (elem.getFirstChild() != null)
- rdf = elem.getFirstChild().getNodeValue();
- }
- }
-
- if (success.equals ("0"))
- throw new NoSuccessException (message, culprit);
- else if (success.equals ("-1"))
- throw new PendingCurationException();
- return new String[] { id, rdf };
- }
-
- /**************************************************************************
- * Return a piece of XML created from the definitions representing input
- * data types and their usage in the given service. Only data considered
- * primary are included. Note that the main job of converting to XML is
- * done by instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- *
- *************************************************************************/
- protected String buildSecondaryInputTag (MobyService service) {
- StringBuffer buf = new StringBuffer();
- MobyData[] secInputs = service.getSecondaryInputs();
- buf.append ("\n");
- for (int i = 0; i < secInputs.length; i++) {
- buf.append (secInputs[i].toXML());
- }
- buf.append (" \n");
- return new String (buf);
- }
-
- /**************************************************************************
- * Return a piece of XML created from the definitions representing output
- * data types and their usage in the given service. Only data considered
- * primary are included. Note that the main job of converting to XML is
- * done by instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- *
- *
- *************************************************************************/
- protected String buildOutputTag (MobyService service) {
- StringBuffer buf = new StringBuffer();
- MobyData[] primaryOutputs = service.getPrimaryOutputs();
- buf.append ("\n");
- for (int i = 0; i < primaryOutputs.length; i++)
- buf.append (primaryOutputs[i].toXML());
- buf.append (" \n");
- return new String (buf);
- }
-
- /**************************************************************************
- * Return a piece of XML represented a query object (an object used
- * to find a service).
- *
- * The returned XML looks like this:
- *
- *
- *
- *
- *
- *
- *
- *
- * ServiceTypeTerm
- * ServiceName
- * moby
- * http://desired.service.provider ;
- * 1|0
- * 1|0
- * 1|0
- *
- * something
- * ....
- * ....
- *
- *************************************************************************/
- protected String buildQueryObject (MobyService service,
- String[] keywords,
- boolean expandObjects,
- boolean expandServices,
- boolean authoritative) {
- if (service == null) {
- service = new MobyService ("dummy");
- service.setCategory ("");
- }
- StringBuffer buf = new StringBuffer();
-
- buf.append ("\n \n");
-
- buf.append ("\n\n");
- MobyData[] po = service.getPrimaryOutputs();
- if (po.length > 0) {
- for (int i = 0; i < po.length; i++)
- buf.append (po[i].toXML());
- }
- buf.append (" \n \n");
-
- buf.append ("" + service.getType() + " \n");
-
- String name = service.getName();
- if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
- buf.append ("" + service.getName() + " \n");
-
- String sigURL = service.getSignatureURL();
- if (!sigURL.equals (""))
- buf.append ("" + sigURL + " \n");
-
- buf.append ("" + service.getCategory() + " \n");
- buf.append ("" + service.getAuthority() + " \n");
-
- buf.append ("");
- buf.append (expandObjects ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("");
- buf.append (expandServices ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("");
- buf.append (authoritative ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("\n");
- if (keywords != null && keywords.length > 0) {
- for (int i = 0; i < keywords.length; i++) {
- buf.append ("");
- buf.append (keywords[i]);
- buf.append (" \n");
- }
- }
- buf.append (" \n");
-
- return new String (buf);
- }
-
- /**************************************************************************
- * Extract one or more MobyService objects from the given XML piece.
- * The XML should look like this:
- *
- * <Services>
- * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
- * <serviceType>Service_Ontology_Term</serviceType>
- * <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
- * <contactEmail>your at email.addy.here</contactEmail>
- * <signatureURL>http://service.RDF.here</signatureURL>
- * <URL>http://service.endpoint.here/scriptname</URL>
- * <authoritative>1</authoritative>
- * <Input>
- * <!-- one or more Simple and/or Complex Primary articles -->
- * </Input>
- * <Output>
- * <!-- one or more Simple and/or Complex Primary articles -->
- * </Output>
- * <secondaryArticles>
- * <!-- one or more Secondary articles -->
- * </secondaryArticles>
- * <Description><![CDATA[free text description here]]></Description>
- * </Service>
- * ... <!-- one or more Service blocks may be returned -->
- * ...
- * ...
- * </Services>
- *
- * @throws MobyException if the XML document is invalid
- *************************************************************************/
- public MobyService[] extractServices (String xml)
- throws MobyException {
-
- Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
- NodeList list = document.getElementsByTagName ("Service");
- MobyService[] results = new MobyService [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyService service = new MobyService (elem.getAttribute ("serviceName"));
- service.setAuthority (elem.getAttribute ("authURI"));
- service.setLSID (elem.getAttribute ("lsid"));
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("Description")) {
- service.setDescription (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("Category")) {
- service.setCategory (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("URL")) {
- service.setURL (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("signatureURL")) {
- service.setSignatureURL (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("contactEmail")) {
- service.setEmailContact (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("serviceType")) {
- service.setType (getFirstValue (children.item (j)));
- MobyServiceType mst = new MobyServiceType(service.getType());
- NamedNodeMap map = (children.item (j).getAttributes());
- if (map != null) {
- Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
- if (node != null)
- mst.setLSID(node.getNodeValue());
- }
- service.setServiceType(mst);
- } else if (nodeName.equals ("authoritative")) {
- String authoritative = getFirstValue (children.item (j));
- service.setAuthoritative (authoritative.equals ("1") ? true : false);
- } else if (nodeName.equals ("Input")) {
- //
- // ...
- //
- //
- // ......
- // ......
- //
- //
- NodeList inputs = children.item (j).getChildNodes();
- for (int k = 0; k < inputs.getLength(); k++) {
- if (inputs.item (k).getNodeName().equals ("Simple")) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
- service.addInput (data);
- } else if (inputs.item (k).getNodeName().equals ("Collection")) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
- service.addInput (data);
- }
- }
- } else if (nodeName.equals ("Output")) {
- //
- //
- //
- NodeList inputs = children.item (j).getChildNodes();
- for (int k = 0; k < inputs.getLength(); k++) {
- if (inputs.item (k).getNodeName().equals ("Simple")) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
- service.addOutput (data);
- } else if (inputs.item (k).getNodeName().equals ("Collection")) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
- service.addOutput (data);
- }
- }
-
- } else if (nodeName.equals ("secondaryArticles")) {
- //
- // ...
- //
- NodeList parameters = children.item (j).getChildNodes();
- for (int k = 0; k < parameters.getLength(); k++) {
- if (parameters.item (k).getNodeName().equals ("Parameter")) {
- MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
- service.addInput (data);
- }
- }
- }
- }
- results [i] = service;
- }
- return results;
- }
-
- // protect against null values
- protected String getFirstValue (Node child) {
- Node node = child.getFirstChild();
- if (node == null) return "";
- String value = node.getNodeValue();
- if (value == null) return "";
- return value;
- }
-
- protected String getFirstValue (NodeList children) {
- if (children.item(0) != null && children.item(0).hasChildNodes()) {
- children.item(0).normalize();
- return getFirstValue (children.item(0));
- }
- return "";
- }
-
- /**************************************************************************
- *
- * Implementing SimpleCache interface.
- *
- * Why to have an interface for such trivial thing? Well, because
- * I needed to overwrite the caching mechanism in the subclasses
- * so I needed to have all caching functions as separate methods -
- * that's why I have collect them in an interface.
- *
- *************************************************************************/
- private Hashtable cache; // this is the cache itself
- private boolean useCache; // this signal that we are actually caching things
-
- // not used here
- public String createId (String rootName,
- String semanticType, String syntaxType,
- long lastModified,
- Properties props) {
- return ""; // not used here
- }
-
- // check existence of a cached object
- public boolean existsInCache (String id) {
- synchronized (cache) {
- if (useCache) return cache.containsKey (id);
- else return false;
- }
- }
-
- // retrieve from cache
- public Object getContents (String id) {
- synchronized (cache) {
- if (useCache) return cache.get (id);
- else return null;
- }
- }
-
- // cache an object
- public void setContents (String id, java.lang.Object data) {
- synchronized (cache) {
- if (useCache) cache.put (id, data);
- }
- }
-
- // in this implementation, it clears the whole cache, regardless
- // what 'id' is passed
- public void removeFromCache (String id) {
- cache.clear();
- }
-
- /**************************************************************************
- *
- * And the other methods related to caching (but not part of the
- * SimpleCache interface).
- *
- **************************************************************************/
-
- /**************************************************************************
- * By default, caching is enabled to reduce network traffic.
- * Setting this to false will clear the cache, and not cache any
- * further calls unless it is set to true again.
- *
- * @param shouldCache whether retrieveXXX call results should be
- * cached in case they are called again (i.e. don't request
- * MobyCentral every time)
- **************************************************************************/
- public void setCacheMode (boolean shouldCache) {
- useCache = shouldCache;
- if (! useCache)
- removeFromCache (null);
- }
-
- /**************************************************************************
- * Find if caching is currently enabled.
- *
- * @return true if caching is enabled
- **************************************************************************/
- public boolean getCacheMode(){
- return useCache;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceNames>
- * <serviceName name="serviceName" authURI='authority.info.here'/>
- * ...
- * ...
- * </serviceNames>
- *
- *
- * @deprecated Replaced by {@link
- * #getServiceNamesByAuthority}. The reason is that this method
- * returns a random result if there are more services with the
- * same name but belonging to different authorities.
- *
- *************************************************************************/
- public Map getServiceNames()
- throws MobyException {
-
- String result = (String)doCall ("retrieveServiceNames",
- new Object[] {});
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceName");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- results.put (elem.getAttribute ("name"),
- elem.getAttribute ("authURI"));
- }
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceNames>
- * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
- * ...
- * ...
- * </serviceNames>
- *
- *
- * @return a Map which has authorities as keys, and String arrays
- * with service names as a values.
- *************************************************************************/
- public Map getServiceNamesByAuthority()
- throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML (result, true);
- }
-
- /**************************************************************************
- * Similar to {@link #getServiceNamesByAuthority} but the
- * resulting Map contains slightly more.
- *
- * @return a Map which has authorities as keys, and arrays of
- * MobyServices as a values. Each MobyService is filled with its
- * name, authority and LSID.
- *************************************************************************/
- public Map getServicesByAuthority()
- throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML (result, false);
- }
-
- //
- protected String getServiceNamesByAuthorityAsXML()
- throws MobyException {
- return (String)doCall ("retrieveServiceNames",
- new Object[] {});
- }
-
- // if onlyNames == true
- // Map: authority name -> String[]
- // (filled with service namea)
- // else
- // Map: authority name -> MobyService[]
- // (filled with service name, authority and lsid)
- protected Map createServicesByAuthorityFromXML (String result,
- boolean onlyNames)
- throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceName");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String name = elem.getAttribute ("name");
- String auth = elem.getAttribute ("authURI");
- Vector v =
- (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
- if (onlyNames) {
- v.addElement (name);
- } else {
- MobyService ms = new MobyService (name);
- ms.setAuthority (auth);
- ms.setLSID (elem.getAttribute ("lsid"));
- v.addElement (ms);
- }
- results.put (auth, v);
- }
-
- // change values of type Vector to MobyService[] or String[]
- for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = (Map.Entry)it.next();
- Vector v = (Vector)entry.getValue();
- if (onlyNames) {
- String[] sNames = new String [v.size()];
- v.copyInto (sNames);
- entry.setValue (sNames);
- } else {
- MobyService[] mss = new MobyService [v.size()];
- v.copyInto (mss);
- entry.setValue (mss);
- }
- }
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceProviders>
- * <serviceProvider name="authority.URI.here"/>
- * ...
- * ...
- * </serviceProviders>
- *
- *************************************************************************/
- public String[] getProviders()
- throws MobyException {
-
- String cacheId = "retrieveServiceProviders";
- String[] cachedResults = (String[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result = (String)doCall ("retrieveServiceProviders",
- new Object[] {});
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceProvider");
- String[] results = new String [list.getLength()];
- for (int i = 0; i < list.getLength(); i++)
- results[i] = ((Element)list.item (i)).getAttribute ("name");
-
- // Add this data to the cache in case we get called again
- setContents (cacheId, results);
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceTypes>
- * <serviceType name="serviceName" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * <contactEmail>...</contactEmail>
- * <authURI>...</authURI>
- * </serviceType>
- * ...
- * ...
- * </serviceTypes>
- *
- *************************************************************************/
- public Map getServiceTypes()
- throws MobyException {
- String result = getServiceTypesAsXML();
- Map results = new TreeMap (getStringComparator());
- MobyServiceType[] types = createServiceTypesFromXML (result);
- for (int i = 0; i < types.length; i++) {
- results.put (types[i].getName(),
- types[i].getDescription());
- }
- return results;
- }
-
- //
- protected String getServiceTypesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveServiceTypes",
- new Object[] {});
- }
-
- // but be aware that the created MobyServiceTypes are not complete
- // - they do not have the relationship information; that's why
- // this method is not public; the full service types are available
- // from CentralDigest implementations
- protected MobyServiceType[] createServiceTypesFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceType");
- if (list == null || list.getLength() == 0)
- return new MobyServiceType[] {};
- MobyServiceType[] results = new MobyServiceType [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
- st.setLSID (elem.getAttribute ("lsid"));
- st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
- st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
- st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
- results[i] = st;
- }
- java.util.Arrays.sort (results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <Namespaces>
- * <Namespace name="namespace" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * <contactEmail>...</contactEmail>
- * <authURI>...</authURI>
- * </Namespace>
- * ...
- * ...
- * </Namespaces>
- *
- *************************************************************************/
- public MobyNamespace[] getFullNamespaces()
- throws MobyException {
-
- String result = getNamespacesAsXML();
- return createNamespacesFromXML (result);
- }
-
- //
- protected String getNamespacesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveNamespaces",
- new Object[] {});
- }
-
- //
- protected MobyNamespace[] createNamespacesFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
- if (list == null || list.getLength() == 0) {
- return new MobyNamespace[] {};
- }
- MobyNamespace[] results = new MobyNamespace [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
- nm.setLSID (elem.getAttribute ("lsid"));
- nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
- nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
- nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
- results[i] = nm;
- }
-
- java.util.Arrays.sort (results);
- return results;
- }
-
- /**************************************************************************
- *
- * @deprecated Replaced by {@link #getFullNamespaces} that gives
- * more information for the same price.
- *************************************************************************/
- public Map getNamespaces()
- throws MobyException {
-
- Map results = new TreeMap (getStringComparator());
- MobyNamespace[] namespaces = getFullNamespaces();
- for (int i = 0; i < namespaces.length; i++) {
- results.put (namespaces[i].getName(),
- namespaces[i].getDescription());
- }
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <objectNames>
- * <Object name="objectName" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * </Object>
- * ...
- * ...
- * </objectNames>
- *
- *************************************************************************/
- public Map getDataTypeNames()
- throws MobyException {
- String result = getDataTypeNamesAsXML();
- return createDataTypeNamesFromXML (result, true);
- }
-
- //
- protected String getDataTypeNamesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveObjectNames",
- new Object[] {});
- }
-
- // if onlyNames == true
- // Map: data type name -> description (String)
- // else
- // Map: data type name -> MobyDataType[]
- // (filled with name, description, and lsid)
- protected Map createDataTypeNamesFromXML (String result,
- boolean onlyNames)
- throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Object");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String name = elem.getAttribute ("name");
- if (name == null)
- continue; // ignore no-named data types
- String desc = "";
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("Description")) {
- desc = getFirstValue (children.item (j));
- break;
- }
- }
- if (onlyNames) {
- results.put (name, desc);
- } else {
- MobyDataType dt = new MobyDataType (name);
- dt.setDescription (desc);
- dt.setLSID (elem.getAttribute ("lsid"));
- results.put (name, dt);
- }
- }
- return results;
- }
-
-
- /**************************************************************************
- * Parses and imports the following XML. An example:
- *
- *
- * <retrieveObjectDefinition>
- * <objectType lsid="...">go_term</objectType>
- * <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
- * <authURI>http://www.illuminae.com</authURI>
- * <contactEmail>markw at illuminae.com</contactEmail>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType articleName=''>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
- * <objectType articleName='Term'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType articleName='Definition'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:has'>
- * <objectType articleName='Problems'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType articleName='Issues'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * </Relationship>
- * </retrieveObjectDefinition>
- *
- *************************************************************************/
- public MobyDataType getDataType (String dataTypeName)
- throws MobyException, NoSuccessException {
-
- String result = getDataTypeAsXML (dataTypeName);
- return createDataTypeFromXML (result, dataTypeName);
- }
-
- public MobyDataType[] getDataTypes()
- throws MobyException, NoSuccessException {
- Map datatypeMap = getDataTypeNames();
- MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
- int i = 0;
- for(String dataTypeName: datatypeMap.keySet()){
- datatypes[i++] = getDataType(dataTypeName);
- }
- return datatypes;
- }
-
- protected String getDataTypeAsXML (String dataTypeName)
- throws MobyException, NoSuccessException {
-
- return (String)doCall ("retrieveObjectDefinition",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- " "
- });
- }
-
- protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
- throws MobyException, NoSuccessException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
- NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
- if (list == null || list.getLength() == 0)
- throw new NoSuccessException ("Data Type name was not found.",
- dataTypeName);
- MobyDataType data = null;
- Element elem = (Element)list.item (0);
- NodeList children = elem.getChildNodes();
-
- // first find the "real" (LSID-ized) data type name
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("objectType")) {
- data = new MobyDataType (getFirstValue (children.item (j)));
- data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
- break;
- }
- }
-
- // if not found (unprobable) use the name given by the caller
- if (data == null)
- data = new MobyDataType (dataTypeName);
-
- // now fill the data type object with the rest of attributes
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("Description")) {
- data.setDescription (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("authURI")) {
- data.setAuthority (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("contactEmail")) {
- data.setEmailContact (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("Relationship")) {
- String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
- if (relationshipType.endsWith ("isa")) {
-
- NodeList parents = children.item (j).getChildNodes();
- for (int k = 0; k < parents.getLength(); k++) {
- if (parents.item (k).getNodeName().equals ("objectType")) {
- data.addParentName (getFirstValue (parents.item (k)));
- }
- }
- } else if (relationshipType.endsWith ("hasa")) {
-
- NodeList belows = children.item (j).getChildNodes();
- for (int k = 0; k < belows.getLength(); k++) {
- if (belows.item (k).getNodeName().equals ("objectType")) {
- data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
- getFirstValue (belows.item (k)),
- Central.iHASA );
- }
- }
- } else if (relationshipType.endsWith ("has")) {
-
- NodeList belows = children.item (j).getChildNodes();
- for (int k = 0; k < belows.getLength(); k++) {
- if (belows.item (k).getNodeName().equals ("objectType")) {
- data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
- belows.item (k).getFirstChild().getNodeValue(),
- Central.iHAS );
- }
- }
- }
- }
- }
- return data;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getServiceWSDL (String serviceName)
- throws MobyException, NoSuccessException {
-
- Map names = getServiceNames();
-
- for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = (Map.Entry)it.next();
- if ( ((String)entry.getKey()).equals (serviceName) )
- return getServiceWSDL (serviceName, (String)entry.getValue());
- }
-
- throw new NoSuccessException ("Service not found.", serviceName);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getServiceWSDL (String serviceName, String authority)
- throws MobyException, NoSuccessException {
-
- String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
- String cachedResults = (String)getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("retrieveService",
- new Object[] {
- "" +
- " "
- });
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- Element service = document.getDocumentElement();
- Node wsdl = service.getFirstChild();
- if (wsdl == null)
- throw new NoSuccessException ("Service not found OR WSDL is not available.",
- serviceName + " (" + authority + ")");
-
- String results = wsdl.getNodeValue();
- setContents (cacheId, results);
- return results;
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterDataTypeXML (MobyDataType dataType) {
-
- // build the ISA tag (expressing hierarchy of data types)
- String[] names = dataType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < names.length; i++) {
- buf.append ("");
- buf.append (names[i]);
- buf.append (" ");
- buf.append ("\n");
- }
-
- // build the HASA/HAS tags (expressing containments of data types)
- MobyRelationship[] children = dataType.getChildren();
- StringBuffer buf2 = new StringBuffer(); // for HASA
- StringBuffer buf3 = new StringBuffer(); // for HAS
- for (int i = 0; i < children.length; i++) {
- if (children[i].getRelationshipType() == Central.iHASA) {
- buf2.append ("");
- buf2.append (children[i].getDataTypeName());
- buf2.append (" ");
- } else if (children[i].getRelationshipType() == Central.iHAS) {
- buf3.append ("");
- buf3.append (children[i].getDataTypeName());
- buf3.append (" ");
- }
- }
-
- return
- "" +
- "" + dataType.getName() + " " +
- "" +
- " " +
- "" + new String (buf) +
- " " +
- "" + new String (buf2) +
- " " +
- "" + new String (buf3) +
- " " +
- "" + dataType.getAuthority() + " " +
- "" + dataType.getEmailContact() + " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerDataType (MobyDataType dataType)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerObjectClass",
- new Object[] { getRegisterDataTypeXML (dataType) });
- dataType.setId (checkRegistration (result, dataType)[0]);
- }
-
- /*************************************************************************
- * B
- *************************************************************************/
- public void unregisterDataType (MobyDataType dataType)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterObjectClass",
- new Object[] {
- "" +
- "" + dataType.getName() + " " +
- " "
- });
- checkRegistration (result, dataType);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
-
- // build the ISA tag (expressing hierarchy of service types)
- String[] names = serviceType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < names.length; i++) {
- buf.append ("");
- buf.append (names[i]);
- buf.append (" ");
- buf.append ("\n");
- }
-
- return
- "" +
- "" + serviceType.getName() + " " +
- "" + serviceType.getEmailContact() + " " +
- "" + serviceType.getAuthority() + " " +
- "" +
- " " +
- "" + new String (buf) +
- " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerServiceType (MobyServiceType serviceType)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerServiceType",
- new Object[] { getRegisterServiceTypeXML (serviceType) });
- serviceType.setId (checkRegistration (result, serviceType)[0]);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterServiceType (MobyServiceType serviceType)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterServiceType",
- new Object[] {
- "" +
- "" + serviceType.getName() + " " +
- " "
- });
- checkRegistration (result, serviceType);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterNamespaceXML (MobyNamespace namespace) {
- return
- "" +
- "" + namespace.getName() + " " +
- "" + namespace.getEmailContact() + " " +
- "" + namespace.getAuthority() + " " +
- "" +
- " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerNamespace (MobyNamespace namespace)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("registerNamespace",
- new Object[] { getRegisterNamespaceXML (namespace) });
- namespace.setId (checkRegistration (result, namespace)[0]);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterNamespace (MobyNamespace namespace)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterNamespace",
- new Object[] {
- "" +
- "" + namespace.getName() + " " +
- " "
- });
- checkRegistration (result, namespace);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterServiceXML (MobyService service) {
- return
- "" +
- "" + service.getCategory() + " " +
- "" + service.getName() + " " +
- "" + service.getType() + " " +
- "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
- "" + service.getAuthority() + " " +
- "" + escapeXML (service.getSignatureURL()) + " " +
- "" + escapeXML (service.getURL()) + " " +
- "" + service.getEmailContact() + " " +
- "" + (service.isAuthoritative() ? "1" : "0") + " " +
- "" +
- " " +
- buildPrimaryInputTag (service) +
- buildSecondaryInputTag (service) +
- buildOutputTag (service) +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerService (MobyService service)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerService",
- new Object[] { getRegisterServiceXML (service) });
- String[] registered = checkRegistration (result, service);
- service.setId (registered [0]);
- service.setRDF (registered [1]);
- String pathToRDF = service.getPathToRDF();
- if ( ! pathToRDF.equals ("") ) {
- File fileRDF = new File (pathToRDF);
- try {
- PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
- fileout.println (registered [1]);
- fileout.close();
- } catch (IOException e) {
- StringBuffer buf = new StringBuffer (100);
- buf.append ("Failed to save RDF in '");
- buf.append (fileRDF.getAbsolutePath() + "'. ");
- buf.append (e.toString());
- try {
- File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
- PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
- fileout.println (registered [1]);
- fileout.close();
- buf.append ("\nReturned RDF file was therefore stored in: ");
- buf.append (tmpFile.getAbsolutePath());
- } catch (IOException e2) {
- buf.append ("\nEven saving in a temporary file failed: ");
- buf.append (e2.toString());
- }
- throw new MobyException (buf.toString());
- }
- }
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterService (MobyService service)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterService",
- new Object[] {
- "" +
- "" + service.getAuthority() + " " +
- "" + service.getName() + " " +
- " "
- });
- checkRegistration (result, service);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (String serviceType)
- throws MobyException {
- if (serviceType == null)
- return new MobyService[] {};
- MobyService pattern = new MobyService ("dummy");
- pattern.setCategory ("");
- pattern.setType (serviceType);
- return findService (pattern, null);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (String[] keywords)
- throws MobyException {
- if (keywords == null)
- return new MobyService[] {};
- return findService (null, keywords);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (MobyService pattern)
- throws MobyException {
- if (pattern == null)
- return new MobyService[] {};
- return findService (pattern, null);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (MobyService pattern, String[] keywords)
- throws MobyException {
- return findService (pattern, keywords, true, true);
- }
-
- /**************************************************************************
- * All 'findService' methods end up here.
- *************************************************************************/
- public MobyService[] findService (MobyService pattern, String[] keywords,
- boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes)
- throws MobyException {
- if (pattern == null) {
- pattern = new MobyService ("dummy");
- pattern.setCategory ("");
- }
-
- String result =
- getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
- MobyService[] services = extractServices (result);
- return services;
- }
-
- // ...actually all 'findService' methods end up here
- protected String getServicesAsXML (MobyService pattern, String[] keywords,
- boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes)
- throws MobyException {
- String[] query = new String[] {
- "" +
- buildQueryObject (pattern, keywords,
- includeParentDataTypes,
- includeChildrenServiceTypes,
- false) +
- " "
- };
- return (String)doCall ("findService", query);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String call (String methodName, String inputXML)
- throws MobyException {
- Object result;
- if (inputXML == null || inputXML.equals (""))
- result = doCall (methodName, new Object[] { });
- else
- result = doCall (methodName, new Object[] { inputXML });
- return (String)result;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- protected static String resultToString (Object result)
- throws MobyException {
- if (result == null)
- throw new MobyException ("Returned result is null.");
- if (result instanceof String)
- return (String)result;
- if (result instanceof String[]) {
- String[] tmp = (String[])result;
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < tmp.length; i++)
- buf.append (tmp[i]);
- return new String (buf);
- }
- if (result instanceof byte[])
- return new String ((byte[])result);
-
- throw new MobyException ("Unknown type of result: " + result.getClass().getName());
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public boolean setDebug (boolean enabled) {
- boolean oldMode = debug;
- debug = enabled;
- return oldMode;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
- * <serviceType>urn:lsid:biomoby.org:servicetype:analysis</serviceType>
- * <serviceType>urn:lsid:biomoby.org:servicetype:service</serviceType>
- * </Relationship>
- * </Relationships>
- *
- *************************************************************************/
- public String[] getServiceTypeRelationships (String serviceTypeName,
- boolean expand)
- throws MobyException {
- String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
- return createServiceTypeRelationshipsFromXML (result);
- }
-
- //
- protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
- boolean expand)
- throws MobyException {
- return
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + serviceTypeName + " " +
- "" + Central.ISA + " " +
- "" + (expand ? "1" : "0") + " " +
- " "
- });
- }
-
- //
- protected String[] createServiceTypeRelationshipsFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("serviceType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- }
- String[] results = new String [v.size()];
- v.copyInto (results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- *<Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
- * </Relationship>
- *</Relationships>
- *
- *
- * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
- * attributes 'lsid' and 'articleName' in <objectType> element.
- *************************************************************************/
- public Map getDataTypeRelationships (String dataTypeName)
- throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName;
- Map cachedResults = (Map)getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- "" + Central.ISA + " " +
- "" + Central.HASA + " " +
- "" + Central.HAS + " " +
- "1 " +
- " "
- });
-
- // parse returned XML
- Map results = new HashMap();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
-
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String relType = elem.getAttribute ("relationshipType");
- NodeList children = elem.getChildNodes();
- Vector v = new Vector();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("objectType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- String[] names = new String [v.size()];
- v.copyInto (names);
- results.put (relType, names);
- }
-
- setContents (cacheId, results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- *<Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- *</Relationships>
- *
- *************************************************************************/
- public String[] getDataTypeRelationships (String dataTypeName,
- String relationshipType)
- throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
- String[] cachedResults = (String[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- "" + relationshipType + " " +
- "1 " +
- " "
- });
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
-
- // it should always be just one element in this list
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("objectType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- }
- String[] results = new String [v.size()];
- v.copyInto (results);
-
- setContents (cacheId, results);
- return results;
- }
-
-// /**************************************************************************
-// *
-// *************************************************************************/
-// public MobyRelationship[] getRelationships (String dataTypeName)
-// throws MobyException {
-// return null;
-// }
-
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getRegistryEndpoint() {
- return endpoint.toString();
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getRegistryNamespace() {
- return uri;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <resourceURLs>
- * <Resource name="Service" url="..." />
- * <Resource name="Object" url="..." />
- * <Resource name="Namespace" url="..." />
- * <Resource name="ServiceInstance" url="..." />
- * <Resource name="Full" url="..." />
- * </resourceURLs>
- *
- *************************************************************************/
- public MobyResourceRef[] getResourceRefs()
- throws MobyException {
-
- String cacheId = "retrieveResourceURLs";
- MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result = (String)doCall ("retrieveResourceURLs",
- new Object[] {});
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Resource");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- try {
- v.addElement
- (new MobyResourceRef (elem.getAttribute ("name"),
- new URL ((String)elem.getAttribute ("url")),
- elem.getAttribute ("type")));
- } catch (MalformedURLException e2) {
- if (debug)
- System.err.println ("Bad URL: " + elem.getAttribute ("url"));
- }
- }
-
- MobyResourceRef[] results = new MobyResourceRef [v.size()];
- v.copyInto (results);
-
- // Add this data to the cache in case we get called again
- setContents (cacheId, results);
-
- return results;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public InputStream getResource (String resourceName)
- throws MobyException {
-
- MobyResourceRef[] resourceRefs = getResourceRefs();
- for (int i = 0; i < resourceRefs.length; i++) {
- if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
- return Utils.getInputStream (resourceRefs[i].getResourceLocation());
- }
- }
- throw new MobyException ("No resource found for '" + resourceName + "'.");
- }
-
- /**************************************************************************
- * Return a case-insensitive comparator of Strings. It is used to
- * create various TreeMaps where keys are strings.
- *************************************************************************/
- protected static Comparator getStringComparator() {
- return new Comparator() {
- public int compare (Object o1, Object o2) {
- return ((String)o1).compareToIgnoreCase ((String)o2);
- }
- };
- }
-
- // cache URL/URI so we only check once
- private static String CHECKED_URL = null;
- private static String CHECKED_URI = null;
-
- /**
- * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
- * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
- * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
- *
- * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
- */
- public static CentralImpl getDefaultCentral() throws MobyException{
- return getDefaultCentral(null);
- }
-
- public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
- if(reg == null && defaultCentrals.containsKey("")){
- return defaultCentrals.get("");
- }
- else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
- return defaultCentrals.get(reg.getEndpoint());
- }
-
- String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
- ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
- URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
- if(resURL != null){
- System.err.println("Loading "+resURL);
- try{
- LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
- for(String line = reader.readLine(); line != null; line = reader.readLine()){
- if(!line.trim().startsWith("#")){
- className = line.trim();
- break;
- }
- }
- } catch(Exception e){
- logger.log(Level.WARNING,
- "Error reading " + resURL,
- e);
- }
- }
- try{
- System.err.println("Central class is "+className);
- Class clazz = Class.forName(className);
- if(reg == null){ // should use default nullary c-tor
- defaultCentrals.put("", (CentralImpl) clazz.newInstance());
- }
- else{ // should have (String endpoint, String namespace) c-tor
- for(Constructor ctor: clazz.getDeclaredConstructors()){
- Class[] params = ctor.getParameterTypes();
- if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
- params[1].getName().equals("java.lang.String") ){
- defaultCentrals.put(reg.getEndpoint(),
- (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
- break;
- }
- }
- if(!defaultCentrals.containsKey(reg.getEndpoint())){
- logger.log(Level.WARNING,
- "Could not find required (String endpoint, String namespace)" +
- "constructor for class " + className);
- }
- }
- } catch(Exception e){
- logger.log(Level.WARNING,
- "Could not load class " + className,
- e);
- if(reg == null){
- defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
- }
- else{
- defaultCentrals.put(reg.getEndpoint(),
- new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
- }
- }
-
- return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
- }
-
- /**
- *
- * @return a String representing the Default mobycentral endpoint. If the
- * system property 'moby.check.default' exists and is set to true,
- * then the URL http://biomoby.org/mobycentral is queried and the
- * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
- * is returned.
- */
- public static String getDefaultURL() {
- boolean check = false;
- try {
- check = Boolean.getBoolean("moby.check.default");
- } catch (Exception e) {
-
- }
-
- if (check) {
- // return the last checked url if we have done this before
- if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
- return CHECKED_URL;
- }
-
- // create a HttpClient object
- HttpClient client = new HttpClient();
- // set up the Head method
- HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
- // do not follow redirects or we will get a 411 error
- method.setFollowRedirects(false);
- // retry 3 times
- method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
- // set the user agent ... should probably make this something more reasonable
- method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
- try {
- // Execute the method.
- int statusCode = client.executeMethod(method);
-
- if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
- System.err.println("Method failed: "
- + method.getStatusLine());
- } else {
- try {
- String location = method.getResponseHeader("location").getValue();
- CHECKED_URL = location;
- try {
- CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
- } catch (MalformedURLException murle ) {
- CHECKED_URI = DEFAULT_NAMESPACE;
- }
- return CHECKED_URL;
- } catch (NullPointerException npe) {
- return DEFAULT_ENDPOINT;
- }
- }
- } catch (HttpException e) {
- System.err.println("Fatal protocol violation: "
- + e.getMessage());
- e.printStackTrace();
- } catch (IOException e) {
- System.err.println("Fatal transport error: " + e.getMessage());
- e.printStackTrace();
- } finally {
- // Release the connection.
- method.releaseConnection();
- }
-
- } else {
- return DEFAULT_ENDPOINT;
- }
- return DEFAULT_ENDPOINT;
- }
-
- /**
- *
- * @return a String representing the default mobycentral uri. If the
- * system property 'moby.check.default' exists and is set to true,
- * then the URL http://biomoby.org/mobycentral is queried and the
- * default central namespace is returned, otherwise DEFAULT_NAMESPACE
- * is returned.
- */
- public static String getDefaultURI() {
- boolean check = false;
- try {
- check = Boolean.getBoolean("moby.check.default");
- } catch (Exception e) {
-
- }
- if (check) {
- if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
- return CHECKED_URI;
- }
- // need to check ...
- getDefaultURL();
- return CHECKED_URI;
- } else {
- return DEFAULT_NAMESPACE;
- }
- }
- /**************************************************************************
- * Convert non-suitable characters in a XML string into their
- * entity references.
- *
- * Adapted from jDom.
- *
- * @param str input to be converted
- * @return If there were any non-suitable characters, return a new
- * string with those characters escaped, otherwise return the
- * unmodified input string
- *
- *************************************************************************/
- public String escapeXML (String str) {
- StringBuffer buffer = null;
- char ch;
- String entity;
- for (int i = 0; i < str.length(); i++) {
- ch = str.charAt (i);
- switch (ch) {
- case '<' :
- entity = "<";
- break;
- case '>' :
- entity = ">";
- break;
- case '&' :
- entity = "&";
- break;
- default :
- entity = null;
- break;
- }
- if (buffer == null) {
- if (entity != null) {
- // An entity occurred, so we'll have to use StringBuffer
- // (allocate room for it plus a few more entities).
- buffer = new StringBuffer (str.length() + 20);
- // Copy previous skipped characters and fall through
- // to pickup current character
- buffer.append (str.substring (0, i));
- buffer.append (entity);
- }
- } else {
- if (entity == null) {
- buffer.append (ch);
- } else {
- buffer.append (entity);
- }
- }
- }
-
- // If there were any entities, return the escaped characters
- // that we put in the StringBuffer. Otherwise, just return
- // the unmodified input string.
- return (buffer == null) ? str : buffer.toString();
- }
-
- /*************************************************************************
- * Format an exception.
- *************************************************************************/
- public static String formatFault (AxisFault e, String endpoint, QName method) {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- formatFault (e, new PrintStream (baos), endpoint, method);
- return baos.toString();
- }
-
- /*************************************************************************
- * Format an exception.
- *************************************************************************/
- public static void formatFault (AxisFault e, PrintStream out,
- String endpoint, QName method) {
-
- out.println ("===ERROR===");
- out.println ("Fault details:");
- // for some obvious errors I do not print all details (with a lenghty trace stack)
- String faultString = e.getFaultString();
- if ( (! faultString.startsWith ("java.net.ConnectException")) &&
- (faultString.indexOf ("Could not find class for the service named:") == -1)
- ) {
- org.w3c.dom.Element[] details = e.getFaultDetails();
- for (int i = 0; i < details.length; i++) {
- String s = details[i].toString().replaceAll ("<", "<");
- s = s.replaceAll (">", ">");
- out.println (s);
- }
- }
- out.println ("Fault string: " + faultString);
- out.println ("Fault code: " + e.getFaultCode());
- out.println ("Fault actor: " + e.getFaultActor());
- if (endpoint != null || method != null)
- out.println ("When calling:");
- if (endpoint != null)
- out.println ("\t" + endpoint);
- if (method != null)
- out.println ("\t" + method);
- out.println ("===========");
- }
-
-
-}
+// CentralImpl.java
+// A default client to the Moby Central service.
+//
+// senger at ebi.ac.uk
+// February 2003
+//
+
+package org.biomoby.client;
+
+import org.biomoby.registry.meta.Registry;
+import org.biomoby.shared.Central;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSet;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+import org.biomoby.shared.MobyRelationship;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.NoSuccessException;
+import org.biomoby.shared.PendingCurationException;
+import org.biomoby.shared.MobyResourceRef;
+import org.biomoby.shared.Utils;
+
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.namespace.QName;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import org.apache.axis.AxisFault;
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
+import org.apache.commons.httpclient.Header;
+import org.apache.commons.httpclient.HttpClient;
+import org.apache.commons.httpclient.HttpException;
+import org.apache.commons.httpclient.HttpStatus;
+import org.apache.commons.httpclient.methods.HeadMethod;
+import org.apache.commons.httpclient.params.HttpMethodParams;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
+import java.io.PrintStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+import java.util.TreeMap;
+import java.util.Comparator;
+import java.util.zip.GZIPInputStream;
+import java.util.logging.*;
+
+/**
+ * A default implementation of the
+ * interface {@link org.biomoby.shared.Central Central}
+ * allowing access to a Moby registry.
+ *
+ * This class is supposed to be used by all other clients that wish
+ * to communicate with the Moby Registry, but do not want to know
+ * about all XML details that are necessary for talking with the Moby Central
+ * directly. This is an example of a client program:
+ *
+ * import org.biomoby.shared.Central;
+ * import org.biomoby.shared.MobyException;
+ * import org.biomoby.client.CentralImpl;
+ * import java.util.Map;
+ * import java.util.Iterator;
+ *
+ * public class Test {
+ *
+ * public static void main (String[] args)
+ * throws MobyException {
+ *
+ * Central worker = new CentralImpl();
+ * Map authorities = worker.getServiceNamesByAuthority();
+ *
+ * for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
+ * Map.Entry entry = (Map.Entry)it.next();
+ * System.out.println (entry.getKey());
+ * String[] names = (String[])entry.getValue();
+ * for (int i = 0; i < names.length; i++)
+ * System.out.println ("\t" + names[i]);
+ * }
+ * }
+ * }
+ *
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class CentralImpl
+ implements Central, SimpleCache {
+
+ private URL endpoint;
+ private String uri;
+ protected boolean debug = false;
+
+ /** Common central used to if getDefaultCentral() is called */
+ protected static Map defaultCentrals = new HashMap();
+
+ /** Default location (endpoint) of a Moby registry. */
+ public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
+
+ /** Default namespace used by the contacted Moby registry. */
+ public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
+
+ /**
+ * The META-INF resource file that will be checked to determine what
+ * default class should be instantiated in order to create a Central Implementation
+ * when getDefaultCentral() is called.
+ */
+ public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
+ /** The class to use for getDefaultCentral if all else fails */
+ public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
+ private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+
+ /**
+ * Thread local that gives each thread its own
+ * DocumentBuilderFactory (since it is not thread-safe). Code taken
+ * from Apache's JaxpUtils.
+ */
+ public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
+ protected synchronized Object initialValue() {
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware (true);
+ return dbf;
+ }
+ };
+
+
+ /*************************************************************************
+ * Default constructor. It connects to a default Moby registry
+ * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
+ * (as defined int {@link #DEFAULT_NAMESPACE}).
+ *************************************************************************/
+ public CentralImpl()
+ throws MobyException {
+ this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry to use.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser is available
+ *************************************************************************/
+ public CentralImpl (String endpoint)
+ throws MobyException {
+ this (endpoint, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry and what
+ * namespace to use. If any of the parameters is null, its default
+ * value is used instead.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser was found
+ *************************************************************************/
+ public CentralImpl (String endpoint, String namespace)
+ throws MobyException {
+
+ if (endpoint == null || "".equals (endpoint.trim()))
+ endpoint = DEFAULT_ENDPOINT;
+ if (namespace == null || "".equals (namespace.trim()))
+ namespace = DEFAULT_NAMESPACE;
+
+ try {
+ this.endpoint = new URL (endpoint);
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Bad URL: " + endpoint);
+ }
+ this.uri = namespace;
+
+ cache = new Hashtable();
+ useCache = true;
+ }
+
+ /*************************************************************************
+ * Loads a DOM Document from an InputStream. Uses thread-safe
+ * mechanism.
+ *************************************************************************/
+ public static Document loadDocument (InputStream input)
+ throws MobyException {
+ try {
+ DocumentBuilderFactory dbf
+ = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
+ DocumentBuilder db = dbf.newDocumentBuilder();
+ return (db.parse (input));
+ } catch (Exception e) {
+ throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
+ }
+ }
+
+ /*************************************************************************
+ * Call 'method' with 'parameters' and return its result.
+ *************************************************************************/
+ protected Object doCall (String method, Object[] parameters)
+ throws MobyException {
+
+ Call call = null;
+ try {
+ Service service = new Service();
+ call = (Call) service.createCall();
+ call.setTargetEndpointAddress (endpoint);
+ call.setTimeout (new Integer (0));
+
+ call.setSOAPActionURI (uri + "#" + method);
+
+ if (debug) {
+ System.err.println ("METHOD CALL: " + method);
+ System.err.println ("------------");
+ if (parameters.length > 0)
+ System.err.println (parameters[0] + "\n");
+ System.err.println ("------------\n");
+
+ Object result = call.invoke (uri, method, parameters);
+
+ System.err.println ("METHOD RETURN:");
+ System.err.println ("------------");
+ if (result != null)
+ System.err.println (result + "\n");
+ System.err.println ("------------\n");
+
+ return resultToString (result);
+
+ } else {
+ return resultToString (call.invoke (uri, method, parameters));
+ }
+
+ } catch (AxisFault e) {
+ throw new MobyException
+ (formatFault (e,
+ endpoint.toString(),
+ (call == null ? null : call.getOperationName())),
+ e);
+// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+
+ } catch (Exception e) {
+ throw new MobyException (e.toString(), e);
+// e.printStackTrace();
+ }
+ }
+
+
+ /**************************************************************************
+ * Parse the given XML sniplet to find tag 'success'. If it has value '1'
+ * look further for tag 'id' and return it back (or return an empty string
+ * if ID is not there). Otherwise raise an exception with the 'culprit'
+ * and with the message from the tag 'message'.
+ *
+ * The return value is a two-element long array. The first element
+ * is the ID (given by BioMobe registry), and the second element
+ * is RDF corresponding with the registered object (BioMoby
+ * returns this only for service instances, so for other objects
+ * this will be null).
+ *
+ * This is how the XML is supposed to look:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * Success takes the value "1" to indicate success, "0" to
+ * indicate failure, and "-1" to indicate "Pending Curation".
+ *************************************************************************/
+ protected String[] checkRegistration (String xml, Object culprit)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String id = "", success = "0", message = "", rdf = "";
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ Element root = document.getDocumentElement();
+
+ NodeList children = root.getChildNodes();
+ for (int i = 0; i < children.getLength(); i++) {
+ if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
+ continue;
+ Element elem = (Element)children.item (i);
+ if (elem.getNodeName().equals ("id")) {
+ if (elem.getFirstChild() != null)
+ id = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals("success")) {
+ if (elem.getFirstChild() != null)
+ success = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("message")) {
+ if (elem.getFirstChild() != null)
+ message = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("RDF")) {
+ if (elem.getFirstChild() != null)
+ rdf = elem.getFirstChild().getNodeValue();
+ }
+ }
+
+ if (success.equals ("0"))
+ throw new NoSuccessException (message, culprit);
+ else if (success.equals ("-1"))
+ throw new PendingCurationException();
+ return new String[] { id, rdf };
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing input
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildSecondaryInputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] secInputs = service.getSecondaryInputs();
+ buf.append ("\n");
+ for (int i = 0; i < secInputs.length; i++) {
+ buf.append (secInputs[i].toXML());
+ }
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing output
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildOutputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] primaryOutputs = service.getPrimaryOutputs();
+ buf.append ("\n");
+ for (int i = 0; i < primaryOutputs.length; i++)
+ buf.append (primaryOutputs[i].toXML());
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML represented a query object (an object used
+ * to find a service).
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * ServiceTypeTerm
+ * ServiceName
+ * moby
+ * http://desired.service.provider ;
+ * 1|0
+ * 1|0
+ * 1|0
+ *
+ * something
+ * ....
+ * ....
+ *
+ *************************************************************************/
+ protected String buildQueryObject (MobyService service,
+ String[] keywords,
+ boolean expandObjects,
+ boolean expandServices,
+ boolean authoritative) {
+ if (service == null) {
+ service = new MobyService ("dummy");
+ service.setCategory ("");
+ }
+ StringBuffer buf = new StringBuffer();
+
+ buf.append ("\n \n");
+
+ buf.append ("\n\n");
+ MobyData[] po = service.getPrimaryOutputs();
+ if (po.length > 0) {
+ for (int i = 0; i < po.length; i++)
+ buf.append (po[i].toXML());
+ }
+ buf.append (" \n \n");
+
+ buf.append ("" + service.getType() + " \n");
+
+ String name = service.getName();
+ if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
+ buf.append ("" + service.getName() + " \n");
+
+ String sigURL = service.getSignatureURL();
+ if (!sigURL.equals (""))
+ buf.append ("" + sigURL + " \n");
+
+ buf.append ("" + service.getCategory() + " \n");
+ buf.append ("" + service.getAuthority() + " \n");
+
+ buf.append ("");
+ buf.append (expandObjects ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (expandServices ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (authoritative ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("\n");
+ if (keywords != null && keywords.length > 0) {
+ for (int i = 0; i < keywords.length; i++) {
+ buf.append ("");
+ buf.append (keywords[i]);
+ buf.append (" \n");
+ }
+ }
+ buf.append (" \n");
+
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Extract one or more MobyService objects from the given XML piece.
+ * The XML should look like this:
+ *
+ * <Services>
+ * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
+ * <serviceType>Service_Ontology_Term</serviceType>
+ * <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
+ * <contactEmail>your at email.addy.here</contactEmail>
+ * <signatureURL>http://service.RDF.here</signatureURL>
+ * <URL>http://service.endpoint.here/scriptname</URL>
+ * <authoritative>1</authoritative>
+ * <Input>
+ * <!-- one or more Simple and/or Complex Primary articles -->
+ * </Input>
+ * <Output>
+ * <!-- one or more Simple and/or Complex Primary articles -->
+ * </Output>
+ * <secondaryArticles>
+ * <!-- one or more Secondary articles -->
+ * </secondaryArticles>
+ * <Description><![CDATA[free text description here]]></Description>
+ * </Service>
+ * ... <!-- one or more Service blocks may be returned -->
+ * ...
+ * ...
+ * </Services>
+ *
+ * @throws MobyException if the XML document is invalid
+ *************************************************************************/
+ public MobyService[] extractServices (String xml)
+ throws MobyException {
+
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ NodeList list = document.getElementsByTagName ("Service");
+ MobyService[] results = new MobyService [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyService service = new MobyService (elem.getAttribute ("serviceName"));
+ service.setAuthority (elem.getAttribute ("authURI"));
+ service.setLSID (elem.getAttribute ("lsid"));
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ service.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Category")) {
+ service.setCategory (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("URL")) {
+ service.setURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("signatureURL")) {
+ service.setSignatureURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ service.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("serviceType")) {
+ service.setType (getFirstValue (children.item (j)));
+ MobyServiceType mst = new MobyServiceType(service.getType());
+ NamedNodeMap map = (children.item (j).getAttributes());
+ if (map != null) {
+ Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
+ if (node != null)
+ mst.setLSID(node.getNodeValue());
+ }
+ service.setServiceType(mst);
+ } else if (nodeName.equals ("authoritative")) {
+ String authoritative = getFirstValue (children.item (j));
+ service.setAuthoritative (authoritative.equals ("1") ? true : false);
+ } else if (nodeName.equals ("Input")) {
+ //
+ // ...
+ //
+ //
+ // ......
+ // ......
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addInput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addInput (data);
+ }
+ }
+ } else if (nodeName.equals ("Output")) {
+ //
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addOutput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addOutput (data);
+ }
+ }
+
+ } else if (nodeName.equals ("secondaryArticles")) {
+ //
+ // ...
+ //
+ NodeList parameters = children.item (j).getChildNodes();
+ for (int k = 0; k < parameters.getLength(); k++) {
+ if (parameters.item (k).getNodeName().equals ("Parameter")) {
+ MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
+ service.addInput (data);
+ }
+ }
+ }
+ }
+ results [i] = service;
+ }
+ return results;
+ }
+
+ // protect against null values
+ protected String getFirstValue (Node child) {
+ Node node = child.getFirstChild();
+ if (node == null) return "";
+ String value = node.getNodeValue();
+ if (value == null) return "";
+ return value;
+ }
+
+ protected String getFirstValue (NodeList children) {
+ if (children.item(0) != null && children.item(0).hasChildNodes()) {
+ children.item(0).normalize();
+ return getFirstValue (children.item(0));
+ }
+ return "";
+ }
+
+ /**************************************************************************
+ *
+ * Implementing SimpleCache interface.
+ *
+ * Why to have an interface for such trivial thing? Well, because
+ * I needed to overwrite the caching mechanism in the subclasses
+ * so I needed to have all caching functions as separate methods -
+ * that's why I have collect them in an interface.
+ *
+ *************************************************************************/
+ private Hashtable cache; // this is the cache itself
+ private boolean useCache; // this signal that we are actually caching things
+
+ // not used here
+ public String createId (String rootName,
+ String semanticType, String syntaxType,
+ long lastModified,
+ Properties props) {
+ return ""; // not used here
+ }
+
+ // check existence of a cached object
+ public boolean existsInCache (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.containsKey (id);
+ else return false;
+ }
+ }
+
+ // retrieve from cache
+ public Object getContents (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.get (id);
+ else return null;
+ }
+ }
+
+ // cache an object
+ public void setContents (String id, java.lang.Object data) {
+ synchronized (cache) {
+ if (useCache) cache.put (id, data);
+ }
+ }
+
+ // in this implementation, it clears the whole cache, regardless
+ // what 'id' is passed
+ public void removeFromCache (String id) {
+ cache.clear();
+ }
+
+ /**************************************************************************
+ *
+ * And the other methods related to caching (but not part of the
+ * SimpleCache interface).
+ *
+ **************************************************************************/
+
+ /**************************************************************************
+ * By default, caching is enabled to reduce network traffic.
+ * Setting this to false will clear the cache, and not cache any
+ * further calls unless it is set to true again.
+ *
+ * @param shouldCache whether retrieveXXX call results should be
+ * cached in case they are called again (i.e. don't request
+ * MobyCentral every time)
+ **************************************************************************/
+ public void setCacheMode (boolean shouldCache) {
+ useCache = shouldCache;
+ if (! useCache)
+ removeFromCache (null);
+ }
+
+ /**************************************************************************
+ * Find if caching is currently enabled.
+ *
+ * @return true if caching is enabled
+ **************************************************************************/
+ public boolean getCacheMode(){
+ return useCache;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceNames>
+ * <serviceName name="serviceName" authURI='authority.info.here'/>
+ * ...
+ * ...
+ * </serviceNames>
+ *
+ *
+ * @deprecated Replaced by {@link
+ * #getServiceNamesByAuthority}. The reason is that this method
+ * returns a random result if there are more services with the
+ * same name but belonging to different authorities.
+ *
+ *************************************************************************/
+ public Map getServiceNames()
+ throws MobyException {
+
+ String result = (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ results.put (elem.getAttribute ("name"),
+ elem.getAttribute ("authURI"));
+ }
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceNames>
+ * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
+ * ...
+ * ...
+ * </serviceNames>
+ *
+ *
+ * @return a Map which has authorities as keys, and String arrays
+ * with service names as a values.
+ *************************************************************************/
+ public Map getServiceNamesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, true);
+ }
+
+ /**************************************************************************
+ * Similar to {@link #getServiceNamesByAuthority} but the
+ * resulting Map contains slightly more.
+ *
+ * @return a Map which has authorities as keys, and arrays of
+ * MobyServices as a values. Each MobyService is filled with its
+ * name, authority and LSID.
+ *************************************************************************/
+ public Map getServicesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, false);
+ }
+
+ //
+ protected String getServiceNamesByAuthorityAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ }
+
+ // if onlyNames == true
+ // Map: authority name -> String[]
+ // (filled with service namea)
+ // else
+ // Map: authority name -> MobyService[]
+ // (filled with service name, authority and lsid)
+ protected Map createServicesByAuthorityFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ String auth = elem.getAttribute ("authURI");
+ Vector v =
+ (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+ if (onlyNames) {
+ v.addElement (name);
+ } else {
+ MobyService ms = new MobyService (name);
+ ms.setAuthority (auth);
+ ms.setLSID (elem.getAttribute ("lsid"));
+ v.addElement (ms);
+ }
+ results.put (auth, v);
+ }
+
+ // change values of type Vector to MobyService[] or String[]
+ for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ Vector v = (Vector)entry.getValue();
+ if (onlyNames) {
+ String[] sNames = new String [v.size()];
+ v.copyInto (sNames);
+ entry.setValue (sNames);
+ } else {
+ MobyService[] mss = new MobyService [v.size()];
+ v.copyInto (mss);
+ entry.setValue (mss);
+ }
+ }
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceProviders>
+ * <serviceProvider name="authority.URI.here"/>
+ * ...
+ * ...
+ * </serviceProviders>
+ *
+ *************************************************************************/
+ public String[] getProviders()
+ throws MobyException {
+
+ String cacheId = "retrieveServiceProviders";
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveServiceProviders",
+ new Object[] {});
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceProvider");
+ String[] results = new String [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++)
+ results[i] = ((Element)list.item (i)).getAttribute ("name");
+
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceTypes>
+ * <serviceType name="serviceName" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * <contactEmail>...</contactEmail>
+ * <authURI>...</authURI>
+ * </serviceType>
+ * ...
+ * ...
+ * </serviceTypes>
+ *
+ *************************************************************************/
+ public Map getServiceTypes()
+ throws MobyException {
+ String result = getServiceTypesAsXML();
+ Map results = new TreeMap (getStringComparator());
+ MobyServiceType[] types = createServiceTypesFromXML (result);
+ for (int i = 0; i < types.length; i++) {
+ results.put (types[i].getName(),
+ types[i].getDescription());
+ }
+ return results;
+ }
+
+ //
+ protected String getServiceTypesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceTypes",
+ new Object[] {});
+ }
+
+ // but be aware that the created MobyServiceTypes are not complete
+ // - they do not have the relationship information; that's why
+ // this method is not public; the full service types are available
+ // from CentralDigest implementations
+ protected MobyServiceType[] createServiceTypesFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceType");
+ if (list == null || list.getLength() == 0)
+ return new MobyServiceType[] {};
+ MobyServiceType[] results = new MobyServiceType [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
+ st.setLSID (elem.getAttribute ("lsid"));
+ st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = st;
+ }
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <Namespaces>
+ * <Namespace name="namespace" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * <contactEmail>...</contactEmail>
+ * <authURI>...</authURI>
+ * </Namespace>
+ * ...
+ * ...
+ * </Namespaces>
+ *
+ *************************************************************************/
+ public MobyNamespace[] getFullNamespaces()
+ throws MobyException {
+
+ String result = getNamespacesAsXML();
+ return createNamespacesFromXML (result);
+ }
+
+ //
+ protected String getNamespacesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveNamespaces",
+ new Object[] {});
+ }
+
+ //
+ protected MobyNamespace[] createNamespacesFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
+ if (list == null || list.getLength() == 0) {
+ return new MobyNamespace[] {};
+ }
+ MobyNamespace[] results = new MobyNamespace [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
+ nm.setLSID (elem.getAttribute ("lsid"));
+ nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = nm;
+ }
+
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ * @deprecated Replaced by {@link #getFullNamespaces} that gives
+ * more information for the same price.
+ *************************************************************************/
+ public Map getNamespaces()
+ throws MobyException {
+
+ Map results = new TreeMap (getStringComparator());
+ MobyNamespace[] namespaces = getFullNamespaces();
+ for (int i = 0; i < namespaces.length; i++) {
+ results.put (namespaces[i].getName(),
+ namespaces[i].getDescription());
+ }
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <objectNames>
+ * <Object name="objectName" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * </Object>
+ * ...
+ * ...
+ * </objectNames>
+ *
+ *************************************************************************/
+ public Map getDataTypeNames()
+ throws MobyException {
+ String result = getDataTypeNamesAsXML();
+ return createDataTypeNamesFromXML (result, true);
+ }
+
+ //
+ protected String getDataTypeNamesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveObjectNames",
+ new Object[] {});
+ }
+
+ // if onlyNames == true
+ // Map: data type name -> description (String)
+ // else
+ // Map: data type name -> MobyDataType[]
+ // (filled with name, description, and lsid)
+ protected Map createDataTypeNamesFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Object");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ if (name == null)
+ continue; // ignore no-named data types
+ String desc = "";
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("Description")) {
+ desc = getFirstValue (children.item (j));
+ break;
+ }
+ }
+ if (onlyNames) {
+ results.put (name, desc);
+ } else {
+ MobyDataType dt = new MobyDataType (name);
+ dt.setDescription (desc);
+ dt.setLSID (elem.getAttribute ("lsid"));
+ results.put (name, dt);
+ }
+ }
+ return results;
+ }
+
+
+ /**************************************************************************
+ * Parses and imports the following XML. An example:
+ *
+ *
+ * <retrieveObjectDefinition>
+ * <objectType lsid="...">go_term</objectType>
+ * <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
+ * <authURI>http://www.illuminae.com</authURI>
+ * <contactEmail>markw at illuminae.com</contactEmail>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType articleName=''>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
+ * <objectType articleName='Term'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType articleName='Definition'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:has'>
+ * <objectType articleName='Problems'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType articleName='Issues'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * </Relationship>
+ * </retrieveObjectDefinition>
+ *
+ *************************************************************************/
+ public MobyDataType getDataType (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ String result = getDataTypeAsXML (dataTypeName);
+ return createDataTypeFromXML (result, dataTypeName);
+ }
+
+ public MobyDataType[] getDataTypes()
+ throws MobyException, NoSuccessException {
+ Map datatypeMap = getDataTypeNames();
+ MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
+ int i = 0;
+ for(String dataTypeName: datatypeMap.keySet()){
+ datatypes[i++] = getDataType(dataTypeName);
+ }
+ return datatypes;
+ }
+
+ protected String getDataTypeAsXML (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ return (String)doCall ("retrieveObjectDefinition",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ " "
+ });
+ }
+
+ protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
+ NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
+ if (list == null || list.getLength() == 0)
+ throw new NoSuccessException ("Data Type name was not found.",
+ dataTypeName);
+ MobyDataType data = null;
+ Element elem = (Element)list.item (0);
+ NodeList children = elem.getChildNodes();
+
+ // first find the "real" (LSID-ized) data type name
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("objectType")) {
+ data = new MobyDataType (getFirstValue (children.item (j)));
+ data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
+ break;
+ }
+ }
+
+ // if not found (unprobable) use the name given by the caller
+ if (data == null)
+ data = new MobyDataType (dataTypeName);
+
+ // now fill the data type object with the rest of attributes
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ data.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("authURI")) {
+ data.setAuthority (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ data.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Relationship")) {
+ String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
+ if (relationshipType.endsWith ("isa")) {
+
+ NodeList parents = children.item (j).getChildNodes();
+ for (int k = 0; k < parents.getLength(); k++) {
+ if (parents.item (k).getNodeName().equals ("objectType")) {
+ data.addParentName (getFirstValue (parents.item (k)));
+ }
+ }
+ } else if (relationshipType.endsWith ("hasa")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ getFirstValue (belows.item (k)),
+ Central.iHASA );
+ }
+ }
+ } else if (relationshipType.endsWith ("has")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ belows.item (k).getFirstChild().getNodeValue(),
+ Central.iHAS );
+ }
+ }
+ }
+ }
+ }
+ return data;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName)
+ throws MobyException, NoSuccessException {
+
+ Map names = getServiceNames();
+
+ for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ if ( ((String)entry.getKey()).equals (serviceName) )
+ return getServiceWSDL (serviceName, (String)entry.getValue());
+ }
+
+ throw new NoSuccessException ("Service not found.", serviceName);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName, String authority)
+ throws MobyException, NoSuccessException {
+
+ String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
+ String cachedResults = (String)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("retrieveService",
+ new Object[] {
+ "" +
+ " "
+ });
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ Element service = document.getDocumentElement();
+ Node wsdl = service.getFirstChild();
+ if (wsdl == null)
+ throw new NoSuccessException ("Service not found OR WSDL is not available.",
+ serviceName + " (" + authority + ")");
+
+ String results = wsdl.getNodeValue();
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterDataTypeXML (MobyDataType dataType) {
+
+ // build the ISA tag (expressing hierarchy of data types)
+ String[] names = dataType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ // build the HASA/HAS tags (expressing containments of data types)
+ MobyRelationship[] children = dataType.getChildren();
+ StringBuffer buf2 = new StringBuffer(); // for HASA
+ StringBuffer buf3 = new StringBuffer(); // for HAS
+ for (int i = 0; i < children.length; i++) {
+ if (children[i].getRelationshipType() == Central.iHASA) {
+ buf2.append ("");
+ buf2.append (children[i].getDataTypeName());
+ buf2.append (" ");
+ } else if (children[i].getRelationshipType() == Central.iHAS) {
+ buf3.append ("");
+ buf3.append (children[i].getDataTypeName());
+ buf3.append (" ");
+ }
+ }
+
+ return
+ "" +
+ "" + dataType.getName() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ "" + new String (buf2) +
+ " " +
+ "" + new String (buf3) +
+ " " +
+ "" + dataType.getAuthority() + " " +
+ "" + dataType.getEmailContact() + " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerObjectClass",
+ new Object[] { getRegisterDataTypeXML (dataType) });
+ dataType.setId (checkRegistration (result, dataType)[0]);
+ }
+
+ /*************************************************************************
+ * B
+ *************************************************************************/
+ public void unregisterDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterObjectClass",
+ new Object[] {
+ "" +
+ "" + dataType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, dataType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
+
+ // build the ISA tag (expressing hierarchy of service types)
+ String[] names = serviceType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ return
+ "" +
+ "" + serviceType.getName() + " " +
+ "" + serviceType.getEmailContact() + " " +
+ "" + serviceType.getAuthority() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerServiceType",
+ new Object[] { getRegisterServiceTypeXML (serviceType) });
+ serviceType.setId (checkRegistration (result, serviceType)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterServiceType",
+ new Object[] {
+ "" +
+ "" + serviceType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, serviceType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterNamespaceXML (MobyNamespace namespace) {
+ return
+ "" +
+ "" + namespace.getName() + " " +
+ "" + namespace.getEmailContact() + " " +
+ "" + namespace.getAuthority() + " " +
+ "" +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("registerNamespace",
+ new Object[] { getRegisterNamespaceXML (namespace) });
+ namespace.setId (checkRegistration (result, namespace)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterNamespace",
+ new Object[] {
+ "" +
+ "" + namespace.getName() + " " +
+ " "
+ });
+ checkRegistration (result, namespace);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceXML (MobyService service) {
+ return
+ "" +
+ "" + service.getCategory() + " " +
+ "" + service.getName() + " " +
+ "" + service.getType() + " " +
+ "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
+ "" + service.getAuthority() + " " +
+ "" + escapeXML (service.getSignatureURL()) + " " +
+ "" + escapeXML (service.getURL()) + " " +
+ "" + service.getEmailContact() + " " +
+ "" + (service.isAuthoritative() ? "1" : "0") + " " +
+ "" +
+ " " +
+ buildPrimaryInputTag (service) +
+ buildSecondaryInputTag (service) +
+ buildOutputTag (service) +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerService",
+ new Object[] { getRegisterServiceXML (service) });
+ String[] registered = checkRegistration (result, service);
+ service.setId (registered [0]);
+ service.setRDF (registered [1]);
+ String pathToRDF = service.getPathToRDF();
+ if ( ! pathToRDF.equals ("") ) {
+ File fileRDF = new File (pathToRDF);
+ try {
+ PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
+ fileout.println (registered [1]);
+ fileout.close();
+ } catch (IOException e) {
+ StringBuffer buf = new StringBuffer (100);
+ buf.append ("Failed to save RDF in '");
+ buf.append (fileRDF.getAbsolutePath() + "'. ");
+ buf.append (e.toString());
+ try {
+ File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
+ PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
+ fileout.println (registered [1]);
+ fileout.close();
+ buf.append ("\nReturned RDF file was therefore stored in: ");
+ buf.append (tmpFile.getAbsolutePath());
+ } catch (IOException e2) {
+ buf.append ("\nEven saving in a temporary file failed: ");
+ buf.append (e2.toString());
+ }
+ throw new MobyException (buf.toString());
+ }
+ }
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterService",
+ new Object[] {
+ "" +
+ "" + service.getAuthority() + " " +
+ "" + service.getName() + " " +
+ " "
+ });
+ checkRegistration (result, service);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String serviceType)
+ throws MobyException {
+ if (serviceType == null)
+ return new MobyService[] {};
+ MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ pattern.setType (serviceType);
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String[] keywords)
+ throws MobyException {
+ if (keywords == null)
+ return new MobyService[] {};
+ return findService (null, keywords);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern)
+ throws MobyException {
+ if (pattern == null)
+ return new MobyService[] {};
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords)
+ throws MobyException {
+ return findService (pattern, keywords, true, true);
+ }
+
+ /**************************************************************************
+ * All 'findService' methods end up here.
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ if (pattern == null) {
+ pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ }
+
+ String result =
+ getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
+ MobyService[] services = extractServices (result);
+ return services;
+ }
+
+ // ...actually all 'findService' methods end up here
+ protected String getServicesAsXML (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ String[] query = new String[] {
+ "" +
+ buildQueryObject (pattern, keywords,
+ includeParentDataTypes,
+ includeChildrenServiceTypes,
+ false) +
+ " "
+ };
+ return (String)doCall ("findService", query);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String call (String methodName, String inputXML)
+ throws MobyException {
+ Object result;
+ if (inputXML == null || inputXML.equals (""))
+ result = doCall (methodName, new Object[] { });
+ else
+ result = doCall (methodName, new Object[] { inputXML });
+ return (String)result;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected static String resultToString (Object result)
+ throws MobyException {
+ if (result == null)
+ throw new MobyException ("Returned result is null.");
+ if (result instanceof String)
+ return (String)result;
+ if (result instanceof String[]) {
+ String[] tmp = (String[])result;
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < tmp.length; i++)
+ buf.append (tmp[i]);
+ return new String (buf);
+ }
+ if (result instanceof byte[])
+ return new String ((byte[])result);
+
+ throw new MobyException ("Unknown type of result: " + result.getClass().getName());
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean setDebug (boolean enabled) {
+ boolean oldMode = debug;
+ debug = enabled;
+ return oldMode;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
+ * <serviceType>urn:lsid:biomoby.org:servicetype:analysis</serviceType>
+ * <serviceType>urn:lsid:biomoby.org:servicetype:service</serviceType>
+ * </Relationship>
+ * </Relationships>
+ *
+ *************************************************************************/
+ public String[] getServiceTypeRelationships (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
+ return createServiceTypeRelationshipsFromXML (result);
+ }
+
+ //
+ protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ return
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + serviceTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + (expand ? "1" : "0") + " " +
+ " "
+ });
+ }
+
+ //
+ protected String[] createServiceTypeRelationshipsFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("serviceType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ *<Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
+ * </Relationship>
+ *</Relationships>
+ *
+ *
+ * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
+ * attributes 'lsid' and 'articleName' in <objectType> element.
+ *************************************************************************/
+ public Map getDataTypeRelationships (String dataTypeName)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName;
+ Map cachedResults = (Map)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + Central.HASA + " " +
+ "" + Central.HAS + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Map results = new HashMap();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String relType = elem.getAttribute ("relationshipType");
+ NodeList children = elem.getChildNodes();
+ Vector v = new Vector();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ String[] names = new String [v.size()];
+ v.copyInto (names);
+ results.put (relType, names);
+ }
+
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ *<Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ *</Relationships>
+ *
+ *************************************************************************/
+ public String[] getDataTypeRelationships (String dataTypeName,
+ String relationshipType)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + relationshipType + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ // it should always be just one element in this list
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+
+ setContents (cacheId, results);
+ return results;
+ }
+
+// /**************************************************************************
+// *
+// *************************************************************************/
+// public MobyRelationship[] getRelationships (String dataTypeName)
+// throws MobyException {
+// return null;
+// }
+
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getRegistryEndpoint() {
+ return endpoint.toString();
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getRegistryNamespace() {
+ return uri;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <resourceURLs>
+ * <Resource name="Service" url="..." />
+ * <Resource name="Object" url="..." />
+ * <Resource name="Namespace" url="..." />
+ * <Resource name="ServiceInstance" url="..." />
+ * <Resource name="Full" url="..." />
+ * </resourceURLs>
+ *
+ *************************************************************************/
+ public MobyResourceRef[] getResourceRefs()
+ throws MobyException {
+
+ String cacheId = "retrieveResourceURLs";
+ MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveResourceURLs",
+ new Object[] {});
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Resource");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ try {
+ v.addElement
+ (new MobyResourceRef (elem.getAttribute ("name"),
+ new URL ((String)elem.getAttribute ("url")),
+ elem.getAttribute ("type")));
+ } catch (MalformedURLException e2) {
+ if (debug)
+ System.err.println ("Bad URL: " + elem.getAttribute ("url"));
+ }
+ }
+
+ MobyResourceRef[] results = new MobyResourceRef [v.size()];
+ v.copyInto (results);
+
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
+
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public InputStream getResource (String resourceName)
+ throws MobyException {
+
+ MobyResourceRef[] resourceRefs = getResourceRefs();
+ for (int i = 0; i < resourceRefs.length; i++) {
+ if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
+ return Utils.getInputStream (resourceRefs[i].getResourceLocation());
+ }
+ }
+ throw new MobyException ("No resource found for '" + resourceName + "'.");
+ }
+
+ /**************************************************************************
+ * Return a case-insensitive comparator of Strings. It is used to
+ * create various TreeMaps where keys are strings.
+ *************************************************************************/
+ protected static Comparator getStringComparator() {
+ return new Comparator() {
+ public int compare (Object o1, Object o2) {
+ return ((String)o1).compareToIgnoreCase ((String)o2);
+ }
+ };
+ }
+
+ // cache URL/URI so we only check once
+ private static String CHECKED_URL = null;
+ private static String CHECKED_URI = null;
+
+ /**
+ * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
+ * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
+ * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+ *
+ * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
+ */
+ public static CentralImpl getDefaultCentral() throws MobyException{
+ return getDefaultCentral(null);
+ }
+
+ public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
+ if(reg == null && defaultCentrals.containsKey("")){
+ return defaultCentrals.get("");
+ }
+ else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+ return defaultCentrals.get(reg.getEndpoint());
+ }
+
+ String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+ ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+ URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+ if(resURL != null){
+ System.err.println("Loading "+resURL);
+ try{
+ LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+ for(String line = reader.readLine(); line != null; line = reader.readLine()){
+ if(!line.trim().startsWith("#")){
+ className = line.trim();
+ break;
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Error reading " + resURL,
+ e);
+ }
+ }
+ try{
+ System.err.println("Central class is "+className);
+ Class clazz = Class.forName(className);
+ if(reg == null){ // should use default nullary c-tor
+ defaultCentrals.put("", (CentralImpl) clazz.newInstance());
+ }
+ else{ // should have (String endpoint, String namespace) c-tor
+ for(Constructor ctor: clazz.getDeclaredConstructors()){
+ Class[] params = ctor.getParameterTypes();
+ if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+ params[1].getName().equals("java.lang.String") ){
+ defaultCentrals.put(reg.getEndpoint(),
+ (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+ break;
+ }
+ }
+ if(!defaultCentrals.containsKey(reg.getEndpoint())){
+ logger.log(Level.WARNING,
+ "Could not find required (String endpoint, String namespace)" +
+ "constructor for class " + className);
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Could not load class " + className,
+ e);
+ if(reg == null){
+ defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
+ }
+ else{
+ defaultCentrals.put(reg.getEndpoint(),
+ new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+ }
+ }
+
+ return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
+ }
+
+ /**
+ *
+ * @return a String representing the Default mobycentral endpoint. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
+ * is returned.
+ */
+ public static String getDefaultURL() {
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+
+ if (check) {
+ // return the last checked url if we have done this before
+ if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
+ return CHECKED_URL;
+ }
+
+ // create a HttpClient object
+ HttpClient client = new HttpClient();
+ // set up the Head method
+ HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
+ // do not follow redirects or we will get a 411 error
+ method.setFollowRedirects(false);
+ // retry 3 times
+ method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
+ // set the user agent ... should probably make this something more reasonable
+ method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
+ try {
+ // Execute the method.
+ int statusCode = client.executeMethod(method);
+
+ if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
+ System.err.println("Method failed: "
+ + method.getStatusLine());
+ } else {
+ try {
+ String location = method.getResponseHeader("location").getValue();
+ CHECKED_URL = location;
+ try {
+ CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
+ } catch (MalformedURLException murle ) {
+ CHECKED_URI = DEFAULT_NAMESPACE;
+ }
+ return CHECKED_URL;
+ } catch (NullPointerException npe) {
+ return DEFAULT_ENDPOINT;
+ }
+ }
+ } catch (HttpException e) {
+ System.err.println("Fatal protocol violation: "
+ + e.getMessage());
+ e.printStackTrace();
+ } catch (IOException e) {
+ System.err.println("Fatal transport error: " + e.getMessage());
+ e.printStackTrace();
+ } finally {
+ // Release the connection.
+ method.releaseConnection();
+ }
+
+ } else {
+ return DEFAULT_ENDPOINT;
+ }
+ return DEFAULT_ENDPOINT;
+ }
+
+ /**
+ *
+ * @return a String representing the default mobycentral uri. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central namespace is returned, otherwise DEFAULT_NAMESPACE
+ * is returned.
+ */
+ public static String getDefaultURI() {
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+ if (check) {
+ if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
+ return CHECKED_URI;
+ }
+ // need to check ...
+ getDefaultURL();
+ return CHECKED_URI;
+ } else {
+ return DEFAULT_NAMESPACE;
+ }
+ }
+ /**************************************************************************
+ * Convert non-suitable characters in a XML string into their
+ * entity references.
+ *
+ * Adapted from jDom.
+ *
+ * @param str input to be converted
+ * @return If there were any non-suitable characters, return a new
+ * string with those characters escaped, otherwise return the
+ * unmodified input string
+ *
+ *************************************************************************/
+ public String escapeXML (String str) {
+ StringBuffer buffer = null;
+ char ch;
+ String entity;
+ for (int i = 0; i < str.length(); i++) {
+ ch = str.charAt (i);
+ switch (ch) {
+ case '<' :
+ entity = "<";
+ break;
+ case '>' :
+ entity = ">";
+ break;
+ case '&' :
+ entity = "&";
+ break;
+ default :
+ entity = null;
+ break;
+ }
+ if (buffer == null) {
+ if (entity != null) {
+ // An entity occurred, so we'll have to use StringBuffer
+ // (allocate room for it plus a few more entities).
+ buffer = new StringBuffer (str.length() + 20);
+ // Copy previous skipped characters and fall through
+ // to pickup current character
+ buffer.append (str.substring (0, i));
+ buffer.append (entity);
+ }
+ } else {
+ if (entity == null) {
+ buffer.append (ch);
+ } else {
+ buffer.append (entity);
+ }
+ }
+ }
+
+ // If there were any entities, return the escaped characters
+ // that we put in the StringBuffer. Otherwise, just return
+ // the unmodified input string.
+ return (buffer == null) ? str : buffer.toString();
+ }
+
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static String formatFault (AxisFault e, String endpoint, QName method) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ formatFault (e, new PrintStream (baos), endpoint, method);
+ return baos.toString();
+ }
+
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static void formatFault (AxisFault e, PrintStream out,
+ String endpoint, QName method) {
+
+ out.println ("===ERROR===");
+ out.println ("Fault details:");
+ // for some obvious errors I do not print all details (with a lenghty trace stack)
+ String faultString = e.getFaultString();
+ if ( (! faultString.startsWith ("java.net.ConnectException")) &&
+ (faultString.indexOf ("Could not find class for the service named:") == -1)
+ ) {
+ org.w3c.dom.Element[] details = e.getFaultDetails();
+ for (int i = 0; i < details.length; i++) {
+ String s = details[i].toString().replaceAll ("<", "<");
+ s = s.replaceAll (">", ">");
+ out.println (s);
+ }
+ }
+ out.println ("Fault string: " + faultString);
+ out.println ("Fault code: " + e.getFaultCode());
+ out.println ("Fault actor: " + e.getFaultActor());
+ if (endpoint != null || method != null)
+ out.println ("When calling:");
+ if (endpoint != null)
+ out.println ("\t" + endpoint);
+ if (method != null)
+ out.println ("\t" + method);
+ out.println ("===========");
+ }
+
+
+}
From groscurt at dev.open-bio.org Wed Dec 3 10:21:13 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 10:21:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031521.mB3FLDqF013719@dev.open-bio.org>
groscurt
Wed Dec 3 10:21:13 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv13676/src/main/org/biomoby/service/dashboard
Modified Files:
SimpleClientPanel.java ServiceCallerModel.java
DashboardProperties.java
Log Message:
changes made for the authentication... without formatting this time
moby-live/Java/src/main/org/biomoby/service/dashboard SimpleClientPanel.java,1.13,1.14 ServiceCallerModel.java,1.7,1.8 DashboardProperties.java,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java 2008/11/26 08:54:21 1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java 2008/12/03 15:21:12 1.14
@@ -1,791 +1,838 @@
-// SimpleClientPanel.java
-//
-// Created: December 2005
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.service.dashboard;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.util.Date;
-
-import javax.swing.BorderFactory;
-import javax.swing.Box;
-import javax.swing.ButtonGroup;
-import javax.swing.Icon;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JPasswordField;
-import javax.swing.JRadioButton;
-import javax.swing.JSplitPane;
-import javax.swing.JTextField;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import org.biomoby.service.dashboard.data.DataContainer;
-import org.biomoby.service.dashboard.data.ServiceInputPanel;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.tulsoft.shared.UUtils;
-import org.tulsoft.tools.gui.AwtUtils;
-import org.tulsoft.tools.gui.JFileChooserWithHistory;
-import org.tulsoft.tools.gui.JTextFieldWithHistory;
-import org.tulsoft.tools.gui.SwingUtils;
-
-/**
- * A panel allowing to formulate input data and to call an arbitrary Biomoby service. Its interface is however not that
- * user-friendly, and it is supposed to be used more or less for testing purposes in time when a new service is being
- * created and developed.
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-public class SimpleClientPanel extends AbstractPanel {
-
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory
- .getLog( SimpleClientPanel.class );
-
- /**
- * A property name. Its value contains a name of color that will be used to display service name.
- */
- protected static final String P_S_TITLE_COLOR = "simpleclient.service.title.color";
-
- /**
- * A property name. Its value contains a name of color that will be used as background for editable console with XML
- * input.
- */
- protected static final String P_S_EDIT_BGCOLOR = "simpleclient.service.edit.bgcolor";
-
- // some texts
- protected static final String INIT_SELECT = "
Start by selecting a service \n" + " ";
- data.setData( emptyMsg );
- input.setText( emptyMsg );
- }
-
- // finally, call the service
- stopButton.setEnabled( true );
- callerModel.runIt( data );
-
- }
- catch ( MobyException e ) {
- exception = e;
-
- }
- catch ( Error e ) {
- exception = new MobyException( e.toString() );
- }
- return null; // not used here
- }
-
- // runs on the event-dispatching thread
- public void finished() {
- if ( wasCancelled ) {
- // service was interrupted by the Stop button - do
- // nothing (the whole GUI should be already in a good
- // state - the button 'Stop' took care about it)
- return;
- }
-
- if ( exception == null ) {
-
- // handle results here (using renderers...)
- if ( propertyChannel.getString( DP_INP_PING ).toLowerCase().equals( "true" ) ) {
- propertyChannel.fire( DP_STATUS_MSG, service.getName() + " isAlive." );
- }
- else {
- propertyChannel.fire( DP_STATUS_MSG, "Service invocation finished." );
- }
-
- if ( !DP_CS_NONE.equals( propertyChannel.getString( DP_CALL_SERVICE ) ) ) {
- results.updateComponent( data );
- }
-
- }
- else {
- if ( propertyChannel.getString( DP_INP_PING ).toLowerCase().equals( "true" ) ) {
- propertyChannel.fire( DP_STATUS_MSG, service.getName() + " is dead." );
- results.removeResults();
- }
- else {
- propertyChannel.fire( DP_STATUS_MSG, "Service invocation failed." );
- error( CALLER_ERROR, exception );
- }
- exception.printStackTrace();
- }
- serviceFinished();
- }
- }
-
- /*******************************************************************************************************************
- * Called when a call to a service finished.
- ******************************************************************************************************************/
- protected void serviceFinished() {
- runButton.setEnabled( true );
- stopButton.setEnabled( false );
- }
-
- /*******************************************************************************************************************
- * Called when a service is selected in a service tree (or in a 'recently used services' combo box), and also at the
- * beginning when a service name is retrieved from user preferences.
- *
- * Get selected service from a registry model and generate a new 'input data panel' to reflect input data of the
- * selected service.
- ******************************************************************************************************************/
- protected void selectService( final String serviceName ) {
- final Object source = this;
- final SwingWorker worker = new SwingWorker() {
- MobyService service;
- MobyDataType[] dataTypes;
-
- public Object construct() {
- try {
- service = registryModel.getService( serviceName );
- dataTypes = registryModel.getDataTypes( source );
- }
- catch ( MobyException e ) {
- error( ServicesTree.SERVICES_ACCESS_ERROR, e );
- }
- return service; // not used here
- }
-
- // runs on the event-dispatching thread.
- public void finished() {
- if ( service == null ) {
- deselectService();
- }
- else {
- updateInputDataPanel( service, dataTypes );
- selService.setText( service.getName() );
- // selectionAllowed = false;
- // recentServices.setText (service.getName());
- // selectionAllowed = true;
- propertyChannel.put( DP_SC_SERVICE, service );
- runButton.setEnabled( true );
-
- }
- }
- };
- worker.start();
- }
-
- /*******************************************************************************************************************
- * Called when no service is selected in order to display this fact on various places in the panel.
- ******************************************************************************************************************/
- protected void deselectService() {
- selService.setText( "" );
- updateInputDataPanel( INIT_SELECT );
- propertyChannel.remove( DP_SC_SERVICE );
- runButton.setEnabled( false );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getName() {
- return "Simple Client";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getDescription() {
- return "A panel allowing to create input data and to call an arbitrary Biomoby service. "
- + "Its purpose is mostly for the service developers to test their new services.";
- }
-
- /*******************************************************************************************************************
- *
- * Customized tree of services...
- *
- ******************************************************************************************************************/
- protected class CustomServicesTree extends ServicesTree {
-
- /***************************************************************************************************************
- * Construtor
- **************************************************************************************************************/
- public CustomServicesTree( RegistryModel model, CommonConsole console ) {
- super( model, console );
- }
-
- /***************************************************************************************************************
- *
- **************************************************************************************************************/
- protected void createPopups( String title ) {
- super.createPopups( title );
- removeFromPopups( AC_RELOAD );
- removeSeparatorAfter( AC_COLLAPSE );
- }
-
- /***************************************************************************************************************
- * Service selected in a service tree...
- **************************************************************************************************************/
- protected void selected( DefaultMutableTreeNode node ) {
- if ( node == null ) {
- // nothing selected
- deselectService();
- return;
- }
- updateInputDataPanel( "Loading..." );
- selService.setText( "" );
- final CommonNode nodeObject = ( CommonNode ) node.getUserObject();
- String currentServiceName = nodeObject.getValue();
- selectService( currentServiceName );
- setPrefValue( DP_SC_SERVICE_NAME, currentServiceName );
- }
- }
-
-}
+// SimpleClientPanel.java
+//
+// Created: December 2005
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.service.dashboard;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.util.Date;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JPasswordField;
+import javax.swing.JRadioButton;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import org.biomoby.service.dashboard.data.DataContainer;
+import org.biomoby.service.dashboard.data.ServiceInputPanel;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.tulsoft.shared.UUtils;
+import org.tulsoft.tools.gui.AwtUtils;
+import org.tulsoft.tools.gui.JFileChooserWithHistory;
+import org.tulsoft.tools.gui.JTextFieldWithHistory;
+import org.tulsoft.tools.gui.SwingUtils;
+
+/**
+ * A panel allowing to formulate input data and to call an arbitrary
+ * Biomoby service. Its interface is however not that user-friendly,
+ * and it is supposed to be used more or less for testing purposes in
+ * time when a new service is being created and developed.
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class SimpleClientPanel
+ extends AbstractPanel {
+
+ private static org.apache.commons.logging.Log log =
+ org.apache.commons.logging.LogFactory.getLog (SimpleClientPanel.class);
+
+ /** A property name. Its value contains a name of color that will
+ * be used to display service name.
+ */
+ protected static final String P_S_TITLE_COLOR = "simpleclient.service.title.color";
+
+ /** A property name. Its value contains a name of color that will
+ * be used as background for editable console with XML input.
+ */
+ protected static final String P_S_EDIT_BGCOLOR = "simpleclient.service.edit.bgcolor";
+
+ // some texts
+ protected static final String INIT_SELECT =
+ "
Start by selecting a service \n" +
+ " ";
+ data.setData(emptyMsg);
+ input.setText(emptyMsg);
+ }
+
+ // finally, call the service
+ stopButton.setEnabled (true);
+ callerModel.runIt (data);
+
+ } catch (MobyException e) {
+ exception = e;
+
+ } catch (Error e) {
+ exception = new MobyException (e.toString());
+ }
+ return null; // not used here
+ }
+
+ // runs on the event-dispatching thread
+ public void finished() {
+ if (wasCancelled) {
+ // service was interrupted by the Stop button - do
+ // nothing (the whole GUI should be already in a good
+ // state - the button 'Stop' took care about it)
+ return;
+ }
+
+ if (exception == null) {
+
+ // handle results here (using renderers...)
+ if (propertyChannel.getString(DP_INP_PING).toLowerCase().equals("true")) {
+ propertyChannel.fire (DP_STATUS_MSG, service.getName()+" isAlive.");
+ } else {
+ propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
+ }
+
+ if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE))) {
+ results.updateComponent (data);
+ }
+
+ } else {
+ if (propertyChannel.getString(DP_INP_PING).toLowerCase().equals("true")) {
+ propertyChannel.fire (DP_STATUS_MSG, service.getName()+" is dead.");
+ results.removeResults();
+ } else {
+ propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
+ error (CALLER_ERROR, exception);
+ }
+ exception.printStackTrace();
+ }
+ serviceFinished();
+ }
+ }
+
+ /**************************************************************************
+ * Called when a call to a service finished.
+ **************************************************************************/
+ protected void serviceFinished() {
+ runButton.setEnabled (true);
+ stopButton.setEnabled (false);
+ }
+
+ /**************************************************************************
+ * Called when a service is selected in a service tree (or in a
+ * 'recently used services' combo box), and also at the beginning
+ * when a service name is retrieved from user preferences.
+ *
+ * Get selected service from a registry model and generate a new
+ * 'input data panel' to reflect input data of the selected
+ * service.
+ **************************************************************************/
+ protected void selectService (final String serviceName) {
+ final Object source = this;
+ final SwingWorker worker = new SwingWorker() {
+ MobyService service;
+ MobyDataType[] dataTypes;
+ public Object construct() {
+ try {
+ service = registryModel.getService (serviceName);
+ dataTypes = registryModel.getDataTypes (source);
+ } catch (MobyException e) {
+ error (ServicesTree.SERVICES_ACCESS_ERROR, e);
+ }
+ return service; // not used here
+ }
+
+ // runs on the event-dispatching thread.
+ public void finished() {
+ if (service == null) {
+ deselectService();
+ } else {
+ updateInputDataPanel (service, dataTypes);
+ selService.setText (service.getName());
+// selectionAllowed = false;
+// recentServices.setText (service.getName());
+// selectionAllowed = true;
+ propertyChannel.put (DP_SC_SERVICE, service);
+ runButton.setEnabled (true);
+
+ }
+ }
+ };
+ worker.start();
+ }
+
+ /**************************************************************************
+ * Called when no service is selected in order to display this
+ * fact on various places in the panel.
+ **************************************************************************/
+ protected void deselectService() {
+ selService.setText ("");
+ updateInputDataPanel (INIT_SELECT);
+ propertyChannel.remove (DP_SC_SERVICE);
+ runButton.setEnabled (false);
+ }
+
+ /**************************************************************************
+ *
+ **************************************************************************/
+ public String getName() {
+ return "Simple Client";
+ }
+
+ /**************************************************************************
+ *
+ **************************************************************************/
+ public String getDescription() {
+ return
+ "A panel allowing to create input data and to call an arbitrary Biomoby service. " +
+ "Its purpose is mostly for the service developers to test their new services.";
+ }
+
+ /**************************************************************************
+ *
+ * Customized tree of services...
+ *
+ **************************************************************************/
+ protected class CustomServicesTree
+ extends ServicesTree {
+
+ /*********************************************************************
+ * Construtor
+ ********************************************************************/
+ public CustomServicesTree (RegistryModel model,
+ CommonConsole console) {
+ super (model, console);
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ protected void createPopups (String title) {
+ super.createPopups (title);
+ removeFromPopups (AC_RELOAD);
+ removeSeparatorAfter (AC_COLLAPSE);
+ }
+
+ /*********************************************************************
+ * Service selected in a service tree...
+ ********************************************************************/
+ protected void selected (DefaultMutableTreeNode node) {
+ if (node == null) {
+ // nothing selected
+ deselectService();
+ return;
+ }
+ updateInputDataPanel ("Loading...");
+ selService.setText ("");
+ final CommonNode nodeObject = (CommonNode)node.getUserObject();
+ String currentServiceName = nodeObject.getValue();
+ selectService (currentServiceName);
+ setPrefValue (DP_SC_SERVICE_NAME, currentServiceName);
+ }
+ }
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java 2008/11/26 08:54:21 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java 2008/12/03 15:21:13 1.8
@@ -1,168 +1,180 @@
-// ServiceCallerModel.java
-//
-// Created: February 2006
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.service.dashboard;
-
-import org.apache.axis.client.Call;
-import org.biomoby.client.ExtendedProtocolClient;
-import org.biomoby.client.ExtendedServiceLocator;
-import org.biomoby.client.MobyServiceLocator;
-import org.biomoby.service.dashboard.data.DataContainer;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.parser.MobyJob;
-import org.biomoby.shared.parser.MobyPackage;
-import org.tulsoft.shared.UUtils;
-
-/**
- * A model that achieves its task by calling (local, remote, or none) Biomoby service. It delegates the task of calling
- * a service to a true Biomoby client (that extends BaseClient ).
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-public class ServiceCallerModel extends AbstractModel {
-
- // private static org.apache.commons.logging.Log log =
- // org.apache.commons.logging.LogFactory.getLog (ServiceCallerModel.class);
-
- /*******************************************************************************************************************
- * Call a service. This is the main purpose of this model.
- *
- *
- * @param data
- * contains input data and this method replaces them by result data
- ******************************************************************************************************************/
- public void runIt( DataContainer data ) throws MobyException {
- SimpleClient worker = new SimpleClient( data );
- worker.process();
- }
-
- /*******************************************************************************************************************
- *
- * A real client - the main worker for this model..
- *
- ******************************************************************************************************************/
- protected class SimpleClient extends ExtendedProtocolClient {
-
- DataContainer data;
-
- /***************************************************************************************************************
- * Constructor.
- **************************************************************************************************************/
- public SimpleClient( DataContainer data ) {
- super();
- this.data = data;
- }
-
- /***************************************************************************************************************
- * What service to call and where to find it.
- **************************************************************************************************************/
- public MobyServiceLocator getServiceLocator() throws MobyException {
- return new MyServiceLocator();
- }
-
- /***************************************************************************************************************
- * Not used here...
- **************************************************************************************************************/
- public boolean fillRequest( MobyJob request, MobyPackage inputContext ) throws MobyException {
- return true;
- }
-
- /***************************************************************************************************************
- * Not used here...
- **************************************************************************************************************/
- public boolean useResponse( MobyJob response, MobyPackage responseContext ) throws MobyException {
- return true;
- }
-
- /***************************************************************************************************************
- * Return input XML (from a data container obtained in the constructor).
- **************************************************************************************************************/
- public String fillRequest() throws MobyException {
-
- if ( data == null ) throw new MobyException( "No input data given." );
-
- return ( String ) data.getData();
- }
-
- /**
- * Sets the authentication for the service call. If the user has checked the corresponding box in the Dashboard
- * the values are stored in the propertychannel.
- */
- protected void setAuthentication( Call call ) {
- String user = propertyChannel.getString( DashboardProperties.DP_USER_AUTHENTICATION );
- if ( !isEmpty( user ) ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, new String( ( char[] ) propertyChannel
- .get( DashboardProperties.DP_PASSWORD_AUTHENTICATION ) ) );
- }
- }
-
- /***************************************************************************************************************
- *
- **************************************************************************************************************/
- public boolean useResponse( String xmlResponse ) throws MobyException {
-
- data.setData( xmlResponse );
-
- // do nothing more if it is just an input echo
- if ( ( ( ExtendedServiceLocator ) getServiceLocator() ).isLoop() ) return false;
-
- return false;
- }
- }
-
- /*******************************************************************************************************************
- *
- * A service locator filled from the property channel.
- *
- ******************************************************************************************************************/
- protected class MyServiceLocator extends ExtendedServiceLocator {
-
- public MyServiceLocator() throws MobyException {
- super();
-
- // fill this locator by a service
- MobyService selService = ( MobyService ) propertyChannel.get( DP_SC_SERVICE );
- if ( selService == null ) throw new MobyException( "No service given." );
- MobyService clonedService = new MobyService( selService.getName(), selService.getAuthority() );
- clonedService.setURL( selService.getURL() );
- setService( clonedService );
-
- // fill how to call this service
- String howToCall = propertyChannel.getString( DP_CALL_SERVICE );
- if ( DP_CS_NEWURL.equals( howToCall ) ) {
- String sEndpoint = propertyChannel.getString( DP_ENDPOINT );
- if ( !UUtils.isEmpty( sEndpoint ) ) clonedService.setURL( sEndpoint );
-
- }
- else if ( DP_CS_REGISTRY.equals( howToCall ) ) {
- clonedService.setURL( null );
- setRegistryEndpoint( propertyChannel.getString( DP_REGISTRY_ENDPOINT ) );
- setRegistryNamespace( propertyChannel.getString( DP_REGISTRY_NAMESPACE ) );
-
- }
- else if ( DP_CS_CLASS.equals( howToCall ) ) {
- String localClass = propertyChannel.getString( DP_IMPL_CLASS );
- if ( UUtils.isEmpty( localClass ) ) throw new MobyException( "No local class given." );
- setLocalClass( localClass );
-
- }
- else if ( DP_CS_NONE.equals( howToCall ) ) {
- setLoop( true );
- }
-
- setAsBytes( propertyChannel.getBoolean( DP_INP_ASBYTES, false ) );
-
- }
- }
-
-}
+// ServiceCallerModel.java
+//
+// Created: February 2006
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.service.dashboard;
+
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.parser.MobyPackage;
+import org.biomoby.shared.parser.MobyJob;
+import org.biomoby.client.ExtendedProtocolClient;
+import org.biomoby.client.MobyServiceLocator;
+import org.biomoby.client.ExtendedServiceLocator;
+import org.biomoby.service.dashboard.data.DataContainer;
+
+import org.tulsoft.shared.UUtils;
+
+/**
+ * A model that achieves its task by calling (local, remote, or none)
+ * Biomoby service. It delegates the task of calling a service to a
+ * true Biomoby client (that extends BaseClient ).
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class ServiceCallerModel
+ extends AbstractModel {
+
+// private static org.apache.commons.logging.Log log =
+// org.apache.commons.logging.LogFactory.getLog (ServiceCallerModel.class);
+
+ /**************************************************************************
+ * Call a service. This is the main purpose of this model.
+ *
+ * @param data contains input data and this method replaces them
+ * by result data
+ *************************************************************************/
+ public void runIt (DataContainer data)
+ throws MobyException {
+ SimpleClient worker = new SimpleClient (data);
+ worker.process();
+ }
+
+ /**************************************************************************
+ *
+ * A real client - the main worker for this model..
+ *
+ *************************************************************************/
+ protected class SimpleClient
+ extends ExtendedProtocolClient {
+
+ DataContainer data;
+
+ /**************************************************************************
+ * Constructor.
+ *************************************************************************/
+ public SimpleClient (DataContainer data) {
+ super();
+ this.data = data;
+ }
+
+ /**************************************************************************
+ * What service to call and where to find it.
+ *************************************************************************/
+ public MobyServiceLocator getServiceLocator()
+ throws MobyException {
+ return new MyServiceLocator();
+ }
+
+ /**************************************************************************
+ * Not used here...
+ *************************************************************************/
+ public boolean fillRequest (MobyJob request, MobyPackage inputContext)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * Not used here...
+ *************************************************************************/
+ public boolean useResponse (MobyJob response,
+ MobyPackage responseContext)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * Return input XML (from a data container obtained in the
+ * constructor).
+ *************************************************************************/
+ public String fillRequest()
+ throws MobyException {
+
+ if (data == null)
+ throw new MobyException ("No input data given.");
+
+ return (String)data.getData();
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean useResponse (String xmlResponse)
+ throws MobyException {
+
+ data.setData (xmlResponse);
+
+ // do nothing more if it is just an input echo
+ if ( ((ExtendedServiceLocator)getServiceLocator()).isLoop())
+ return false;
+
+ return false;
+ }
+ }
+
+ /**************************************************************************
+ *
+ * A service locator filled from the property channel.
+ *
+ *************************************************************************/
+ protected class MyServiceLocator
+ extends ExtendedServiceLocator {
+
+ public MyServiceLocator()
+ throws MobyException {
+ super();
+
+ // fill this locator by a service
+ MobyService selService = (MobyService)propertyChannel.get (DP_SC_SERVICE);
+ if (selService == null)
+ throw new MobyException ("No service given.");
+ MobyService clonedService = new MobyService (selService.getName(), selService.getAuthority());
+ clonedService.setURL (selService.getURL());
+ setService (clonedService);
+
+ // fill how to call this service
+ String howToCall = propertyChannel.getString (DP_CALL_SERVICE);
+ if (DP_CS_NEWURL.equals (howToCall)) {
+ String sEndpoint = propertyChannel.getString (DP_ENDPOINT);
+ if (! UUtils.isEmpty (sEndpoint))
+ clonedService.setURL (sEndpoint);
+
+ } else if (DP_CS_REGISTRY.equals (howToCall)) {
+ clonedService.setURL (null);
+ setRegistryEndpoint (propertyChannel.getString (DP_REGISTRY_ENDPOINT));
+ setRegistryNamespace (propertyChannel.getString (DP_REGISTRY_NAMESPACE));
+
+ } else if (DP_CS_CLASS.equals (howToCall)) {
+ String localClass = propertyChannel.getString (DP_IMPL_CLASS);
+ if (UUtils.isEmpty (localClass))
+ throw new MobyException ("No local class given.");
+ setLocalClass (localClass);
+
+ } else if (DP_CS_NONE.equals (howToCall)) {
+ setLoop (true);
+ }
+
+ setAsBytes (propertyChannel.getBoolean (DP_INP_ASBYTES, false));
+
+ // sets the user and the password
+ // the getString method returns an empty string in case the
+ // key is not in the propertychannel, therefore the test if
+ // the value is not empty
+ String user = propertyChannel.getString(DP_USER_AUTHENTICATION);
+ if(user.length() > 0) {
+ setUser( user );
+ }
+ String password = propertyChannel.getString(DP_PASSWORD_AUTHENTICATION);
+ if(password.length() > 0) {
+ setPassword( password );
+ }
+ }
+ }
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java 2008/11/26 08:54:21 1.30
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java 2008/12/03 15:21:13 1.31
@@ -9,10 +9,10 @@
package org.biomoby.service.dashboard;
/**
- * A list of names of most/all recognized properties that can be fired by dashboard panels, and a list of names of Java
- * properties that can be used to configure the dashboard.
- *
- *
+ * A list of names of most/all recognized properties that can be fired
+ * by dashboard panels, and a list of names of Java properties that
+ * can be used to configure the dashboard.
+ *
* @author Martin Senger
* @version $Id$
*/
@@ -44,9 +44,9 @@
static final String DP_FL_BIOCASE = "biocase";
static final String DP_FL_HIBERNATE = "hibernate";
- static final String DP_SEL_SERVICES = "selectedServices"; // type: Vector with service/authority name
- static final String DP_SEL_AUTHORITIES = "selectedAuthorities"; // type: Vector with authority name
- static final String DP_DEPL_SERVICES = "servicesToDeploy"; // type: Map with serviceName => className
+ static final String DP_SEL_SERVICES = "selectedServices"; // type: Vector with service/authority name
+ static final String DP_SEL_AUTHORITIES = "selectedAuthorities"; // type: Vector with authority name
+ static final String DP_DEPL_SERVICES = "servicesToDeploy"; // type: Map with serviceName => className
static final String DP_LOCAL_DEPLOY = "use-local-deploy";
static final String DP_TOMCAT_HOME = "tomcatHome";
@@ -82,10 +82,10 @@
static final String DP_DETACH_VIEW = "detachViewers";
- // static final String DP_SC_IN_DATA = "sc-inputData";
+// static final String DP_SC_IN_DATA = "sc-inputData";
static final String DP_SC_IN_FILE = "sc-inputFromFile";
static final String DP_SC_INPUT_FILE = "sc-inputFile";
- static final String DP_SC_SERVICE = "dp-sc-service"; // type: MobyService
+ static final String DP_SC_SERVICE = "dp-sc-service"; // type: MobyService
static final String DP_SC_SERVICE_NAME = "dp-sc-service-name";
static final String DP_SC_SERVICES = "dp-sc-recent-services";
@@ -97,21 +97,21 @@
static final String DP_DATATYPE_NAME = "dp-datatype-name";
// names of properties used in property channel storage
- static final String DP_REGISTRY_MODEL = "dp-registry-model"; // type: RegistryModel
- static final String DP_ANT_MODEL = "dp-ant-model"; // type: AntModel
+ static final String DP_REGISTRY_MODEL = "dp-registry-model"; // type: RegistryModel
+ static final String DP_ANT_MODEL = "dp-ant-model"; // type: AntModel
static final String DP_REGISTRY_SYNONYM = "dp-registry-synonym";
- static final String DP_REG_INFO = "dp-reg-info"; // type: Boolean
+ static final String DP_REG_INFO = "dp-reg-info"; // type: Boolean
static final String DP_REGISTRY_ENDPOINT = "dp-registry-endpoint";
static final String DP_REGISTRY_NAMESPACE = "dp-registry-namespace";
static final String DP_CACHE_DIR = "dp-cache-dir";
- static final String DP_USE_CACHE = "dp-use-cache"; // type: Boolean
+ static final String DP_USE_CACHE = "dp-use-cache"; // type: Boolean
static final String DP_REG_DT_NAME = "dp-reg-dt-name";
static final String DP_REG_DT_AUTH = "dp-reg-dt-auth";
static final String DP_REG_DT_EMAIL = "dp-reg-dt-email";
static final String DP_REG_DT_DESC = "dp-reg-dt-desc";
- static final String DP_REG_DT_TREE = "dp-reg-dt-tree"; // type: MobyDataType
+ static final String DP_REG_DT_TREE = "dp-reg-dt-tree"; // type: MobyDataType
static final String DP_REG_NS_NAME = "dp-reg-ns-name";
static final String DP_REG_NS_AUTH = "dp-reg-ns-auth";
@@ -132,88 +132,97 @@
static final String DP_REG_S_RDF_URL = "dp-reg-s-rdf-url";
static final String DP_REG_S_RDF_PATH = "dp-reg-s-rdf-path";
static final String DP_REG_S_XML_PATH = "dp-reg-s-xml-path";
- static final String DP_USE_SIGNATURE = "dp-use-signature"; // type: Boolean
- static final String DP_USE_AUTHORITATIVE = "dp-use-auth"; // type: Boolean
+ static final String DP_USE_SIGNATURE = "dp-use-signature"; // type: Boolean
+ static final String DP_USE_AUTHORITATIVE = "dp-use-auth"; // type: Boolean
static final String DP_REG_S_TYPE = "dp-reg-s-type";
static final String DP_REG_VERBOSE = "dp-reg-verbose";
- static final String DP_S_SELECTED = "dp-s-selected"; // type: MobyService
+ static final String DP_S_SELECTED = "dp-s-selected"; // type: MobyService
- /**
- * A property name. Its value contains a title that will appear in big fonts on top of the dashboard. It may be
- * empty if property {@link #DP_TITLE_ICON} is defined; otherwise a default value will be used.
+ /** A property name. Its value contains a title that will appear
+ * in big fonts on top of the dashboard. It may be empty if
+ * property {@link #DP_TITLE_ICON} is defined; otherwise a default
+ * value will be used.
*/
static final String DP_TITLE = "dashboard.title";
- /**
- * A property name. Its value contains a filename with an icon accompanying a dashboard title (defined by property
- * {@link #DP_TITLE}. No default value used. Specify here either an absolute path (not recommended) or a relative
- * path whose beginning can be found somewhere on the CLASSPATH.
+ /** A property name. Its value contains a filename with an icon
+ * accompanying a dashboard title (defined by property {@link
+ * #DP_TITLE}. No default value used. Specify here either an
+ * absolute path (not recommended) or a relative path whose
+ * beginning can be found somewhere on the CLASSPATH.
*/
static final String DP_TITLE_ICON = "dashboard.title.icon";
- /**
- * A property name. Its value contains a filename with the main dashboard icon. Specify here either an absolute path
- * (not recommended) or a relative path whose beginning can be found somewhere on the CLASSPATH.
+ /** A property name. Its value contains a filename with the main
+ * dashboard icon. Specify here either an absolute path (not
+ * recommended) or a relative path whose beginning can be found
+ * somewhere on the CLASSPATH.
*/
static final String DP_ICON = "dashboard.icon";
- /**
- * A property name. Its value contains a color name used to paint main dashboard background. The name can be a color
- * name, or a number in various format (see GraphColours for details).
+ /** A property name. Its value contains a color name used to paint
+ * main dashboard background. The name can be a color name, or a
+ * number in various format (see GraphColours for
+ * details).
*/
static final String DP_BGCOLOR = "dashboard.bgcolor";
- /**
- * A property name. Its value contains a short description what a dashboard can do generally. Often, however, it is
- * more convenient to put the description in a file and to use property {@link #DP_DESCRIPTION_FILE}.
+ /** A property name. Its value contains a short description what a
+ dashboard can do generally. Often, however, it is more
+ convenient to put the description in a file and to use
+ property {@link #DP_DESCRIPTION_FILE}.
*/
static final String DP_DESCRIPTION = "dashboard.description";
- /**
- * A property name. Its value contains a file name with a short description what a dashboard can do generally.
+ /** A property name. Its value contains a file name with a short
+ description what a dashboard can do generally.
*/
static final String DP_DESCRIPTION_FILE = "dashboard.description.file";
- /**
- * A property name. Its value contains a short description of a project that uses this dashboard. Often, however, it
- * is more convenient to put the description in a file and to use property {@link #DP_P_DESCRIPTION_FILE}.
+ /** A property name. Its value contains a short description of a
+ project that uses this dashboard. Often, however, it is more
+ convenient to put the description in a file and to use
+ property {@link #DP_P_DESCRIPTION_FILE}.
*/
static final String DP_P_DESCRIPTION = "project.description";
- /**
- * A property name. Its value contains a file name with a short description of a project that uses this dashboard.
+ /** A property name. Its value contains a file name with a short
+ description of a project that uses this dashboard.
*/
static final String DP_P_DESCRIPTION_FILE = "project.description.file";
- /**
- * A property name. Its value contains a name of a contact person, possibly with an email address.
+ /** A property name. Its value contains a name of a contact
+ person, possibly with an email address.
*/
static final String DP_CONTACT = "dashboard.contact";
- /**
- * A property name. Its value contains a directory name with the local cache of a BiMoby Central registry.
+ /** A property name. Its value contains a directory name with the
+ * local cache of a BiMoby Central registry.
*/
static final String DP_REGISTRY_CACHE_DIR = "registry.cache.dir";
- /**
- * A property name. Its value contains a name or a comma-separated list of names of BioMoby registries that will be
- * displayed in the RegistryPanel. If this property is missing, the list is taken from the hard-coded known
- * registries in the Java source file.
- *
- *
- * The names (values of this property) are equivalent to the 'synonym' attribute of the Registry class.
+ /** A property name. Its value contains a name or a
+ * comma-separated list of names of BioMoby registries that will
+ * be displayed in the RegistryPanel. If this property is missing,
+ * the list is taken from the hard-coded known registries in the
+ * Java source file.
+ *
+ * The names (values of this property) are equivalent to the
+ * 'synonym' attribute of the Registry class.
*/
static final String DP_WANTED_REGISTRIES = "dashboard.wanted.registries";
- /**
- * A property name. Its value contains a name (synonym) of a default BioMoby registry. By default, the default
- * registry is taken either from the first element in {@link #DP_WANTED_REGISTRIES} or from
+ /** A property name. Its value contains a name (synonym) of a
+ * default BioMoby registry. By default, the default registry is
+ * taken either from the first element in {@link
+ * #DP_WANTED_REGISTRIES} or from
* Registries.DEFAULT_REGISTRY_SYNONYM .
*/
static final String DP_DEFAULT_REGISTRY = "dashboard.default.registry";
+
/**
* A property name. Its value contains the user name used for the authentication required for the servlet container
* the service is hosted at.
From groscurt at dev.open-bio.org Wed Dec 3 10:21:13 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 10:21:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031521.mB3FLD8Y013747@dev.open-bio.org>
groscurt
Wed Dec 3 10:21:13 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv13676/src/main/org/biomoby/client
Modified Files:
MobyRequest.java BaseClient.java MobyServiceLocator.java
Log Message:
changes made for the authentication... without formatting this time
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.41,1.42 BaseClient.java,1.13,1.14 MobyServiceLocator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/11/26 08:53:43 1.41
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/12/03 15:21:13 1.42
@@ -1,1028 +1,1030 @@
-
-package org.biomoby.client;
-
-import java.io.*;
-import java.util.*;
-
-import javax.xml.namespace.QName;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.rpc.Service;
-import javax.xml.transform.TransformerException;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.message.MessageElement;
-import org.apache.xml.utils.PrefixResolver;
-import org.apache.xml.utils.PrefixResolverDefault;
-import org.apache.xpath.XPath;
-import org.apache.xpath.XPathContext;
-import org.apache.xpath.objects.XNodeSet;
-import org.apache.xpath.objects.XObject;
-
-import org.biomoby.shared.*;
-import org.biomoby.shared.data.*;
-import org.biomoby.shared.parser.MobyTags; // defined the Moby XML element names
-import org.biomoby.w3c.addressing.EndpointReference;
-import org.omg.lsae.notifications.AnalysisEvent;
-
-import org.w3c.dom.*;
-
-/**
- * This class handles the WSDL transaction to request a response from a remote SOAP Web service that handles the MOBY format. It depends on having already retrieved the definition of the Web
- * service via the MOBY central registry using the jMOBY
- * API, and for now it uses the Apache Axis Web services framework,
- * as well as Apache Xalan. There are code comments for the few lines that rely on Axis classes rather than the JAX-RPC
- * interfaces.
- *
- * @author Paul Gordon gordonp at ucalgary.ca
- */
-public class MobyRequest {
-
- protected MobyService mobyService = null;
- protected MobyContentInstance inputData = null;
- protected MobyContentInstance outputData = null;
- protected Central mobyCentral = null;
- protected PrefixResolver mobyPrefixResolver = null;
-
- protected Hashtable wsdlCache = null;
- protected String lastWsdlCacheKey = null;
- protected DocumentBuilder docBuilder = null;
- protected Service service = null;
-
- protected Class stringType;
- protected static boolean debug = false;
- protected PrintStream debugPS = System.err;
- protected XPathContext xpath_context;
- protected String responseString = null;
-
- private XPath stringEncodedXPath;
- private XPath base64EncodedXPath;
- private XPath simpleChildXPath;
- private XPath collectionChildXPath;
-
- private int autoID = 0;
-
- // Used as invocation callback if MobyRequest is acting as a server,
- // or is executing services as a client asynchronously
- private Vector< MobyRequestEventHandler > eventHandlers;
-
- private String user;
- private String password;
-
- /**
- * Default constructor. You should have a Central instance around since you're going to be retrieving MobyServices
- * to pass into here. Lets reuse it.
- *
- * @param central An instance of a Moby central object so we can make requests about object types, etc.
- * @throws ParserConfigurationException if JAXP doesn't have any valid DOM-building XML parsers set up for use
- */
- public MobyRequest( Central central ) throws ParserConfigurationException {
- mobyCentral = central;
- wsdlCache = new Hashtable();
-
- eventHandlers = new Vector< MobyRequestEventHandler >();
-
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware( true );
- docBuilder = dbf.newDocumentBuilder();
-
- try {
- stringType = Class.forName( "java.lang.String" );
- }
- catch ( ClassNotFoundException classe ) {
- debugPS.println( "WARNING: Something is very wrong, could not find Class definition of String: " + classe );
- }
-
- xpath_context = new XPathContext();
- mobyPrefixResolver = new MobyPrefixResolver();
-
- // Now compile the XPath statements that will be used fetch data from the server response
- try {
- base64EncodedXPath = new XPath( "//*[starts-with(substring-after(@" + MobyPrefixResolver.XSI1999_PREFIX
- + ":type, ':'), \"base64\") or starts-with(substring-after(@" + MobyPrefixResolver.XSI2001_PREFIX
- + ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT );
- stringEncodedXPath = new XPath( "//*[substring-after(@" + MobyPrefixResolver.XSI1999_PREFIX
- + ":type, ':')=\"string\" or substring-after(@" + MobyPrefixResolver.XSI2001_PREFIX
- + ":type, ':')=\"string\"] | //" + MobyPrefixResolver.SOAP_ENC_PREFIX + ":string", null,
- mobyPrefixResolver, XPath.SELECT );
- simpleChildXPath = new XPath( "moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT );
- collectionChildXPath = new XPath( "moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT );
- }
- catch ( TransformerException te ) {
- debugPS.println( "Syntax error encountered while compiling XPath "
- + "statements for internal use (code bug?): " + te );
- }
- setDebugMode( System.getProperty( "moby.debug" ) != null );
- }
-
- /**
- * @param mode if true, debugging information is printed to the stream returned by getDebugOutputStream
- */
- public void setDebugMode(boolean mode) {
- debug = mode;
- }
-
- /**
- * Standard error is used unless this method is called.
- *
- * @param ps the OutputStream to which debugging information is sent.
- * @throws IllegalArgumentException if the stream is null
- */
- public void setDebugPrintStream(PrintStream ps) throws IllegalArgumentException {
- if ( ps == null ) {
- throw new IllegalArgumentException( "The OutputStream specified to MobyRequest was null" );
- }
- debugPS = ps;
- }
-
- /**
- * @param user the user for a possible service authentication
- * @param password the passoword for a possible service authentication
- */
- public void setAuthentication(String user, String password) {
- this.user = user;
- this.password = password;
- }
-
- /**
- * @return the instance of the class implementing Central that we are using
- */
- public Central getCentralImpl() {
- return mobyCentral;
- }
-
- /**
- * @param mobyservice the MobyService that should be executed when invokeService is called
- */
- public void setService(MobyService mobyservice) {
- if ( mobyservice == null ) {
- mobyService = null;
- }
- else if ( mobyService == null || !mobyservice.equals( mobyService ) ) {
- mobyService = mobyservice;
- }
- }
-
- /**
- * @return the MobyService that will be executed when invokeService is called
- */
- public MobyService getService() {
- return mobyService;
- }
-
- /**
- * @return the Raw MOBY XML response as a string
- */
- public String getResponseXML() {
- return responseString;
- }
-
- /**
- * Sets the input data for the MOBY service request. The length of the input array, and the number of input
- * parameters required by the service must be equal when invokeService() is called. This method strictly enforces
- * that the input be of the appropriate type for the service.
- *
- * Note that there is no requirement to use MobyDataInstance.setXmlMode() before passing in data, this class will
- * temporarily set the XML mode of the data when it is required.
- *
- * @throws IllegalArgumentException if the input does not fit the criteria of the service (e.g. wrong data type)
- */
- public void setInput(MobyContentInstance data) throws MobyException {
- inputData = data;
- }
-
- /**
- * Takes the data in the array, with their current articleNames, as input for the service
- */
- public void setInput(MobyDataInstance[] data) throws MobyException {
- MobyDataJob job = new MobyDataJob();
- for ( MobyDataInstance param : data ) {
- job.put( param.getName(), param );
- }
- inputData = new MobyContentInstance();
- inputData.put( job );
- }
-
- /**
- * Convenience method to run services that take one argument. If the service requires the input to have a name, it
- * will be automatically assigned.
- */
- public void setInput(MobyDataInstance datum) throws MobyException {
- setInput( datum, "" );
- }
-
- /**
- * Convenience method to run services that take one named argument.
- */
- public void setInput(MobyDataInstance datum, String paramName) throws MobyException {
- inputData = new MobyContentInstance( datum, paramName );
- }
-
- /**
- * @return the MobyService that will be executed when invokeService is called
- */
- public MobyContentInstance getInput() {
- return inputData;
- }
-
- /**
- * Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
- */
- public void setSecondaryInput(Collection< MobyDataSecondaryInstance > secondaryData) throws MobyException {
- setSecondaryInput( secondaryData.toArray( new MobyDataSecondaryInstance[ secondaryData.size() ] ) );
- }
-
- /**
- * This method will assign the provided secondary parameters to all primary input data currently in this object.
- * This is covenient if you are running 100 seqs through BLAST and only want to set the parameters once. If you
- * instead want to set secondary input differently for all primary inputs, you'll need to create a custom
- * MobyContentInstance as input to setInput().
- *
- * @throws MobyException if a parameter name is blank, or overrides a primary parameter
- */
- public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException {
-
- Iterator queryNames = inputData.keySet().iterator();
- // For each query
- while (queryNames.hasNext()) {
- MobyDataJob queryParams = inputData.get( queryNames.next() );
- // Set all the secondary params (overwrites any old ones)
- for ( int i = 0; i < secondaryData.length; i++ ) {
- String secName = secondaryData[ i ].getName();
- if ( secName == null || secName.length() == 0 ) {
- throw new MobyException( "A secondary parameter cannot have a blank name (array index " + i + ")" );
- }
- if ( queryParams.containsKey( secName ) && queryParams.get( secName ) instanceof MobyPrimaryData ) {
- throw new MobyException( "A secondary parameter cannot override an existing primary parameter "
- + "with the same name (" + secName + ")" );
- }
- queryParams.put( secName, secondaryData[ i ] );
- }
- }
- }
-
- /**
- * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the
- * correspondingly indexed input request.
- *
- * @throws MobyException if you try to get the results before calling InvokeService
- */
- public MobyContentInstance getOutput() throws MobyException {
- if ( outputData == null ) {
- throw new MobyException( "Trying to access MOBY service results " + "before the service is invoked" );
- }
- else {
- return outputData;
- }
- }
-
- /**
- * The main method of the class. If all of the MOBY input objects are properly defined according to the Web service
- * definition, a SOAP request will be sent to the remote server, and the method will return one or more MOBY objects
- * (synchronous). Call this method after calling setService, and setInput. If you do not call setSecondaryInput, the
- * default secondary parameter values will be used.
- *
- * @return the results of the remote Web service in response to the give input
- *
- * @throws MobyException i.e. there was something wrong with the input, output or remote service's logic
- * @throws SOAPException i.e. there was a problem with the underlying transaction/transport layer
- */
- public MobyContentInstance invokeService() throws Exception, MobyException, SOAPException, NoSuccessException {
- return mobyService.isAsynchronous()
- ? invokeService( inputData, new StringBuffer() )
- : invokeService( inputData, ( StringBuffer ) null );
- }
-
- // Used internally for asynchronous thread calls that all need the XML data
- // and can't rely on the answer from thread-insensitive getResponseXML()
- private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML) throws Exception,
- MobyException, SOAPException, NoSuccessException {
- return invokeService( inData, contentsXML, null, 0 );
- }
-
- private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML,
- MobyRequestEventHandler handler, int requestId) throws Exception, MobyException, SOAPException,
- NoSuccessException {
-
- if ( mobyService == null ) {
- throw new MobyException( "Tried to invoke null service from MobyRequest (call setService first)" );
- }
-
- Element mobyDOM = null;
- if ( mobyService.isAsynchronous() ) {
- // Async is "simpler", because it had to merge DOMs together into a single MobyContentInstance anyway
- MobyContentInstance mci = performAsyncSOAPRequest( mobyService, inData, handler, requestId );
- StringWriter writer = new StringWriter();
- MobyDataUtils.toXMLDocument( writer, mci );
- contentsXML.append( writer.toString() );
- return mci;
- }
- else {
- String mobyXML = convertMOBYDataToMOBYRequest( inData );
- Call call = getServiceFromWSDL();
- if ( user != null && password != null ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, password );
- }
- mobyDOM = performSOAPRequest( call, mobyXML, contentsXML );
- // The following parses the DOM and extracts all the appropriate jMOBY objects to represent the XML in Java
- return MobyDataUtils.fromXMLDocument( mobyDOM, mobyService.getServiceType().getRegistry() );
- }
- }
-
- protected MobyContentInstance performAsyncSOAPRequest(MobyService mservice, MobyContentInstance inData,
- MobyRequestEventHandler handler, int requestId) throws Exception {
- String mobyXML = convertMOBYDataToMOBYRequest( inData );
- EndpointReference epr = AsyncClient.sendRequest( mservice, mobyXML );
-
- // Essentially cloning, so removing ids doesn't change the
- // MobyContentInstance "data" (which we will use again later on)
- MobyContentInstance finalContents = new MobyContentInstance();
- Set< String > queryIDs = new HashSet< String >( inData.keySet() );
- try {
- // Should add some timeout here...
- while (!queryIDs.isEmpty()) {
- // todo: make this setable
- Thread.sleep( 5000 );
-
- AnalysisEvent[] events = AsyncClient.poll( epr, queryIDs );
-
- Vector< String > newDataAvailable = new Vector< String >();
- for ( AnalysisEvent event : events ) {
- if ( event != null && event.isCompleted() ) {
- queryIDs.remove( event.getQueryId() );
- newDataAvailable.add( event.getQueryId() );
- }
- }
-
- if ( newDataAvailable.size() > 0 ) {
- // Parse and merge the new data into the existing contents
- InputStream resultStream = AsyncClient.getResultStream( epr, newDataAvailable );
- Element mobyDOM = asyncSoapTextToMobyDOM( resultStream );
- MobyContentInstance newResults = MobyDataUtils.fromXMLDocument( mobyDOM,
- mservice.getServiceType()
- .getRegistry() );
- // The merge
- for ( String jobid : newResults.keySet() ) {
- finalContents.put( jobid, newResults.get( jobid ) );
- }
-
- // Inform the handler that some data has been added to the response (for incremental display?)
- if ( handler != null ) {
- MobyRequestEvent mre = new MobyRequestEvent( finalContents, this, mservice, null, requestId );
- StringWriter xmlWriter = new StringWriter();
- MobyDataUtils.toXMLDocument( xmlWriter, finalContents );
-
- mre.setContentsXML( xmlWriter.toString() );
- if ( !queryIDs.isEmpty() ) {
- // Send an update event only if we aren't finished yet.
- // If we are finished, the client is going to get this event as the
- // invocation thread finishes up (no need to double up).
- handler.processEvent( mre );
- }
- }
- }
- }
- }
- catch ( Exception e ) {
- e.printStackTrace();
- AsyncClient.destroy( epr );
- throw new Exception( "Exception occured while polling the service invocation: " + e );
- }
-
- return finalContents;
- }
-
- private Element asyncSoapTextToMobyDOM(InputStream inStream) throws Exception {
- Element soapDOM = null;
- synchronized ( docBuilder ) {
- soapDOM = docBuilder.parse( inStream ).getDocumentElement();
- }
- final boolean IS_ASYNC_SERVICE_CALL = true;
- return decodeSOAPMessage( soapDOM, null, null, IS_ASYNC_SERVICE_CALL );
- }
-
- /**
- * Asynchronous call to invokeService. A callback to the passed-in handler will be made when the response is ready,
- * or there is an exception.
- *
- * @return the id that the callback event will return from getID(), allowing a client to distinguish between
- * multiple concurrent invocation callbacks
- */
- public synchronized int invokeService(MobyRequestEventHandler handler) {
- int id = autoID++;
-
- Thread t = new InvocationThread( this, inputData, handler, id ); // see internal class definition below
- t.start();
-
- return id;
- }
-
- // This is the class that asynchronously calls the service and does a callback to
- // the handler specified in the invocation.
- class InvocationThread extends Thread {
- MobyContentInstance data;
- MobyService mservice;
- MobyRequest mobyRequest;
- MobyRequestEventHandler handler;
- int requestId;
-
- InvocationThread( MobyRequest mr, MobyContentInstance inData, MobyRequestEventHandler h, int id ) {
- data = inData;
- mobyRequest = mr;
- mservice = mobyRequest.getService();
- handler = h;
- requestId = id;
-
- // Name the thread after the service being run, mostly for ease of debugging
- setName( mservice.getName() + requestId );
- }
-
- public void run() {
- MobyRequestEvent requestEvent = new MobyRequestEvent( data, mobyRequest, mservice, null, requestId );
- // Tell the handler we're starting the request, with the given data
- handler.start( requestEvent );
-
- MobyRequestEvent responseEvent = null;
- MobyContentInstance content = null;
- StringBuffer contentsXML = new StringBuffer(); // to be filled in by the RPC call below
- try {
- content = mobyRequest.invokeService( data, contentsXML, handler, requestId ); // RPC call...
- }
- catch ( Exception e ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, e, requestId );
- }
- catch ( Error err ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, err, requestId );
- }
- if ( responseEvent == null ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, null, requestId );
- }
- // We've got the raw XML laying around, so why not provide it unmolested to the callback?
- responseEvent.setContentsXML( contentsXML.toString() );
- handler.processEvent( responseEvent );
- handler.stop( mobyRequest, requestId );
- }
- }
-
- public void addEventHandler(MobyRequestEventHandler h) {
- eventHandlers.add( h );
- }
-
- public void removeEventHandler(MobyRequestEventHandler h) {
- eventHandlers.remove( h );
- }
-
- public void sendResponse(MobyRequestEvent mre) {
- // Not yet implemented, need to conform to some web.xml specification here...
- }
-
- /**
- * This method retrieves from Moby Central a copy of the WSDL document for the service (or uses an internally cached
- * copy from a previous invocation), and sets the variables for the SOAP call appropriately so you can consequently
- * call performSOAPRequest.
- */
- protected Call getServiceFromWSDL() throws MobyException, NoSuccessException {
- // String wsdl = null;
-
- // // Since this is how we retrieve a service from Central, use the same values as the key to the hash
- // String wsdlCacheKey = mobyService.getName() + "@" + mobyService.getAuthority();
-
- // // This is the same call as last time, so we don't need to change the setup
- // if(wsdlCacheKey.equals(lastWsdlCacheKey)){
- // return setCallFromWSDL((String) wsdlCache.get(wsdlCacheKey));
- // }
- // // We haven't encountered this service yet
- // else if(!wsdlCache.containsKey(wsdlCacheKey)){
- // wsdl = mobyCentral.getServiceWSDL(mobyService.getName(), mobyService.getAuthority());
- // wsdlCache.put(wsdlCacheKey, wsdl);
- // }
- // // We've dealt with this one before
- // else{
- // wsdl = (String) wsdlCache.get(wsdlCacheKey);
- // }
-
- // lastWsdlCacheKey = wsdlCacheKey; // Keep track of the last invocation
-
- // Get ready to do SOAP
- return setCallFromWSDL( null );
- }
-
- /**
- * Creates the SOAP Call that will be invoked later. This should be based on the WSDL document and parameter
- * information from the MobyService, but these are currently not up to snuff.
- */
- protected Call setCallFromWSDL(String wsdl) throws MobyException, SOAPException {
- if ( service == null ) {
- service = new org.apache.axis.client.Service(); // AXIS SPECIFIC This acts as a factory for Calls
- }
-
- Call soapCall;
- try {
- soapCall = ( Call ) service.createCall();// create a fresh Call each time
- }
- catch ( javax.xml.rpc.ServiceException se ) {
- throw new SOAPException( "Could not instatiate call to SOAP Service: " + se );
- }
-
- // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll
- // have to do the call's info setting manually.
- // ((org.apache.axis.client.Call) soapCall).setSOAPService(soapService);
- soapCall.removeAllParameters();
- soapCall.setTargetEndpointAddress( mobyService.getURL() );
- soapCall.setPortName( new QName( "http://biomoby.org/", mobyService.getName() + "PortType" ) );
- // soapCall.setOperationName(new QName("http://biomoby.org/",
- // mobyService.getName()));
- soapCall.setSOAPActionURI( "http://biomoby.org/#" + mobyService.getName() );
- return soapCall;
- }
-
- /**
- * Calls the invoke() method of the JAX-RPC Call interface.
- */
- protected Element performSOAPRequest(Call soapCall, String mobyInputXML, StringBuffer contentsXMLOutput)
- throws SOAPException {
- // First, turn the input objects into a MOBY XML request
- String[] mobyXMLInputData = new String[ 1 ];
-
- // Setup
- mobyXMLInputData[ 0 ] = mobyInputXML;
-
- if ( debug )
- debugPS.println( "returnType just before invoke call is " + soapCall.getReturnType() );
- Object returnedObject = null;
- try {
- returnedObject = soapCall.invoke( new QName( "http://biomoby.org/", mobyService.getName() ),
- mobyXMLInputData );
- }
- catch ( Exception e ) {
- e.printStackTrace();
- // System.err.println("Input: "+mobyInputXML);
- throw new SOAPException( "While invoking SOAP Call: " + e );
- }
-
- try {
- if ( debug ) {
- debugPS.println( "SOAP Response was:\n" );
- debugPS.println( soapCall.getResponseMessage().getSOAPPart().getEnvelope() );
- }
- Element resultDom = ( ( MessageElement ) soapCall.getResponseMessage().getSOAPPart().getEnvelope() ).getAsDOM();
- return decodeSOAPMessage( resultDom, contentsXMLOutput, mobyInputXML );
- }
- catch ( Exception e ) {
- e.printStackTrace();
- throw new SOAPException( "Could not get SOAP response as DOM Element: " + e );
- }
-
- }
-
- public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML) throws SOAPException,
- MobyException {
- return decodeSOAPMessage( n, contentsXMLOutput, inputXML, false );
- }
-
- /**
- * Isolates the MOBY Data from the SOAP message returned by the remote service host.
- *
- * @throws SOAPException if the MOBY payload cannot be found in the SOAP message
- * @throws MobyException if the MOBY message is not well-formed XML
- *
- * @return The root element of the MOBY response DOM
- */
- public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML, boolean async)
- throws SOAPException, MobyException {
- if ( n == null ) {
- throw new SOAPException( "SOAP Message given to decode is null" );
- }
-
- NodeList node_list = null;
- XPath responseElementXPath = null;
- try {
- if ( async ) {
- responseElementXPath = new XPath( "//" + MobyPrefixResolver.WSRP_PREFIX + ":"
- + AsyncClient.WSRP_MULTI_PROPERTY_TAG_NAME + "Response", null, mobyPrefixResolver, XPath.SELECT );
- }
- else {
- responseElementXPath = new XPath( "//" + MobyPrefixResolver.MOBY_TRANSPORT_PREFIX + ":"
- + mobyService.getName() + "Response | //" + mobyService.getName() + "Response | " + "//"
- + MobyPrefixResolver.MOBY_TRANSPORT_PREFIX + ":" + mobyService.getName() + " | //"
- + mobyService.getName(), null, mobyPrefixResolver, XPath.SELECT );
- }
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select SOAP nodes due to exception "
- + "while compiling XPath statement (code bug?):" + te );
- }
- try {
- node_list = runXPath( responseElementXPath, n );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select SOAP nodes due to exception " + "while executing XPath statement:"
- + te );
- }
-
- if ( node_list == null || node_list.getLength() == 0 ) {
- throw new SOAPException( "Could not find a response element in SOAP payload (service "
- + mobyService.getName() + ")" );
- }
-
- if ( node_list.getLength() > 1 ) {
- throw new SOAPException( "Found more than one response element in SOAP payload, "
- + "unable to resolve ambiguity of the payload (service provider error?)" );
- }
-
- Node[] responseNodes = null;
- if ( async ) {
- Vector< Node > nodes = new Vector< Node >();
- NodeList resultNodeList = node_list.item( 0 ).getChildNodes();
- for ( int i = 0; resultNodeList != null && i < resultNodeList.getLength(); i++ ) {
- if ( ! ( resultNodeList.item( i ) instanceof Element ) ) {
- continue;
- }
- Element resultElement = ( Element ) resultNodeList.item( i );
- if ( resultElement.getLocalName().startsWith( AsyncClient.MOBY_RESULT_PROPERTY_PREFIX ) ) {
- nodes.add( resultElement );
- }
- }
- responseNodes = nodes.toArray( new Node[ nodes.size() ] );
- }
- else {
- responseNodes = new Node[]{node_list.item( 0 )};
- }
-
- Element domRoot = null; // Where the result will be put
-
- for ( Node responseNode : responseNodes ) {
- // Find base64 encoded elements in the SOAP message using XPath and
- // replace them with the real decoded contents
- node_list = null;
- try {
- node_list = runXPath( base64EncodedXPath, responseNode );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select base64 encoded SOAP nodes due to exception "
- + "while executing XPath statement:" + te );
- }
- if ( debug && node_list != null ) {
- debugPS.println( "There were " + node_list.getLength() + " base64 encoded elements in the data" );
- }
-
- // Do decoding for each base64 part found
- for ( int i = 0; node_list != null && i < node_list.getLength(); i++ ) {
- org.w3c.dom.Node change = node_list.item( i );
- /* Make sure the text data is all put into one contiguous piece for decoding */
- change.normalize();
-
- byte[] decodedBytes = org.apache.axis.encoding.Base64.decode( change.getFirstChild().getNodeValue() );
- String newText = new String( decodedBytes );
- if ( debug ) {
- debugPS.println( "New decoded text is" + newText );
- }
-
- // Swap out this node for the decoded data
- change.getParentNode().replaceChild( n.getOwnerDocument().createTextNode( new String( decodedBytes ) ),
- change );
- }
-
- // Now see if there are any strings that need decoding
- node_list = null;
- try {
- node_list = runXPath( stringEncodedXPath, responseNode );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select string encoded SOAP nodes due to exception "
- + "while executing XPath statement:" + te );
- }
-
- // Do concatenation for each plain string part found
- for ( int i = 0; node_list != null && i < node_list.getLength(); i++ ) {
- org.w3c.dom.Node change = node_list.item( i );
- /* Make sure the text data is all put into one contiguous piece for decoding */
- change.normalize();
- String plainString = "";
- int j = 0;
- for ( NodeList children = change.getChildNodes(); children != null && j < children.getLength(); j++ ) {
- Node child = children.item( j );
- if ( child instanceof CDATASection || child instanceof Text ) {
- plainString += child.getNodeValue();
- if ( debug ) {
- debugPS.println( "Plain string is now " + plainString );
- }
- }
- }
-
- // Swap out this node for the decoded data
- change.getParentNode().replaceChild( n.getOwnerDocument().createCDATASection( plainString ), change );
- }
- if ( debug && node_list != null ) {
- debugPS.println( "There were " + node_list.getLength()
- + " XML Schema string encoded elements in the data" );
- }
-
- // Parse the MOBY XML document payload
- responseNode.normalize();
- NodeList children = responseNode.getChildNodes();
- if ( children == null ) {
- throw new MobyException( "The MOBY payload has no contents at all" );
- }
- if ( children.getLength() != 1 ) {
- if ( debug ) {
- debugPS.println( "Warning: MOBY Payload appears to have more than "
- + "just text in it, skipping the non-text sections" );
- }
- }
-
- Element predefinedDOM = null; // Choice of ripping DOM Element for moby payload out of SOAP DOM
- String localResponseString = ""; // or storing raw XML strings, to be converted to a DOM later
- for ( int j = 0; j < children.getLength(); j++ ) {
- Node child = children.item( j );
- if ( child instanceof CDATASection || child instanceof Text ) {
- // Unescape XML special characters in the string, so we can later on
- // parse the payload as regular XML.
- // Ignore whitespace-only node
- if ( child.getNodeValue().matches( "^\\s+$" ) ) {
- continue;
- }
- if ( debug ) {
- debugPS.println( "Concatenating text in response " + child.getNodeValue() );
- }
- localResponseString += child.getNodeValue();// .replaceAll("<", "<").replaceAll(">",
- // ">").replaceAll("(&|F)", "&");
- }
- if ( child instanceof Element && child.getLocalName().equals( MobyTags.MOBY ) ) {
- debugPS.println( "Warning: The MOBY contents was found as raw XML inside the SOAP response!\n"
- + "This is illegal according to the MOBY-API, please inform the service\n "
- + " provider, as parsing such text may not be supported in the future" );
- localResponseString = null;
- // Store the moby payload root element's DOM represntation, so we don't
- // have to serialize it to the localResponseString and then parse it out
- // again (that would be wasteful).
- predefinedDOM = ( Element ) child;
- break;
- }
- }
-
- if ( localResponseString != null ) {
- if ( localResponseString.length() == 0 ) {
- throw new MobyException( "The MOBY payload has no text contents at all" );
- }
- if ( Character.isWhitespace( localResponseString.charAt( 0 ) ) ) {
- localResponseString = localResponseString.trim();
- }
- }
-
- // Check if the payload is an XML document. If not, try a last ditch effort
- // by base64 decoding the contents. This is technically not allowable in the
- // MOBY spec, but we are being lenient.
- if ( localResponseString != null && !localResponseString.startsWith( "\n" + localResponseString;
- debugPS.println( "Warning: The MOBY contents was missing an XML declaration, but it is "
- + "required by the MOBY API, and may stop working in the future without it. Please "
- + "contact the client's provider to correct this." );
- }
- else {
- String oldResponse = localResponseString;
- localResponseString = new String( org.apache.axis.encoding.Base64.decode( localResponseString ) );
- if ( !localResponseString.startsWith( " entry : data.entrySet() ) {
- String queryName = entry.getKey();
- MobyDataJob query = entry.getValue();
-
- // Additionally, we check if they are MobyDataInstances below
- Map< String, MobyPrimaryData > primaryParams = new HashMap< String, MobyPrimaryData >();
- Map< String, MobySecondaryData > secondaryParams = new HashMap< String, MobySecondaryData >();
-
- // To store the primary input parameter name as given by the user,
- // in case we need it later on for parameter renaming...
- String primaryParamName = null;
-
- for ( Map.Entry< String, MobyDataInstance > subentry : query.entrySet() ) {
- String name = subentry.getKey();
- MobyDataInstance param = subentry.getValue();
- if ( param == null ) {
- throw new MobyException( "Query " + queryName + " contained a null input parameter (" + name + ")" );
- }
- else if ( param instanceof MobyPrimaryData ) {
- primaryParams.put( name, ( MobyPrimaryData ) param );
- primaryParamName = name;
- }
- else if ( param instanceof MobySecondaryData ) {
- secondaryParams.put( name, ( MobySecondaryData ) param );
- }
- else {
- System.err.println( "Input parameter " + name + " (query " + queryName
- + ") was not a MobyPrimaryData or MobySecondaryData "
- + "as expected, but rather was of class " + param.getClass().getName() );
- }
- }
-
- if ( inputs != null && inputs.length != primaryParams.size() ) {
- throw new MobyException( "Service " + mobyService.getName() + " was provided " + primaryParams.size()
- + " primary input parameter(s), but takes " + inputs.length + " (query " + queryName + ")" );
- }
- if ( secondaries != null ) {
- // If no secondaries provided, fill them in by default
- if ( secondaries.length != 0 ) {
- for ( MobySecondaryData secondary : secondaries ) {
- if ( !secondaryParams.containsKey( secondary.getName() ) ) {
- if ( debug ) {
- System.err.println( "Setting default secondary param value for missing param "
- + secondary );
- }
- query.put( secondary.getName(), new MobyDataSecondaryInstance( secondary ) );
- }
- }
- }
- if ( secondaries.length != secondaryParams.size() ) {
- throw new MobyException( "Service " + mobyService.getName() + " was provided "
- + secondaryParams.size() + " secondary input parameter(s), but takes " + secondaries.length
- + " (query " + queryName + "). Extra secondary" + " parameters must have been specified" );
- }
- }
-
- // If there was one anonymous input, assign the name automatically in
- // the case the service requires it to be named. This is the only
- // unambiguous case in which we can do this.
- if ( inputs.length == 1 ) {
- String serviceParamName = inputs[ 0 ].getName(); // name as req'd by the service
-
- // name isn't the same as required currently
- if ( serviceParamName != null && serviceParamName.length() > 0
- && !serviceParamName.equals( primaryParamName ) ) {
- // take out the old parameter
- MobyPrimaryData theInputToRename = ( MobyPrimaryData ) query.remove( primaryParamName );
-
- // Add in the same parameter, but with the appropriate name
- query.put( serviceParamName, ( MobyDataInstance ) theInputToRename );
- }
- }
- }
-
- ByteArrayOutputStream mobyRequest = new ByteArrayOutputStream();
- try {
- MobyDataUtils.toXMLDocument( mobyRequest, data );
- }
- catch ( MobyException me ) {
- throw me;
- }
- catch ( Exception e ) {
- e.printStackTrace();
- throw new MobyException( "Could not create MOBY payload XML from input data: " + e );
- }
-
- if ( debug ) {
- debugPS.println( "Input to MOBY Service is:" );
- debugPS.print( mobyRequest.toString() );
- }
-
- return mobyRequest.toString();
- }
-
- /**
- * A method that sets up the execution environment for and runs a compiled XPath statement against a DOM node You
- * should call releaseXPath when you're done with the results
- *
- * @return the list of Nodes that satisfy the XPath in this Node's context
- */
- protected NodeList runXPath(XPath xpath, Node n) throws TransformerException {
- NodeList result = null;
- int dtm_node_handle = xpath_context.getDTMHandleFromNode( n );
- PrefixResolver node_prefix_resolver = new PrefixResolverDefault( n );
- XObject xobject = xpath.execute( xpath_context, n, node_prefix_resolver );
- if ( xobject instanceof XNodeSet ) {
- result = ( ( XNodeSet ) xobject ).nodelist();
- }
- else if ( debug && xobject != null ) {
- debugPS.println( "Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName() );
- debugPS.flush();
- }
- return result;
- }
-
- protected void releaseXPath(Node n) {
- xpath_context.release( xpath_context.getDTM( xpath_context.getDTMHandleFromNode( n ) ), false );
- }
-}
+package org.biomoby.client;
+
+import java.io.*;
+import java.util.*;
+
+import javax.xml.namespace.QName;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.rpc.Service;
+import javax.xml.transform.TransformerException;
+
+import org.apache.axis.client.Call;
+import org.apache.axis.message.MessageElement;
+import org.apache.xml.utils.PrefixResolver;
+import org.apache.xml.utils.PrefixResolverDefault;
+import org.apache.xpath.XPath;
+import org.apache.xpath.XPathContext;
+import org.apache.xpath.objects.XNodeSet;
+import org.apache.xpath.objects.XObject;
+
+import org.biomoby.shared.*;
+import org.biomoby.shared.data.*;
+import org.biomoby.shared.parser.MobyTags; // defined the Moby XML element names
+import org.biomoby.w3c.addressing.EndpointReference;
+import org.omg.lsae.notifications.AnalysisEvent;
+
+import org.w3c.dom.*;
+
+/**
+ * This class handles the WSDL transaction to request a response
+ * from a remote SOAP Web service that handles the
+ * MOBY format. It depends on
+ * having already retrieved the definition of the Web service via
+ * the MOBY central registry using the
+ * jMOBY API,
+ * and for now it uses the
+ * Apache
+ * Axis Web services framework, as well as Apache Xalan. There are code comments for the
+ * few lines that rely on Axis classes rather than the JAX-RPC interfaces.
+ *
+ * @author Paul Gordon gordonp at ucalgary.ca
+ */
+public class MobyRequest{
+
+ protected MobyService mobyService = null;
+ protected MobyContentInstance inputData = null;
+ protected MobyContentInstance outputData = null;
+ protected Central mobyCentral = null;
+ protected PrefixResolver mobyPrefixResolver = null;
+
+ protected Hashtable wsdlCache = null;
+ protected String lastWsdlCacheKey = null;
+ protected DocumentBuilder docBuilder = null;
+ protected Service service = null;
+
+ protected Class stringType;
+ protected static boolean debug = false;
+ protected PrintStream debugPS = System.err;
+ protected XPathContext xpath_context;
+ protected String responseString = null;
+
+ private XPath stringEncodedXPath;
+ private XPath base64EncodedXPath;
+ private XPath simpleChildXPath;
+ private XPath collectionChildXPath;
+ private String user;
+ private String password;
+
+ private int autoID = 0;
+
+ // Used as invocation callback if MobyRequest is acting as a server,
+ // or is executing services as a client asynchronously
+ private Vector eventHandlers;
+
+ /**
+ * Default constructor. You should have a Central instance around since you're going to
+ * be retrieving MobyServices to pass into here. Lets reuse it.
+ *
+ * @param central An instance of a Moby central object so we can make requests about object types, etc.
+ * @throws ParserConfigurationException if JAXP doesn't have any valid DOM-building XML parsers set up for use
+ */
+ public MobyRequest(Central central) throws ParserConfigurationException{
+ mobyCentral = central;
+ wsdlCache = new Hashtable();
+
+ eventHandlers = new Vector();
+
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ docBuilder = dbf.newDocumentBuilder();
+
+ try{
+ stringType = Class.forName("java.lang.String");
+ }catch(ClassNotFoundException classe){
+ debugPS.println("WARNING: Something is very wrong, could not find Class definition of String: " + classe);
+ }
+
+ xpath_context = new XPathContext();
+ mobyPrefixResolver = new MobyPrefixResolver();
+
+ // Now compile the XPath statements that will be used fetch data from the server response
+ try{
+ base64EncodedXPath = new XPath("//*[starts-with(substring-after(@"+
+ MobyPrefixResolver.XSI1999_PREFIX+
+ ":type, ':'), \"base64\") or starts-with(substring-after(@"+
+ MobyPrefixResolver.XSI2001_PREFIX+
+ ":type, ':'), \"base64\")]", null,
+ mobyPrefixResolver, XPath.SELECT);
+ stringEncodedXPath = new XPath("//*[substring-after(@"+
+ MobyPrefixResolver.XSI1999_PREFIX+
+ ":type, ':')=\"string\" or substring-after(@"+
+ MobyPrefixResolver.XSI2001_PREFIX+
+ ":type, ':')=\"string\"] | //"+
+ MobyPrefixResolver.SOAP_ENC_PREFIX+":string", null,
+ mobyPrefixResolver, XPath.SELECT);
+ simpleChildXPath = new XPath("moby:Simple | Simple", null,
+ mobyPrefixResolver, XPath.SELECT);
+ collectionChildXPath = new XPath("moby:Collection | Collection", null,
+ mobyPrefixResolver, XPath.SELECT);
+ }
+ catch(TransformerException te){
+ debugPS.println("Syntax error encountered while compiling XPath " +
+ "statements for internal use (code bug?): " + te);
+ }
+ setDebugMode(System.getProperty("moby.debug") != null);
+ }
+
+ public void setAuthentication(String user, String password){
+ this.user = user;
+ this.password = password;
+ }
+
+ /**
+ * @param mode if true, debugging information is printed to the stream returned by getDebugOutputStream
+ */
+ public void setDebugMode(boolean mode){
+ debug = mode;
+ }
+
+ /**
+ * Standard error is used unless this method is called.
+ *
+ * @param ps the OutputStream to which debugging information is sent.
+ * @throws IllegalArgumentException if the stream is null
+ */
+ public void setDebugPrintStream(PrintStream ps) throws IllegalArgumentException{
+ if(ps == null){
+ throw new IllegalArgumentException("The OutputStream specified to MobyRequest was null");
+ }
+ debugPS = ps;
+ }
+
+ /**
+ * @return the instance of the class implementing Central that we are using
+ */
+ public Central getCentralImpl(){
+ return mobyCentral;
+ }
+
+ /**
+ * @param mobyservice the MobyService that should be executed when invokeService is called
+ */
+ public void setService(MobyService mobyservice){
+ if(mobyservice == null){
+ mobyService = null;
+ }
+ else if(mobyService == null || !mobyservice.equals(mobyService)){
+ mobyService = mobyservice;
+ }
+ }
+
+ /**
+ * @return the MobyService that will be executed when invokeService is called
+ */
+ public MobyService getService(){
+ return mobyService;
+ }
+
+ /**
+ * @return the Raw MOBY XML response as a string
+ */
+ public String getResponseXML(){
+ return responseString;
+ }
+
+ /**
+ * Sets the input data for the MOBY service request. The length of the input array, and the
+ * number of input parameters required by the service must be equal when invokeService() is called.
+ * This method strictly enforces that the input be of the appropriate type for the service.
+ *
+ * Note that there is no requirement to use MobyDataInstance.setXmlMode() before passing in
+ * data, this class will temporarily set the XML mode of the data when it is required.
+ *
+ * @throws IllegalArgumentException if the input does not fit the criteria of the service (e.g. wrong data type)
+ */
+ public void setInput(MobyContentInstance data) throws MobyException{
+ inputData = data;
+ }
+
+ /**
+ * Takes the data in the array, with their current articleNames, as input for the service
+ */
+ public void setInput(MobyDataInstance[] data) throws MobyException{
+ MobyDataJob job = new MobyDataJob();
+ for(MobyDataInstance param: data){
+ job.put(param.getName(), param);
+ }
+ inputData = new MobyContentInstance();
+ inputData.put(job);
+ }
+
+ /**
+ * Convenience method to run services that take one argument. If the service
+ * requires the input to have a name, it will be automatically assigned.
+ */
+ public void setInput(MobyDataInstance datum) throws MobyException{
+ setInput(datum, "");
+ }
+
+ /**
+ * Convenience method to run services that take one named argument.
+ */
+ public void setInput(MobyDataInstance datum, String paramName) throws MobyException{
+ inputData = new MobyContentInstance(datum, paramName);
+ }
+
+ /**
+ * @return the MobyService that will be executed when invokeService is called
+ */
+ public MobyContentInstance getInput(){
+ return inputData;
+ }
+
+ /**
+ * Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
+ */
+ public void setSecondaryInput(Collection secondaryData) throws MobyException{
+ setSecondaryInput(secondaryData.toArray(new MobyDataSecondaryInstance[secondaryData.size()]));
+ }
+
+ /**
+ * This method will assign the provided secondary parameters to all primary input data currently
+ * in this object. This is covenient if you are running 100 seqs through BLAST and only want to set
+ * the parameters once. If you instead want to set secondary input differently for all primary inputs, you'll
+ * need to create a custom MobyContentInstance as input to setInput().
+ *
+ * @throws MobyException if a parameter name is blank, or overrides a primary parameter
+ */
+ public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException{
+
+ Iterator queryNames = inputData.keySet().iterator();
+ // For each query
+ while(queryNames.hasNext()){
+ MobyDataJob queryParams = inputData.get(queryNames.next());
+ // Set all the secondary params (overwrites any old ones)
+ for(int i = 0; i < secondaryData.length; i++){
+ String secName = secondaryData[i].getName();
+ if(secName == null || secName.length() == 0){
+ throw new MobyException("A secondary parameter cannot have a blank name (array index " + i + ")");
+ }
+ if(queryParams.containsKey(secName) && queryParams.get(secName) instanceof MobyPrimaryData){
+ throw new MobyException("A secondary parameter cannot override an existing primary parameter " +
+ "with the same name (" + secName + ")");
+ }
+ queryParams.put(secName, secondaryData[i]);
+ }
+ }
+ }
+
+ /**
+ * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the correspondingly indexed input request.
+ *
+ * @throws MobyException if you try to get the results before calling InvokeService
+ */
+ public MobyContentInstance getOutput() throws MobyException{
+ if(outputData == null){
+ throw new MobyException("Trying to access MOBY service results " +
+ "before the service is invoked");
+ }
+ else{
+ return outputData;
+ }
+ }
+
+ /**
+ * The main method of the class. If all of the MOBY input objects
+ * are properly defined according to the Web service definition,
+ * a SOAP request will be sent to the remote server, and the method
+ * will return one or more MOBY objects (synchronous).
+ * Call this method after calling setService, and setInput. If you do not call
+ * setSecondaryInput, the default secondary parameter values will be used.
+ *
+ * @return the results of the remote Web service in response to the give input
+ *
+ * @throws MobyException i.e. there was something wrong with the input, output or remote service's logic
+ * @throws SOAPException i.e. there was a problem with the underlying transaction/transport layer
+ */
+ public MobyContentInstance invokeService() throws Exception, MobyException, SOAPException, NoSuccessException{
+ return mobyService.isAsynchronous() ? invokeService(inputData, new StringBuffer()) : invokeService(inputData, (StringBuffer) null);
+ }
+
+ // Used internally for asynchronous thread calls that all need the XML data
+ // and can't rely on the answer from thread-insensitive getResponseXML()
+ private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML)
+ throws Exception, MobyException, SOAPException, NoSuccessException{
+ return invokeService(inData, contentsXML, null, 0);
+ }
+
+ private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML, MobyRequestEventHandler handler, int requestId)
+ throws Exception, MobyException, SOAPException, NoSuccessException{
+
+ if(mobyService == null){
+ throw new MobyException("Tried to invoke null service from MobyRequest (call setService first)");
+ }
+
+ Element mobyDOM = null;
+ if(mobyService.isAsynchronous()){
+ // Async is "simpler", because it had to merge DOMs together into a single MobyContentInstance anyway
+ MobyContentInstance mci = performAsyncSOAPRequest(mobyService, inData, handler, requestId);
+ StringWriter writer = new StringWriter();
+ MobyDataUtils.toXMLDocument(writer, mci);
+ contentsXML.append(writer.toString());
+ return mci;
+ }
+ else{
+ String mobyXML = convertMOBYDataToMOBYRequest(inData);
+ Call call = getServiceFromWSDL();
+ if(user != null && password != null) {
+ call.setProperty( Call.USERNAME_PROPERTY, user );
+ call.setProperty( Call.PASSWORD_PROPERTY, password );
+ }
+ mobyDOM = performSOAPRequest(call, mobyXML, contentsXML);
+ // The following parses the DOM and extracts all the appropriate jMOBY objects to represent the XML in Java
+ return MobyDataUtils.fromXMLDocument(mobyDOM, mobyService.getServiceType().getRegistry());
+ }
+ }
+
+ protected MobyContentInstance performAsyncSOAPRequest(MobyService mservice, MobyContentInstance inData,
+ MobyRequestEventHandler handler, int requestId)
+ throws Exception{
+ String mobyXML = convertMOBYDataToMOBYRequest(inData);
+ EndpointReference epr = AsyncClient.sendRequest(mservice, mobyXML);
+
+ // Essentially cloning, so removing ids doesn't change the
+ // MobyContentInstance "data" (which we will use again later on)
+ MobyContentInstance finalContents = new MobyContentInstance();
+ Set queryIDs = new HashSet(inData.keySet());
+ try {
+ // Should add some timeout here...
+ while(!queryIDs.isEmpty()){
+ // todo: make this setable
+ Thread.sleep(5000);
+
+ AnalysisEvent[] events =
+ AsyncClient.poll(epr, queryIDs);
+
+ Vector newDataAvailable = new Vector();
+ for(AnalysisEvent event: events){
+ if(event != null && event.isCompleted()){
+ queryIDs.remove(event.getQueryId());
+ newDataAvailable.add(event.getQueryId());
+ }
+ }
+
+ if(newDataAvailable.size() > 0){
+ // Parse and merge the new data into the existing contents
+ InputStream resultStream = AsyncClient.getResultStream(epr, newDataAvailable);
+ Element mobyDOM = asyncSoapTextToMobyDOM(resultStream);
+ MobyContentInstance newResults = MobyDataUtils.fromXMLDocument(mobyDOM, mservice.getServiceType().getRegistry());
+ // The merge
+ for(String jobid: newResults.keySet()){
+ finalContents.put(jobid, newResults.get(jobid));
+ }
+
+ // Inform the handler that some data has been added to the response (for incremental display?)
+ if(handler != null){
+ MobyRequestEvent mre = new MobyRequestEvent(finalContents, this, mservice, null, requestId);
+ StringWriter xmlWriter = new StringWriter();
+ MobyDataUtils.toXMLDocument(xmlWriter, finalContents);
+
+ mre.setContentsXML(xmlWriter.toString());
+ if(!queryIDs.isEmpty()){
+ // Send an update event only if we aren't finished yet.
+ // If we are finished, the client is going to get this event as the
+ // invocation thread finishes up (no need to double up).
+ handler.processEvent(mre);
+ }
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ AsyncClient.destroy(epr);
+ throw new Exception("Exception occured while polling the service invocation: " + e);
+ }
+
+ return finalContents;
+ }
+
+ private Element asyncSoapTextToMobyDOM(InputStream inStream) throws Exception{
+ Element soapDOM = null;
+ synchronized(docBuilder){
+ soapDOM = docBuilder.parse(inStream).getDocumentElement();
+ }
+ final boolean IS_ASYNC_SERVICE_CALL = true;
+ return decodeSOAPMessage(soapDOM, null, null, IS_ASYNC_SERVICE_CALL);
+ }
+
+ /**
+ * Asynchronous call to invokeService. A callback to the passed-in handler will be made when
+ * the response is ready, or there is an exception.
+ *
+ * @return the id that the callback event will return from getID(), allowing a client to distinguish between multiple concurrent invocation callbacks
+ */
+ public synchronized int invokeService(MobyRequestEventHandler handler){
+ int id = autoID++;
+
+ Thread t = new InvocationThread(this, inputData, handler, id); // see internal class definition below
+ t.start();
+
+ return id;
+ }
+
+ // This is the class that asynchronously calls the service and does a callback to
+ // the handler specified in the invocation.
+ class InvocationThread extends Thread {
+ MobyContentInstance data;
+ MobyService mservice;
+ MobyRequest mobyRequest;
+ MobyRequestEventHandler handler;
+ int requestId;
+
+ InvocationThread(MobyRequest mr, MobyContentInstance inData, MobyRequestEventHandler h, int id){
+ data = inData;
+ mobyRequest = mr;
+ mservice = mobyRequest.getService();
+ handler = h;
+ requestId = id;
+
+ // Name the thread after the service being run, mostly for ease of debugging
+ setName(mservice.getName()+requestId);
+ }
+
+ public void run() {
+ MobyRequestEvent requestEvent = new MobyRequestEvent(data, mobyRequest, mservice, null, requestId);
+ // Tell the handler we're starting the request, with the given data
+ handler.start(requestEvent);
+
+ MobyRequestEvent responseEvent = null;
+ MobyContentInstance content = null;
+ StringBuffer contentsXML = new StringBuffer(); //to be filled in by the RPC call below
+ try{
+ content = mobyRequest.invokeService(data, contentsXML, handler, requestId); //RPC call...
+ }
+ catch(Exception e){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, e, requestId);
+ }
+ catch(Error err){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, err, requestId);
+ }
+ if(responseEvent == null){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, null, requestId);
+ }
+ // We've got the raw XML laying around, so why not provide it unmolested to the callback?
+ responseEvent.setContentsXML(contentsXML.toString());
+ handler.processEvent(responseEvent);
+ handler.stop(mobyRequest, requestId);
+ }
+ }
+
+ public void addEventHandler(MobyRequestEventHandler h){
+ eventHandlers.add(h);
+ }
+
+ public void removeEventHandler(MobyRequestEventHandler h){
+ eventHandlers.remove(h);
+ }
+
+ public void sendResponse(MobyRequestEvent mre){
+ // Not yet implemented, need to conform to some web.xml specification here...
+ }
+
+ /**
+ * This method retrieves from Moby Central a copy of the WSDL document for the service
+ * (or uses an internally cached copy from a previous invocation), and sets the variables for the
+ * SOAP call appropriately so you can consequently call performSOAPRequest.
+ */
+ protected Call getServiceFromWSDL() throws MobyException, NoSuccessException{
+// String wsdl = null;
+
+// // Since this is how we retrieve a service from Central, use the same values as the key to the hash
+// String wsdlCacheKey = mobyService.getName() + "@" + mobyService.getAuthority();
+
+// // This is the same call as last time, so we don't need to change the setup
+// if(wsdlCacheKey.equals(lastWsdlCacheKey)){
+// return setCallFromWSDL((String) wsdlCache.get(wsdlCacheKey));
+// }
+// // We haven't encountered this service yet
+// else if(!wsdlCache.containsKey(wsdlCacheKey)){
+// wsdl = mobyCentral.getServiceWSDL(mobyService.getName(), mobyService.getAuthority());
+// wsdlCache.put(wsdlCacheKey, wsdl);
+// }
+// // We've dealt with this one before
+// else{
+// wsdl = (String) wsdlCache.get(wsdlCacheKey);
+// }
+
+// lastWsdlCacheKey = wsdlCacheKey; // Keep track of the last invocation
+
+ // Get ready to do SOAP
+ return setCallFromWSDL(null);
+ }
+
+ /**
+ * Creates the SOAP Call that will be invoked later. This should be based on the WSDL document
+ * and parameter information from the MobyService, but these are currently not up to snuff.
+ */
+ protected Call setCallFromWSDL(String wsdl) throws MobyException, SOAPException{
+ if(service == null){
+ service = new org.apache.axis.client.Service(); // AXIS SPECIFIC This acts as a factory for Calls
+ }
+
+ Call soapCall;
+ try{
+ soapCall = (Call) service.createCall();//create a fresh Call each time
+ }catch(javax.xml.rpc.ServiceException se){
+ throw new SOAPException("Could not instatiate call to SOAP Service: " + se);
+ }
+
+ // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll
+ // have to do the call's info setting manually.
+ //((org.apache.axis.client.Call) soapCall).setSOAPService(soapService);
+ soapCall.removeAllParameters();
+ soapCall.setTargetEndpointAddress(mobyService.getURL());
+ soapCall.setPortName(new QName("http://biomoby.org/",
+ mobyService.getName() + "PortType"));
+ //soapCall.setOperationName(new QName("http://biomoby.org/",
+ // mobyService.getName()));
+ soapCall.setSOAPActionURI("http://biomoby.org/#" + mobyService.getName());
+ return soapCall;
+ }
+
+ /**
+ * Calls the invoke() method of the JAX-RPC Call interface.
+ */
+ protected Element performSOAPRequest(Call soapCall, String mobyInputXML, StringBuffer contentsXMLOutput) throws SOAPException{
+ // First, turn the input objects into a MOBY XML request
+ String[] mobyXMLInputData = new String[1];
+
+ //Setup
+ mobyXMLInputData[0] = mobyInputXML;
+
+ if(debug)
+ debugPS.println("returnType just before invoke call is " + soapCall.getReturnType());
+ Object returnedObject = null;
+ try{
+ returnedObject = soapCall.invoke(new QName("http://biomoby.org/",
+ mobyService.getName()), mobyXMLInputData);
+ }
+ catch(Exception e){
+ e.printStackTrace();
+ //System.err.println("Input: "+mobyInputXML);
+ throw new SOAPException("While invoking SOAP Call: " + e);
+ }
+
+ try{
+ if(debug){
+ debugPS.println("SOAP Response was:\n");
+ debugPS.println(soapCall.getResponseMessage().getSOAPPart().getEnvelope());
+ }
+ Element resultDom = ((MessageElement) soapCall.getResponseMessage().getSOAPPart().getEnvelope()).getAsDOM();
+ return decodeSOAPMessage(resultDom, contentsXMLOutput, mobyInputXML);
+ } catch(Exception e){
+ e.printStackTrace();
+ throw new SOAPException("Could not get SOAP response as DOM Element: "+ e);
+ }
+
+ }
+
+ public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML)
+ throws SOAPException, MobyException{
+ return decodeSOAPMessage(n, contentsXMLOutput, inputXML, false);
+ }
+
+ /**
+ * Isolates the MOBY Data from the SOAP message returned by the remote service host.
+ *
+ * @throws SOAPException if the MOBY payload cannot be found in the SOAP message
+ * @throws MobyException if the MOBY message is not well-formed XML
+ *
+ * @return The root element of the MOBY response DOM
+ */
+ public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML, boolean async)
+ throws SOAPException, MobyException{
+ if(n == null){
+ throw new SOAPException("SOAP Message given to decode is null");
+ }
+
+ NodeList node_list = null;
+ XPath responseElementXPath = null;
+ try{
+ if(async){
+ responseElementXPath = new XPath("//"+MobyPrefixResolver.WSRP_PREFIX +
+ ":"+AsyncClient.WSRP_MULTI_PROPERTY_TAG_NAME+"Response",
+ null, mobyPrefixResolver, XPath.SELECT);
+ }
+ else{
+ responseElementXPath = new XPath("//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+
+ ":"+mobyService.getName()+"Response | //" +
+ mobyService.getName()+"Response | " +
+ "//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+
+ ":"+mobyService.getName() + " | //" +
+ mobyService.getName(),
+ null, mobyPrefixResolver, XPath.SELECT);
+ }
+ }catch(TransformerException te){
+ throw new SOAPException("Cannot select SOAP nodes due to exception "+
+ "while compiling XPath statement (code bug?):" +te);
+ }
+ try{
+ node_list = runXPath(responseElementXPath, n);
+ }catch(TransformerException te){
+ throw new SOAPException("Cannot select SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+
+ if(node_list == null || node_list.getLength() == 0){
+ throw new SOAPException("Could not find a response element in SOAP payload (service " +
+ mobyService.getName() + ")");
+ }
+
+ if(node_list.getLength() > 1){
+ throw new SOAPException("Found more than one response element in SOAP payload, " +
+ "unable to resolve ambiguity of the payload (service provider error?)");
+ }
+
+ Node[] responseNodes = null;
+ if(async){
+ Vector nodes = new Vector();
+ NodeList resultNodeList = node_list.item(0).getChildNodes();
+ for(int i = 0; resultNodeList != null && i < resultNodeList.getLength(); i++){
+ if(!(resultNodeList.item(i) instanceof Element)){
+ continue;
+ }
+ Element resultElement = (Element) resultNodeList.item(i);
+ if(resultElement.getLocalName().startsWith(AsyncClient.MOBY_RESULT_PROPERTY_PREFIX)){
+ nodes.add(resultElement);
+ }
+ }
+ responseNodes = nodes.toArray(new Node[nodes.size()]);
+ }
+ else{
+ responseNodes = new Node[]{node_list.item(0)};
+ }
+
+ Element domRoot = null; // Where the result will be put
+
+ for(Node responseNode: responseNodes){
+ // Find base64 encoded elements in the SOAP message using XPath and
+ // replace them with the real decoded contents
+ node_list = null;
+ try{
+ node_list = runXPath(base64EncodedXPath, responseNode);
+ }
+ catch(TransformerException te){
+ throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+ if(debug && node_list != null){
+ debugPS.println("There were " + node_list.getLength() +
+ " base64 encoded elements in the data");
+ }
+
+ // Do decoding for each base64 part found
+ for(int i = 0; node_list != null && i < node_list.getLength(); i++){
+ org.w3c.dom.Node change = node_list.item(i);
+ /* Make sure the text data is all put into one contiguous piece for decoding*/
+ change.normalize();
+
+ byte[] decodedBytes = org.apache.axis.encoding.Base64.decode(change.getFirstChild().getNodeValue());
+ String newText = new String(decodedBytes);
+ if(debug){
+ debugPS.println("New decoded text is" + newText);
+ }
+
+ // Swap out this node for the decoded data
+ change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(new String(decodedBytes)),
+ change);
+ }
+
+ // Now see if there are any strings that need decoding
+ node_list = null;
+ try{
+ node_list = runXPath(stringEncodedXPath, responseNode);
+ }
+ catch(TransformerException te){
+ throw new SOAPException("Cannot select string encoded SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+
+ // Do concatenation for each plain string part found
+ for(int i = 0; node_list != null && i < node_list.getLength(); i++){
+ org.w3c.dom.Node change = node_list.item(i);
+ /* Make sure the text data is all put into one contiguous piece for decoding*/
+ change.normalize();
+ String plainString = "";
+ int j = 0;
+ for(NodeList children = change.getChildNodes();
+ children != null && j < children.getLength();
+ j++){
+ Node child = children.item(j);
+ if(child instanceof CDATASection || child instanceof Text){
+ plainString += child.getNodeValue();
+ if(debug){
+ debugPS.println("Plain string is now " + plainString);
+ }
+ }
+ }
+
+ // Swap out this node for the decoded data
+ change.getParentNode().replaceChild(n.getOwnerDocument().createCDATASection(plainString), change);
+ }
+ if(debug && node_list != null){
+ debugPS.println("There were " + node_list.getLength() +
+ " XML Schema string encoded elements in the data");
+ }
+
+ // Parse the MOBY XML document payload
+ responseNode.normalize();
+ NodeList children = responseNode.getChildNodes();
+ if(children == null){
+ throw new MobyException("The MOBY payload has no contents at all");
+ }
+ if(children.getLength() != 1){
+ if(debug){
+ debugPS.println("Warning: MOBY Payload appears to have more than " +
+ "just text in it, skipping the non-text sections");
+ }
+ }
+
+ Element predefinedDOM = null; // Choice of ripping DOM Element for moby payload out of SOAP DOM
+ String localResponseString = ""; // or storing raw XML strings, to be converted to a DOM later
+ for(int j = 0; j < children.getLength(); j++){
+ Node child = children.item(j);
+ if(child instanceof CDATASection || child instanceof Text){
+ // Unescape XML special characters in the string, so we can later on
+ // parse the payload as regular XML.
+ // Ignore whitespace-only node
+ if(child.getNodeValue().matches("^\\s+$")){
+ continue;
+ }
+ if(debug){
+ debugPS.println("Concatenating text in response " + child.getNodeValue());
+ }
+ localResponseString += child.getNodeValue();//.replaceAll("<", "<").replaceAll(">", ">").replaceAll("(&|F)", "&");
+ }
+ if(child instanceof Element && child.getLocalName().equals(MobyTags.MOBY)){
+ debugPS.println("Warning: The MOBY contents was found as raw XML inside the SOAP response!\n" +
+ "This is illegal according to the MOBY-API, please inform the service\n " +
+ " provider, as parsing such text may not be supported in the future");
+ localResponseString = null;
+ // Store the moby payload root element's DOM represntation, so we don't
+ // have to serialize it to the localResponseString and then parse it out
+ // again (that would be wasteful).
+ predefinedDOM = (Element) child;
+ break;
+ }
+ }
+
+ if(localResponseString != null){
+ if(localResponseString.length() == 0){
+ throw new MobyException("The MOBY payload has no text contents at all");
+ }
+ if(Character.isWhitespace(localResponseString.charAt(0))){
+ localResponseString = localResponseString.trim();
+ }
+ }
+
+ // Check if the payload is an XML document. If not, try a last ditch effort
+ // by base64 decoding the contents. This is technically not allowable in the
+ // MOBY spec, but we are being lenient.
+ if(localResponseString != null && !localResponseString.startsWith("\n"+localResponseString;
+ debugPS.println("Warning: The MOBY contents was missing an XML declaration, but it is " +
+ "required by the MOBY API, and may stop working in the future without it. Please " +
+ "contact the client's provider to correct this.");
+ }
+ else{
+ String oldResponse = localResponseString;
+ localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString));
+ if(!localResponseString.startsWith(" entry: data.entrySet()){
+ String queryName = entry.getKey();
+ MobyDataJob query = entry.getValue();
+
+ // Additionally, we check if they are MobyDataInstances below
+ Map primaryParams = new HashMap();
+ Map secondaryParams = new HashMap();
+
+ // To store the primary input parameter name as given by the user,
+ // in case we need it later on for parameter renaming...
+ String primaryParamName = null;
+
+ for(Map.Entry subentry: query.entrySet()){
+ String name = subentry.getKey();
+ MobyDataInstance param = subentry.getValue();
+ if(param == null){
+ throw new MobyException("Query " + queryName +
+ " contained a null input parameter (" + name + ")");
+ }
+ else if(param instanceof MobyPrimaryData){
+ primaryParams.put(name, (MobyPrimaryData) param);
+ primaryParamName = name;
+ }
+ else if(param instanceof MobySecondaryData){
+ secondaryParams.put(name, (MobySecondaryData) param);
+ }
+ else{
+ System.err.println("Input parameter " + name + " (query " + queryName +
+ ") was not a MobyPrimaryData or MobySecondaryData " +
+ "as expected, but rather was of class " + param.getClass().getName());
+ }
+ }
+
+ if(inputs != null && inputs.length != primaryParams.size()){
+ throw new MobyException("Service " + mobyService.getName() + " was provided " +
+ primaryParams.size() +
+ " primary input parameter(s), but takes " + inputs.length +
+ " (query " + queryName + ")");
+ }
+ if(secondaries != null){
+ // If no secondaries provided, fill them in by default
+ if(secondaries.length != 0){
+ for(MobySecondaryData secondary: secondaries){
+ if(!secondaryParams.containsKey(secondary.getName())){
+ if(debug){
+ System.err.println("Setting default secondary param value for missing param " + secondary);
+ }
+ query.put(secondary.getName(), new MobyDataSecondaryInstance(secondary));
+ }
+ }
+ }
+ if(secondaries.length != secondaryParams.size()){
+ throw new MobyException("Service " + mobyService.getName() + " was provided " +
+ secondaryParams.size() +
+ " secondary input parameter(s), but takes " + secondaries.length +
+ " (query " + queryName + "). Extra secondary" +
+ " parameters must have been specified");
+ }
+ }
+
+ // If there was one anonymous input, assign the name automatically in
+ // the case the service requires it to be named. This is the only
+ // unambiguous case in which we can do this.
+ if(inputs.length == 1){
+ String serviceParamName = inputs[0].getName(); // name as req'd by the service
+
+ // name isn't the same as required currently
+ if(serviceParamName != null && serviceParamName.length() > 0 &&
+ !serviceParamName.equals(primaryParamName)){
+ // take out the old parameter
+ MobyPrimaryData theInputToRename = (MobyPrimaryData) query.remove(primaryParamName);
+
+ // Add in the same parameter, but with the appropriate name
+ query.put(serviceParamName, (MobyDataInstance) theInputToRename);
+ }
+ }
+ }
+
+ ByteArrayOutputStream mobyRequest = new ByteArrayOutputStream();
+ try{
+ MobyDataUtils.toXMLDocument(mobyRequest, data);
+ }
+ catch(MobyException me){
+ throw me;
+ }
+ catch(Exception e){
+ e.printStackTrace();
+ throw new MobyException("Could not create MOBY payload XML from input data: " +e);
+ }
+
+ if(debug){
+ debugPS.println("Input to MOBY Service is:");
+ debugPS.print(mobyRequest.toString());
+ }
+
+ return mobyRequest.toString();
+ }
+
+ /**
+ * A method that sets up the execution environment for and runs a compiled XPath statement against a DOM node
+ * You should call releaseXPath when you're done with the results
+ * @return the list of Nodes that satisfy the XPath in this Node's context
+ */
+ protected NodeList runXPath(XPath xpath, Node n) throws TransformerException{
+ NodeList result = null;
+ int dtm_node_handle = xpath_context.getDTMHandleFromNode(n);
+ PrefixResolver node_prefix_resolver = new PrefixResolverDefault(n);
+ XObject xobject = xpath.execute(xpath_context, n, node_prefix_resolver);
+ if(xobject instanceof XNodeSet){
+ result = ((XNodeSet) xobject).nodelist();
+ }
+ else if(debug && xobject != null){
+ debugPS.println("Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName());
+ debugPS.flush();
+ }
+ return result;
+ }
+
+ protected void releaseXPath(Node n){
+ xpath_context.release(xpath_context.getDTM(xpath_context.getDTMHandleFromNode(n)), false);
+ }
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2008/11/26 08:53:43 1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2008/12/03 15:21:13 1.14
@@ -1,429 +1,487 @@
-// BaseClient.java
-//
-// Created: August 2005
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.client;
-
-import java.io.StringReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-
-import org.apache.axis.client.Call;
-import org.apache.commons.lang.StringUtils;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.parser.JDOMUtils;
-import org.biomoby.shared.parser.MobyJob;
-import org.biomoby.shared.parser.MobyPackage;
-import org.biomoby.shared.parser.MobyTags;
-import org.biomoby.shared.parser.ServiceException;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-import org.tulsoft.shared.GException;
-import org.tulsoft.tools.soap.axis.AxisCall;
-
-/**
- * This is a base class for Biomoby clients. It takes care about converting user input into Biomoby XML, sending it in a
- * SOAP message to a Biomoby service, waiting for the response and parsing it from Biomoby XML. It also divides requests
- * and responses into so-called jobs - each of them corresponds to a Biomoby query (a Biomoby single network
- * request may contain more queries/jobs).
- *
- *
- * Any client can override various methods - but the ones she/he must override in a subclass are those
- * telling what service to call ({@link #getServiceLocator}), what data to put in a request ({@link #fillRequest(MobyJob,MobyPackage) fillRequest}),
- * and what to do with a response ({@link #useResponse(MobyJob,MobyPackage) useResponse}.
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-abstract public class BaseClient {
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog( BaseClient.class );
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- static protected boolean notEmpty(String value) {
- return StringUtils.isNotBlank( value );
- }
- static protected boolean isEmpty(String value) {
- return StringUtils.isBlank( value );
- }
-
- /*******************************************************************************************************************
- * The main method that packs input data, invokes a BioMoby service and uses its response. Use this method if the
- * input data should have just one job (which is a usual case) - otherwise use method {@link #process(int)}.
- *
- *
- * @throws MobyException if (a) a sub-class throws it during the filling data or using response, or (b) a Biomoby
- * service invocation fails
- ******************************************************************************************************************/
- public void process() throws MobyException {
- process( 1 );
- }
-
- /*******************************************************************************************************************
- * The main method that packs input data, invokes a BioMoby service and uses its response. The input data may
- * consist from more than one job (query) - the 'jobCount' is a suggestion how many jobs will be included, but this
- * can be changed by the implementing sub-class.
- *
- *
- * Usually a client developer does not need to overwrite this method. She or he makes the real input data filling in
- * the {@link #fillRequest} method, and uses the response in the {@link #useResponse} method.
- *
- *
- * @throws MobyException if (a) a sub-class throws it during the filling data or using response, or (b) a Biomoby
- * service invocation fails
- ******************************************************************************************************************/
- public void process(int jobCount) throws MobyException {
-
- String xmlResponse = null;
-
- // input: raw-level processing
- String xmlInput = fillRequest();
- if ( xmlInput != null ) {
- if ( ( xmlInput = interceptRequest( xmlInput ) ) == null )
- return;
- }
-
- // input: usual processing (i.e. collect XML in iterations)
- else {
- MobyPackage mobyInput = new MobyPackage();
- if ( !fillRequest( mobyInput, jobCount ) )
- return;
- xmlInput = mobyInput.toXML();
- if ( ( xmlInput = interceptRequest( xmlInput ) ) == null )
- return;
- }
-
- // calling service
- xmlResponse = callRemoteService( xmlInput );
-
- // output: raw-level processing
- if ( !useResponse( xmlResponse ) )
- return;
-
- // output: usual processing (again by iterations)
- MobyPackage mobyResponse = MobyPackage.createFromXML( xmlResponse );
- useResponse( mobyResponse );
- }
-
- public String interceptRequest(String xmlInput) throws MobyException {
- return xmlInput;
- }
-
- /*******************************************************************************************************************
- * Create raw XML input. Override this method if you have already an input XML, or you want to create it yourself.
- *
- *
- * @return a full XML input for a Biomoby service (in this case no other fillRequest methods will
- * called); return null if no XML was created and a usual process to gather it will be used
- *
- * @throws MobyException if an XML cannot be created
- ******************************************************************************************************************/
- public String fillRequest() throws MobyException {
- return null;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected String filterMobyResponseType(Object result) throws MobyException {
- if ( result instanceof String )
- return ( String ) result;
- else if ( result instanceof byte[] )
- return new String( ( byte[] ) result );
- else
- throw new MobyException(
- "The Biomoby data should be sent/received either as type String or base64/byte[]. "
- + "But they are of type '" + result.getClass().getName() + "'." );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected String callBiomobyService(MobyServiceLocator locator, String xmlInput) throws MobyException {
-
- MobyService service = locator.getService();
- String serviceName = service.getName();
- boolean asBytes = locator.isAsBytes();
- String serviceEndpoint = service.getURL();
- int timeout = locator.getSuggestedTimeout();
-
- try {
- URL target = new URL( serviceEndpoint );
- AxisCall call = new AxisCall( target, timeout );
- // to allow service calls which need authentication
- setAuthentication( call.getCall() );
- call.getCall().setSOAPActionURI( MobyService.BIOMOBY_SERVICE_URI + "#" + serviceName );
-
- return filterMobyResponseType( call.doCall( MobyService.BIOMOBY_SERVICE_URI, serviceName,
- new Object[]{sendingFilter( xmlInput, asBytes )} ) );
- }
- catch ( MalformedURLException e ) {
- throw new MobyException( "Service endpoint '" + serviceEndpoint + "' is not a valid URL." );
- }
- catch ( GException e ) {
- throw new MobyException( e.getMessage(), e );
- }
- }
-
- /**
- * Sets the authentication for the call. The default implementation does not do anything !
- *
- * @param call
- */
- protected void setAuthentication(Call call) {
- return;
- }
-
- //
- protected Object sendingFilter(String input, boolean asBytes) {
- if ( asBytes ) {
- log.debug( "Data sent as a byte array" );
- return input.getBytes();
- }
- else {
- return input;
- }
- }
-
- /*******************************************************************************************************************
- * Call a SOAP-based BioMoby service. In order to find what service to call and what are its characteristics (such
- * as its endpoint) it will call method {@link #getServiceLocator} that should be implemented by a sub-class.
- *
- *
- * Once it has the service locator, this class does one of the following, in this order:
- *
- *
- * The locator must contain at least a service name. If it does not, an exception is raised.
- *
- * If the locator contains a service endpoint, a call is made to this endpoint, using also the service name as
- * a method name.
- *
- * If the locator has a registry endpoint, an enquiry to the registry is made to find an endpoint of a service
- * corresponding with the given service name. Once found, the service is called.
- *
- * The same as the previous one but using a default registry.
- *
- * @param xmlInput data will be sent to the called Biomoby service
- *
- * @return service response (still in XML)
- *
- * @throws MobyException (a) if service call (or a call to registry; for example because the registry does not know
- * given service) fails, or (b) if the used {@link MobyServiceLocator} does not contain a service name.
- *
- ******************************************************************************************************************/
- public String callRemoteService(String xmlInput) throws MobyException {
-
- // 1) service name is a must
- MobyServiceLocator locator = getServiceLocator();
- MobyService service = locator.getService();
- if ( service == null )
- throw new MobyException( "MobyService locator returned an empty service object.\n"
- + "I do not know what service to call..." );
- String serviceName = service.getName();
- if ( isEmpty( serviceName ) || MobyService.DUMMY_NAME.equals( serviceName ) )
- throw new MobyException( "MobyService locator returned an empty service name.\n"
- + "I do not know what service to call..." );
-
- // 2) try service endpoint
- String serviceEndpoint = service.getURL();
- if ( notEmpty( serviceEndpoint ) )
- return callBiomobyService( locator, xmlInput );
-
- // 3) find service endpoint in a Biomoby registry
- Central worker = new CentralImpl( locator.getRegistryEndpoint(), locator.getRegistryNamespace() );
- MobyService[] services = worker.findService( service );
- if ( services == null || services.length == 0 )
- throw new MobyException( "Service " + service.toShortString() + " is not known in Biomoby registry: \n"
- + "\t" + worker.getRegistryEndpoint() + "\n" + "\t" + worker.getRegistryNamespace() );
- // ...and call the service
- serviceEndpoint = services[ 0 ].getURL();
- if ( notEmpty( serviceEndpoint ) ) {
- service.setURL( serviceEndpoint );
- return callBiomobyService( locator, xmlInput );
- }
-
- // what else can I do?
- throw new MobyException( "Registry has not returned any URL for service " + service.toShortString() );
- }
-
- /*******************************************************************************************************************
- * Fill the whole 'mobyInput' - put there any number of jobs (queries) as you wish (you do not need to follow the
- * 'jobCount' hint suggesting how many jobs should be put there).
- *
- *
- * Usually there is not need to overwrite this method. It serves as an inter-mediator between the main
- * {@link #process} method and the individual request fillings (done by a sub-class in method
- * {@link #fillRequest(MobyJob,MobyPackage)}).
- *
- *
- * @return false if you wish to cancel whole request (nothing will be sent to a Biomoby service); otherwise return
- * true.
- *
- * @param mobyInput is an empty shell that you are supposed to fill with the input data for a Biomoby service
- * execution
- *
- * @param jobCount is only a suggestion how many requests/job should be created (it comes from the {@link #process}
- * method) - but it does not need to be obeyed
- *
- ******************************************************************************************************************/
- public boolean fillRequest(MobyPackage mobyInput, int jobCount) throws MobyException {
-
- if ( jobCount < 0 )
- jobCount = 0;
- for ( int i = 0; i < jobCount; i++ ) {
- MobyJob request = new MobyJob( "job_" + i );
- if ( !fillRequest( request, mobyInput ) )
- break;
- mobyInput.addJob( request );
- }
- return ( mobyInput.size() > 0 );
- }
-
- /*******************************************************************************************************************
- * A raw-level processing. Use it if you need access to raw XML coming from a service.
- *
- *
- * @param xmlResponse is a raw XML response returned from a BioMoby service
- *
- * @return false if the response should be considered fully processed (in this case no other 'useResponse' will be
- * called); true indicates that normal processing of the response will follow; by default, this class (BaseClient )
- * returns true
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'mobyResponse' is broken
- ******************************************************************************************************************/
- public boolean useResponse(String xmlResponse) throws MobyException {
- return true;
- }
-
- /*******************************************************************************************************************
- * A high-level processing. Use it if you need access to all jobs (queries) - that returned from a service - in the
- * same time. Otherwise use the processing on the job level (method {@link #useResponse(MobyJob,MobyPackage)}.
- *
- *
- * @param mobyResponse is a full response returned from a BioMoby service
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'mobyResponse' is broken
- ******************************************************************************************************************/
- public void useResponse(MobyPackage mobyResponse) throws MobyException {
-
- // iterate over all input jobs
- for ( int i = 0; i < mobyResponse.size(); i++ ) {
- if ( !useResponse( mobyResponse.getJob( i ), mobyResponse ) )
- return;
- }
- }
-
- /*******************************************************************************************************************
- * Extracts errors from a raw service response. It is iseful when one does not want to create a whole
- * MobyPackage from a response, but just find whether a response is good or bad.
- *
- *
- * @param xmlResponse is a full response returned from a BioMoby service
- *
- * @return a slightly formatted list of exceptions (of severity error ) extracted from the response; or
- * null if there are no errors there
- ******************************************************************************************************************/
- public String errorsInResponse(String xmlResponse) {
- try {
- StringBuffer buf = new StringBuffer();
- SAXBuilder builder = new SAXBuilder();
- Document doc = builder.build( new StringReader( xmlResponse ) );
- Element root = doc.getRootElement();
- Element mobyContent = JDOMUtils.getChild( root, MobyTags.MOBYCONTENT );
- Element serviceNotes = JDOMUtils.getChild( mobyContent, MobyTags.SERVICENOTES );
- ServiceException[] exceptions = ServiceException.extractExceptions( serviceNotes );
- for ( int i = 0; i < exceptions.length; i++ ) {
- if ( exceptions[ i ].getSeverity() != ServiceException.ERROR )
- continue;
- if ( buf.length() > 0 )
- buf.append( "\n" );
- buf.append( exceptions[ i ].getErrorCodeAsString() );
- buf.append( ": " );
- buf.append( exceptions[ i ].getMessage() );
- }
- return ( buf.length() == 0 ? null : new String( buf ) );
-
- }
- catch ( Exception e ) {
- return e.toString();
- }
- }
-
- //
- // Abstract methods
- //
-
- /*******************************************************************************************************************
- * Return characteristics of a BioMoby service that will be called, and that reveal where to find such service.
- *
- *
- * @see #callRemoteService
- *
- * @return an object defining a location of a BioMoby service
- * @throws MobyException if service locator cannot be returned/created (e.g. because there is not enough information
- * about what service to call)
- ******************************************************************************************************************/
- abstract public MobyServiceLocator getServiceLocator() throws MobyException;
-
- /*******************************************************************************************************************
- * Crate data (fill them into 'request') for one Moby job (query). The request will be sent within given
- * 'inputContext' - but it is not yet there (because you may wish not to put it there - see the return value), and
- * it is not the task of this method to put it there (just fill the 'request').
- *
- *
- * This is a method that should be implemented by a client developer, and it is the place where the client's
- * business logic sits.
- *
- *
- * @return true if this request should be included into the input data (package) that will be sent to a biomoby
- * service; or return false if you do not wish to create any more requests for this particular package (also
- * this 'request' will not be used)
- *
- * @param request is an object that you are supposed to fill with input data for one service invocation; it already
- * has a name (so called 'query id' in the BioMoby speak) but you are free to change it
- *
- * @param inputContext is an envelope where all requests will be stored and sent to a Biomoby service; you do not
- * need to do anything with it here unless you wish; note that all already created requests are there,
- * but not the one you are just creating in this method
- *
- * @throws MobyException if you need so (from whatever reason in your business logic); if thrown then nothing will
- * be sent to a Biomoby service
- *
- ******************************************************************************************************************/
- abstract public boolean fillRequest(MobyJob request, MobyPackage inputContext) throws MobyException;
-
- /*******************************************************************************************************************
- * Process a single job returned from a BioMoby service.
- *
- *
- * This is a method that should be implemented by a client developer, and it is the place where the client's
- * business logic using the response sits.
- *
- *
- * @param response is an object that you are supposed to use
- *
- * @param responseContext is an envelope where the full response (all its jobs) is located; you do not need to do
- * anything with it here unless you wish (e.g. it gives you knowledge about how many jobs are in the full
- * response, or it gives you access to the so-called 'service notes')
- *
- * @return false if you do not wish to get any more responses/jobs; otherwise return true
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'response' is broken
- *
- ******************************************************************************************************************/
- abstract public boolean useResponse(MobyJob response, MobyPackage responseContext) throws MobyException;
-
-}
+// BaseClient.java
+//
+// Created: August 2005
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.client;
+
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.parser.JDOMUtils;
+import org.biomoby.shared.Central;
+import org.biomoby.client.CentralImpl;
+import org.biomoby.shared.parser.MobyPackage;
+import org.biomoby.shared.parser.MobyJob;
+import org.biomoby.shared.parser.ServiceException;
+import org.biomoby.shared.parser.MobyTags;
+
+import org.tulsoft.tools.soap.axis.AxisCall;
+import org.tulsoft.shared.GException;
+
+import org.apache.axis.client.Call;
+import org.apache.commons.lang.StringUtils;
+
+import org.jdom.input.SAXBuilder;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.Namespace;
+
+import java.net.URL;
+import java.net.MalformedURLException;
+import java.io.StringReader;
+
+/**
+ * This is a base class for Biomoby clients. It takes care about
+ * converting user input into Biomoby XML, sending it in a SOAP
+ * message to a Biomoby service, waiting for the response and parsing
+ * it from Biomoby XML. It also divides requests and responses into
+ * so-called jobs - each of them corresponds to a Biomoby
+ * query (a Biomoby single network request may contain more
+ * queries/jobs).
+ *
+ * Any client can override various methods - but the ones she/he
+ * must override in a subclass are those telling what service
+ * to call ({@link #getServiceLocator}), what data to put in a request
+ * ({@link #fillRequest(MobyJob,MobyPackage) fillRequest}), and what
+ * to do with a response ({@link #useResponse(MobyJob,MobyPackage)
+ * useResponse}.
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+abstract public class BaseClient {
+
+ private static org.apache.commons.logging.Log log =
+ org.apache.commons.logging.LogFactory.getLog (BaseClient.class);
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ static protected boolean notEmpty (String value) {
+ return StringUtils.isNotBlank (value);
+ }
+ static protected boolean isEmpty (String value) {
+ return StringUtils.isBlank (value);
+ }
+
+ /**************************************************************************
+ * The main method that packs input data, invokes a BioMoby
+ * service and uses its response. Use this method if the input
+ * data should have just one job (which is a usual case) -
+ * otherwise use method {@link #process(int)}.
+ *
+ * @throws MobyException if (a) a sub-class throws it during the
+ * filling data or using response, or (b) a Biomoby service
+ * invocation fails
+ *************************************************************************/
+ public void process()
+ throws MobyException {
+ process (1);
+ }
+
+ /**************************************************************************
+ * The main method that packs input data, invokes a BioMoby
+ * service and uses its response. The input data may consist from
+ * more than one job (query) - the 'jobCount' is a suggestion how
+ * many jobs will be included, but this can be changed by the
+ * implementing sub-class.
+ *
+ * Usually a client developer does not need to overwrite this
+ * method. She or he makes the real input data filling in the
+ * {@link #fillRequest} method, and uses the response in the
+ * {@link #useResponse} method.
+ *
+ * @throws MobyException if (a) a sub-class throws it during the
+ * filling data or using response, or (b) a Biomoby service
+ * invocation fails
+ *************************************************************************/
+ public void process (int jobCount)
+ throws MobyException {
+
+ String xmlResponse = null;
+
+ // input: raw-level processing
+ String xmlInput = fillRequest();
+ if (xmlInput != null) {
+ if ( (xmlInput = interceptRequest (xmlInput)) == null )
+ return;
+ }
+
+ // input: usual processing (i.e. collect XML in iterations)
+ else {
+ MobyPackage mobyInput = new MobyPackage();
+ if (! fillRequest (mobyInput, jobCount)) return;
+ xmlInput = mobyInput.toXML();
+ if ( (xmlInput = interceptRequest (xmlInput)) == null )
+ return;
+ }
+
+ // calling service
+ xmlResponse = callRemoteService (xmlInput);
+
+ // output: raw-level processing
+ if (! useResponse (xmlResponse)) return;
+
+ // output: usual processing (again by iterations)
+ MobyPackage mobyResponse = MobyPackage.createFromXML (xmlResponse);
+ useResponse (mobyResponse);
+ }
+
+ public String interceptRequest (String xmlInput)
+ throws MobyException {
+ return xmlInput;
+ }
+
+ /**************************************************************************
+ * Create raw XML input. Override this method if you have already
+ * an input XML, or you want to create it yourself.
+ *
+ * @return a full XML input for a Biomoby service (in this case no
+ * other fillRequest methods will called); return null if
+ * no XML was created and a usual process to gather it will be used
+ *
+ * @throws MobyException if an XML cannot be created
+ *************************************************************************/
+ public String fillRequest()
+ throws MobyException {
+ return null;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected String filterMobyResponseType (Object result)
+ throws MobyException {
+ if (result instanceof String)
+ return (String)result;
+ else if (result instanceof byte[])
+ return new String ((byte[])result);
+ else
+ throw new MobyException
+ ("The Biomoby data should be sent/received either as type String or base64/byte[]. " +
+ "But they are of type '" + result.getClass().getName() + "'.");
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected String callBiomobyService (MobyServiceLocator locator,
+ String xmlInput)
+ throws MobyException {
+
+
+ MobyService service = locator.getService();
+ String serviceName = service.getName();
+ boolean asBytes = locator.isAsBytes();
+ String serviceEndpoint = service.getURL();
+ int timeout = locator.getSuggestedTimeout();
+
+ try {
+ URL target = new URL (serviceEndpoint);
+ AxisCall call = new AxisCall (target, timeout);
+ // if the locator has authentication information.
+ if(locator.hasAuthentication()) {
+ call.getCall().setProperty( Call.USERNAME_PROPERTY, locator.getUser() );
+ call.getCall().setProperty( Call.PASSWORD_PROPERTY, locator.getPassword() );
+ }
+ call.getCall().setSOAPActionURI (MobyService.BIOMOBY_SERVICE_URI + "#" + serviceName);
+ return filterMobyResponseType
+ (call.doCall (MobyService.BIOMOBY_SERVICE_URI,
+ serviceName,
+ new Object[] { sendingFilter (xmlInput, asBytes) }));
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Service endpoint '" + serviceEndpoint +
+ "' is not a valid URL.");
+ } catch (GException e) {
+ throw new MobyException (e.getMessage(), e);
+ }
+ }
+
+ //
+ protected Object sendingFilter (String input, boolean asBytes) {
+ if (asBytes) {
+ log.debug ("Data sent as a byte array");
+ return input.getBytes();
+ } else {
+ return input;
+ }
+ }
+
+ /**************************************************************************
+ * Call a SOAP-based BioMoby service. In order to find what
+ * service to call and what are its characteristics (such as its
+ * endpoint) it will call method {@link #getServiceLocator} that
+ * should be implemented by a sub-class.
+ *
+ * Once it has the service locator, this class does one of the
+ * following, in this order:
+ *
+ * The locator must contain at least a service name. If it
+ * does not, an exception is raised.
+ *
+ * If the locator contains a service endpoint, a call is
+ * made to this endpoint, using also the service name as a
+ * method name.
+ *
+ * If the locator has a registry endpoint, an enquiry to
+ * the registry is made to find an endpoint of a service
+ * corresponding with the given service name. Once found, the
+ * service is called.
+ *
+ * The same as the previous one but using a default
+ * registry.
+ *
+ * @param xmlInput data will be sent to the called Biomoby service
+ *
+ * @return service response (still in XML)
+ *
+ * @throws MobyException (a) if service call (or a call to
+ * registry; for example because the registry does not know given
+ * service) fails, or (b) if the used {@link MobyServiceLocator}
+ * does not contain a service name.
+ *
+ *************************************************************************/
+ public String callRemoteService (String xmlInput)
+ throws MobyException {
+
+ // 1) service name is a must
+ MobyServiceLocator locator = getServiceLocator();
+ MobyService service = locator.getService();
+ if (service == null)
+ throw new MobyException ("MobyService locator returned an empty service object.\n" +
+ "I do not know what service to call...");
+ String serviceName = service.getName();
+ if (isEmpty (serviceName) ||
+ MobyService.DUMMY_NAME.equals (serviceName))
+ throw new MobyException ("MobyService locator returned an empty service name.\n" +
+ "I do not know what service to call...");
+
+ // 2) try service endpoint
+ String serviceEndpoint = service.getURL();
+ if (notEmpty (serviceEndpoint))
+ return callBiomobyService (locator, xmlInput);
+
+ // 3) find service endpoint in a Biomoby registry
+ Central worker = new CentralImpl (locator.getRegistryEndpoint(),
+ locator.getRegistryNamespace());
+ MobyService[] services = worker.findService (service);
+ if (services == null || services.length == 0)
+ throw new MobyException ("Service " + service.toShortString() +
+ " is not known in Biomoby registry: \n" +
+ "\t" + worker.getRegistryEndpoint() + "\n" +
+ "\t" + worker.getRegistryNamespace());
+ // ...and call the service
+ serviceEndpoint = services[0].getURL();
+ if (notEmpty (serviceEndpoint)) {
+ service.setURL (serviceEndpoint);
+ return callBiomobyService (locator, xmlInput);
+ }
+
+ // what else can I do?
+ throw new MobyException ("Registry has not returned any URL for service " +
+ service.toShortString());
+ }
+
+ /**************************************************************************
+ * Fill the whole 'mobyInput' - put there any number of jobs
+ * (queries) as you wish (you do not need to follow the 'jobCount'
+ * hint suggesting how many jobs should be put there).
+ *
+ * Usually there is not need to overwrite this method. It serves
+ * as an inter-mediator between the main {@link #process} method
+ * and the individual request fillings (done by a sub-class in
+ * method {@link #fillRequest(MobyJob,MobyPackage)}).
+ *
+ * @return false if you wish to cancel whole request (nothing will
+ * be sent to a Biomoby service); otherwise return true.
+ *
+ * @param mobyInput is an empty shell that you are supposed to
+ * fill with the input data for a Biomoby service execution
+ *
+ * @param jobCount is only a suggestion how many requests/job
+ * should be created (it comes from the {@link #process} method) -
+ * but it does not need to be obeyed
+ *
+ *************************************************************************/
+ public boolean fillRequest (MobyPackage mobyInput, int jobCount)
+ throws MobyException {
+
+ if (jobCount < 0) jobCount = 0;
+ for (int i = 0; i < jobCount; i++) {
+ MobyJob request = new MobyJob ("job_" + i);
+ if (! fillRequest (request, mobyInput))
+ break;
+ mobyInput.addJob (request);
+ }
+ return (mobyInput.size() > 0);
+ }
+
+ /**************************************************************************
+ * A raw-level processing. Use it if you need access to raw XML
+ * coming from a service.
+ *
+ * @param xmlResponse is a raw XML response returned from a
+ * BioMoby service
+ *
+ * @return false if the response should be considered fully
+ * processed (in this case no other 'useResponse' will be called);
+ * true indicates that normal processing of the response will
+ * follow; by default, this class (BaseClient ) returns true
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'mobyResponse' is broken
+ *************************************************************************/
+ public boolean useResponse (String xmlResponse)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * A high-level processing. Use it if you need access to all jobs
+ * (queries) - that returned from a service - in the same time.
+ * Otherwise use the processing on the job level (method {@link
+ * #useResponse(MobyJob,MobyPackage)}.
+ *
+ * @param mobyResponse is a full response returned from a BioMoby
+ * service
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'mobyResponse' is broken
+ *************************************************************************/
+ public void useResponse (MobyPackage mobyResponse)
+ throws MobyException {
+
+ // iterate over all input jobs
+ for (int i = 0; i < mobyResponse.size(); i++) {
+ if (! useResponse (mobyResponse.getJob (i),
+ mobyResponse))
+ return;
+ }
+ }
+
+ /**************************************************************************
+ * Extracts errors from a raw service response. It is iseful when
+ * one does not want to create a whole MobyPackage from a
+ * response, but just find whether a response is good or bad.
+ *
+ * @param xmlResponse is a full response returned from a BioMoby
+ * service
+ *
+ * @return a slightly formatted list of exceptions (of severity
+ * error ) extracted from the response; or null if there
+ * are no errors there
+ *************************************************************************/
+ public String errorsInResponse (String xmlResponse) {
+ try {
+ StringBuffer buf = new StringBuffer();
+ SAXBuilder builder = new SAXBuilder();
+ Document doc =
+ builder.build (new StringReader (xmlResponse));
+ Element root = doc.getRootElement();
+ Element mobyContent = JDOMUtils.getChild (root, MobyTags.MOBYCONTENT);
+ Element serviceNotes = JDOMUtils.getChild (mobyContent, MobyTags.SERVICENOTES);
+ ServiceException[] exceptions =
+ ServiceException.extractExceptions (serviceNotes);
+ for (int i = 0; i < exceptions.length; i++) {
+ if (exceptions[i].getSeverity() != ServiceException.ERROR)
+ continue;
+ if (buf.length() > 0)
+ buf.append ("\n");
+ buf.append (exceptions[i].getErrorCodeAsString());
+ buf.append (": ");
+ buf.append (exceptions[i].getMessage());
+ }
+ return (buf.length() == 0 ? null : new String (buf));
+
+ } catch (Exception e) {
+ return e.toString();
+ }
+ }
+
+
+ //
+ // Abstract methods
+ //
+
+ /**************************************************************************
+ * Return characteristics of a BioMoby service that will be
+ * called, and that reveal where to find such service.
+ *
+ * @see #callRemoteService
+ *
+ * @return an object defining a location of a BioMoby service
+ * @throws MobyException if service locator cannot be
+ * returned/created (e.g. because there is not enough information
+ * about what service to call)
+ *************************************************************************/
+ abstract public MobyServiceLocator getServiceLocator()
+ throws MobyException;
+
+ /**************************************************************************
+ * Crate data (fill them into 'request') for one Moby job
+ * (query). The request will be sent within given 'inputContext' -
+ * but it is not yet there (because you may wish not to put it
+ * there - see the return value), and it is not the task of this
+ * method to put it there (just fill the 'request').
+ *
+ * This is a method that should be implemented by a client
+ * developer, and it is the place where the client's business
+ * logic sits.
+ *
+ * @return true if this request should be included into the input
+ * data (package) that will be sent to a biomoby service; or
+ * return false if you do not wish to create any more requests for
+ * this particular package (also this 'request' will not be used)
+ *
+ * @param request is an object that you are supposed to fill with
+ * input data for one service invocation; it already has a name
+ * (so called 'query id' in the BioMoby speak) but you are free to change it
+ *
+ * @param inputContext is an envelope where all requests will be
+ * stored and sent to a Biomoby service; you do not need to do
+ * anything with it here unless you wish; note that all already
+ * created requests are there, but not the one you are just
+ * creating in this method
+ *
+ * @throws MobyException if you need so (from whatever reason in
+ * your business logic); if thrown then nothing will be sent to a
+ * Biomoby service
+ *
+ *************************************************************************/
+ abstract public boolean fillRequest (MobyJob request, MobyPackage inputContext)
+ throws MobyException;
+
+ /**************************************************************************
+ * Process a single job returned from a BioMoby service.
+ *
+ * This is a method that should be implemented by a client
+ * developer, and it is the place where the client's business
+ * logic using the response sits.
+ *
+ * @param response is an object that you are supposed to use
+ *
+ * @param responseContext is an envelope where the full response
+ * (all its jobs) is located; you do not need to do anything with
+ * it here unless you wish (e.g. it gives you knowledge about how
+ * many jobs are in the full response, or it gives you access to
+ * the so-called 'service notes')
+ *
+ * @return false if you do not wish to get any more
+ * responses/jobs; otherwise return true
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'response' is broken
+ *
+ *************************************************************************/
+ abstract public boolean useResponse (MobyJob response,
+ MobyPackage responseContext)
+ throws MobyException;
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2006/02/19 18:42:55 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/03 15:21:13 1.5
@@ -33,6 +33,8 @@
protected String registryNamespace;
protected boolean asBytes = false;
protected int timeout = 0;
+ protected String user;
+ protected String password;
/**************************************************************************
* Default constructor.
@@ -131,6 +133,44 @@
public void setAsBytes (boolean enabled) {
asBytes = enabled;
}
-
-
+
+ /*****************************************
+ * Sets the user for authentication
+ * @param user
+ ***************************************/
+ public void setUser(String user) {
+ this.user = user;
+ }
+
+ /***************************************
+ * Sets the password for authentication
+ * @param password
+ ***************************************/
+ public void setPassword(String password) {
+ this.password = password;
+ }
+
+ /******************************************
+ * Returns the user for the authentication
+ * @return user
+ ******************************************/
+ public String getUser() {
+ return user;
+ }
+
+ /**********************************************
+ * Returns the password for the authentication
+ * @return password
+ **********************************************/
+ public String getPassword() {
+ return password;
+ }
+
+ /***************************************************
+ * Returns true if the user AND the password is set
+ * @return
+ ***************************************************/
+ public boolean hasAuthentication() {
+ return user != null && password != null;
+ }
}
From groscurt at dev.open-bio.org Wed Dec 3 07:09:41 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 07:09:41 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031209.mB3C9f1X011972@dev.open-bio.org>
groscurt
Wed Dec 3 07:09:40 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv11937/src/main/org/biomoby/client
Modified Files:
CentralImpl.java
Log Message:
reformatted it to the original version and removed the System.properties for the service authentication
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.58,1.59
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/11/26 08:53:43 1.58
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/12/03 12:09:40 1.59
@@ -69,50 +69,53 @@
import java.util.logging.*;
/**
- * A default implementation of the interface {@link org.biomoby.shared.Central Central} allowing access to a Moby
- * registry.
- *
- * This class is supposed to be used by all other clients that wish to communicate with the Moby Registry, but do not
- * want to know about all XML details that are necessary for talking with the Moby Central directly. This is an example
- * of a client program:
- *
- *
+ * A default implementation of the
+ * interface {@link org.biomoby.shared.Central Central}
+ * allowing access to a Moby registry.
+ *
+ * This class is supposed to be used by all other clients that wish
+ * to communicate with the Moby Registry, but do not want to know
+ * about all XML details that are necessary for talking with the Moby Central
+ * directly. This is an example of a client program:
+ *
* import org.biomoby.shared.Central;
* import org.biomoby.shared.MobyException;
* import org.biomoby.client.CentralImpl;
* import java.util.Map;
* import java.util.Iterator;
- *
+ *
* public class Test {
- *
- * public static void main( String[] args ) throws MobyException {
- *
- * Central worker = new CentralImpl();
- * Map authorities = worker.getServiceNamesByAuthority();
- *
- * for ( Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
- * Map.Entry entry = ( Map.Entry ) it.next();
- * System.out.println( entry.getKey() );
- * String[] names = ( String[] ) entry.getValue();
- * for ( int i = 0; i < names.length; i++ )
- * System.out.println( "\t" + names[ i ] );
- * }
- * }
+ *
+ * public static void main (String[] args)
+ * throws MobyException {
+ *
+ * Central worker = new CentralImpl();
+ * Map authorities = worker.getServiceNamesByAuthority();
+ *
+ * for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
+ * Map.Entry entry = (Map.Entry)it.next();
+ * System.out.println (entry.getKey());
+ * String[] names = (String[])entry.getValue();
+ * for (int i = 0; i < names.length; i++)
+ * System.out.println ("\t" + names[i]);
+ * }
+ * }
* }
- *
- *
+ *
+ *
* @author Martin Senger
* @version $Id$
*/
-public class CentralImpl implements Central, SimpleCache {
+public class CentralImpl
+ implements Central, SimpleCache {
private URL endpoint;
private String uri;
protected boolean debug = false;
/** Common central used to if getDefaultCentral() is called */
- protected static Map< String, CentralImpl > defaultCentrals = new HashMap< String, CentralImpl >();
+ protected static Map defaultCentrals = new HashMap();
/** Default location (endpoint) of a Moby registry. */
public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
@@ -121,322 +124,368 @@
public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
/**
- * The META-INF resource file that will be checked to determine what default class should be instantiated in order
- * to create a Central Implementation when getDefaultCentral() is called.
+ * The META-INF resource file that will be checked to determine what
+ * default class should be instantiated in order to create a Central Implementation
+ * when getDefaultCentral() is called.
*/
public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
/** The class to use for getDefaultCentral if all else fails */
public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
- private static Logger logger = Logger.getLogger( "org.biomoby.client.CentralImpl" );
+ private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
- /**
- * Thread local that gives each thread its own DocumentBuilderFactory (since it is not thread-safe). Code taken from
- * Apache's JaxpUtils.
- */
- public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
- protected synchronized Object initialValue() {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware( true );
- return dbf;
- }
- };
-
- /*******************************************************************************************************************
- * Default constructor. It connects to a default Moby registry (as defined in {@link #DEFAULT_ENDPOINT}) using a
- * default namespace (as defined int {@link #DEFAULT_NAMESPACE}).
- ******************************************************************************************************************/
- public CentralImpl() throws MobyException {
- this( DEFAULT_ENDPOINT, DEFAULT_NAMESPACE );
+ /**
+ * Thread local that gives each thread its own
+ * DocumentBuilderFactory (since it is not thread-safe). Code taken
+ * from Apache's JaxpUtils.
+ */
+ public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
+ protected synchronized Object initialValue() {
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware (true);
+ return dbf;
+ }
+ };
+
+
+ /*************************************************************************
+ * Default constructor. It connects to a default Moby registry
+ * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
+ * (as defined int {@link #DEFAULT_NAMESPACE}).
+ *************************************************************************/
+ public CentralImpl()
+ throws MobyException {
+ this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Constructor allowing to specify which Moby Registry to use.
- *
- * @throws MobyException
- * if 'endpoint' is not a valid URL, or if no DOM parser is available
- ******************************************************************************************************************/
- public CentralImpl( String endpoint ) throws MobyException {
- this( endpoint, DEFAULT_NAMESPACE );
- }
-
- /*******************************************************************************************************************
- * Constructor allowing to specify which Moby Registry and what namespace to use. If any of the parameters is null,
- * its default value is used instead.
- *
- *
- * @throws MobyException
- * if 'endpoint' is not a valid URL, or if no DOM parser was found
- ******************************************************************************************************************/
- public CentralImpl( String endpoint, String namespace ) throws MobyException {
-
- if ( endpoint == null || "".equals( endpoint.trim() ) ) endpoint = DEFAULT_ENDPOINT;
- if ( namespace == null || "".equals( namespace.trim() ) ) namespace = DEFAULT_NAMESPACE;
-
- try {
- this.endpoint = new URL( endpoint );
- }
- catch ( MalformedURLException e ) {
- throw new MobyException( "Bad URL: " + endpoint );
- }
- this.uri = namespace;
-
- cache = new Hashtable< String, Object >();
- useCache = true;
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser is available
+ *************************************************************************/
+ public CentralImpl (String endpoint)
+ throws MobyException {
+ this (endpoint, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry and what
+ * namespace to use. If any of the parameters is null, its default
+ * value is used instead.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser was found
+ *************************************************************************/
+ public CentralImpl (String endpoint, String namespace)
+ throws MobyException {
+
+ if (endpoint == null || "".equals (endpoint.trim()))
+ endpoint = DEFAULT_ENDPOINT;
+ if (namespace == null || "".equals (namespace.trim()))
+ namespace = DEFAULT_NAMESPACE;
+
+ try {
+ this.endpoint = new URL (endpoint);
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Bad URL: " + endpoint);
+ }
+ this.uri = namespace;
+
+ cache = new Hashtable();
+ useCache = true;
+ }
+
+ /*************************************************************************
+ * Loads a DOM Document from an InputStream. Uses thread-safe
+ * mechanism.
+ *************************************************************************/
+ public static Document loadDocument (InputStream input)
+ throws MobyException {
+ try {
+ DocumentBuilderFactory dbf
+ = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
+ DocumentBuilder db = dbf.newDocumentBuilder();
+ return (db.parse (input));
+ } catch (Exception e) {
+ throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
}
-
- /*******************************************************************************************************************
- * Loads a DOM Document from an InputStream. Uses thread-safe mechanism.
- ******************************************************************************************************************/
- public static Document loadDocument( InputStream input ) throws MobyException {
- try {
- DocumentBuilderFactory dbf = ( DocumentBuilderFactory ) DOCUMENT_BUILDER_FACTORIES.get();
- DocumentBuilder db = dbf.newDocumentBuilder();
- return ( db.parse( input ) );
- }
- catch ( Exception e ) {
- throw new MobyException( "Problem with reading XML input: " + e.toString(), e );
- }
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Call 'method' with 'parameters' and return its result.
- ******************************************************************************************************************/
- protected Object doCall( String method, Object[] parameters ) throws MobyException {
-
- Call call = null;
- try {
- Service service = new Service();
- call = ( Call ) service.createCall();
- call.setTargetEndpointAddress( endpoint );
- call.setTimeout( new Integer( 0 ) );
-
- String user = System.getProperty( "user" );
- String password = System.getProperty( "password" );
-
- if ( user != null && password != null ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, password );
- }
-
- call.setSOAPActionURI( uri + "#" + method );
-
- if ( debug ) {
- System.err.println( "METHOD CALL: " + method );
- System.err.println( "------------" );
- if ( parameters.length > 0 ) System.err.println( parameters[ 0 ] + "\n" );
- System.err.println( "------------\n" );
-
- Object result = call.invoke( uri, method, parameters );
-
- System.err.println( "METHOD RETURN:" );
- System.err.println( "------------" );
- if ( result != null ) System.err.println( result + "\n" );
- System.err.println( "------------\n" );
-
- return resultToString( result );
-
- }
- else {
- return resultToString( call.invoke( uri, method, parameters ) );
- }
-
- }
- catch ( AxisFault e ) {
- throw new MobyException( formatFault( e, endpoint.toString(), ( call == null ? null : call
- .getOperationName() ) ), e );
- // (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
-
- }
- catch ( Exception e ) {
- throw new MobyException( e.toString(), e );
- // e.printStackTrace();
- }
- }
-
- /*******************************************************************************************************************
- * Parse the given XML sniplet to find tag 'success'. If it has value '1' look further for tag 'id' and return it
- * back (or return an empty string if ID is not there). Otherwise raise an exception with the 'culprit' and with the
- * message from the tag 'message'.
- *
- *
- * The return value is a two-element long array. The first element is the ID (given by BioMobe registry), and the
- * second element is RDF corresponding with the registered object (BioMoby returns this only for service instances,
- * so for other objects this will be null).
- *
- *
- * This is how the XML is supposed to look:
- *
- * Success takes the value "1" to indicate success, "0" to indicate failure, and "-1" to indicate "Pending
- * Curation".
- ******************************************************************************************************************/
- protected String[] checkRegistration( String xml, Object culprit ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String id = "", success = "0", message = "", rdf = "";
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( xml.getBytes() ) );
- Element root = document.getDocumentElement();
-
- NodeList children = root.getChildNodes();
- for ( int i = 0; i < children.getLength(); i++ ) {
- if ( children.item( i ).getNodeType() != Node.ELEMENT_NODE ) continue;
- Element elem = ( Element ) children.item( i );
- if ( elem.getNodeName().equals( "id" ) ) {
- if ( elem.getFirstChild() != null ) id = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "success" ) ) {
- if ( elem.getFirstChild() != null ) success = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "message" ) ) {
- if ( elem.getFirstChild() != null ) message = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "RDF" ) ) {
- if ( elem.getFirstChild() != null ) rdf = elem.getFirstChild().getNodeValue();
- }
- }
-
- if ( success.equals( "0" ) )
- throw new NoSuccessException( message, culprit );
- else if ( success.equals( "-1" ) ) throw new PendingCurationException();
- return new String[] { id, rdf };
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML created from the definitions representing input data types and their usage in the given
- * service. Only data considered primary are included. Note that the main job of converting to XML is done by
- * instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- ******************************************************************************************************************/
- protected String buildSecondaryInputTag( MobyService service ) {
- StringBuffer buf = new StringBuffer();
- MobyData[] secInputs = service.getSecondaryInputs();
- buf.append( "\n" );
- for ( int i = 0; i < secInputs.length; i++ ) {
- buf.append( secInputs[ i ].toXML() );
- }
- buf.append( " \n" );
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML created from the definitions representing output data types and their usage in the given
- * service. Only data considered primary are included. Note that the main job of converting to XML is done by
- * instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- ******************************************************************************************************************/
- protected String buildOutputTag( MobyService service ) {
- StringBuffer buf = new StringBuffer();
- MobyData[] primaryOutputs = service.getPrimaryOutputs();
- buf.append( "\n" );
- for ( int i = 0; i < primaryOutputs.length; i++ )
- buf.append( primaryOutputs[ i ].toXML() );
- buf.append( " \n" );
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML represented a query object (an object used to find a service).
- *
+ *************************************************************************/
+ protected Object doCall (String method, Object[] parameters)
+ throws MobyException {
+
+ Call call = null;
+ try {
+ Service service = new Service();
+ call = (Call) service.createCall();
+ call.setTargetEndpointAddress (endpoint);
+ call.setTimeout (new Integer (0));
+
+ call.setSOAPActionURI (uri + "#" + method);
+
+ if (debug) {
+ System.err.println ("METHOD CALL: " + method);
+ System.err.println ("------------");
+ if (parameters.length > 0)
+ System.err.println (parameters[0] + "\n");
+ System.err.println ("------------\n");
+
+ Object result = call.invoke (uri, method, parameters);
+
+ System.err.println ("METHOD RETURN:");
+ System.err.println ("------------");
+ if (result != null)
+ System.err.println (result + "\n");
+ System.err.println ("------------\n");
+
+ return resultToString (result);
+
+ } else {
+ return resultToString (call.invoke (uri, method, parameters));
+ }
+
+ } catch (AxisFault e) {
+ throw new MobyException
+ (formatFault (e,
+ endpoint.toString(),
+ (call == null ? null : call.getOperationName())),
+ e);
+// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+
+ } catch (Exception e) {
+ throw new MobyException (e.toString(), e);
+// e.printStackTrace();
+ }
+ }
+
+
+ /**************************************************************************
+ * Parse the given XML sniplet to find tag 'success'. If it has value '1'
+ * look further for tag 'id' and return it back (or return an empty string
+ * if ID is not there). Otherwise raise an exception with the 'culprit'
+ * and with the message from the tag 'message'.
+ *
+ * The return value is a two-element long array. The first element
+ * is the ID (given by BioMobe registry), and the second element
+ * is RDF corresponding with the registered object (BioMoby
+ * returns this only for service instances, so for other objects
+ * this will be null).
+ *
+ * This is how the XML is supposed to look:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * Success takes the value "1" to indicate success, "0" to
+ * indicate failure, and "-1" to indicate "Pending Curation".
+ *************************************************************************/
+ protected String[] checkRegistration (String xml, Object culprit)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String id = "", success = "0", message = "", rdf = "";
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ Element root = document.getDocumentElement();
+
+ NodeList children = root.getChildNodes();
+ for (int i = 0; i < children.getLength(); i++) {
+ if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
+ continue;
+ Element elem = (Element)children.item (i);
+ if (elem.getNodeName().equals ("id")) {
+ if (elem.getFirstChild() != null)
+ id = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals("success")) {
+ if (elem.getFirstChild() != null)
+ success = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("message")) {
+ if (elem.getFirstChild() != null)
+ message = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("RDF")) {
+ if (elem.getFirstChild() != null)
+ rdf = elem.getFirstChild().getNodeValue();
+ }
+ }
+
+ if (success.equals ("0"))
+ throw new NoSuccessException (message, culprit);
+ else if (success.equals ("-1"))
+ throw new PendingCurationException();
+ return new String[] { id, rdf };
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing input
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
* The returned XML looks like this:
- *
- *
- *
- * ServiceTypeTerm ServiceName moby
- * http://desired.service.provider ; 1|0 1|0
- * 1|0 something .... ....
- ******************************************************************************************************************/
- protected String buildQueryObject( MobyService service, String[] keywords, boolean expandObjects,
- boolean expandServices, boolean authoritative ) {
- if ( service == null ) {
- service = new MobyService( "dummy" );
- service.setCategory( "" );
- }
- StringBuffer buf = new StringBuffer();
-
- buf.append( "\n \n" );
-
- buf.append( "\n\n" );
- MobyData[] po = service.getPrimaryOutputs();
- if ( po.length > 0 ) {
- for ( int i = 0; i < po.length; i++ )
- buf.append( po[ i ].toXML() );
- }
- buf.append( " \n \n" );
-
- buf.append( "" + service.getType() + " \n" );
-
- String name = service.getName();
- if ( !name.equals( "" ) && !name.equals( "dummy" ) && !name.equals( MobyService.DUMMY_NAME ) )
- buf.append( "" + service.getName() + " \n" );
-
- String sigURL = service.getSignatureURL();
- if ( !sigURL.equals( "" ) ) buf.append( "" + sigURL + " \n" );
-
- buf.append( "" + service.getCategory() + " \n" );
- buf.append( "" + service.getAuthority() + " \n" );
-
- buf.append( "" );
- buf.append( expandObjects ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "" );
- buf.append( expandServices ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "" );
- buf.append( authoritative ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "\n" );
- if ( keywords != null && keywords.length > 0 ) {
- for ( int i = 0; i < keywords.length; i++ ) {
- buf.append( "" );
- buf.append( keywords[ i ] );
- buf.append( " \n" );
- }
- }
- buf.append( " \n" );
-
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Extract one or more MobyService objects from the given XML piece. The XML should look like this:
- *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildSecondaryInputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] secInputs = service.getSecondaryInputs();
+ buf.append ("\n");
+ for (int i = 0; i < secInputs.length; i++) {
+ buf.append (secInputs[i].toXML());
+ }
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing output
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildOutputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] primaryOutputs = service.getPrimaryOutputs();
+ buf.append ("\n");
+ for (int i = 0; i < primaryOutputs.length; i++)
+ buf.append (primaryOutputs[i].toXML());
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML represented a query object (an object used
+ * to find a service).
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * ServiceTypeTerm
+ * ServiceName
+ * moby
+ * http://desired.service.provider ;
+ * 1|0
+ * 1|0
+ * 1|0
+ *
+ * something
+ * ....
+ * ....
+ *
+ *************************************************************************/
+ protected String buildQueryObject (MobyService service,
+ String[] keywords,
+ boolean expandObjects,
+ boolean expandServices,
+ boolean authoritative) {
+ if (service == null) {
+ service = new MobyService ("dummy");
+ service.setCategory ("");
+ }
+ StringBuffer buf = new StringBuffer();
+
+ buf.append ("\n \n");
+
+ buf.append ("\n\n");
+ MobyData[] po = service.getPrimaryOutputs();
+ if (po.length > 0) {
+ for (int i = 0; i < po.length; i++)
+ buf.append (po[i].toXML());
+ }
+ buf.append (" \n \n");
+
+ buf.append ("" + service.getType() + " \n");
+
+ String name = service.getName();
+ if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
+ buf.append ("" + service.getName() + " \n");
+
+ String sigURL = service.getSignatureURL();
+ if (!sigURL.equals (""))
+ buf.append ("" + sigURL + " \n");
+
+ buf.append ("" + service.getCategory() + " \n");
+ buf.append ("" + service.getAuthority() + " \n");
+
+ buf.append ("");
+ buf.append (expandObjects ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (expandServices ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (authoritative ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("\n");
+ if (keywords != null && keywords.length > 0) {
+ for (int i = 0; i < keywords.length; i++) {
+ buf.append ("");
+ buf.append (keywords[i]);
+ buf.append (" \n");
+ }
+ }
+ buf.append (" \n");
+
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Extract one or more MobyService objects from the given XML piece.
+ * The XML should look like this:
*
* <Services>
- * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
+ * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
* <serviceType>Service_Ontology_Term</serviceType>
* <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
* <contactEmail>your at email.addy.here</contactEmail>
@@ -459,359 +508,359 @@
* ...
* </Services>
*
- *
- * @throws MobyException
- * if the XML document is invalid
- ******************************************************************************************************************/
- public MobyService[] extractServices( String xml ) throws MobyException {
-
- Document document = loadDocument( new ByteArrayInputStream( xml.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Service" );
- MobyService[] results = new MobyService[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyService service = new MobyService( elem.getAttribute( "serviceName" ) );
- service.setAuthority( elem.getAttribute( "authURI" ) );
- service.setLSID( elem.getAttribute( "lsid" ) );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "Description" ) ) {
- service.setDescription( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "Category" ) ) {
- service.setCategory( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "URL" ) ) {
- service.setURL( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "signatureURL" ) ) {
- service.setSignatureURL( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "contactEmail" ) ) {
- service.setEmailContact( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "serviceType" ) ) {
- service.setType( getFirstValue( children.item( j ) ) );
- MobyServiceType mst = new MobyServiceType( service.getType() );
- NamedNodeMap map = ( children.item( j ).getAttributes() );
- if ( map != null ) {
- Node node = map.getNamedItemNS( children.item( j ).getNamespaceURI(), "lsid" );
- if ( node != null ) mst.setLSID( node.getNodeValue() );
- }
- service.setServiceType( mst );
- }
- else if ( nodeName.equals( "authoritative" ) ) {
- String authoritative = getFirstValue( children.item( j ) );
- service.setAuthoritative( authoritative.equals( "1" ) ? true : false );
- }
- else if ( nodeName.equals( "Input" ) ) {
- //
- // ...
- //
- //
- // ......
- // ......
- //
- //
- NodeList inputs = children.item( j ).getChildNodes();
- for ( int k = 0; k < inputs.getLength(); k++ ) {
- if ( inputs.item( k ).getNodeName().equals( "Simple" ) ) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple( ( Element ) inputs.item( k ) );
- service.addInput( data );
- }
- else if ( inputs.item( k ).getNodeName().equals( "Collection" ) ) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet( ( Element ) inputs.item( k ) );
- service.addInput( data );
- }
- }
- }
- else if ( nodeName.equals( "Output" ) ) {
- //
- //
- //
- NodeList inputs = children.item( j ).getChildNodes();
- for ( int k = 0; k < inputs.getLength(); k++ ) {
- if ( inputs.item( k ).getNodeName().equals( "Simple" ) ) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple( ( Element ) inputs.item( k ) );
- service.addOutput( data );
- }
- else if ( inputs.item( k ).getNodeName().equals( "Collection" ) ) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet( ( Element ) inputs.item( k ) );
- service.addOutput( data );
- }
- }
-
- }
- else if ( nodeName.equals( "secondaryArticles" ) ) {
- //
- // ...
- //
- NodeList parameters = children.item( j ).getChildNodes();
- for ( int k = 0; k < parameters.getLength(); k++ ) {
- if ( parameters.item( k ).getNodeName().equals( "Parameter" ) ) {
- MobySecondaryData data = new MobySecondaryData( ( Element ) parameters.item( k ) );
- service.addInput( data );
- }
- }
- }
+ * @throws MobyException if the XML document is invalid
+ *************************************************************************/
+ public MobyService[] extractServices (String xml)
+ throws MobyException {
+
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ NodeList list = document.getElementsByTagName ("Service");
+ MobyService[] results = new MobyService [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyService service = new MobyService (elem.getAttribute ("serviceName"));
+ service.setAuthority (elem.getAttribute ("authURI"));
+ service.setLSID (elem.getAttribute ("lsid"));
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ service.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Category")) {
+ service.setCategory (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("URL")) {
+ service.setURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("signatureURL")) {
+ service.setSignatureURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ service.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("serviceType")) {
+ service.setType (getFirstValue (children.item (j)));
+ MobyServiceType mst = new MobyServiceType(service.getType());
+ NamedNodeMap map = (children.item (j).getAttributes());
+ if (map != null) {
+ Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
+ if (node != null)
+ mst.setLSID(node.getNodeValue());
+ }
+ service.setServiceType(mst);
+ } else if (nodeName.equals ("authoritative")) {
+ String authoritative = getFirstValue (children.item (j));
+ service.setAuthoritative (authoritative.equals ("1") ? true : false);
+ } else if (nodeName.equals ("Input")) {
+ //
+ // ...
+ //
+ //
+ // ......
+ // ......
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addInput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addInput (data);
+ }
+ }
+ } else if (nodeName.equals ("Output")) {
+ //
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addOutput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addOutput (data);
+ }
+ }
+
+ } else if (nodeName.equals ("secondaryArticles")) {
+ //
+ // ...
+ //
+ NodeList parameters = children.item (j).getChildNodes();
+ for (int k = 0; k < parameters.getLength(); k++) {
+ if (parameters.item (k).getNodeName().equals ("Parameter")) {
+ MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
+ service.addInput (data);
+ }
}
- results[ i ] = service;
}
- return results;
+ }
+ results [i] = service;
+ }
+ return results;
}
// protect against null values
- protected String getFirstValue( Node child ) {
- Node node = child.getFirstChild();
- if ( node == null ) return "";
- String value = node.getNodeValue();
- if ( value == null ) return "";
- return value;
+ protected String getFirstValue (Node child) {
+ Node node = child.getFirstChild();
+ if (node == null) return "";
+ String value = node.getNodeValue();
+ if (value == null) return "";
+ return value;
+ }
+
+ protected String getFirstValue (NodeList children) {
+ if (children.item(0) != null && children.item(0).hasChildNodes()) {
+ children.item(0).normalize();
+ return getFirstValue (children.item(0));
}
-
- protected String getFirstValue( NodeList children ) {
- if ( children.item( 0 ) != null && children.item( 0 ).hasChildNodes() ) {
- children.item( 0 ).normalize();
- return getFirstValue( children.item( 0 ) );
- }
- return "";
+ return "";
}
- /*******************************************************************************************************************
+ /**************************************************************************
*
* Implementing SimpleCache interface.
- *
- * Why to have an interface for such trivial thing? Well, because I needed to overwrite the caching mechanism in the
- * subclasses so I needed to have all caching functions as separate methods - that's why I have collect them in an
- * interface.
- *
- ******************************************************************************************************************/
- private Hashtable< String, Object > cache; // this is the cache itself
- private boolean useCache; // this signal that we are actually caching things
+ *
+ * Why to have an interface for such trivial thing? Well, because
+ * I needed to overwrite the caching mechanism in the subclasses
+ * so I needed to have all caching functions as separate methods -
+ * that's why I have collect them in an interface.
+ *
+ *************************************************************************/
+ private Hashtable cache; // this is the cache itself
+ private boolean useCache; // this signal that we are actually caching things
// not used here
- public String createId( String rootName, String semanticType, String syntaxType, long lastModified, Properties props ) {
- return ""; // not used here
+ public String createId (String rootName,
+ String semanticType, String syntaxType,
+ long lastModified,
+ Properties props) {
+ return ""; // not used here
}
// check existence of a cached object
- public boolean existsInCache( String id ) {
- synchronized ( cache ) {
- if ( useCache )
- return cache.containsKey( id );
- else
- return false;
- }
+ public boolean existsInCache (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.containsKey (id);
+ else return false;
+ }
}
// retrieve from cache
- public Object getContents( String id ) {
- synchronized ( cache ) {
- if ( useCache )
- return cache.get( id );
- else
- return null;
- }
+ public Object getContents (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.get (id);
+ else return null;
+ }
}
// cache an object
- public void setContents( String id, java.lang.Object data ) {
- synchronized ( cache ) {
- if ( useCache ) cache.put( id, data );
- }
+ public void setContents (String id, java.lang.Object data) {
+ synchronized (cache) {
+ if (useCache) cache.put (id, data);
+ }
}
// in this implementation, it clears the whole cache, regardless
// what 'id' is passed
- public void removeFromCache( String id ) {
- cache.clear();
+ public void removeFromCache (String id) {
+ cache.clear();
}
- /*******************************************************************************************************************
- *
- * And the other methods related to caching (but not part of the SimpleCache interface).
- *
- ******************************************************************************************************************/
-
- /*******************************************************************************************************************
- * By default, caching is enabled to reduce network traffic. Setting this to false will clear the cache, and not
- * cache any further calls unless it is set to true again.
- *
- *
- * @param shouldCache
- * whether retrieveXXX call results should be cached in case they are called again (i.e. don't request
- * MobyCentral every time)
- ******************************************************************************************************************/
- public void setCacheMode( boolean shouldCache ) {
- useCache = shouldCache;
- if ( !useCache ) removeFromCache( null );
+ /**************************************************************************
+ *
+ * And the other methods related to caching (but not part of the
+ * SimpleCache interface).
+ *
+ **************************************************************************/
+
+ /**************************************************************************
+ * By default, caching is enabled to reduce network traffic.
+ * Setting this to false will clear the cache, and not cache any
+ * further calls unless it is set to true again.
+ *
+ * @param shouldCache whether retrieveXXX call results should be
+ * cached in case they are called again (i.e. don't request
+ * MobyCentral every time)
+ **************************************************************************/
+ public void setCacheMode (boolean shouldCache) {
+ useCache = shouldCache;
+ if (! useCache)
+ removeFromCache (null);
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Find if caching is currently enabled.
- *
+ *
* @return true if caching is enabled
- ******************************************************************************************************************/
- public boolean getCacheMode() {
- return useCache;
+ **************************************************************************/
+ public boolean getCacheMode(){
+ return useCache;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceNames>
- * <serviceName name="serviceName" authURI='authority.info.here'/>
+ * <serviceName name="serviceName" authURI='authority.info.here'/>
* ...
* ...
* </serviceNames>
*
- *
- * @deprecated Replaced by {@link #getServiceNamesByAuthority}. The reason is that this method returns a random
- * result if there are more services with the same name but belonging to different authorities.
- *
- *
- ******************************************************************************************************************/
- public Map< String, String > getServiceNames() throws MobyException {
-
- String result = ( String ) doCall( "retrieveServiceNames", new Object[] {} );
- // parse returned XML
- Map< String, String > results = new TreeMap< String, String >( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceName" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- results.put( elem.getAttribute( "name" ), elem.getAttribute( "authURI" ) );
- }
+ *
+ * @deprecated Replaced by {@link
+ * #getServiceNamesByAuthority}. The reason is that this method
+ * returns a random result if there are more services with the
+ * same name but belonging to different authorities.
+ *
+ *************************************************************************/
+ public Map getServiceNames()
+ throws MobyException {
+
+ String result = (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ results.put (elem.getAttribute ("name"),
+ elem.getAttribute ("authURI"));
+ }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceNames>
- * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
+ * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
* ...
* ...
* </serviceNames>
*
- *
- * @return a Map which has authorities as keys, and String arrays with service names as a values.
- ******************************************************************************************************************/
- public Map getServiceNamesByAuthority() throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML( result, true );
- }
-
- /*******************************************************************************************************************
- * Similar to {@link #getServiceNamesByAuthority} but the resulting Map contains slightly more.
- *
- *
- * @return a Map which has authorities as keys, and arrays of MobyServices as a values. Each MobyService is filled
- * with its name, authority and LSID.
- ******************************************************************************************************************/
- public Map getServicesByAuthority() throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML( result, false );
+ *
+ * @return a Map which has authorities as keys, and String arrays
+ * with service names as a values.
+ *************************************************************************/
+ public Map getServiceNamesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, true);
+ }
+
+ /**************************************************************************
+ * Similar to {@link #getServiceNamesByAuthority} but the
+ * resulting Map contains slightly more.
+ *
+ * @return a Map which has authorities as keys, and arrays of
+ * MobyServices as a values. Each MobyService is filled with its
+ * name, authority and LSID.
+ *************************************************************************/
+ public Map getServicesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, false);
}
//
- protected String getServiceNamesByAuthorityAsXML() throws MobyException {
- return ( String ) doCall( "retrieveServiceNames", new Object[] {} );
+ protected String getServiceNamesByAuthorityAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceNames",
+ new Object[] {});
}
// if onlyNames == true
- // Map: authority name -> String[]
- // (filled with service namea)
+ // Map: authority name -> String[]
+ // (filled with service namea)
// else
- // Map: authority name -> MobyService[]
- // (filled with service name, authority and lsid)
- protected Map createServicesByAuthorityFromXML( String result, boolean onlyNames ) throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceName" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String name = elem.getAttribute( "name" );
- String auth = elem.getAttribute( "authURI" );
- Vector< Object > v = ( results.containsKey( auth ) ? ( Vector ) results.get( auth )
- : new Vector< Object >() );
- if ( onlyNames ) {
- v.addElement( name );
- }
- else {
- MobyService ms = new MobyService( name );
- ms.setAuthority( auth );
- ms.setLSID( elem.getAttribute( "lsid" ) );
- v.addElement( ms );
- }
- results.put( auth, v );
- }
-
- // change values of type Vector to MobyService[] or String[]
- for ( Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = ( Map.Entry ) it.next();
- Vector v = ( Vector ) entry.getValue();
- if ( onlyNames ) {
- String[] sNames = new String[ v.size() ];
- v.copyInto( sNames );
- entry.setValue( sNames );
- }
- else {
- MobyService[] mss = new MobyService[ v.size() ];
- v.copyInto( mss );
- entry.setValue( mss );
- }
+ // Map: authority name -> MobyService[]
+ // (filled with service name, authority and lsid)
+ protected Map createServicesByAuthorityFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ String auth = elem.getAttribute ("authURI");
+ Vector v =
+ (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+ if (onlyNames) {
+ v.addElement (name);
+ } else {
+ MobyService ms = new MobyService (name);
+ ms.setAuthority (auth);
+ ms.setLSID (elem.getAttribute ("lsid"));
+ v.addElement (ms);
+ }
+ results.put (auth, v);
+ }
+
+ // change values of type Vector to MobyService[] or String[]
+ for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ Vector v = (Vector)entry.getValue();
+ if (onlyNames) {
+ String[] sNames = new String [v.size()];
+ v.copyInto (sNames);
+ entry.setValue (sNames);
+ } else {
+ MobyService[] mss = new MobyService [v.size()];
+ v.copyInto (mss);
+ entry.setValue (mss);
}
+ }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceProviders>
- * <serviceProvider name="authority.URI.here"/>
+ * <serviceProvider name="authority.URI.here"/>
* ...
* ...
* </serviceProviders>
*
- ******************************************************************************************************************/
- public String[] getProviders() throws MobyException {
+ *************************************************************************/
+ public String[] getProviders()
+ throws MobyException {
- String cacheId = "retrieveServiceProviders";
- String[] cachedResults = ( String[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
+ String cacheId = "retrieveServiceProviders";
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
- String result = ( String ) doCall( "retrieveServiceProviders", new Object[] {} );
+ String result = (String)doCall ("retrieveServiceProviders",
+ new Object[] {});
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceProvider" );
- String[] results = new String[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ )
- results[ i ] = ( ( Element ) list.item( i ) ).getAttribute( "name" );
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceProvider");
+ String[] results = new String [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++)
+ results[i] = ((Element)list.item (i)).getAttribute ("name");
- // Add this data to the cache in case we get called again
- setContents( cacheId, results );
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceTypes>
- * <serviceType name="serviceName" lsid="...">
+ * <serviceType name="serviceName" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* <contactEmail>...</contactEmail>
* <authURI>...</authURI>
@@ -820,52 +869,57 @@
* ...
* </serviceTypes>
*
- ******************************************************************************************************************/
- public Map getServiceTypes() throws MobyException {
- String result = getServiceTypesAsXML();
- Map results = new TreeMap( getStringComparator() );
- MobyServiceType[] types = createServiceTypesFromXML( result );
- for ( int i = 0; i < types.length; i++ ) {
- results.put( types[ i ].getName(), types[ i ].getDescription() );
- }
- return results;
+ *************************************************************************/
+ public Map getServiceTypes()
+ throws MobyException {
+ String result = getServiceTypesAsXML();
+ Map results = new TreeMap (getStringComparator());
+ MobyServiceType[] types = createServiceTypesFromXML (result);
+ for (int i = 0; i < types.length; i++) {
+ results.put (types[i].getName(),
+ types[i].getDescription());
+ }
+ return results;
}
//
- protected String getServiceTypesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveServiceTypes", new Object[] {} );
+ protected String getServiceTypesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceTypes",
+ new Object[] {});
}
// but be aware that the created MobyServiceTypes are not complete
// - they do not have the relationship information; that's why
// this method is not public; the full service types are available
// from CentralDigest implementations
- protected MobyServiceType[] createServiceTypesFromXML( String result ) throws MobyException {
+ protected MobyServiceType[] createServiceTypesFromXML (String result)
+ throws MobyException {
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceType" );
- if ( list == null || list.getLength() == 0 ) return new MobyServiceType[] {};
- MobyServiceType[] results = new MobyServiceType[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyServiceType st = new MobyServiceType( elem.getAttribute( "name" ) );
- st.setLSID( elem.getAttribute( "lsid" ) );
- st.setDescription( getFirstValue( elem.getElementsByTagName( "Description" ) ) );
- st.setEmailContact( getFirstValue( elem.getElementsByTagName( "contactEmail" ) ) );
- st.setAuthority( getFirstValue( elem.getElementsByTagName( "authURI" ) ) );
- results[ i ] = st;
- }
- java.util.Arrays.sort( results );
- return results;
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceType");
+ if (list == null || list.getLength() == 0)
+ return new MobyServiceType[] {};
+ MobyServiceType[] results = new MobyServiceType [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
+ st.setLSID (elem.getAttribute ("lsid"));
+ st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = st;
+ }
+ java.util.Arrays.sort (results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <Namespaces>
- * <Namespace name="namespace" lsid="...">
+ * <Namespace name="namespace" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* <contactEmail>...</contactEmail>
* <authURI>...</authURI>
@@ -874,122 +928,133 @@
* ...
* </Namespaces>
*
- ******************************************************************************************************************/
- public MobyNamespace[] getFullNamespaces() throws MobyException {
+ *************************************************************************/
+ public MobyNamespace[] getFullNamespaces()
+ throws MobyException {
- String result = getNamespacesAsXML();
- return createNamespacesFromXML( result );
+ String result = getNamespacesAsXML();
+ return createNamespacesFromXML (result);
}
//
- protected String getNamespacesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveNamespaces", new Object[] {} );
+ protected String getNamespacesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveNamespaces",
+ new Object[] {});
}
//
- protected MobyNamespace[] createNamespacesFromXML( String result ) throws MobyException {
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getDocumentElement().getElementsByTagName( "Namespace" );
- if ( list == null || list.getLength() == 0 ) {
- return new MobyNamespace[] {};
- }
- MobyNamespace[] results = new MobyNamespace[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyNamespace nm = new MobyNamespace( elem.getAttribute( "name" ) );
- nm.setLSID( elem.getAttribute( "lsid" ) );
- nm.setDescription( getFirstValue( elem.getElementsByTagName( "Description" ) ) );
- nm.setEmailContact( getFirstValue( elem.getElementsByTagName( "contactEmail" ) ) );
- nm.setAuthority( getFirstValue( elem.getElementsByTagName( "authURI" ) ) );
- results[ i ] = nm;
- }
+ protected MobyNamespace[] createNamespacesFromXML (String result)
+ throws MobyException {
- java.util.Arrays.sort( results );
- return results;
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
+ if (list == null || list.getLength() == 0) {
+ return new MobyNamespace[] {};
+ }
+ MobyNamespace[] results = new MobyNamespace [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
+ nm.setLSID (elem.getAttribute ("lsid"));
+ nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = nm;
+ }
+
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ * @deprecated Replaced by {@link #getFullNamespaces} that gives
+ * more information for the same price.
+ *************************************************************************/
+ public Map getNamespaces()
+ throws MobyException {
+
+ Map results = new TreeMap (getStringComparator());
+ MobyNamespace[] namespaces = getFullNamespaces();
+ for (int i = 0; i < namespaces.length; i++) {
+ results.put (namespaces[i].getName(),
+ namespaces[i].getDescription());
}
-
- /*******************************************************************************************************************
- *
- * @deprecated Replaced by {@link #getFullNamespaces} that gives more information for the same price.
- *
- ******************************************************************************************************************/
- public Map getNamespaces() throws MobyException {
-
- Map results = new TreeMap( getStringComparator() );
- MobyNamespace[] namespaces = getFullNamespaces();
- for ( int i = 0; i < namespaces.length; i++ ) {
- results.put( namespaces[ i ].getName(), namespaces[ i ].getDescription() );
- }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <objectNames>
- * <Object name="objectName" lsid="...">
+ * <Object name="objectName" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* </Object>
* ...
* ...
* </objectNames>
*
- ******************************************************************************************************************/
- public Map getDataTypeNames() throws MobyException {
- String result = getDataTypeNamesAsXML();
- return createDataTypeNamesFromXML( result, true );
+ *************************************************************************/
+ public Map getDataTypeNames()
+ throws MobyException {
+ String result = getDataTypeNamesAsXML();
+ return createDataTypeNamesFromXML (result, true);
}
//
- protected String getDataTypeNamesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveObjectNames", new Object[] {} );
+ protected String getDataTypeNamesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveObjectNames",
+ new Object[] {});
}
// if onlyNames == true
- // Map: data type name -> description (String)
+ // Map: data type name -> description (String)
// else
- // Map: data type name -> MobyDataType[]
- // (filled with name, description, and lsid)
- protected Map createDataTypeNamesFromXML( String result, boolean onlyNames ) throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Object" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String name = elem.getAttribute( "name" );
- if ( name == null ) continue; // ignore no-named data types
- String desc = "";
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "Description" ) ) {
- desc = getFirstValue( children.item( j ) );
- break;
- }
- }
- if ( onlyNames ) {
- results.put( name, desc );
- }
- else {
- MobyDataType dt = new MobyDataType( name );
- dt.setDescription( desc );
- dt.setLSID( elem.getAttribute( "lsid" ) );
- results.put( name, dt );
- }
+ // Map: data type name -> MobyDataType[]
+ // (filled with name, description, and lsid)
+ protected Map createDataTypeNamesFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Object");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ if (name == null)
+ continue; // ignore no-named data types
+ String desc = "";
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("Description")) {
+ desc = getFirstValue (children.item (j));
+ break;
}
- return results;
+ }
+ if (onlyNames) {
+ results.put (name, desc);
+ } else {
+ MobyDataType dt = new MobyDataType (name);
+ dt.setDescription (desc);
+ dt.setLSID (elem.getAttribute ("lsid"));
+ results.put (name, dt);
+ }
+ }
+ return results;
}
- /*******************************************************************************************************************
+
+ /**************************************************************************
* Parses and imports the following XML. An example:
- *
+ *
*
* <retrieveObjectDefinition>
- * <objectType lsid="...">go_term</objectType>
+ * <objectType lsid="...">go_term</objectType>
* <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
* <authURI>http://www.illuminae.com</authURI>
* <contactEmail>markw at illuminae.com</contactEmail>
@@ -1006,448 +1071,529 @@
* </Relationship>
* </retrieveObjectDefinition>
*
- ******************************************************************************************************************/
- public MobyDataType getDataType( String dataTypeName ) throws MobyException, NoSuccessException {
-
- String result = getDataTypeAsXML( dataTypeName );
- return createDataTypeFromXML( result, dataTypeName );
- }
-
- public MobyDataType[] getDataTypes() throws MobyException, NoSuccessException {
- Map< String, String > datatypeMap = getDataTypeNames();
- MobyDataType[] datatypes = new MobyDataType[ datatypeMap.size() ];
- int i = 0;
- for ( String dataTypeName : datatypeMap.keySet() ) {
- datatypes[ i++ ] = getDataType( dataTypeName );
- }
- return datatypes;
- }
-
- protected String getDataTypeAsXML( String dataTypeName ) throws MobyException, NoSuccessException {
-
- return ( String ) doCall( "retrieveObjectDefinition", new Object[] { ""
- + "" + dataTypeName + " " + " " } );
- }
-
- protected MobyDataType createDataTypeFromXML( String xmlSource, String dataTypeName ) throws MobyException,
- NoSuccessException {
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( xmlSource.getBytes() ) );
- NodeList list = document.getElementsByTagName( "retrieveObjectDefinition" );
- if ( list == null || list.getLength() == 0 )
- throw new NoSuccessException( "Data Type name was not found.", dataTypeName );
- MobyDataType data = null;
- Element elem = ( Element ) list.item( 0 );
- NodeList children = elem.getChildNodes();
-
- // first find the "real" (LSID-ized) data type name
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "objectType" ) ) {
- data = new MobyDataType( getFirstValue( children.item( j ) ) );
- data.setLSID( ( ( Element ) children.item( j ) ).getAttribute( "lsid" ) );
- break;
- }
- }
-
- // if not found (unprobable) use the name given by the caller
- if ( data == null ) data = new MobyDataType( dataTypeName );
-
- // now fill the data type object with the rest of attributes
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "Description" ) ) {
- data.setDescription( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "authURI" ) ) {
- data.setAuthority( getFirstValue( children.item( j ) ) );
+ *************************************************************************/
+ public MobyDataType getDataType (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ String result = getDataTypeAsXML (dataTypeName);
+ return createDataTypeFromXML (result, dataTypeName);
+ }
+
+ public MobyDataType[] getDataTypes()
+ throws MobyException, NoSuccessException {
+ Map datatypeMap = getDataTypeNames();
+ MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
+ int i = 0;
+ for(String dataTypeName: datatypeMap.keySet()){
+ datatypes[i++] = getDataType(dataTypeName);
+ }
+ return datatypes;
+ }
+
+ protected String getDataTypeAsXML (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ return (String)doCall ("retrieveObjectDefinition",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ " "
+ });
+ }
+
+ protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
+ NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
+ if (list == null || list.getLength() == 0)
+ throw new NoSuccessException ("Data Type name was not found.",
+ dataTypeName);
+ MobyDataType data = null;
+ Element elem = (Element)list.item (0);
+ NodeList children = elem.getChildNodes();
+
+ // first find the "real" (LSID-ized) data type name
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("objectType")) {
+ data = new MobyDataType (getFirstValue (children.item (j)));
+ data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
+ break;
+ }
+ }
+
+ // if not found (unprobable) use the name given by the caller
+ if (data == null)
+ data = new MobyDataType (dataTypeName);
+
+ // now fill the data type object with the rest of attributes
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ data.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("authURI")) {
+ data.setAuthority (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ data.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Relationship")) {
+ String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
+ if (relationshipType.endsWith ("isa")) {
+
+ NodeList parents = children.item (j).getChildNodes();
+ for (int k = 0; k < parents.getLength(); k++) {
+ if (parents.item (k).getNodeName().equals ("objectType")) {
+ data.addParentName (getFirstValue (parents.item (k)));
+ }
+ }
+ } else if (relationshipType.endsWith ("hasa")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ getFirstValue (belows.item (k)),
+ Central.iHASA );
+ }
+ }
+ } else if (relationshipType.endsWith ("has")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ belows.item (k).getFirstChild().getNodeValue(),
+ Central.iHAS );
}
- else if ( nodeName.equals( "contactEmail" ) ) {
- data.setEmailContact( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "Relationship" ) ) {
- String relationshipType = ( ( Element ) children.item( j ) ).getAttribute( "relationshipType" );
- if ( relationshipType.endsWith( "isa" ) ) {
-
- NodeList parents = children.item( j ).getChildNodes();
- for ( int k = 0; k < parents.getLength(); k++ ) {
- if ( parents.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addParentName( getFirstValue( parents.item( k ) ) );
- }
- }
- }
- else if ( relationshipType.endsWith( "hasa" ) ) {
-
- NodeList belows = children.item( j ).getChildNodes();
- for ( int k = 0; k < belows.getLength(); k++ ) {
- if ( belows.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addChild( ( ( Element ) belows.item( k ) ).getAttribute( "articleName" ),
- getFirstValue( belows.item( k ) ), Central.iHASA );
- }
- }
- }
- else if ( relationshipType.endsWith( "has" ) ) {
-
- NodeList belows = children.item( j ).getChildNodes();
- for ( int k = 0; k < belows.getLength(); k++ ) {
- if ( belows.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addChild( ( ( Element ) belows.item( k ) ).getAttribute( "articleName" ), belows.item(
- k ).getFirstChild().getNodeValue(), Central.iHAS );
- }
- }
- }
}
}
- return data;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getServiceWSDL( String serviceName ) throws MobyException, NoSuccessException {
-
- Map names = getServiceNames();
-
- for ( Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = ( Map.Entry ) it.next();
- if ( ( ( String ) entry.getKey() ).equals( serviceName ) )
- return getServiceWSDL( serviceName, ( String ) entry.getValue() );
- }
-
- throw new NoSuccessException( "Service not found.", serviceName );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getServiceWSDL( String serviceName, String authority ) throws MobyException, NoSuccessException {
-
- String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
- String cachedResults = ( String ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "retrieveService",
- new Object[] { "" + " " } );
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- Element service = document.getDocumentElement();
- Node wsdl = service.getFirstChild();
- if ( wsdl == null )
- throw new NoSuccessException( "Service not found OR WSDL is not available.", serviceName + " (" + authority
- + ")" );
-
- String results = wsdl.getNodeValue();
- setContents( cacheId, results );
- return results;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterDataTypeXML( MobyDataType dataType ) {
-
- // build the ISA tag (expressing hierarchy of data types)
- String[] names = dataType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < names.length; i++ ) {
- buf.append( "" );
- buf.append( names[ i ] );
- buf.append( " " );
- buf.append( "\n" );
- }
-
- // build the HASA/HAS tags (expressing containments of data types)
- MobyRelationship[] children = dataType.getChildren();
- StringBuffer buf2 = new StringBuffer(); // for HASA
- StringBuffer buf3 = new StringBuffer(); // for HAS
- for ( int i = 0; i < children.length; i++ ) {
- if ( children[ i ].getRelationshipType() == Central.iHASA ) {
- buf2.append( "" );
- buf2.append( children[ i ].getDataTypeName() );
- buf2.append( " " );
- }
- else if ( children[ i ].getRelationshipType() == Central.iHAS ) {
- buf3.append( "" );
- buf3.append( children[ i ].getDataTypeName() );
- buf3.append( " " );
- }
}
-
- return "" + "" + dataType.getName() + " "
- + "" + " "
- + "" + new String( buf ) + " "
- + "" + new String( buf2 ) + " "
- + "" + new String( buf3 ) + " " + ""
- + dataType.getAuthority() + " " + "" + dataType.getEmailContact()
- + " " + " ";
}
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerDataType( MobyDataType dataType ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerObjectClass", new Object[] { getRegisterDataTypeXML( dataType ) } );
- dataType.setId( checkRegistration( result, dataType )[ 0 ] );
+ return data;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName)
+ throws MobyException, NoSuccessException {
+
+ Map names = getServiceNames();
+
+ for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ if ( ((String)entry.getKey()).equals (serviceName) )
+ return getServiceWSDL (serviceName, (String)entry.getValue());
+ }
+
+ throw new NoSuccessException ("Service not found.", serviceName);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName, String authority)
+ throws MobyException, NoSuccessException {
+
+ String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
+ String cachedResults = (String)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("retrieveService",
+ new Object[] {
+ "" +
+ " "
+ });
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ Element service = document.getDocumentElement();
+ Node wsdl = service.getFirstChild();
+ if (wsdl == null)
+ throw new NoSuccessException ("Service not found OR WSDL is not available.",
+ serviceName + " (" + authority + ")");
+
+ String results = wsdl.getNodeValue();
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterDataTypeXML (MobyDataType dataType) {
+
+ // build the ISA tag (expressing hierarchy of data types)
+ String[] names = dataType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ // build the HASA/HAS tags (expressing containments of data types)
+ MobyRelationship[] children = dataType.getChildren();
+ StringBuffer buf2 = new StringBuffer(); // for HASA
+ StringBuffer buf3 = new StringBuffer(); // for HAS
+ for (int i = 0; i < children.length; i++) {
+ if (children[i].getRelationshipType() == Central.iHASA) {
+ buf2.append ("");
+ buf2.append (children[i].getDataTypeName());
+ buf2.append (" ");
+ } else if (children[i].getRelationshipType() == Central.iHAS) {
+ buf3.append ("");
+ buf3.append (children[i].getDataTypeName());
+ buf3.append (" ");
+ }
+ }
+
+ return
+ "" +
+ "" + dataType.getName() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ "" + new String (buf2) +
+ " " +
+ "" + new String (buf3) +
+ " " +
+ "" + dataType.getAuthority() + " " +
+ "" + dataType.getEmailContact() + " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerObjectClass",
+ new Object[] { getRegisterDataTypeXML (dataType) });
+ dataType.setId (checkRegistration (result, dataType)[0]);
}
- /*******************************************************************************************************************
+ /*************************************************************************
* B
- ******************************************************************************************************************/
- public void unregisterDataType( MobyDataType dataType ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterObjectClass", new Object[] { ""
- + "" + dataType.getName() + " " + " " } );
- checkRegistration( result, dataType );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterServiceTypeXML( MobyServiceType serviceType ) {
-
- // build the ISA tag (expressing hierarchy of service types)
- String[] names = serviceType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < names.length; i++ ) {
- buf.append( "" );
- buf.append( names[ i ] );
- buf.append( " " );
- buf.append( "\n" );
- }
-
- return "" + "" + serviceType.getName() + " " + ""
- + serviceType.getEmailContact() + " " + "" + serviceType.getAuthority()
- + " " + "" + " "
- + "" + new String( buf ) + " "
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerServiceType( MobyServiceType serviceType ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerServiceType",
- new Object[] { getRegisterServiceTypeXML( serviceType ) } );
- serviceType.setId( checkRegistration( result, serviceType )[ 0 ] );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterServiceType( MobyServiceType serviceType ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterServiceType", new Object[] { ""
- + "" + serviceType.getName() + " " + " " } );
- checkRegistration( result, serviceType );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterNamespaceXML( MobyNamespace namespace ) {
- return "" + "" + namespace.getName() + " " + ""
- + namespace.getEmailContact() + " " + "" + namespace.getAuthority()
- + " " + "" + " "
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerNamespace( MobyNamespace namespace ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "registerNamespace", new Object[] { getRegisterNamespaceXML( namespace ) } );
- namespace.setId( checkRegistration( result, namespace )[ 0 ] );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterNamespace( MobyNamespace namespace ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterNamespace", new Object[] { ""
- + "" + namespace.getName() + " " + " " } );
- checkRegistration( result, namespace );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterServiceXML( MobyService service ) {
- return "" + "" + service.getCategory() + " " + ""
- + service.getName() + " " + "" + service.getType() + " "
- + "" + ( service.getLSID() == null ? "" : service.getLSID().trim() ) + " "
- + "" + service.getAuthority() + " " + ""
- + escapeXML( service.getSignatureURL() ) + " " + "" + escapeXML( service.getURL() )
- + " " + "" + service.getEmailContact() + " "
- + "" + ( service.isAuthoritative() ? "1" : "0" ) + " "
- + "" + " "
- + buildPrimaryInputTag( service ) + buildSecondaryInputTag( service ) + buildOutputTag( service )
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerService( MobyService service ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerService", new Object[] { getRegisterServiceXML( service ) } );
- String[] registered = checkRegistration( result, service );
- service.setId( registered[ 0 ] );
- service.setRDF( registered[ 1 ] );
- String pathToRDF = service.getPathToRDF();
- if ( !pathToRDF.equals( "" ) ) {
- File fileRDF = new File( pathToRDF );
- try {
- PrintStream fileout = new PrintStream( new FileOutputStream( fileRDF ) );
- fileout.println( registered[ 1 ] );
- fileout.close();
- }
- catch ( IOException e ) {
- StringBuffer buf = new StringBuffer( 100 );
- buf.append( "Failed to save RDF in '" );
- buf.append( fileRDF.getAbsolutePath() + "'. " );
- buf.append( e.toString() );
- try {
- File tmpFile = File.createTempFile( service.getName() + "-", ".rdf" );
- PrintStream fileout = new PrintStream( new FileOutputStream( tmpFile ) );
- fileout.println( registered[ 1 ] );
- fileout.close();
- buf.append( "\nReturned RDF file was therefore stored in: " );
- buf.append( tmpFile.getAbsolutePath() );
- }
- catch ( IOException e2 ) {
- buf.append( "\nEven saving in a temporary file failed: " );
- buf.append( e2.toString() );
- }
- throw new MobyException( buf.toString() );
- }
- }
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterService( MobyService service ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterService", new Object[] { "" + ""
- + service.getAuthority() + " " + "" + service.getName() + " "
- + " " } );
- checkRegistration( result, service );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( String serviceType ) throws MobyException {
- if ( serviceType == null ) return new MobyService[] {};
- MobyService pattern = new MobyService( "dummy" );
- pattern.setCategory( "" );
- pattern.setType( serviceType );
- return findService( pattern, null );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( String[] keywords ) throws MobyException {
- if ( keywords == null ) return new MobyService[] {};
- return findService( null, keywords );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern ) throws MobyException {
- if ( pattern == null ) return new MobyService[] {};
- return findService( pattern, null );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern, String[] keywords ) throws MobyException {
- return findService( pattern, keywords, true, true );
+ *************************************************************************/
+ public void unregisterDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterObjectClass",
+ new Object[] {
+ "" +
+ "" + dataType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, dataType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
+
+ // build the ISA tag (expressing hierarchy of service types)
+ String[] names = serviceType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ return
+ "" +
+ "" + serviceType.getName() + " " +
+ "" + serviceType.getEmailContact() + " " +
+ "" + serviceType.getAuthority() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerServiceType",
+ new Object[] { getRegisterServiceTypeXML (serviceType) });
+ serviceType.setId (checkRegistration (result, serviceType)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterServiceType",
+ new Object[] {
+ "" +
+ "" + serviceType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, serviceType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterNamespaceXML (MobyNamespace namespace) {
+ return
+ "" +
+ "" + namespace.getName() + " " +
+ "" + namespace.getEmailContact() + " " +
+ "" + namespace.getAuthority() + " " +
+ "" +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("registerNamespace",
+ new Object[] { getRegisterNamespaceXML (namespace) });
+ namespace.setId (checkRegistration (result, namespace)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterNamespace",
+ new Object[] {
+ "" +
+ "" + namespace.getName() + " " +
+ " "
+ });
+ checkRegistration (result, namespace);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceXML (MobyService service) {
+ return
+ "" +
+ "" + service.getCategory() + " " +
+ "" + service.getName() + " " +
+ "" + service.getType() + " " +
+ "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
+ "" + service.getAuthority() + " " +
+ "" + escapeXML (service.getSignatureURL()) + " " +
+ "" + escapeXML (service.getURL()) + " " +
+ "" + service.getEmailContact() + " " +
+ "" + (service.isAuthoritative() ? "1" : "0") + " " +
+ "" +
+ " " +
+ buildPrimaryInputTag (service) +
+ buildSecondaryInputTag (service) +
+ buildOutputTag (service) +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerService",
+ new Object[] { getRegisterServiceXML (service) });
+ String[] registered = checkRegistration (result, service);
+ service.setId (registered [0]);
+ service.setRDF (registered [1]);
+ String pathToRDF = service.getPathToRDF();
+ if ( ! pathToRDF.equals ("") ) {
+ File fileRDF = new File (pathToRDF);
+ try {
+ PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
+ fileout.println (registered [1]);
+ fileout.close();
+ } catch (IOException e) {
+ StringBuffer buf = new StringBuffer (100);
+ buf.append ("Failed to save RDF in '");
+ buf.append (fileRDF.getAbsolutePath() + "'. ");
+ buf.append (e.toString());
+ try {
+ File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
+ PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
+ fileout.println (registered [1]);
+ fileout.close();
+ buf.append ("\nReturned RDF file was therefore stored in: ");
+ buf.append (tmpFile.getAbsolutePath());
+ } catch (IOException e2) {
+ buf.append ("\nEven saving in a temporary file failed: ");
+ buf.append (e2.toString());
+ }
+ throw new MobyException (buf.toString());
+ }
+ }
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterService",
+ new Object[] {
+ "" +
+ "" + service.getAuthority() + " " +
+ "" + service.getName() + " " +
+ " "
+ });
+ checkRegistration (result, service);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String serviceType)
+ throws MobyException {
+ if (serviceType == null)
+ return new MobyService[] {};
+ MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ pattern.setType (serviceType);
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String[] keywords)
+ throws MobyException {
+ if (keywords == null)
+ return new MobyService[] {};
+ return findService (null, keywords);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern)
+ throws MobyException {
+ if (pattern == null)
+ return new MobyService[] {};
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords)
+ throws MobyException {
+ return findService (pattern, keywords, true, true);
}
- /*******************************************************************************************************************
+ /**************************************************************************
* All 'findService' methods end up here.
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes ) throws MobyException {
- if ( pattern == null ) {
- pattern = new MobyService( "dummy" );
- pattern.setCategory( "" );
- }
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ if (pattern == null) {
+ pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ }
- String result = getServicesAsXML( pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes );
- MobyService[] services = extractServices( result );
- return services;
+ String result =
+ getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
+ MobyService[] services = extractServices (result);
+ return services;
}
// ...actually all 'findService' methods end up here
- protected String getServicesAsXML( MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes ) throws MobyException {
- String[] query = new String[] { ""
- + buildQueryObject( pattern, keywords, includeParentDataTypes, includeChildrenServiceTypes, false )
- + " " };
- return ( String ) doCall( "findService", query );
+ protected String getServicesAsXML (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ String[] query = new String[] {
+ "" +
+ buildQueryObject (pattern, keywords,
+ includeParentDataTypes,
+ includeChildrenServiceTypes,
+ false) +
+ " "
+ };
+ return (String)doCall ("findService", query);
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String call( String methodName, String inputXML ) throws MobyException {
- Object result;
- if ( inputXML == null || inputXML.equals( "" ) )
- result = doCall( methodName, new Object[] {} );
- else
- result = doCall( methodName, new Object[] { inputXML } );
- return ( String ) result;
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String call (String methodName, String inputXML)
+ throws MobyException {
+ Object result;
+ if (inputXML == null || inputXML.equals (""))
+ result = doCall (methodName, new Object[] { });
+ else
+ result = doCall (methodName, new Object[] { inputXML });
+ return (String)result;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected static String resultToString (Object result)
+ throws MobyException {
+ if (result == null)
+ throw new MobyException ("Returned result is null.");
+ if (result instanceof String)
+ return (String)result;
+ if (result instanceof String[]) {
+ String[] tmp = (String[])result;
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < tmp.length; i++)
+ buf.append (tmp[i]);
+ return new String (buf);
}
+ if (result instanceof byte[])
+ return new String ((byte[])result);
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected static String resultToString( Object result ) throws MobyException {
- if ( result == null ) throw new MobyException( "Returned result is null." );
- if ( result instanceof String ) return ( String ) result;
- if ( result instanceof String[] ) {
- String[] tmp = ( String[] ) result;
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < tmp.length; i++ )
- buf.append( tmp[ i ] );
- return new String( buf );
- }
- if ( result instanceof byte[] ) return new String( ( byte[] ) result );
-
- throw new MobyException( "Unknown type of result: " + result.getClass().getName() );
+ throw new MobyException ("Unknown type of result: " + result.getClass().getName());
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public boolean setDebug( boolean enabled ) {
- boolean oldMode = debug;
- debug = enabled;
- return oldMode;
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean setDebug (boolean enabled) {
+ boolean oldMode = debug;
+ debug = enabled;
+ return oldMode;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
@@ -1456,45 +1602,55 @@
* </Relationship>
* </Relationships>
*
- ******************************************************************************************************************/
- public String[] getServiceTypeRelationships( String serviceTypeName, boolean expand ) throws MobyException {
- String result = getServiceTypeRelationshipsAsXML( serviceTypeName, expand );
- return createServiceTypeRelationshipsFromXML( result );
+ *************************************************************************/
+ public String[] getServiceTypeRelationships (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
+ return createServiceTypeRelationshipsFromXML (result);
}
//
- protected String getServiceTypeRelationshipsAsXML( String serviceTypeName, boolean expand ) throws MobyException {
- return ( String ) doCall( "Relationships", new Object[] { "" + "" + serviceTypeName
- + " " + "" + Central.ISA + " "
- + "" + ( expand ? "1" : "0" ) + " " + " " } );
+ protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ return
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + serviceTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + (expand ? "1" : "0") + " " +
+ " "
+ });
}
//
- protected String[] createServiceTypeRelationshipsFromXML( String result ) throws MobyException {
+ protected String[] createServiceTypeRelationshipsFromXML (String result)
+ throws MobyException {
- // parse returned XML
- Vector< String > v = new Vector< String >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "serviceType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("serviceType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
}
- String[] results = new String[ v.size() ];
- v.copyInto( results );
- return results;
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
- * lt;Relationships>
+ *<Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
* <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
@@ -1503,411 +1659,431 @@
* <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
* </Relationship>
- * lt;/Relationships>
+ *</Relationships>
*
- *
- * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an attributes 'lsid' and 'articleName' in
- * <objectType> element.
- ******************************************************************************************************************/
- public Map getDataTypeRelationships( String dataTypeName ) throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName;
- Map cachedResults = ( Map ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "Relationships", new Object[] { "" + ""
- + dataTypeName + " " + "" + Central.ISA + " "
- + "" + Central.HASA + " " + "" + Central.HAS
- + " " + "1 " + " " } );
-
- // parse returned XML
- Map results = new HashMap();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
-
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String relType = elem.getAttribute( "relationshipType" );
- NodeList children = elem.getChildNodes();
- Vector< String > v = new Vector< String >();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "objectType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
- String[] names = new String[ v.size() ];
- v.copyInto( names );
- results.put( relType, names );
+ *
+ * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
+ * attributes 'lsid' and 'articleName' in <objectType> element.
+ *************************************************************************/
+ public Map getDataTypeRelationships (String dataTypeName)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName;
+ Map cachedResults = (Map)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + Central.HASA + " " +
+ "" + Central.HAS + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Map results = new HashMap();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String relType = elem.getAttribute ("relationshipType");
+ NodeList children = elem.getChildNodes();
+ Vector v = new Vector();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
}
+ String[] names = new String [v.size()];
+ v.copyInto (names);
+ results.put (relType, names);
+ }
- setContents( cacheId, results );
- return results;
+ setContents (cacheId, results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
- * lt;Relationships>
+ *<Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
* <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
* </Relationship>
- * lt;/Relationships>
+ *</Relationships>
*
- ******************************************************************************************************************/
- public String[] getDataTypeRelationships( String dataTypeName, String relationshipType ) throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
- String[] cachedResults = ( String[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "Relationships", new Object[] { "" + ""
- + dataTypeName + " " + "" + relationshipType + " "
- + "1 " + " " } );
-
- // parse returned XML
- Vector< String > v = new Vector< String >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
-
- // it should always be just one element in this list
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "objectType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
+ *************************************************************************/
+ public String[] getDataTypeRelationships (String dataTypeName,
+ String relationshipType)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + relationshipType + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ // it should always be just one element in this list
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
}
- String[] results = new String[ v.size() ];
- v.copyInto( results );
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
- setContents( cacheId, results );
- return results;
+ setContents (cacheId, results);
+ return results;
}
- // /**************************************************************************
- // *
- // *************************************************************************/
- // public MobyRelationship[] getRelationships (String dataTypeName)
- // throws MobyException {
- // return null;
- // }
+// /**************************************************************************
+// *
+// *************************************************************************/
+// public MobyRelationship[] getRelationships (String dataTypeName)
+// throws MobyException {
+// return null;
+// }
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
+
+ /**************************************************************************
+ *
+ *************************************************************************/
public String getRegistryEndpoint() {
- return endpoint.toString();
+ return endpoint.toString();
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
+ /**************************************************************************
+ *
+ *************************************************************************/
public String getRegistryNamespace() {
- return uri;
+ return uri;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <resourceURLs>
- * <Resource name="Service" url="..." />
- * <Resource name="Object" url="..." />
- * <Resource name="Namespace" url="..." />
- * <Resource name="ServiceInstance" url="..." />
- * <Resource name="Full" url="..." />
+ * <Resource name="Service" url="..." />
+ * <Resource name="Object" url="..." />
+ * <Resource name="Namespace" url="..." />
+ * <Resource name="ServiceInstance" url="..." />
+ * <Resource name="Full" url="..." />
* </resourceURLs>
*
- ******************************************************************************************************************/
- public MobyResourceRef[] getResourceRefs() throws MobyException {
-
- String cacheId = "retrieveResourceURLs";
- MobyResourceRef[] cachedResults = ( MobyResourceRef[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "retrieveResourceURLs", new Object[] {} );
-
- // parse returned XML
- Vector< MobyResourceRef > v = new Vector< MobyResourceRef >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Resource" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- try {
- v.addElement( new MobyResourceRef( elem.getAttribute( "name" ), new URL( ( String ) elem
- .getAttribute( "url" ) ), elem.getAttribute( "type" ) ) );
- }
- catch ( MalformedURLException e2 ) {
- if ( debug ) System.err.println( "Bad URL: " + elem.getAttribute( "url" ) );
- }
+ *************************************************************************/
+ public MobyResourceRef[] getResourceRefs()
+ throws MobyException {
+
+ String cacheId = "retrieveResourceURLs";
+ MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveResourceURLs",
+ new Object[] {});
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Resource");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ try {
+ v.addElement
+ (new MobyResourceRef (elem.getAttribute ("name"),
+ new URL ((String)elem.getAttribute ("url")),
+ elem.getAttribute ("type")));
+ } catch (MalformedURLException e2) {
+ if (debug)
+ System.err.println ("Bad URL: " + elem.getAttribute ("url"));
}
+ }
- MobyResourceRef[] results = new MobyResourceRef[ v.size() ];
- v.copyInto( results );
+ MobyResourceRef[] results = new MobyResourceRef [v.size()];
+ v.copyInto (results);
- // Add this data to the cache in case we get called again
- setContents( cacheId, results );
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
- return results;
+ return results;
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public InputStream getResource( String resourceName ) throws MobyException {
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public InputStream getResource (String resourceName)
+ throws MobyException {
- MobyResourceRef[] resourceRefs = getResourceRefs();
- for ( int i = 0; i < resourceRefs.length; i++ ) {
- if ( resourceName.equalsIgnoreCase( resourceRefs[ i ].getResourceName() ) ) {
- return Utils.getInputStream( resourceRefs[ i ].getResourceLocation() );
- }
+ MobyResourceRef[] resourceRefs = getResourceRefs();
+ for (int i = 0; i < resourceRefs.length; i++) {
+ if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
+ return Utils.getInputStream (resourceRefs[i].getResourceLocation());
}
- throw new MobyException( "No resource found for '" + resourceName + "'." );
+ }
+ throw new MobyException ("No resource found for '" + resourceName + "'.");
}
- /*******************************************************************************************************************
- * Return a case-insensitive comparator of Strings. It is used to create various TreeMaps where keys are strings.
- ******************************************************************************************************************/
+ /**************************************************************************
+ * Return a case-insensitive comparator of Strings. It is used to
+ * create various TreeMaps where keys are strings.
+ *************************************************************************/
protected static Comparator getStringComparator() {
- return new Comparator() {
- public int compare( Object o1, Object o2 ) {
- return ( ( String ) o1 ).compareToIgnoreCase( ( String ) o2 );
- }
+ return new Comparator() {
+ public int compare (Object o1, Object o2) {
+ return ((String)o1).compareToIgnoreCase ((String)o2);
+ }
};
}
-
- // cache URL/URI so we only check once
+
+ // cache URL/URI so we only check once
private static String CHECKED_URL = null;
private static String CHECKED_URI = null;
-
+
/**
- * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared class hierarchy
- * that implicitly check the registry will use the same cache. Otherwise, methods such as
- * MobyNamespace.getNamespace() must be passed a Central object parameter as well.
- *
+ * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
+ * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
+ * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+ *
* @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
*/
- public static CentralImpl getDefaultCentral() throws MobyException {
- return getDefaultCentral( null );
+ public static CentralImpl getDefaultCentral() throws MobyException{
+ return getDefaultCentral(null);
}
- public static CentralImpl getDefaultCentral( Registry reg ) throws MobyException {
- if ( reg == null && defaultCentrals.containsKey( "" ) ) {
- return defaultCentrals.get( "" );
- }
- else if ( reg != null && defaultCentrals.containsKey( reg.getEndpoint() ) ) {
- return defaultCentrals.get( reg.getEndpoint() );
- }
+ public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
+ if(reg == null && defaultCentrals.containsKey("")){
+ return defaultCentrals.get("");
+ }
+ else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+ return defaultCentrals.get(reg.getEndpoint());
+ }
- String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
- ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
- URL resURL = classLoader.getResource( "META-INF/" + CENTRAL_IMPL_RESOURCE_NAME );
- if ( resURL != null ) {
- System.err.println( "Loading " + resURL );
- try {
- LineNumberReader reader = new LineNumberReader( new InputStreamReader( resURL.openStream() ) );
- for ( String line = reader.readLine(); line != null; line = reader.readLine() ) {
- if ( !line.trim().startsWith( "#" ) ) {
- className = line.trim();
- break;
- }
- }
- }
- catch ( Exception e ) {
- logger.log( Level.WARNING, "Error reading " + resURL, e );
+ String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+ ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+ URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+ if(resURL != null){
+ System.err.println("Loading "+resURL);
+ try{
+ LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+ for(String line = reader.readLine(); line != null; line = reader.readLine()){
+ if(!line.trim().startsWith("#")){
+ className = line.trim();
+ break;
}
}
- try {
- System.err.println( "Central class is " + className );
- Class clazz = Class.forName( className );
- if ( reg == null ) { // should use default nullary c-tor
- defaultCentrals.put( "", ( CentralImpl ) clazz.newInstance() );
- }
- else { // should have (String endpoint, String namespace) c-tor
- for ( Constructor ctor : clazz.getDeclaredConstructors() ) {
- Class[] params = ctor.getParameterTypes();
- if ( params.length == 2 && params[ 0 ].getName().equals( "java.lang.String" )
- && params[ 1 ].getName().equals( "java.lang.String" ) ) {
- defaultCentrals.put( reg.getEndpoint(), ( CentralImpl ) ctor.newInstance( reg.getEndpoint(),
- reg.getNamespace() ) );
- break;
- }
- }
- if ( !defaultCentrals.containsKey( reg.getEndpoint() ) ) {
- logger.log( Level.WARNING, "Could not find required (String endpoint, String namespace)"
- + "constructor for class " + className );
- }
- }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Error reading " + resURL,
+ e);
}
- catch ( Exception e ) {
- logger.log( Level.WARNING, "Could not load class " + className, e );
- if ( reg == null ) {
- defaultCentrals.put( "", new CentralImpl() ); // fallback to this class, no caching, etc.
- }
- else {
- defaultCentrals.put( reg.getEndpoint(), new CentralImpl( reg.getEndpoint(), reg.getNamespace() ) );
+ }
+ try{
+ System.err.println("Central class is "+className);
+ Class clazz = Class.forName(className);
+ if(reg == null){ // should use default nullary c-tor
+ defaultCentrals.put("", (CentralImpl) clazz.newInstance());
+ }
+ else{ // should have (String endpoint, String namespace) c-tor
+ for(Constructor ctor: clazz.getDeclaredConstructors()){
+ Class[] params = ctor.getParameterTypes();
+ if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+ params[1].getName().equals("java.lang.String") ){
+ defaultCentrals.put(reg.getEndpoint(),
+ (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+ break;
}
}
+ if(!defaultCentrals.containsKey(reg.getEndpoint())){
+ logger.log(Level.WARNING,
+ "Could not find required (String endpoint, String namespace)" +
+ "constructor for class " + className);
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Could not load class " + className,
+ e);
+ if(reg == null){
+ defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
+ }
+ else{
+ defaultCentrals.put(reg.getEndpoint(),
+ new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+ }
+ }
- return defaultCentrals.get( reg == null ? "" : reg.getEndpoint() );
+ return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
}
/**
*
- * @return a String representing the Default mobycentral endpoint. If the system property 'moby.check.default'
- * exists and is set to true, then the URL http://biomoby.org/mobycentral is queried and the default central
- * endpoint is returned, otherwise DEFAULT_ENDPOINT is returned.
+ * @return a String representing the Default mobycentral endpoint. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
+ * is returned.
*/
public static String getDefaultURL() {
- boolean check = false;
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+
+ if (check) {
+ // return the last checked url if we have done this before
+ if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
+ return CHECKED_URL;
+ }
+
+ // create a HttpClient object
+ HttpClient client = new HttpClient();
+ // set up the Head method
+ HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
+ // do not follow redirects or we will get a 411 error
+ method.setFollowRedirects(false);
+ // retry 3 times
+ method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
+ // set the user agent ... should probably make this something more reasonable
+ method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
try {
- check = Boolean.getBoolean( "moby.check.default" );
- }
- catch ( Exception e ) {
-
- }
+ // Execute the method.
+ int statusCode = client.executeMethod(method);
- if ( check ) {
- // return the last checked url if we have done this before
- if ( CHECKED_URL != null && CHECKED_URL.trim() != "" ) {
- return CHECKED_URL;
- }
-
- // create a HttpClient object
- HttpClient client = new HttpClient();
- // set up the Head method
- HeadMethod method = new HeadMethod( "http://biomoby.org/mobycentral" );
- // do not follow redirects or we will get a 411 error
- method.setFollowRedirects( false );
- // retry 3 times
- method.getParams().setParameter( HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler( 3, false ) );
- // set the user agent ... should probably make this something more reasonable
- method.getParams().setParameter( HttpMethodParams.USER_AGENT, "jMoby/1.0" );
+ if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
+ System.err.println("Method failed: "
+ + method.getStatusLine());
+ } else {
try {
- // Execute the method.
- int statusCode = client.executeMethod( method );
-
- if ( statusCode != HttpStatus.SC_MOVED_PERMANENTLY ) {
- System.err.println( "Method failed: " + method.getStatusLine() );
- }
- else {
- try {
- String location = method.getResponseHeader( "location" ).getValue();
- CHECKED_URL = location;
- try {
- CHECKED_URI = "http://" + ( new URL( CHECKED_URL ).getAuthority() ) + "/MOBY/Central";
- }
- catch ( MalformedURLException murle ) {
- CHECKED_URI = DEFAULT_NAMESPACE;
- }
- return CHECKED_URL;
- }
- catch ( NullPointerException npe ) {
- return DEFAULT_ENDPOINT;
- }
- }
- }
- catch ( HttpException e ) {
- System.err.println( "Fatal protocol violation: " + e.getMessage() );
- e.printStackTrace();
- }
- catch ( IOException e ) {
- System.err.println( "Fatal transport error: " + e.getMessage() );
- e.printStackTrace();
- }
- finally {
- // Release the connection.
- method.releaseConnection();
+ String location = method.getResponseHeader("location").getValue();
+ CHECKED_URL = location;
+ try {
+ CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
+ } catch (MalformedURLException murle ) {
+ CHECKED_URI = DEFAULT_NAMESPACE;
}
-
- }
- else {
+ return CHECKED_URL;
+ } catch (NullPointerException npe) {
return DEFAULT_ENDPOINT;
+ }
}
+ } catch (HttpException e) {
+ System.err.println("Fatal protocol violation: "
+ + e.getMessage());
+ e.printStackTrace();
+ } catch (IOException e) {
+ System.err.println("Fatal transport error: " + e.getMessage());
+ e.printStackTrace();
+ } finally {
+ // Release the connection.
+ method.releaseConnection();
+ }
+
+ } else {
return DEFAULT_ENDPOINT;
}
-
+ return DEFAULT_ENDPOINT;
+ }
+
/**
*
- * @return a String representing the default mobycentral uri. If the system property 'moby.check.default' exists and
- * is set to true, then the URL http://biomoby.org/mobycentral is queried and the default central namespace
- * is returned, otherwise DEFAULT_NAMESPACE is returned.
+ * @return a String representing the default mobycentral uri. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central namespace is returned, otherwise DEFAULT_NAMESPACE
+ * is returned.
*/
public static String getDefaultURI() {
- boolean check = false;
- try {
- check = Boolean.getBoolean( "moby.check.default" );
- }
- catch ( Exception e ) {
-
- }
- if ( check ) {
- if ( CHECKED_URI != null && CHECKED_URI.trim() != "" ) {
- return CHECKED_URI;
- }
- // need to check ...
- getDefaultURL();
- return CHECKED_URI;
- }
- else {
- return DEFAULT_NAMESPACE;
- }
- }
-
- /*******************************************************************************************************************
- * Convert non-suitable characters in a XML string into their entity references.
- *
- *
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+ if (check) {
+ if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
+ return CHECKED_URI;
+ }
+ // need to check ...
+ getDefaultURL();
+ return CHECKED_URI;
+ } else {
+ return DEFAULT_NAMESPACE;
+ }
+ }
+ /**************************************************************************
+ * Convert non-suitable characters in a XML string into their
+ * entity references.
+ *
* Adapted from jDom.
- *
- * @param str
- * input to be converted
- * @return If there were any non-suitable characters, return a new string with those characters escaped, otherwise
- * return the unmodified input string
- *
- ******************************************************************************************************************/
- public String escapeXML( String str ) {
+ *
+ * @param str input to be converted
+ * @return If there were any non-suitable characters, return a new
+ * string with those characters escaped, otherwise return the
+ * unmodified input string
+ *
+ *************************************************************************/
+ public String escapeXML (String str) {
StringBuffer buffer = null;
char ch;
String entity;
- for ( int i = 0; i < str.length(); i++ ) {
- ch = str.charAt( i );
- switch ( ch ) {
- case '<':
- entity = "<";
- break;
- case '>':
- entity = ">";
- break;
- case '&':
- entity = "&";
- break;
- default:
- entity = null;
- break;
+ for (int i = 0; i < str.length(); i++) {
+ ch = str.charAt (i);
+ switch (ch) {
+ case '<' :
+ entity = "<";
+ break;
+ case '>' :
+ entity = ">";
+ break;
+ case '&' :
+ entity = "&";
+ break;
+ default :
+ entity = null;
+ break;
}
- if ( buffer == null ) {
- if ( entity != null ) {
+ if (buffer == null) {
+ if (entity != null) {
// An entity occurred, so we'll have to use StringBuffer
// (allocate room for it plus a few more entities).
- buffer = new StringBuffer( str.length() + 20 );
+ buffer = new StringBuffer (str.length() + 20);
// Copy previous skipped characters and fall through
// to pickup current character
- buffer.append( str.substring( 0, i ) );
- buffer.append( entity );
- }
- }
- else {
- if ( entity == null ) {
- buffer.append( ch );
+ buffer.append (str.substring (0, i));
+ buffer.append (entity);
}
- else {
- buffer.append( entity );
+ } else {
+ if (entity == null) {
+ buffer.append (ch);
+ } else {
+ buffer.append (entity);
}
}
}
@@ -1915,43 +2091,49 @@
// If there were any entities, return the escaped characters
// that we put in the StringBuffer. Otherwise, just return
// the unmodified input string.
- return ( buffer == null ) ? str : buffer.toString();
+ return (buffer == null) ? str : buffer.toString();
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Format an exception.
- ******************************************************************************************************************/
- public static String formatFault( AxisFault e, String endpoint, QName method ) {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- formatFault( e, new PrintStream( baos ), endpoint, method );
- return baos.toString();
+ *************************************************************************/
+ public static String formatFault (AxisFault e, String endpoint, QName method) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ formatFault (e, new PrintStream (baos), endpoint, method);
+ return baos.toString();
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Format an exception.
- ******************************************************************************************************************/
- public static void formatFault( AxisFault e, PrintStream out, String endpoint, QName method ) {
-
- out.println( "===ERROR===" );
- out.println( "Fault details:" );
- // for some obvious errors I do not print all details (with a lenghty trace stack)
- String faultString = e.getFaultString();
- if ( ( !faultString.startsWith( "java.net.ConnectException" ) )
- && ( faultString.indexOf( "Could not find class for the service named:" ) == -1 ) ) {
- org.w3c.dom.Element[] details = e.getFaultDetails();
- for ( int i = 0; i < details.length; i++ ) {
- String s = details[ i ].toString().replaceAll( "<", "<" );
- s = s.replaceAll( ">", ">" );
- out.println( s );
- }
- }
- out.println( "Fault string: " + faultString );
- out.println( "Fault code: " + e.getFaultCode() );
- out.println( "Fault actor: " + e.getFaultActor() );
- if ( endpoint != null || method != null ) out.println( "When calling:" );
- if ( endpoint != null ) out.println( "\t" + endpoint );
- if ( method != null ) out.println( "\t" + method );
- out.println( "===========" );
+ *************************************************************************/
+ public static void formatFault (AxisFault e, PrintStream out,
+ String endpoint, QName method) {
+
+ out.println ("===ERROR===");
+ out.println ("Fault details:");
+ // for some obvious errors I do not print all details (with a lenghty trace stack)
+ String faultString = e.getFaultString();
+ if ( (! faultString.startsWith ("java.net.ConnectException")) &&
+ (faultString.indexOf ("Could not find class for the service named:") == -1)
+ ) {
+ org.w3c.dom.Element[] details = e.getFaultDetails();
+ for (int i = 0; i < details.length; i++) {
+ String s = details[i].toString().replaceAll ("<", "<");
+ s = s.replaceAll (">", ">");
+ out.println (s);
+ }
+ }
+ out.println ("Fault string: " + faultString);
+ out.println ("Fault code: " + e.getFaultCode());
+ out.println ("Fault actor: " + e.getFaultActor());
+ if (endpoint != null || method != null)
+ out.println ("When calling:");
+ if (endpoint != null)
+ out.println ("\t" + endpoint);
+ if (method != null)
+ out.println ("\t" + method);
+ out.println ("===========");
}
+
}
From kawas at dev.open-bio.org Thu Dec 4 10:31:27 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 4 Dec 2008 10:31:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812041531.mB4FVRR8016254@dev.open-bio.org>
kawas
Thu Dec 4 10:31:27 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv16218/Perl/MOBY-Server
Modified Files:
MANIFEST
Log Message:
added share/cgi/service_unit_tester.pl to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST 2008/11/20 19:40:41 1.9
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST 2008/12/04 15:31:26 1.10
@@ -97,6 +97,7 @@
share/cgi/OntologyServer.cgi
share/cgi/RESOURCES
share/cgi/service_tester.pl
+share/cgi/service_unit_tester.pl
share/cgi/ServicePingerValidator
share/cgi/ValidateService
share/config/mobycentral.config.template
From groscurt at dev.open-bio.org Wed Dec 17 05:21:57 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 05:21:57 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171021.mBHALvuv005113@dev.open-bio.org>
groscurt
Wed Dec 17 05:21:57 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test
In directory dev.open-bio.org:/tmp/cvs-serv5054/src/main/de/mpg/mpiz_koeln/featureClient/test
Modified Files:
SimpleSingleCall.java SingleCallWithParameters.java
MultiCallWithParameters.java MultiCallByDefinition.java
ComplexSingleCall.java SimpleMultiCall.java
SingleMultiServiceCall.java
Log Message:
moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test SimpleSingleCall.java,1.1,1.2 SingleCallWithParameters.java,1.1,1.2 MultiCallWithParameters.java,1.1,1.2 MultiCallByDefinition.java,1.1,1.2 ComplexSingleCall.java,1.1,1.2 SimpleMultiCall.java,1.1,1.2 SingleMultiServiceCall.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.MobyObject;
@@ -19,7 +18,7 @@
client.setTimeout( 45 );
client.addService( "mpiz-koeln.mpg.de", "ID2IDs" );
client.setServiceInputSingleCall( "", "NP_176539.1" );
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
Collection< MobyObject > collection = mobyServiceResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.AminoAcidSequence;
@@ -38,7 +37,7 @@
client.setServiceInputSingleCall( organism, sequence, geneName );
- List< FeatureClientResult > result = client.call();
+ Collection < FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
Collection< FASTA_AA > fastas = mobyServiceResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -79,7 +78,7 @@
client.addServiceInputMultiCall( "gene2", organism, sequence, geneName );
// the service is called
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// the map stores for each identifier given the list of results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -34,7 +33,7 @@
client.addServiceInputMultiCall( "AGI_LocusCode", "AT1G12000" );
// call the service, which will be found
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// as we have called the service multiple times we get back for each identifier the returned results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 10:21:56 1.2
@@ -34,7 +34,7 @@
client.setServiceInputSingleCall( sequence );
// start the call and retrieve the results
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult featureClientResult : result ) {
// as the service was called once we get back the result for this service call
Collection< AminoAcidSequence > sequences = featureClientResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -29,7 +28,7 @@
client.addServiceInputMultiCall( "GO", "0004396" );
// call the service
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// the map stores for each id of the input object a list of results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.MobyService;
@@ -27,7 +26,7 @@
client.setServiceInputSingleCall( "AGI_LocusCode", "AT1G12000" );
// call the service
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// you can get which service returned the current result
From groscurt at dev.open-bio.org Wed Dec 17 09:07:17 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:07:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171407.mBHE7H6U005665@dev.open-bio.org>
groscurt
Wed Dec 17 09:07:16 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv5630/src/main/org/biomoby/shared
Modified Files:
MobyService.java
Log Message:
added hashCode method, based on the uniquename as used in the equals method
moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/10/21 16:38:44 1.25
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/12/17 14:07:16 1.26
@@ -102,6 +102,10 @@
if (obj == null) return false;
return getUniqueName().equals ( ((MobyService)obj).getUniqueName() );
}
+
+ public int hashCode() {
+ return getUniqueName().hashCode();
+ }
/**************************************************************************
* Default constructor.
From groscurt at dev.open-bio.org Wed Dec 17 09:09:00 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:09:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171409.mBHE90wZ005705@dev.open-bio.org>
groscurt
Wed Dec 17 09:09:00 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv5670/src/main/org/biomoby/client
Modified Files:
MobyServiceLocator.java
Log Message:
javadoc had a warning...
moby-live/Java/src/main/org/biomoby/client MobyServiceLocator.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/03 15:21:13 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/17 14:09:00 1.6
@@ -168,7 +168,7 @@
/***************************************************
* Returns true if the user AND the password is set
- * @return
+ * @return if authentication shall be used
***************************************************/
public boolean hasAuthentication() {
return user != null && password != null;
From groscurt at dev.open-bio.org Wed Dec 17 09:09:54 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:09:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171409.mBHE9sdL005791@dev.open-bio.org>
groscurt
Wed Dec 17 09:09:54 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test
In directory dev.open-bio.org:/tmp/cvs-serv5728/src/main/de/mpg/mpiz_koeln/featureClient/test
Modified Files:
SingleCallDefinition.java SingleCallWithParameters.java
ComplexSingleCall.java SingleMultiServiceCall.java
MultiCallWithParameters.java SimpleSingleCall.java
SimpleMultiCall.java MultiCallByDefinition.java
Log Message:
minor changes
moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test SingleCallDefinition.java,1.1,1.2 SingleCallWithParameters.java,1.2,1.3 ComplexSingleCall.java,1.2,1.3 SingleMultiServiceCall.java,1.2,1.3 MultiCallWithParameters.java,1.2,1.3 SimpleSingleCall.java,1.2,1.3 SimpleMultiCall.java,1.2,1.3 MultiCallByDefinition.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java 2008/12/17 14:09:54 1.2
@@ -9,14 +9,14 @@
import de.mpg.mpiz_koeln.featureClient.FeatureClientException;
import de.mpg.mpiz_koeln.featureClient.FeatureClientResult;
-public class SingleCallDefinition {
+class SingleCallDefinition {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.addOutput( "Object", "PMID" );
client.setTimeout( 45 );
client.add2Filter( "Locus2GeneAliases", "getCor", "getGeneticElementNameByFreeText", "getGoTermAssociations",
"getConservedDomainLabelFromDomainId", "ExplodeOutCrossReferences" );
- client.setServiceInputSingleCall( "", "Q9SZW4" );
+ client.setSingleCallInput( "", "Q9SZW4" );
Collection< FeatureClientResult > collection = client.call();
for ( FeatureClientResult mobyServiceResult : collection ) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
import de.mpg.mpiz_koeln.featureClient.FeatureClientException;
import de.mpg.mpiz_koeln.featureClient.FeatureClientResult;
-public class SingleCallWithParameters {
+class SingleCallWithParameters {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 120 );
@@ -35,7 +35,7 @@
geneName.setId( "my_gene" );
geneName.setName( "gene_name" );
- client.setServiceInputSingleCall( organism, sequence, geneName );
+ client.setSingleCallInput( organism, sequence, geneName );
Collection < FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 14:09:54 1.3
@@ -2,7 +2,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.AminoAcidSequence;
@@ -18,7 +17,7 @@
* This examples shows how to use the client to call a web service once which consumes a complex data type, such as
* AminoAcidSequence.
*/
-public class ComplexSingleCall {
+class ComplexSingleCall {
public static void main(String[] args) throws MobyException, FeatureClientException {
FeatureClient client = new FeatureClient();
// timeout of the calls is set to 45 seconds
@@ -31,7 +30,7 @@
sequence.set_SequenceString( new MobyString( "MQPVKVYADRRSQPSRAVIIFCRVNQIDFEEVTVDLFKSQHLTPEFRKVNPMGQVPAIVDGR" ) );
sequence.set_Length( new MobyInteger( 50 ) );
// set the input to the client
- client.setServiceInputSingleCall( sequence );
+ client.setSingleCallInput( sequence );
// start the call and retrieve the results
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
/**
* This example shows how to call more service one with one input.
*/
-public class SingleMultiServiceCall {
+class SingleMultiServiceCall {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 30 );
@@ -23,7 +23,7 @@
client.addService( "Locus2Publications" );
// set the input of the service
- client.setServiceInputSingleCall( "AGI_LocusCode", "AT1G12000" );
+ client.setSingleCallInput( "AGI_LocusCode", "AT1G12000" );
// call the service
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 14:09:54 1.3
@@ -18,7 +18,7 @@
* This example shows how to call a service multiple times which consumes more than one input. It also shows the mixture
* of a simple object input and a complex data type input.
*/
-public class MultiCallWithParameters {
+class MultiCallWithParameters {
public static void main( String[] args ) throws MobyException, FeatureClientException {
FeatureClient client = new FeatureClient();
// the service might take longer, so we set the timeout to 120 seconds
@@ -55,7 +55,7 @@
// adds the inputs to the client and give it an identifier, so that you are able to distinguish the several
// calls later. This identifier is completely free to choice !
- client.addServiceInputMultiCall( "gene1", organism, sequence, geneName );
+ client.addMultipleCallInput( "gene1", organism, sequence, geneName );
// we want to call the same service a second time so we build again some input values
organism = new MobyObject();
@@ -75,7 +75,7 @@
geneName.setName( "gene_name" );
// adds the inputs to the client for the second call with a different identifier as before
- client.addServiceInputMultiCall( "gene2", organism, sequence, geneName );
+ client.addMultipleCallInput( "gene2", organism, sequence, geneName );
// the service is called
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 14:09:54 1.3
@@ -12,12 +12,12 @@
/**
* This example shows how to call a service once with a simple object input.
*/
-public class SimpleSingleCall {
+class SimpleSingleCall {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 45 );
client.addService( "mpiz-koeln.mpg.de", "ID2IDs" );
- client.setServiceInputSingleCall( "", "NP_176539.1" );
+ client.setSingleCallInput( "", "NP_176539.1" );
Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
/**
* This example shows how to call a web service multiple times with a simple object input.
*/
-public class SimpleMultiCall {
+class SimpleMultiCall {
public static void main( String[] args ) throws MobyException, FeatureClientException {
// the client queries the default central if no given otherwise
FeatureClient client = new FeatureClient();
@@ -23,9 +23,9 @@
client.addService( "mpiz-koeln.mpg.de", "get_go_information_by_go_term" );
// the three different inputs for the three service calls
- client.addServiceInputMultiCall( "GO", "0044408" );
- client.addServiceInputMultiCall( "GO", "0020015" );
- client.addServiceInputMultiCall( "GO", "0004396" );
+ client.addMultipleCallInput( "GO", "0044408" );
+ client.addMultipleCallInput( "GO", "0020015" );
+ client.addMultipleCallInput( "GO", "0004396" );
// call the service
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 14:09:54 1.3
@@ -18,7 +18,7 @@
*
* It also shows how to filter out services or authorities which shall be not called at all.
*/
-public class MultiCallByDefinition {
+class MultiCallByDefinition {
public static void main( String[] args ) throws MobyException, FeatureClientException {
// create a client to the default moby central in calgary with a timeout of 30 seconds
FeatureClient client = new FeatureClient();
@@ -28,9 +28,9 @@
// exclude services identified by service name or authority
client.add2Filter( "Locus2GeneAliases", "getCor", "bioinfo.icapture.ubc.ca" );
// input for the first call -> it also defines now we search for service which consumes an AGI code
- client.addServiceInputMultiCall( "AGI_LocusCode", "AT4G30110" );
+ client.addMultipleCallInput( "AGI_LocusCode", "AT4G30110" );
// input for the second call
- client.addServiceInputMultiCall( "AGI_LocusCode", "AT1G12000" );
+ client.addMultipleCallInput( "AGI_LocusCode", "AT1G12000" );
// call the service, which will be found
Collection< FeatureClientResult > result = client.call();
From kawas at dev.open-bio.org Tue Dec 2 18:53:11 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 13:53:11 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021853.mB2IrBM9006660@dev.open-bio.org>
kawas
Tue Dec 2 13:53:11 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6624/Perl/MOBY-Server
Modified Files:
Makefile.PL
Log Message:
added XML::SemanticCompare to the makefile (used by MobyUnitTest.pm)
moby-live/Perl/MOBY-Server Makefile.PL,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/11/17 15:25:10 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/12/02 18:53:11 1.11
@@ -29,6 +29,7 @@
requires 'DBD::mysql' => '0.01';
# used in MobyUnitTest
requires 'XML::Simple' => '2.18';
+ requires 'XML::SemanticCompare'=> '0';
# MOBY::Async requires
requires 'WSRF::Lite' => '0.8.2.3';
From kawas at dev.open-bio.org Tue Dec 2 18:53:46 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 13:53:46 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021853.mB2Irkas006720@dev.open-bio.org>
kawas
Tue Dec 2 13:53:46 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv6685/Perl/MOBY-Server/lib/MOBY/Client
Modified Files:
MobyUnitTest.pm
Log Message:
removed logic used to diff XML doms and instead use a module XML::SemanticCompare to do the diff
moby-live/Perl/MOBY-Server/lib/MOBY/Client MobyUnitTest.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm 2008/11/25 17:29:54 1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm 2008/12/02 18:53:46 1.4
@@ -10,6 +10,7 @@
use strict;
use Carp;
+use XML::SemanticCompare;
use vars qw /$VERSION/;
$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/;
@@ -19,7 +20,6 @@
#-----------------------------------------------------------------
# load all modules needed
#-----------------------------------------------------------------
-use XML::Simple;
use XML::LibXML;
use Data::Dumper;
@@ -150,139 +150,9 @@
sub _test_xml {
my ( $self, $xml ) = @_;
return undef if $self->expected_output =~ m//g;
-
- # create object
- my $xml_simple = new XML::Simple(
- ForceArray => 1,
- ForceContent => 1,
-
- #KeepRoot => 1,
- SuppressEmpty => 1,
- keyattr => []
- );
-
- # read both XML files into a HASH
- my $control = undef;
- my $test = undef;
-
- # check for invalid XML
- eval { $control = $xml_simple->XMLin( $self->expected_output ); };
- return undef if $@;
- # check for invalid XML
- eval { $test = $xml_simple->XMLin($xml); };
- return undef if $@;
- return $self->_compare_current_level( $control, $test, (), () );
-}
-
-#-----------------------------------------------------------------
-# _compare_current_level:
-# compares current level of data structures that represent XML
-# documents.
-# If the current level and all child levels match, a true value
-# is returned. Otherwise, undef is returned.
-#-----------------------------------------------------------------
-sub _compare_current_level {
-
- # $control is current level in hash
- # x_ns are the prefixes that we use
- my ( $self, $control, $test, $control_ns, $test_ns ) = @_;
-
- # if either hash is missing they arent equal
- return undef unless $control;
- return undef unless $test;
-
- # get the namespace prefix and uris at the current level
- # for each doc and remove from current level of hash
- for my $key ( keys %$control ) {
- next unless $key =~ m/^xmlns[:]?/;
- $control_ns->{''} = ${$control}->{$key} if $key eq 'xmlns';
- $control_ns->{$1} = ${$control}->{$key} if $key =~ m/xmlns\:(.*)$/g;
- delete $$control->{$key};
- }
- for my $key ( keys %$test ) {
- next unless $key =~ m/^xmlns[:]?/;
- $test_ns->{''} = ${$test}->{$key} if $key eq 'xmlns';
- $test_ns->{$1} = ${$test}->{$key} if $key =~ m/xmlns\:(.*)$/g;
- delete ${$test}->{$key};
- }
-
- # compare current level number of keys
- return undef unless (keys %$control) == (keys %$test);
-
- # number of keys are equal, so start comparing!
- my $matching_nodes = 0;
- for my $key ( keys %$control ) {
- my $success = 1;
- for my $test_key ( keys %$test ) {
- # does the key exist?
- # 'content' is a special case ... because its text content for a node
- if ( ($key eq $test_key and $key eq 'content' )
- or ($self->_get_prefixed_key( $test_key, $test_ns ) eq
- $self->_get_prefixed_key( $key, $control_ns )
- and $self->_get_prefixed_key( $key, $control_ns )))
- {
-
- # are we dealing with scalar values now or more nesting?
- if ( ref( ${$control}->{$key} ) eq 'ARRAY' ) {
- # both items should be an array
- next unless ref(${$test}->{$test_key}) eq 'ARRAY';
- # array sizes should match here ...
- next unless @{${$control}->{$key}} == @{${$test}->{$test_key}};
- # more nesting try matching child nodes
- my $child_matches = 0;
- foreach my $child ( @{ ${$control}->{$key} } ) {
- my $matched = undef;
- foreach my $test_child ( @{ ${$test}->{$test_key} } ) {
- $matched = $self->_compare_current_level( $child, $test_child, $control_ns, $test_ns );
- $child_matches++ if $matched;
- last if $matched;
- } # end inner foreach
- $matching_nodes++ if @{ ${$control}->{$key} } == $child_matches;
- }
- } else {
- # compare scalar values now
- # we dont care about whitespace, so we need to trim the text
- my $c_text = $self->_clear_whitespace(${$control}->{$key});
- my $t_text = $self->_clear_whitespace(${$test}->{$test_key});
- $matching_nodes++ if $c_text eq $t_text;
- last if $c_text eq $t_text;
- }
- }
- } #end inner for
- }
-
- # no differences found!
- return undef unless $matching_nodes == (keys %$control);
- return 1;
-}
-
-#-----------------------------------------------------------------
-# _clear_whitespace: a whitespace trim function
-#-----------------------------------------------------------------
-sub _clear_whitespace {
- my ($self, $text) = @_;
- $text =~ s/^\s+//;
- $text =~ s/\s+$//;
- return $text;
-}
-
-#-----------------------------------------------------------------
-# _get_prefixed_key:
-# goes through and tries to determine what the namespace URI
-# is for a prefix.
-# Once a URI is found, the prefix is swapped with URI and
-# returned.
-#-----------------------------------------------------------------
-sub _get_prefixed_key {
- my ( $self, $key, $ns_hash ) = @_;
- my $prefixed_key = $key;
- my $prefix = $1 if $key =~ m/^([\w]+)\:.*/;
- $prefixed_key =~ s/$prefix/$ns_hash->{$prefix}/ if $prefix;
-
- # check for default xmlns
- $prefixed_key = $ns_hash->{$prefix} . ":" . $key
- if not $prefix and defined $ns_hash->{$prefix};
- return $prefixed_key;
+ # compare the docs
+ my $sc = XML::SemanticCompare->new();
+ return $sc->compare($self->expected_output, $xml);
}
#-----------------------------------------------------------------
@@ -295,21 +165,8 @@
# empty xml, nothing to test
return undef if $xml =~ m//g;
#instantiate a parser
- my $parser = XML::LibXML->new();
- my $tree = undef;
- # try parsing a string or a file
- eval {$tree = $parser->parse_string($xml);};
- eval {$tree = $parser->parse_file($xml);} if $@;
- return undef if $@;
- my $root = $tree->getDocumentElement;
- # evaluate the xpath statement
- my $results = undef;
- eval {$results = $root->find($self->xpath); };
- return undef if $@;
- # no results?
- return undef unless $results;
- # got some hits!
- return 1;
+ my $sc = XML::SemanticCompare->new();
+ return $sc->test_xpath($self->xpath, $xml);
}
#-----------------------------------------------------------------
From kawas at dev.open-bio.org Tue Dec 2 18:54:50 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 13:54:50 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021854.mB2IsoJ1006760@dev.open-bio.org>
kawas
Tue Dec 2 13:54:50 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6725/Perl/MOBY-Server
Modified Files:
Makefile.PL
Log Message:
update wsrf-lite version that we use (significant bug fixes in newest version of WSRF::Lite)
moby-live/Perl/MOBY-Server Makefile.PL,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/12/02 18:53:11 1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/12/02 18:54:50 1.12
@@ -32,7 +32,7 @@
requires 'XML::SemanticCompare'=> '0';
# MOBY::Async requires
- requires 'WSRF::Lite' => '0.8.2.3';
+ requires 'WSRF::Lite' => '0.8.2.6';
if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) {
From kawas at dev.open-bio.org Tue Dec 2 19:15:02 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 14:15:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021915.mB2JF2jT006885@dev.open-bio.org>
kawas
Tue Dec 2 14:15:02 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6850/Perl/MOBY-Server
Modified Files:
Makefile.PL
Log Message:
fix wsrf version
moby-live/Perl/MOBY-Server Makefile.PL,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/12/02 18:54:50 1.12
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/12/02 19:15:02 1.13
@@ -32,7 +32,7 @@
requires 'XML::SemanticCompare'=> '0';
# MOBY::Async requires
- requires 'WSRF::Lite' => '0.8.2.6';
+ requires 'WSRF::Lite' => '0.8.2.5';
if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) {
From kawas at dev.open-bio.org Tue Dec 2 19:15:31 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 14:15:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021915.mB2JFVAS006925@dev.open-bio.org>
kawas
Tue Dec 2 14:15:31 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv6890/Perl/MOBY-Server
Modified Files:
META.yml
Log Message:
updated 'requires'
moby-live/Perl/MOBY-Server META.yml,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml 2008/06/05 14:13:52 1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml 2008/12/02 19:15:31 1.5
@@ -41,4 +41,7 @@
XML::DOM: 0
XML::LibXML: 1.62
XML::XPath: 1.12
-version: 1.05
+ XML::SemanticCompare: 0
+ XML::Simple: 2.18
+ WSRF::Lite: 0.8.2.5
+version: 1.06
From kawas at dev.open-bio.org Tue Dec 2 19:16:19 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 14:16:19 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021916.mB2JGJoK006965@dev.open-bio.org>
kawas
Tue Dec 2 14:16:19 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv6930/Perl/MOBY-Client
Modified Files:
META.yml
Log Message:
updated 'requires'
moby-live/Perl/MOBY-Client META.yml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml 2008/03/05 18:38:40 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/META.yml 2008/12/02 19:16:19 1.3
@@ -23,6 +23,8 @@
SOAP::Lite: 0.60
URI::Escape: 0
XML::LibXML: 0
- WSRF::Lite: 0
+ WSRF::Lite: 0.8.2.5
RDF::Core: 0.51
-version: 1.01
+ XML::Simple: 2.18
+ XML::SemanticCompare: 0.91
+version: 1.03
From kawas at dev.open-bio.org Tue Dec 2 19:16:52 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 14:16:52 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021916.mB2JGqhL007005@dev.open-bio.org>
kawas
Tue Dec 2 14:16:52 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv6970/Perl/MOBY-Client
Modified Files:
Makefile.PL
Log Message:
updated 'requires'
moby-live/Perl/MOBY-Client Makefile.PL,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/11/17 15:30:55 1.9
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/12/02 19:16:52 1.10
@@ -21,6 +21,7 @@
requires 'RDF::Core' => '0.51';
# MOBY::Client::MobyUnitTest depends
requires 'XML::Simple' => '2.18';
+requires 'XML::SemanticCompare' => '0.91';
# MOBY::CommonSubs depends
requires 'HTML::Entities' => 0;
From kawas at dev.open-bio.org Tue Dec 2 19:18:31 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 2 Dec 2008 14:18:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812021918.mB2JIVUe007087@dev.open-bio.org>
kawas
Tue Dec 2 14:18:31 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv7052/Perl/MOBY-Client
Modified Files:
Makefile.PL
Log Message:
updated wsrf version
moby-live/Perl/MOBY-Client Makefile.PL,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/12/02 19:16:52 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2008/12/02 19:18:31 1.11
@@ -27,7 +27,7 @@
requires 'HTML::Entities' => 0;
# MOBY::Async requires
-requires 'WSRF::Lite' => '0.8.2.2.3';
+requires 'WSRF::Lite' => '0.8.2.5';
auto_install;
From senger at dev.open-bio.org Wed Dec 3 12:22:21 2008
From: senger at dev.open-bio.org (Martin Senger)
Date: Wed, 3 Dec 2008 07:22:21 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031222.mB3CMLKI012050@dev.open-bio.org>
senger
Wed Dec 3 07:22:21 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv12031/S/client
Modified Files:
CentralImpl.java
Log Message:
revert to 1.57
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.59,1.60
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.59
retrieving revision 1.60
diff -u -r1.59 -r1.60
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/12/03 12:09:40 1.59
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/12/03 12:22:21 1.60
@@ -1,2139 +1,2139 @@
-// CentralImpl.java
-// A default client to the Moby Central service.
-//
-// senger at ebi.ac.uk
-// February 2003
-//
-
-package org.biomoby.client;
-
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-import org.biomoby.shared.MobyRelationship;
-import org.biomoby.shared.MobySecondaryData;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.MobyServiceType;
-import org.biomoby.shared.NoSuccessException;
-import org.biomoby.shared.PendingCurationException;
-import org.biomoby.shared.MobyResourceRef;
-import org.biomoby.shared.Utils;
-
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.namespace.QName;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import org.apache.axis.AxisFault;
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.Header;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpException;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.methods.HeadMethod;
-import org.apache.commons.httpclient.params.HttpMethodParams;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.LineNumberReader;
-import java.io.PrintStream;
-import java.io.InputStream;
-import java.lang.reflect.Constructor;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Vector;
-import java.util.TreeMap;
-import java.util.Comparator;
-import java.util.zip.GZIPInputStream;
-import java.util.logging.*;
-
-/**
- * A default implementation of the
- * interface {@link org.biomoby.shared.Central Central}
- * allowing access to a Moby registry.
- *
- * This class is supposed to be used by all other clients that wish
- * to communicate with the Moby Registry, but do not want to know
- * about all XML details that are necessary for talking with the Moby Central
- * directly. This is an example of a client program:
- *
- * import org.biomoby.shared.Central;
- * import org.biomoby.shared.MobyException;
- * import org.biomoby.client.CentralImpl;
- * import java.util.Map;
- * import java.util.Iterator;
- *
- * public class Test {
- *
- * public static void main (String[] args)
- * throws MobyException {
- *
- * Central worker = new CentralImpl();
- * Map authorities = worker.getServiceNamesByAuthority();
- *
- * for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
- * Map.Entry entry = (Map.Entry)it.next();
- * System.out.println (entry.getKey());
- * String[] names = (String[])entry.getValue();
- * for (int i = 0; i < names.length; i++)
- * System.out.println ("\t" + names[i]);
- * }
- * }
- * }
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-public class CentralImpl
- implements Central, SimpleCache {
-
- private URL endpoint;
- private String uri;
- protected boolean debug = false;
-
- /** Common central used to if getDefaultCentral() is called */
- protected static Map defaultCentrals = new HashMap();
-
- /** Default location (endpoint) of a Moby registry. */
- public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
-
- /** Default namespace used by the contacted Moby registry. */
- public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
-
- /**
- * The META-INF resource file that will be checked to determine what
- * default class should be instantiated in order to create a Central Implementation
- * when getDefaultCentral() is called.
- */
- public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
- /** The class to use for getDefaultCentral if all else fails */
- public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
- private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
-
- /**
- * Thread local that gives each thread its own
- * DocumentBuilderFactory (since it is not thread-safe). Code taken
- * from Apache's JaxpUtils.
- */
- public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
- protected synchronized Object initialValue() {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware (true);
- return dbf;
- }
- };
-
-
- /*************************************************************************
- * Default constructor. It connects to a default Moby registry
- * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
- * (as defined int {@link #DEFAULT_NAMESPACE}).
- *************************************************************************/
- public CentralImpl()
- throws MobyException {
- this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
- }
-
- /*************************************************************************
- * Constructor allowing to specify which Moby Registry to use.
- *
- * @throws MobyException if 'endpoint' is not a valid URL, or if no
- * DOM parser is available
- *************************************************************************/
- public CentralImpl (String endpoint)
- throws MobyException {
- this (endpoint, DEFAULT_NAMESPACE);
- }
-
- /*************************************************************************
- * Constructor allowing to specify which Moby Registry and what
- * namespace to use. If any of the parameters is null, its default
- * value is used instead.
- *
- * @throws MobyException if 'endpoint' is not a valid URL, or if no
- * DOM parser was found
- *************************************************************************/
- public CentralImpl (String endpoint, String namespace)
- throws MobyException {
-
- if (endpoint == null || "".equals (endpoint.trim()))
- endpoint = DEFAULT_ENDPOINT;
- if (namespace == null || "".equals (namespace.trim()))
- namespace = DEFAULT_NAMESPACE;
-
- try {
- this.endpoint = new URL (endpoint);
- } catch (MalformedURLException e) {
- throw new MobyException ("Bad URL: " + endpoint);
- }
- this.uri = namespace;
-
- cache = new Hashtable();
- useCache = true;
- }
-
- /*************************************************************************
- * Loads a DOM Document from an InputStream. Uses thread-safe
- * mechanism.
- *************************************************************************/
- public static Document loadDocument (InputStream input)
- throws MobyException {
- try {
- DocumentBuilderFactory dbf
- = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
- DocumentBuilder db = dbf.newDocumentBuilder();
- return (db.parse (input));
- } catch (Exception e) {
- throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
- }
- }
-
- /*************************************************************************
- * Call 'method' with 'parameters' and return its result.
- *************************************************************************/
- protected Object doCall (String method, Object[] parameters)
- throws MobyException {
-
- Call call = null;
- try {
- Service service = new Service();
- call = (Call) service.createCall();
- call.setTargetEndpointAddress (endpoint);
- call.setTimeout (new Integer (0));
-
- call.setSOAPActionURI (uri + "#" + method);
-
- if (debug) {
- System.err.println ("METHOD CALL: " + method);
- System.err.println ("------------");
- if (parameters.length > 0)
- System.err.println (parameters[0] + "\n");
- System.err.println ("------------\n");
-
- Object result = call.invoke (uri, method, parameters);
-
- System.err.println ("METHOD RETURN:");
- System.err.println ("------------");
- if (result != null)
- System.err.println (result + "\n");
- System.err.println ("------------\n");
-
- return resultToString (result);
-
- } else {
- return resultToString (call.invoke (uri, method, parameters));
- }
-
- } catch (AxisFault e) {
- throw new MobyException
- (formatFault (e,
- endpoint.toString(),
- (call == null ? null : call.getOperationName())),
- e);
-// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
-
- } catch (Exception e) {
- throw new MobyException (e.toString(), e);
-// e.printStackTrace();
- }
- }
-
-
- /**************************************************************************
- * Parse the given XML sniplet to find tag 'success'. If it has value '1'
- * look further for tag 'id' and return it back (or return an empty string
- * if ID is not there). Otherwise raise an exception with the 'culprit'
- * and with the message from the tag 'message'.
- *
- * The return value is a two-element long array. The first element
- * is the ID (given by BioMobe registry), and the second element
- * is RDF corresponding with the registered object (BioMoby
- * returns this only for service instances, so for other objects
- * this will be null).
- *
- * This is how the XML is supposed to look:
- *
- *
- *
- *
- *
- *
- *
- * Success takes the value "1" to indicate success, "0" to
- * indicate failure, and "-1" to indicate "Pending Curation".
- *************************************************************************/
- protected String[] checkRegistration (String xml, Object culprit)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String id = "", success = "0", message = "", rdf = "";
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
- Element root = document.getDocumentElement();
-
- NodeList children = root.getChildNodes();
- for (int i = 0; i < children.getLength(); i++) {
- if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
- continue;
- Element elem = (Element)children.item (i);
- if (elem.getNodeName().equals ("id")) {
- if (elem.getFirstChild() != null)
- id = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals("success")) {
- if (elem.getFirstChild() != null)
- success = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals ("message")) {
- if (elem.getFirstChild() != null)
- message = elem.getFirstChild().getNodeValue();
- } else if (elem.getNodeName().equals ("RDF")) {
- if (elem.getFirstChild() != null)
- rdf = elem.getFirstChild().getNodeValue();
- }
- }
-
- if (success.equals ("0"))
- throw new NoSuccessException (message, culprit);
- else if (success.equals ("-1"))
- throw new PendingCurationException();
- return new String[] { id, rdf };
- }
-
- /**************************************************************************
- * Return a piece of XML created from the definitions representing input
- * data types and their usage in the given service. Only data considered
- * primary are included. Note that the main job of converting to XML is
- * done by instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- *
- *************************************************************************/
- protected String buildSecondaryInputTag (MobyService service) {
- StringBuffer buf = new StringBuffer();
- MobyData[] secInputs = service.getSecondaryInputs();
- buf.append ("\n");
- for (int i = 0; i < secInputs.length; i++) {
- buf.append (secInputs[i].toXML());
- }
- buf.append (" \n");
- return new String (buf);
- }
-
- /**************************************************************************
- * Return a piece of XML created from the definitions representing output
- * data types and their usage in the given service. Only data considered
- * primary are included. Note that the main job of converting to XML is
- * done by instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- *
- *
- *************************************************************************/
- protected String buildOutputTag (MobyService service) {
- StringBuffer buf = new StringBuffer();
- MobyData[] primaryOutputs = service.getPrimaryOutputs();
- buf.append ("\n");
- for (int i = 0; i < primaryOutputs.length; i++)
- buf.append (primaryOutputs[i].toXML());
- buf.append (" \n");
- return new String (buf);
- }
-
- /**************************************************************************
- * Return a piece of XML represented a query object (an object used
- * to find a service).
- *
- * The returned XML looks like this:
- *
- *
- *
- *
- *
- *
- *
- *
- * ServiceTypeTerm
- * ServiceName
- * moby
- * http://desired.service.provider ;
- * 1|0
- * 1|0
- * 1|0
- *
- * something
- * ....
- * ....
- *
- *************************************************************************/
- protected String buildQueryObject (MobyService service,
- String[] keywords,
- boolean expandObjects,
- boolean expandServices,
- boolean authoritative) {
- if (service == null) {
- service = new MobyService ("dummy");
- service.setCategory ("");
- }
- StringBuffer buf = new StringBuffer();
-
- buf.append ("\n \n");
-
- buf.append ("\n\n");
- MobyData[] po = service.getPrimaryOutputs();
- if (po.length > 0) {
- for (int i = 0; i < po.length; i++)
- buf.append (po[i].toXML());
- }
- buf.append (" \n \n");
-
- buf.append ("" + service.getType() + " \n");
-
- String name = service.getName();
- if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
- buf.append ("" + service.getName() + " \n");
-
- String sigURL = service.getSignatureURL();
- if (!sigURL.equals (""))
- buf.append ("" + sigURL + " \n");
-
- buf.append ("" + service.getCategory() + " \n");
- buf.append ("" + service.getAuthority() + " \n");
-
- buf.append ("");
- buf.append (expandObjects ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("");
- buf.append (expandServices ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("");
- buf.append (authoritative ? "1" : "0");
- buf.append (" \n");
-
- buf.append ("\n");
- if (keywords != null && keywords.length > 0) {
- for (int i = 0; i < keywords.length; i++) {
- buf.append ("");
- buf.append (keywords[i]);
- buf.append (" \n");
- }
- }
- buf.append (" \n");
-
- return new String (buf);
- }
-
- /**************************************************************************
- * Extract one or more MobyService objects from the given XML piece.
- * The XML should look like this:
- *
- * <Services>
- * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
- * <serviceType>Service_Ontology_Term</serviceType>
- * <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
- * <contactEmail>your at email.addy.here</contactEmail>
- * <signatureURL>http://service.RDF.here</signatureURL>
- * <URL>http://service.endpoint.here/scriptname</URL>
- * <authoritative>1</authoritative>
- * <Input>
- * <!-- one or more Simple and/or Complex Primary articles -->
- * </Input>
- * <Output>
- * <!-- one or more Simple and/or Complex Primary articles -->
- * </Output>
- * <secondaryArticles>
- * <!-- one or more Secondary articles -->
- * </secondaryArticles>
- * <Description><![CDATA[free text description here]]></Description>
- * </Service>
- * ... <!-- one or more Service blocks may be returned -->
- * ...
- * ...
- * </Services>
- *
- * @throws MobyException if the XML document is invalid
- *************************************************************************/
- public MobyService[] extractServices (String xml)
- throws MobyException {
-
- Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
- NodeList list = document.getElementsByTagName ("Service");
- MobyService[] results = new MobyService [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyService service = new MobyService (elem.getAttribute ("serviceName"));
- service.setAuthority (elem.getAttribute ("authURI"));
- service.setLSID (elem.getAttribute ("lsid"));
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("Description")) {
- service.setDescription (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("Category")) {
- service.setCategory (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("URL")) {
- service.setURL (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("signatureURL")) {
- service.setSignatureURL (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("contactEmail")) {
- service.setEmailContact (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("serviceType")) {
- service.setType (getFirstValue (children.item (j)));
- MobyServiceType mst = new MobyServiceType(service.getType());
- NamedNodeMap map = (children.item (j).getAttributes());
- if (map != null) {
- Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
- if (node != null)
- mst.setLSID(node.getNodeValue());
- }
- service.setServiceType(mst);
- } else if (nodeName.equals ("authoritative")) {
- String authoritative = getFirstValue (children.item (j));
- service.setAuthoritative (authoritative.equals ("1") ? true : false);
- } else if (nodeName.equals ("Input")) {
- //
- // ...
- //
- //
- // ......
- // ......
- //
- //
- NodeList inputs = children.item (j).getChildNodes();
- for (int k = 0; k < inputs.getLength(); k++) {
- if (inputs.item (k).getNodeName().equals ("Simple")) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
- service.addInput (data);
- } else if (inputs.item (k).getNodeName().equals ("Collection")) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
- service.addInput (data);
- }
- }
- } else if (nodeName.equals ("Output")) {
- //
- //
- //
- NodeList inputs = children.item (j).getChildNodes();
- for (int k = 0; k < inputs.getLength(); k++) {
- if (inputs.item (k).getNodeName().equals ("Simple")) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
- service.addOutput (data);
- } else if (inputs.item (k).getNodeName().equals ("Collection")) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
- service.addOutput (data);
- }
- }
-
- } else if (nodeName.equals ("secondaryArticles")) {
- //
- // ...
- //
- NodeList parameters = children.item (j).getChildNodes();
- for (int k = 0; k < parameters.getLength(); k++) {
- if (parameters.item (k).getNodeName().equals ("Parameter")) {
- MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
- service.addInput (data);
- }
- }
- }
- }
- results [i] = service;
- }
- return results;
- }
-
- // protect against null values
- protected String getFirstValue (Node child) {
- Node node = child.getFirstChild();
- if (node == null) return "";
- String value = node.getNodeValue();
- if (value == null) return "";
- return value;
- }
-
- protected String getFirstValue (NodeList children) {
- if (children.item(0) != null && children.item(0).hasChildNodes()) {
- children.item(0).normalize();
- return getFirstValue (children.item(0));
- }
- return "";
- }
-
- /**************************************************************************
- *
- * Implementing SimpleCache interface.
- *
- * Why to have an interface for such trivial thing? Well, because
- * I needed to overwrite the caching mechanism in the subclasses
- * so I needed to have all caching functions as separate methods -
- * that's why I have collect them in an interface.
- *
- *************************************************************************/
- private Hashtable cache; // this is the cache itself
- private boolean useCache; // this signal that we are actually caching things
-
- // not used here
- public String createId (String rootName,
- String semanticType, String syntaxType,
- long lastModified,
- Properties props) {
- return ""; // not used here
- }
-
- // check existence of a cached object
- public boolean existsInCache (String id) {
- synchronized (cache) {
- if (useCache) return cache.containsKey (id);
- else return false;
- }
- }
-
- // retrieve from cache
- public Object getContents (String id) {
- synchronized (cache) {
- if (useCache) return cache.get (id);
- else return null;
- }
- }
-
- // cache an object
- public void setContents (String id, java.lang.Object data) {
- synchronized (cache) {
- if (useCache) cache.put (id, data);
- }
- }
-
- // in this implementation, it clears the whole cache, regardless
- // what 'id' is passed
- public void removeFromCache (String id) {
- cache.clear();
- }
-
- /**************************************************************************
- *
- * And the other methods related to caching (but not part of the
- * SimpleCache interface).
- *
- **************************************************************************/
-
- /**************************************************************************
- * By default, caching is enabled to reduce network traffic.
- * Setting this to false will clear the cache, and not cache any
- * further calls unless it is set to true again.
- *
- * @param shouldCache whether retrieveXXX call results should be
- * cached in case they are called again (i.e. don't request
- * MobyCentral every time)
- **************************************************************************/
- public void setCacheMode (boolean shouldCache) {
- useCache = shouldCache;
- if (! useCache)
- removeFromCache (null);
- }
-
- /**************************************************************************
- * Find if caching is currently enabled.
- *
- * @return true if caching is enabled
- **************************************************************************/
- public boolean getCacheMode(){
- return useCache;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceNames>
- * <serviceName name="serviceName" authURI='authority.info.here'/>
- * ...
- * ...
- * </serviceNames>
- *
- *
- * @deprecated Replaced by {@link
- * #getServiceNamesByAuthority}. The reason is that this method
- * returns a random result if there are more services with the
- * same name but belonging to different authorities.
- *
- *************************************************************************/
- public Map getServiceNames()
- throws MobyException {
-
- String result = (String)doCall ("retrieveServiceNames",
- new Object[] {});
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceName");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- results.put (elem.getAttribute ("name"),
- elem.getAttribute ("authURI"));
- }
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceNames>
- * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
- * ...
- * ...
- * </serviceNames>
- *
- *
- * @return a Map which has authorities as keys, and String arrays
- * with service names as a values.
- *************************************************************************/
- public Map getServiceNamesByAuthority()
- throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML (result, true);
- }
-
- /**************************************************************************
- * Similar to {@link #getServiceNamesByAuthority} but the
- * resulting Map contains slightly more.
- *
- * @return a Map which has authorities as keys, and arrays of
- * MobyServices as a values. Each MobyService is filled with its
- * name, authority and LSID.
- *************************************************************************/
- public Map getServicesByAuthority()
- throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML (result, false);
- }
-
- //
- protected String getServiceNamesByAuthorityAsXML()
- throws MobyException {
- return (String)doCall ("retrieveServiceNames",
- new Object[] {});
- }
-
- // if onlyNames == true
- // Map: authority name -> String[]
- // (filled with service namea)
- // else
- // Map: authority name -> MobyService[]
- // (filled with service name, authority and lsid)
- protected Map createServicesByAuthorityFromXML (String result,
- boolean onlyNames)
- throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceName");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String name = elem.getAttribute ("name");
- String auth = elem.getAttribute ("authURI");
- Vector v =
- (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
- if (onlyNames) {
- v.addElement (name);
- } else {
- MobyService ms = new MobyService (name);
- ms.setAuthority (auth);
- ms.setLSID (elem.getAttribute ("lsid"));
- v.addElement (ms);
- }
- results.put (auth, v);
- }
-
- // change values of type Vector to MobyService[] or String[]
- for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = (Map.Entry)it.next();
- Vector v = (Vector)entry.getValue();
- if (onlyNames) {
- String[] sNames = new String [v.size()];
- v.copyInto (sNames);
- entry.setValue (sNames);
- } else {
- MobyService[] mss = new MobyService [v.size()];
- v.copyInto (mss);
- entry.setValue (mss);
- }
- }
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceProviders>
- * <serviceProvider name="authority.URI.here"/>
- * ...
- * ...
- * </serviceProviders>
- *
- *************************************************************************/
- public String[] getProviders()
- throws MobyException {
-
- String cacheId = "retrieveServiceProviders";
- String[] cachedResults = (String[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result = (String)doCall ("retrieveServiceProviders",
- new Object[] {});
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceProvider");
- String[] results = new String [list.getLength()];
- for (int i = 0; i < list.getLength(); i++)
- results[i] = ((Element)list.item (i)).getAttribute ("name");
-
- // Add this data to the cache in case we get called again
- setContents (cacheId, results);
-
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <serviceTypes>
- * <serviceType name="serviceName" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * <contactEmail>...</contactEmail>
- * <authURI>...</authURI>
- * </serviceType>
- * ...
- * ...
- * </serviceTypes>
- *
- *************************************************************************/
- public Map getServiceTypes()
- throws MobyException {
- String result = getServiceTypesAsXML();
- Map results = new TreeMap (getStringComparator());
- MobyServiceType[] types = createServiceTypesFromXML (result);
- for (int i = 0; i < types.length; i++) {
- results.put (types[i].getName(),
- types[i].getDescription());
- }
- return results;
- }
-
- //
- protected String getServiceTypesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveServiceTypes",
- new Object[] {});
- }
-
- // but be aware that the created MobyServiceTypes are not complete
- // - they do not have the relationship information; that's why
- // this method is not public; the full service types are available
- // from CentralDigest implementations
- protected MobyServiceType[] createServiceTypesFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("serviceType");
- if (list == null || list.getLength() == 0)
- return new MobyServiceType[] {};
- MobyServiceType[] results = new MobyServiceType [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
- st.setLSID (elem.getAttribute ("lsid"));
- st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
- st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
- st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
- results[i] = st;
- }
- java.util.Arrays.sort (results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <Namespaces>
- * <Namespace name="namespace" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * <contactEmail>...</contactEmail>
- * <authURI>...</authURI>
- * </Namespace>
- * ...
- * ...
- * </Namespaces>
- *
- *************************************************************************/
- public MobyNamespace[] getFullNamespaces()
- throws MobyException {
-
- String result = getNamespacesAsXML();
- return createNamespacesFromXML (result);
- }
-
- //
- protected String getNamespacesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveNamespaces",
- new Object[] {});
- }
-
- //
- protected MobyNamespace[] createNamespacesFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
- if (list == null || list.getLength() == 0) {
- return new MobyNamespace[] {};
- }
- MobyNamespace[] results = new MobyNamespace [list.getLength()];
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
- nm.setLSID (elem.getAttribute ("lsid"));
- nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
- nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
- nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
- results[i] = nm;
- }
-
- java.util.Arrays.sort (results);
- return results;
- }
-
- /**************************************************************************
- *
- * @deprecated Replaced by {@link #getFullNamespaces} that gives
- * more information for the same price.
- *************************************************************************/
- public Map getNamespaces()
- throws MobyException {
-
- Map results = new TreeMap (getStringComparator());
- MobyNamespace[] namespaces = getFullNamespaces();
- for (int i = 0; i < namespaces.length; i++) {
- results.put (namespaces[i].getName(),
- namespaces[i].getDescription());
- }
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <objectNames>
- * <Object name="objectName" lsid="...">
- * <Description><![CDATA[free text description here]]></Description>
- * </Object>
- * ...
- * ...
- * </objectNames>
- *
- *************************************************************************/
- public Map getDataTypeNames()
- throws MobyException {
- String result = getDataTypeNamesAsXML();
- return createDataTypeNamesFromXML (result, true);
- }
-
- //
- protected String getDataTypeNamesAsXML()
- throws MobyException {
- return (String)doCall ("retrieveObjectNames",
- new Object[] {});
- }
-
- // if onlyNames == true
- // Map: data type name -> description (String)
- // else
- // Map: data type name -> MobyDataType[]
- // (filled with name, description, and lsid)
- protected Map createDataTypeNamesFromXML (String result,
- boolean onlyNames)
- throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap (getStringComparator());
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Object");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String name = elem.getAttribute ("name");
- if (name == null)
- continue; // ignore no-named data types
- String desc = "";
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("Description")) {
- desc = getFirstValue (children.item (j));
- break;
- }
- }
- if (onlyNames) {
- results.put (name, desc);
- } else {
- MobyDataType dt = new MobyDataType (name);
- dt.setDescription (desc);
- dt.setLSID (elem.getAttribute ("lsid"));
- results.put (name, dt);
- }
- }
- return results;
- }
-
-
- /**************************************************************************
- * Parses and imports the following XML. An example:
- *
- *
- * <retrieveObjectDefinition>
- * <objectType lsid="...">go_term</objectType>
- * <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
- * <authURI>http://www.illuminae.com</authURI>
- * <contactEmail>markw at illuminae.com</contactEmail>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType articleName=''>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
- * <objectType articleName='Term'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType articleName='Definition'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:has'>
- * <objectType articleName='Problems'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType articleName='Issues'>urn:lsid:biomoby.org:objectclass:string</objectType>
- * </Relationship>
- * </retrieveObjectDefinition>
- *
- *************************************************************************/
- public MobyDataType getDataType (String dataTypeName)
- throws MobyException, NoSuccessException {
-
- String result = getDataTypeAsXML (dataTypeName);
- return createDataTypeFromXML (result, dataTypeName);
- }
-
- public MobyDataType[] getDataTypes()
- throws MobyException, NoSuccessException {
- Map datatypeMap = getDataTypeNames();
- MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
- int i = 0;
- for(String dataTypeName: datatypeMap.keySet()){
- datatypes[i++] = getDataType(dataTypeName);
- }
- return datatypes;
- }
-
- protected String getDataTypeAsXML (String dataTypeName)
- throws MobyException, NoSuccessException {
-
- return (String)doCall ("retrieveObjectDefinition",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- " "
- });
- }
-
- protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
- throws MobyException, NoSuccessException {
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
- NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
- if (list == null || list.getLength() == 0)
- throw new NoSuccessException ("Data Type name was not found.",
- dataTypeName);
- MobyDataType data = null;
- Element elem = (Element)list.item (0);
- NodeList children = elem.getChildNodes();
-
- // first find the "real" (LSID-ized) data type name
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("objectType")) {
- data = new MobyDataType (getFirstValue (children.item (j)));
- data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
- break;
- }
- }
-
- // if not found (unprobable) use the name given by the caller
- if (data == null)
- data = new MobyDataType (dataTypeName);
-
- // now fill the data type object with the rest of attributes
- for (int j = 0; j < children.getLength(); j++) {
- String nodeName = children.item (j).getNodeName();
- if (nodeName.equals ("Description")) {
- data.setDescription (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("authURI")) {
- data.setAuthority (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("contactEmail")) {
- data.setEmailContact (getFirstValue (children.item (j)));
- } else if (nodeName.equals ("Relationship")) {
- String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
- if (relationshipType.endsWith ("isa")) {
-
- NodeList parents = children.item (j).getChildNodes();
- for (int k = 0; k < parents.getLength(); k++) {
- if (parents.item (k).getNodeName().equals ("objectType")) {
- data.addParentName (getFirstValue (parents.item (k)));
- }
- }
- } else if (relationshipType.endsWith ("hasa")) {
-
- NodeList belows = children.item (j).getChildNodes();
- for (int k = 0; k < belows.getLength(); k++) {
- if (belows.item (k).getNodeName().equals ("objectType")) {
- data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
- getFirstValue (belows.item (k)),
- Central.iHASA );
- }
- }
- } else if (relationshipType.endsWith ("has")) {
-
- NodeList belows = children.item (j).getChildNodes();
- for (int k = 0; k < belows.getLength(); k++) {
- if (belows.item (k).getNodeName().equals ("objectType")) {
- data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
- belows.item (k).getFirstChild().getNodeValue(),
- Central.iHAS );
- }
- }
- }
- }
- }
- return data;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getServiceWSDL (String serviceName)
- throws MobyException, NoSuccessException {
-
- Map names = getServiceNames();
-
- for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = (Map.Entry)it.next();
- if ( ((String)entry.getKey()).equals (serviceName) )
- return getServiceWSDL (serviceName, (String)entry.getValue());
- }
-
- throw new NoSuccessException ("Service not found.", serviceName);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getServiceWSDL (String serviceName, String authority)
- throws MobyException, NoSuccessException {
-
- String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
- String cachedResults = (String)getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("retrieveService",
- new Object[] {
- "" +
- " "
- });
-
- // parse returned XML
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- Element service = document.getDocumentElement();
- Node wsdl = service.getFirstChild();
- if (wsdl == null)
- throw new NoSuccessException ("Service not found OR WSDL is not available.",
- serviceName + " (" + authority + ")");
-
- String results = wsdl.getNodeValue();
- setContents (cacheId, results);
- return results;
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterDataTypeXML (MobyDataType dataType) {
-
- // build the ISA tag (expressing hierarchy of data types)
- String[] names = dataType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < names.length; i++) {
- buf.append ("");
- buf.append (names[i]);
- buf.append (" ");
- buf.append ("\n");
- }
-
- // build the HASA/HAS tags (expressing containments of data types)
- MobyRelationship[] children = dataType.getChildren();
- StringBuffer buf2 = new StringBuffer(); // for HASA
- StringBuffer buf3 = new StringBuffer(); // for HAS
- for (int i = 0; i < children.length; i++) {
- if (children[i].getRelationshipType() == Central.iHASA) {
- buf2.append ("");
- buf2.append (children[i].getDataTypeName());
- buf2.append (" ");
- } else if (children[i].getRelationshipType() == Central.iHAS) {
- buf3.append ("");
- buf3.append (children[i].getDataTypeName());
- buf3.append (" ");
- }
- }
-
- return
- "" +
- "" + dataType.getName() + " " +
- "" +
- " " +
- "" + new String (buf) +
- " " +
- "" + new String (buf2) +
- " " +
- "" + new String (buf3) +
- " " +
- "" + dataType.getAuthority() + " " +
- "" + dataType.getEmailContact() + " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerDataType (MobyDataType dataType)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerObjectClass",
- new Object[] { getRegisterDataTypeXML (dataType) });
- dataType.setId (checkRegistration (result, dataType)[0]);
- }
-
- /*************************************************************************
- * B
- *************************************************************************/
- public void unregisterDataType (MobyDataType dataType)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterObjectClass",
- new Object[] {
- "" +
- "" + dataType.getName() + " " +
- " "
- });
- checkRegistration (result, dataType);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
-
- // build the ISA tag (expressing hierarchy of service types)
- String[] names = serviceType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < names.length; i++) {
- buf.append ("");
- buf.append (names[i]);
- buf.append (" ");
- buf.append ("\n");
- }
-
- return
- "" +
- "" + serviceType.getName() + " " +
- "" + serviceType.getEmailContact() + " " +
- "" + serviceType.getAuthority() + " " +
- "" +
- " " +
- "" + new String (buf) +
- " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerServiceType (MobyServiceType serviceType)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerServiceType",
- new Object[] { getRegisterServiceTypeXML (serviceType) });
- serviceType.setId (checkRegistration (result, serviceType)[0]);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterServiceType (MobyServiceType serviceType)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterServiceType",
- new Object[] {
- "" +
- "" + serviceType.getName() + " " +
- " "
- });
- checkRegistration (result, serviceType);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterNamespaceXML (MobyNamespace namespace) {
- return
- "" +
- "" + namespace.getName() + " " +
- "" + namespace.getEmailContact() + " " +
- "" + namespace.getAuthority() + " " +
- "" +
- " " +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerNamespace (MobyNamespace namespace)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("registerNamespace",
- new Object[] { getRegisterNamespaceXML (namespace) });
- namespace.setId (checkRegistration (result, namespace)[0]);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterNamespace (MobyNamespace namespace)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterNamespace",
- new Object[] {
- "" +
- "" + namespace.getName() + " " +
- " "
- });
- checkRegistration (result, namespace);
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public String getRegisterServiceXML (MobyService service) {
- return
- "" +
- "" + service.getCategory() + " " +
- "" + service.getName() + " " +
- "" + service.getType() + " " +
- "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
- "" + service.getAuthority() + " " +
- "" + escapeXML (service.getSignatureURL()) + " " +
- "" + escapeXML (service.getURL()) + " " +
- "" + service.getEmailContact() + " " +
- "" + (service.isAuthoritative() ? "1" : "0") + " " +
- "" +
- " " +
- buildPrimaryInputTag (service) +
- buildSecondaryInputTag (service) +
- buildOutputTag (service) +
- " ";
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void registerService (MobyService service)
- throws MobyException, NoSuccessException, PendingCurationException {
-
- String result =
- (String)doCall ("registerService",
- new Object[] { getRegisterServiceXML (service) });
- String[] registered = checkRegistration (result, service);
- service.setId (registered [0]);
- service.setRDF (registered [1]);
- String pathToRDF = service.getPathToRDF();
- if ( ! pathToRDF.equals ("") ) {
- File fileRDF = new File (pathToRDF);
- try {
- PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
- fileout.println (registered [1]);
- fileout.close();
- } catch (IOException e) {
- StringBuffer buf = new StringBuffer (100);
- buf.append ("Failed to save RDF in '");
- buf.append (fileRDF.getAbsolutePath() + "'. ");
- buf.append (e.toString());
- try {
- File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
- PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
- fileout.println (registered [1]);
- fileout.close();
- buf.append ("\nReturned RDF file was therefore stored in: ");
- buf.append (tmpFile.getAbsolutePath());
- } catch (IOException e2) {
- buf.append ("\nEven saving in a temporary file failed: ");
- buf.append (e2.toString());
- }
- throw new MobyException (buf.toString());
- }
- }
- }
-
- /*************************************************************************
- *
- *************************************************************************/
- public void unregisterService (MobyService service)
- throws MobyException, NoSuccessException, PendingCurationException {
- String result =
- (String)doCall ("deregisterService",
- new Object[] {
- "" +
- "" + service.getAuthority() + " " +
- "" + service.getName() + " " +
- " "
- });
- checkRegistration (result, service);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (String serviceType)
- throws MobyException {
- if (serviceType == null)
- return new MobyService[] {};
- MobyService pattern = new MobyService ("dummy");
- pattern.setCategory ("");
- pattern.setType (serviceType);
- return findService (pattern, null);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (String[] keywords)
- throws MobyException {
- if (keywords == null)
- return new MobyService[] {};
- return findService (null, keywords);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (MobyService pattern)
- throws MobyException {
- if (pattern == null)
- return new MobyService[] {};
- return findService (pattern, null);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public MobyService[] findService (MobyService pattern, String[] keywords)
- throws MobyException {
- return findService (pattern, keywords, true, true);
- }
-
- /**************************************************************************
- * All 'findService' methods end up here.
- *************************************************************************/
- public MobyService[] findService (MobyService pattern, String[] keywords,
- boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes)
- throws MobyException {
- if (pattern == null) {
- pattern = new MobyService ("dummy");
- pattern.setCategory ("");
- }
-
- String result =
- getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
- MobyService[] services = extractServices (result);
- return services;
- }
-
- // ...actually all 'findService' methods end up here
- protected String getServicesAsXML (MobyService pattern, String[] keywords,
- boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes)
- throws MobyException {
- String[] query = new String[] {
- "" +
- buildQueryObject (pattern, keywords,
- includeParentDataTypes,
- includeChildrenServiceTypes,
- false) +
- " "
- };
- return (String)doCall ("findService", query);
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String call (String methodName, String inputXML)
- throws MobyException {
- Object result;
- if (inputXML == null || inputXML.equals (""))
- result = doCall (methodName, new Object[] { });
- else
- result = doCall (methodName, new Object[] { inputXML });
- return (String)result;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- protected static String resultToString (Object result)
- throws MobyException {
- if (result == null)
- throw new MobyException ("Returned result is null.");
- if (result instanceof String)
- return (String)result;
- if (result instanceof String[]) {
- String[] tmp = (String[])result;
- StringBuffer buf = new StringBuffer();
- for (int i = 0; i < tmp.length; i++)
- buf.append (tmp[i]);
- return new String (buf);
- }
- if (result instanceof byte[])
- return new String ((byte[])result);
-
- throw new MobyException ("Unknown type of result: " + result.getClass().getName());
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public boolean setDebug (boolean enabled) {
- boolean oldMode = debug;
- debug = enabled;
- return oldMode;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
- * <serviceType>urn:lsid:biomoby.org:servicetype:analysis</serviceType>
- * <serviceType>urn:lsid:biomoby.org:servicetype:service</serviceType>
- * </Relationship>
- * </Relationships>
- *
- *************************************************************************/
- public String[] getServiceTypeRelationships (String serviceTypeName,
- boolean expand)
- throws MobyException {
- String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
- return createServiceTypeRelationshipsFromXML (result);
- }
-
- //
- protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
- boolean expand)
- throws MobyException {
- return
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + serviceTypeName + " " +
- "" + Central.ISA + " " +
- "" + (expand ? "1" : "0") + " " +
- " "
- });
- }
-
- //
- protected String[] createServiceTypeRelationshipsFromXML (String result)
- throws MobyException {
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("serviceType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- }
- String[] results = new String [v.size()];
- v.copyInto (results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- *<Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
- * </Relationship>
- *</Relationships>
- *
- *
- * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
- * attributes 'lsid' and 'articleName' in <objectType> element.
- *************************************************************************/
- public Map getDataTypeRelationships (String dataTypeName)
- throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName;
- Map cachedResults = (Map)getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- "" + Central.ISA + " " +
- "" + Central.HASA + " " +
- "" + Central.HAS + " " +
- "1 " +
- " "
- });
-
- // parse returned XML
- Map results = new HashMap();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
-
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- String relType = elem.getAttribute ("relationshipType");
- NodeList children = elem.getChildNodes();
- Vector v = new Vector();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("objectType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- String[] names = new String [v.size()];
- v.copyInto (names);
- results.put (relType, names);
- }
-
- setContents (cacheId, results);
- return results;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- *<Relationships>
- * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
- * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
- * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
- * </Relationship>
- *</Relationships>
- *
- *************************************************************************/
- public String[] getDataTypeRelationships (String dataTypeName,
- String relationshipType)
- throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
- String[] cachedResults = (String[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result =
- (String)doCall ("Relationships",
- new Object[] {
- "" +
- "" + dataTypeName + " " +
- "" + relationshipType + " " +
- "1 " +
- " "
- });
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Relationship");
-
- // it should always be just one element in this list
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- NodeList children = elem.getChildNodes();
- for (int j = 0; j < children.getLength(); j++) {
- if (children.item (j).getNodeName().equals ("objectType")) {
- v.addElement (getFirstValue (children.item (j)));
- }
- }
- }
- String[] results = new String [v.size()];
- v.copyInto (results);
-
- setContents (cacheId, results);
- return results;
- }
-
-// /**************************************************************************
-// *
-// *************************************************************************/
-// public MobyRelationship[] getRelationships (String dataTypeName)
-// throws MobyException {
-// return null;
-// }
-
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getRegistryEndpoint() {
- return endpoint.toString();
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public String getRegistryNamespace() {
- return uri;
- }
-
- /**************************************************************************
- * Parses and imports the following XML.
- *
- * <resourceURLs>
- * <Resource name="Service" url="..." />
- * <Resource name="Object" url="..." />
- * <Resource name="Namespace" url="..." />
- * <Resource name="ServiceInstance" url="..." />
- * <Resource name="Full" url="..." />
- * </resourceURLs>
- *
- *************************************************************************/
- public MobyResourceRef[] getResourceRefs()
- throws MobyException {
-
- String cacheId = "retrieveResourceURLs";
- MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
- if (cachedResults != null)
- return cachedResults;
-
- String result = (String)doCall ("retrieveResourceURLs",
- new Object[] {});
-
- // parse returned XML
- Vector v = new Vector();
- Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
- NodeList list = document.getElementsByTagName ("Resource");
- for (int i = 0; i < list.getLength(); i++) {
- Element elem = (Element)list.item (i);
- try {
- v.addElement
- (new MobyResourceRef (elem.getAttribute ("name"),
- new URL ((String)elem.getAttribute ("url")),
- elem.getAttribute ("type")));
- } catch (MalformedURLException e2) {
- if (debug)
- System.err.println ("Bad URL: " + elem.getAttribute ("url"));
- }
- }
-
- MobyResourceRef[] results = new MobyResourceRef [v.size()];
- v.copyInto (results);
-
- // Add this data to the cache in case we get called again
- setContents (cacheId, results);
-
- return results;
- }
-
- /**************************************************************************
- *
- *************************************************************************/
- public InputStream getResource (String resourceName)
- throws MobyException {
-
- MobyResourceRef[] resourceRefs = getResourceRefs();
- for (int i = 0; i < resourceRefs.length; i++) {
- if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
- return Utils.getInputStream (resourceRefs[i].getResourceLocation());
- }
- }
- throw new MobyException ("No resource found for '" + resourceName + "'.");
- }
-
- /**************************************************************************
- * Return a case-insensitive comparator of Strings. It is used to
- * create various TreeMaps where keys are strings.
- *************************************************************************/
- protected static Comparator getStringComparator() {
- return new Comparator() {
- public int compare (Object o1, Object o2) {
- return ((String)o1).compareToIgnoreCase ((String)o2);
- }
- };
- }
-
- // cache URL/URI so we only check once
- private static String CHECKED_URL = null;
- private static String CHECKED_URI = null;
-
- /**
- * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
- * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
- * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
- *
- * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
- */
- public static CentralImpl getDefaultCentral() throws MobyException{
- return getDefaultCentral(null);
- }
-
- public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
- if(reg == null && defaultCentrals.containsKey("")){
- return defaultCentrals.get("");
- }
- else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
- return defaultCentrals.get(reg.getEndpoint());
- }
-
- String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
- ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
- URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
- if(resURL != null){
- System.err.println("Loading "+resURL);
- try{
- LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
- for(String line = reader.readLine(); line != null; line = reader.readLine()){
- if(!line.trim().startsWith("#")){
- className = line.trim();
- break;
- }
- }
- } catch(Exception e){
- logger.log(Level.WARNING,
- "Error reading " + resURL,
- e);
- }
- }
- try{
- System.err.println("Central class is "+className);
- Class clazz = Class.forName(className);
- if(reg == null){ // should use default nullary c-tor
- defaultCentrals.put("", (CentralImpl) clazz.newInstance());
- }
- else{ // should have (String endpoint, String namespace) c-tor
- for(Constructor ctor: clazz.getDeclaredConstructors()){
- Class[] params = ctor.getParameterTypes();
- if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
- params[1].getName().equals("java.lang.String") ){
- defaultCentrals.put(reg.getEndpoint(),
- (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
- break;
- }
- }
- if(!defaultCentrals.containsKey(reg.getEndpoint())){
- logger.log(Level.WARNING,
- "Could not find required (String endpoint, String namespace)" +
- "constructor for class " + className);
- }
- }
- } catch(Exception e){
- logger.log(Level.WARNING,
- "Could not load class " + className,
- e);
- if(reg == null){
- defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
- }
- else{
- defaultCentrals.put(reg.getEndpoint(),
- new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
- }
- }
-
- return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
- }
-
- /**
- *
- * @return a String representing the Default mobycentral endpoint. If the
- * system property 'moby.check.default' exists and is set to true,
- * then the URL http://biomoby.org/mobycentral is queried and the
- * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
- * is returned.
- */
- public static String getDefaultURL() {
- boolean check = false;
- try {
- check = Boolean.getBoolean("moby.check.default");
- } catch (Exception e) {
-
- }
-
- if (check) {
- // return the last checked url if we have done this before
- if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
- return CHECKED_URL;
- }
-
- // create a HttpClient object
- HttpClient client = new HttpClient();
- // set up the Head method
- HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
- // do not follow redirects or we will get a 411 error
- method.setFollowRedirects(false);
- // retry 3 times
- method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
- // set the user agent ... should probably make this something more reasonable
- method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
- try {
- // Execute the method.
- int statusCode = client.executeMethod(method);
-
- if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
- System.err.println("Method failed: "
- + method.getStatusLine());
- } else {
- try {
- String location = method.getResponseHeader("location").getValue();
- CHECKED_URL = location;
- try {
- CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
- } catch (MalformedURLException murle ) {
- CHECKED_URI = DEFAULT_NAMESPACE;
- }
- return CHECKED_URL;
- } catch (NullPointerException npe) {
- return DEFAULT_ENDPOINT;
- }
- }
- } catch (HttpException e) {
- System.err.println("Fatal protocol violation: "
- + e.getMessage());
- e.printStackTrace();
- } catch (IOException e) {
- System.err.println("Fatal transport error: " + e.getMessage());
- e.printStackTrace();
- } finally {
- // Release the connection.
- method.releaseConnection();
- }
-
- } else {
- return DEFAULT_ENDPOINT;
- }
- return DEFAULT_ENDPOINT;
- }
-
- /**
- *
- * @return a String representing the default mobycentral uri. If the
- * system property 'moby.check.default' exists and is set to true,
- * then the URL http://biomoby.org/mobycentral is queried and the
- * default central namespace is returned, otherwise DEFAULT_NAMESPACE
- * is returned.
- */
- public static String getDefaultURI() {
- boolean check = false;
- try {
- check = Boolean.getBoolean("moby.check.default");
- } catch (Exception e) {
-
- }
- if (check) {
- if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
- return CHECKED_URI;
- }
- // need to check ...
- getDefaultURL();
- return CHECKED_URI;
- } else {
- return DEFAULT_NAMESPACE;
- }
- }
- /**************************************************************************
- * Convert non-suitable characters in a XML string into their
- * entity references.
- *
- * Adapted from jDom.
- *
- * @param str input to be converted
- * @return If there were any non-suitable characters, return a new
- * string with those characters escaped, otherwise return the
- * unmodified input string
- *
- *************************************************************************/
- public String escapeXML (String str) {
- StringBuffer buffer = null;
- char ch;
- String entity;
- for (int i = 0; i < str.length(); i++) {
- ch = str.charAt (i);
- switch (ch) {
- case '<' :
- entity = "<";
- break;
- case '>' :
- entity = ">";
- break;
- case '&' :
- entity = "&";
- break;
- default :
- entity = null;
- break;
- }
- if (buffer == null) {
- if (entity != null) {
- // An entity occurred, so we'll have to use StringBuffer
- // (allocate room for it plus a few more entities).
- buffer = new StringBuffer (str.length() + 20);
- // Copy previous skipped characters and fall through
- // to pickup current character
- buffer.append (str.substring (0, i));
- buffer.append (entity);
- }
- } else {
- if (entity == null) {
- buffer.append (ch);
- } else {
- buffer.append (entity);
- }
- }
- }
-
- // If there were any entities, return the escaped characters
- // that we put in the StringBuffer. Otherwise, just return
- // the unmodified input string.
- return (buffer == null) ? str : buffer.toString();
- }
-
- /*************************************************************************
- * Format an exception.
- *************************************************************************/
- public static String formatFault (AxisFault e, String endpoint, QName method) {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- formatFault (e, new PrintStream (baos), endpoint, method);
- return baos.toString();
- }
-
- /*************************************************************************
- * Format an exception.
- *************************************************************************/
- public static void formatFault (AxisFault e, PrintStream out,
- String endpoint, QName method) {
-
- out.println ("===ERROR===");
- out.println ("Fault details:");
- // for some obvious errors I do not print all details (with a lenghty trace stack)
- String faultString = e.getFaultString();
- if ( (! faultString.startsWith ("java.net.ConnectException")) &&
- (faultString.indexOf ("Could not find class for the service named:") == -1)
- ) {
- org.w3c.dom.Element[] details = e.getFaultDetails();
- for (int i = 0; i < details.length; i++) {
- String s = details[i].toString().replaceAll ("<", "<");
- s = s.replaceAll (">", ">");
- out.println (s);
- }
- }
- out.println ("Fault string: " + faultString);
- out.println ("Fault code: " + e.getFaultCode());
- out.println ("Fault actor: " + e.getFaultActor());
- if (endpoint != null || method != null)
- out.println ("When calling:");
- if (endpoint != null)
- out.println ("\t" + endpoint);
- if (method != null)
- out.println ("\t" + method);
- out.println ("===========");
- }
-
-
-}
+// CentralImpl.java
+// A default client to the Moby Central service.
+//
+// senger at ebi.ac.uk
+// February 2003
+//
+
+package org.biomoby.client;
+
+import org.biomoby.registry.meta.Registry;
+import org.biomoby.shared.Central;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSet;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+import org.biomoby.shared.MobyRelationship;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.NoSuccessException;
+import org.biomoby.shared.PendingCurationException;
+import org.biomoby.shared.MobyResourceRef;
+import org.biomoby.shared.Utils;
+
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.namespace.QName;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import org.apache.axis.AxisFault;
+import org.apache.axis.client.Call;
+import org.apache.axis.client.Service;
+import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
+import org.apache.commons.httpclient.Header;
+import org.apache.commons.httpclient.HttpClient;
+import org.apache.commons.httpclient.HttpException;
+import org.apache.commons.httpclient.HttpStatus;
+import org.apache.commons.httpclient.methods.HeadMethod;
+import org.apache.commons.httpclient.params.HttpMethodParams;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
+import java.io.PrintStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Vector;
+import java.util.TreeMap;
+import java.util.Comparator;
+import java.util.zip.GZIPInputStream;
+import java.util.logging.*;
+
+/**
+ * A default implementation of the
+ * interface {@link org.biomoby.shared.Central Central}
+ * allowing access to a Moby registry.
+ *
+ * This class is supposed to be used by all other clients that wish
+ * to communicate with the Moby Registry, but do not want to know
+ * about all XML details that are necessary for talking with the Moby Central
+ * directly. This is an example of a client program:
+ *
+ * import org.biomoby.shared.Central;
+ * import org.biomoby.shared.MobyException;
+ * import org.biomoby.client.CentralImpl;
+ * import java.util.Map;
+ * import java.util.Iterator;
+ *
+ * public class Test {
+ *
+ * public static void main (String[] args)
+ * throws MobyException {
+ *
+ * Central worker = new CentralImpl();
+ * Map authorities = worker.getServiceNamesByAuthority();
+ *
+ * for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
+ * Map.Entry entry = (Map.Entry)it.next();
+ * System.out.println (entry.getKey());
+ * String[] names = (String[])entry.getValue();
+ * for (int i = 0; i < names.length; i++)
+ * System.out.println ("\t" + names[i]);
+ * }
+ * }
+ * }
+ *
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class CentralImpl
+ implements Central, SimpleCache {
+
+ private URL endpoint;
+ private String uri;
+ protected boolean debug = false;
+
+ /** Common central used to if getDefaultCentral() is called */
+ protected static Map defaultCentrals = new HashMap();
+
+ /** Default location (endpoint) of a Moby registry. */
+ public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
+
+ /** Default namespace used by the contacted Moby registry. */
+ public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
+
+ /**
+ * The META-INF resource file that will be checked to determine what
+ * default class should be instantiated in order to create a Central Implementation
+ * when getDefaultCentral() is called.
+ */
+ public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
+ /** The class to use for getDefaultCentral if all else fails */
+ public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
+ private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
+
+ /**
+ * Thread local that gives each thread its own
+ * DocumentBuilderFactory (since it is not thread-safe). Code taken
+ * from Apache's JaxpUtils.
+ */
+ public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
+ protected synchronized Object initialValue() {
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware (true);
+ return dbf;
+ }
+ };
+
+
+ /*************************************************************************
+ * Default constructor. It connects to a default Moby registry
+ * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
+ * (as defined int {@link #DEFAULT_NAMESPACE}).
+ *************************************************************************/
+ public CentralImpl()
+ throws MobyException {
+ this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry to use.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser is available
+ *************************************************************************/
+ public CentralImpl (String endpoint)
+ throws MobyException {
+ this (endpoint, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry and what
+ * namespace to use. If any of the parameters is null, its default
+ * value is used instead.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser was found
+ *************************************************************************/
+ public CentralImpl (String endpoint, String namespace)
+ throws MobyException {
+
+ if (endpoint == null || "".equals (endpoint.trim()))
+ endpoint = DEFAULT_ENDPOINT;
+ if (namespace == null || "".equals (namespace.trim()))
+ namespace = DEFAULT_NAMESPACE;
+
+ try {
+ this.endpoint = new URL (endpoint);
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Bad URL: " + endpoint);
+ }
+ this.uri = namespace;
+
+ cache = new Hashtable();
+ useCache = true;
+ }
+
+ /*************************************************************************
+ * Loads a DOM Document from an InputStream. Uses thread-safe
+ * mechanism.
+ *************************************************************************/
+ public static Document loadDocument (InputStream input)
+ throws MobyException {
+ try {
+ DocumentBuilderFactory dbf
+ = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
+ DocumentBuilder db = dbf.newDocumentBuilder();
+ return (db.parse (input));
+ } catch (Exception e) {
+ throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
+ }
+ }
+
+ /*************************************************************************
+ * Call 'method' with 'parameters' and return its result.
+ *************************************************************************/
+ protected Object doCall (String method, Object[] parameters)
+ throws MobyException {
+
+ Call call = null;
+ try {
+ Service service = new Service();
+ call = (Call) service.createCall();
+ call.setTargetEndpointAddress (endpoint);
+ call.setTimeout (new Integer (0));
+
+ call.setSOAPActionURI (uri + "#" + method);
+
+ if (debug) {
+ System.err.println ("METHOD CALL: " + method);
+ System.err.println ("------------");
+ if (parameters.length > 0)
+ System.err.println (parameters[0] + "\n");
+ System.err.println ("------------\n");
+
+ Object result = call.invoke (uri, method, parameters);
+
+ System.err.println ("METHOD RETURN:");
+ System.err.println ("------------");
+ if (result != null)
+ System.err.println (result + "\n");
+ System.err.println ("------------\n");
+
+ return resultToString (result);
+
+ } else {
+ return resultToString (call.invoke (uri, method, parameters));
+ }
+
+ } catch (AxisFault e) {
+ throw new MobyException
+ (formatFault (e,
+ endpoint.toString(),
+ (call == null ? null : call.getOperationName())),
+ e);
+// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+
+ } catch (Exception e) {
+ throw new MobyException (e.toString(), e);
+// e.printStackTrace();
+ }
+ }
+
+
+ /**************************************************************************
+ * Parse the given XML sniplet to find tag 'success'. If it has value '1'
+ * look further for tag 'id' and return it back (or return an empty string
+ * if ID is not there). Otherwise raise an exception with the 'culprit'
+ * and with the message from the tag 'message'.
+ *
+ * The return value is a two-element long array. The first element
+ * is the ID (given by BioMobe registry), and the second element
+ * is RDF corresponding with the registered object (BioMoby
+ * returns this only for service instances, so for other objects
+ * this will be null).
+ *
+ * This is how the XML is supposed to look:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * Success takes the value "1" to indicate success, "0" to
+ * indicate failure, and "-1" to indicate "Pending Curation".
+ *************************************************************************/
+ protected String[] checkRegistration (String xml, Object culprit)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String id = "", success = "0", message = "", rdf = "";
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ Element root = document.getDocumentElement();
+
+ NodeList children = root.getChildNodes();
+ for (int i = 0; i < children.getLength(); i++) {
+ if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
+ continue;
+ Element elem = (Element)children.item (i);
+ if (elem.getNodeName().equals ("id")) {
+ if (elem.getFirstChild() != null)
+ id = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals("success")) {
+ if (elem.getFirstChild() != null)
+ success = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("message")) {
+ if (elem.getFirstChild() != null)
+ message = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("RDF")) {
+ if (elem.getFirstChild() != null)
+ rdf = elem.getFirstChild().getNodeValue();
+ }
+ }
+
+ if (success.equals ("0"))
+ throw new NoSuccessException (message, culprit);
+ else if (success.equals ("-1"))
+ throw new PendingCurationException();
+ return new String[] { id, rdf };
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing input
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildSecondaryInputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] secInputs = service.getSecondaryInputs();
+ buf.append ("\n");
+ for (int i = 0; i < secInputs.length; i++) {
+ buf.append (secInputs[i].toXML());
+ }
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing output
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildOutputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] primaryOutputs = service.getPrimaryOutputs();
+ buf.append ("\n");
+ for (int i = 0; i < primaryOutputs.length; i++)
+ buf.append (primaryOutputs[i].toXML());
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML represented a query object (an object used
+ * to find a service).
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * ServiceTypeTerm
+ * ServiceName
+ * moby
+ * http://desired.service.provider ;
+ * 1|0
+ * 1|0
+ * 1|0
+ *
+ * something
+ * ....
+ * ....
+ *
+ *************************************************************************/
+ protected String buildQueryObject (MobyService service,
+ String[] keywords,
+ boolean expandObjects,
+ boolean expandServices,
+ boolean authoritative) {
+ if (service == null) {
+ service = new MobyService ("dummy");
+ service.setCategory ("");
+ }
+ StringBuffer buf = new StringBuffer();
+
+ buf.append ("\n \n");
+
+ buf.append ("\n\n");
+ MobyData[] po = service.getPrimaryOutputs();
+ if (po.length > 0) {
+ for (int i = 0; i < po.length; i++)
+ buf.append (po[i].toXML());
+ }
+ buf.append (" \n \n");
+
+ buf.append ("" + service.getType() + " \n");
+
+ String name = service.getName();
+ if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
+ buf.append ("" + service.getName() + " \n");
+
+ String sigURL = service.getSignatureURL();
+ if (!sigURL.equals (""))
+ buf.append ("" + sigURL + " \n");
+
+ buf.append ("" + service.getCategory() + " \n");
+ buf.append ("" + service.getAuthority() + " \n");
+
+ buf.append ("");
+ buf.append (expandObjects ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (expandServices ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (authoritative ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("\n");
+ if (keywords != null && keywords.length > 0) {
+ for (int i = 0; i < keywords.length; i++) {
+ buf.append ("");
+ buf.append (keywords[i]);
+ buf.append (" \n");
+ }
+ }
+ buf.append (" \n");
+
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Extract one or more MobyService objects from the given XML piece.
+ * The XML should look like this:
+ *
+ * <Services>
+ * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
+ * <serviceType>Service_Ontology_Term</serviceType>
+ * <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
+ * <contactEmail>your at email.addy.here</contactEmail>
+ * <signatureURL>http://service.RDF.here</signatureURL>
+ * <URL>http://service.endpoint.here/scriptname</URL>
+ * <authoritative>1</authoritative>
+ * <Input>
+ * <!-- one or more Simple and/or Complex Primary articles -->
+ * </Input>
+ * <Output>
+ * <!-- one or more Simple and/or Complex Primary articles -->
+ * </Output>
+ * <secondaryArticles>
+ * <!-- one or more Secondary articles -->
+ * </secondaryArticles>
+ * <Description><![CDATA[free text description here]]></Description>
+ * </Service>
+ * ... <!-- one or more Service blocks may be returned -->
+ * ...
+ * ...
+ * </Services>
+ *
+ * @throws MobyException if the XML document is invalid
+ *************************************************************************/
+ public MobyService[] extractServices (String xml)
+ throws MobyException {
+
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ NodeList list = document.getElementsByTagName ("Service");
+ MobyService[] results = new MobyService [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyService service = new MobyService (elem.getAttribute ("serviceName"));
+ service.setAuthority (elem.getAttribute ("authURI"));
+ service.setLSID (elem.getAttribute ("lsid"));
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ service.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Category")) {
+ service.setCategory (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("URL")) {
+ service.setURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("signatureURL")) {
+ service.setSignatureURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ service.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("serviceType")) {
+ service.setType (getFirstValue (children.item (j)));
+ MobyServiceType mst = new MobyServiceType(service.getType());
+ NamedNodeMap map = (children.item (j).getAttributes());
+ if (map != null) {
+ Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
+ if (node != null)
+ mst.setLSID(node.getNodeValue());
+ }
+ service.setServiceType(mst);
+ } else if (nodeName.equals ("authoritative")) {
+ String authoritative = getFirstValue (children.item (j));
+ service.setAuthoritative (authoritative.equals ("1") ? true : false);
+ } else if (nodeName.equals ("Input")) {
+ //
+ // ...
+ //
+ //
+ // ......
+ // ......
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addInput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addInput (data);
+ }
+ }
+ } else if (nodeName.equals ("Output")) {
+ //
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addOutput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addOutput (data);
+ }
+ }
+
+ } else if (nodeName.equals ("secondaryArticles")) {
+ //
+ // ...
+ //
+ NodeList parameters = children.item (j).getChildNodes();
+ for (int k = 0; k < parameters.getLength(); k++) {
+ if (parameters.item (k).getNodeName().equals ("Parameter")) {
+ MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
+ service.addInput (data);
+ }
+ }
+ }
+ }
+ results [i] = service;
+ }
+ return results;
+ }
+
+ // protect against null values
+ protected String getFirstValue (Node child) {
+ Node node = child.getFirstChild();
+ if (node == null) return "";
+ String value = node.getNodeValue();
+ if (value == null) return "";
+ return value;
+ }
+
+ protected String getFirstValue (NodeList children) {
+ if (children.item(0) != null && children.item(0).hasChildNodes()) {
+ children.item(0).normalize();
+ return getFirstValue (children.item(0));
+ }
+ return "";
+ }
+
+ /**************************************************************************
+ *
+ * Implementing SimpleCache interface.
+ *
+ * Why to have an interface for such trivial thing? Well, because
+ * I needed to overwrite the caching mechanism in the subclasses
+ * so I needed to have all caching functions as separate methods -
+ * that's why I have collect them in an interface.
+ *
+ *************************************************************************/
+ private Hashtable cache; // this is the cache itself
+ private boolean useCache; // this signal that we are actually caching things
+
+ // not used here
+ public String createId (String rootName,
+ String semanticType, String syntaxType,
+ long lastModified,
+ Properties props) {
+ return ""; // not used here
+ }
+
+ // check existence of a cached object
+ public boolean existsInCache (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.containsKey (id);
+ else return false;
+ }
+ }
+
+ // retrieve from cache
+ public Object getContents (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.get (id);
+ else return null;
+ }
+ }
+
+ // cache an object
+ public void setContents (String id, java.lang.Object data) {
+ synchronized (cache) {
+ if (useCache) cache.put (id, data);
+ }
+ }
+
+ // in this implementation, it clears the whole cache, regardless
+ // what 'id' is passed
+ public void removeFromCache (String id) {
+ cache.clear();
+ }
+
+ /**************************************************************************
+ *
+ * And the other methods related to caching (but not part of the
+ * SimpleCache interface).
+ *
+ **************************************************************************/
+
+ /**************************************************************************
+ * By default, caching is enabled to reduce network traffic.
+ * Setting this to false will clear the cache, and not cache any
+ * further calls unless it is set to true again.
+ *
+ * @param shouldCache whether retrieveXXX call results should be
+ * cached in case they are called again (i.e. don't request
+ * MobyCentral every time)
+ **************************************************************************/
+ public void setCacheMode (boolean shouldCache) {
+ useCache = shouldCache;
+ if (! useCache)
+ removeFromCache (null);
+ }
+
+ /**************************************************************************
+ * Find if caching is currently enabled.
+ *
+ * @return true if caching is enabled
+ **************************************************************************/
+ public boolean getCacheMode(){
+ return useCache;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceNames>
+ * <serviceName name="serviceName" authURI='authority.info.here'/>
+ * ...
+ * ...
+ * </serviceNames>
+ *
+ *
+ * @deprecated Replaced by {@link
+ * #getServiceNamesByAuthority}. The reason is that this method
+ * returns a random result if there are more services with the
+ * same name but belonging to different authorities.
+ *
+ *************************************************************************/
+ public Map getServiceNames()
+ throws MobyException {
+
+ String result = (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ results.put (elem.getAttribute ("name"),
+ elem.getAttribute ("authURI"));
+ }
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceNames>
+ * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
+ * ...
+ * ...
+ * </serviceNames>
+ *
+ *
+ * @return a Map which has authorities as keys, and String arrays
+ * with service names as a values.
+ *************************************************************************/
+ public Map getServiceNamesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, true);
+ }
+
+ /**************************************************************************
+ * Similar to {@link #getServiceNamesByAuthority} but the
+ * resulting Map contains slightly more.
+ *
+ * @return a Map which has authorities as keys, and arrays of
+ * MobyServices as a values. Each MobyService is filled with its
+ * name, authority and LSID.
+ *************************************************************************/
+ public Map getServicesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, false);
+ }
+
+ //
+ protected String getServiceNamesByAuthorityAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ }
+
+ // if onlyNames == true
+ // Map: authority name -> String[]
+ // (filled with service namea)
+ // else
+ // Map: authority name -> MobyService[]
+ // (filled with service name, authority and lsid)
+ protected Map createServicesByAuthorityFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ String auth = elem.getAttribute ("authURI");
+ Vector v =
+ (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+ if (onlyNames) {
+ v.addElement (name);
+ } else {
+ MobyService ms = new MobyService (name);
+ ms.setAuthority (auth);
+ ms.setLSID (elem.getAttribute ("lsid"));
+ v.addElement (ms);
+ }
+ results.put (auth, v);
+ }
+
+ // change values of type Vector to MobyService[] or String[]
+ for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ Vector v = (Vector)entry.getValue();
+ if (onlyNames) {
+ String[] sNames = new String [v.size()];
+ v.copyInto (sNames);
+ entry.setValue (sNames);
+ } else {
+ MobyService[] mss = new MobyService [v.size()];
+ v.copyInto (mss);
+ entry.setValue (mss);
+ }
+ }
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceProviders>
+ * <serviceProvider name="authority.URI.here"/>
+ * ...
+ * ...
+ * </serviceProviders>
+ *
+ *************************************************************************/
+ public String[] getProviders()
+ throws MobyException {
+
+ String cacheId = "retrieveServiceProviders";
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveServiceProviders",
+ new Object[] {});
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceProvider");
+ String[] results = new String [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++)
+ results[i] = ((Element)list.item (i)).getAttribute ("name");
+
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
+
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <serviceTypes>
+ * <serviceType name="serviceName" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * <contactEmail>...</contactEmail>
+ * <authURI>...</authURI>
+ * </serviceType>
+ * ...
+ * ...
+ * </serviceTypes>
+ *
+ *************************************************************************/
+ public Map getServiceTypes()
+ throws MobyException {
+ String result = getServiceTypesAsXML();
+ Map results = new TreeMap (getStringComparator());
+ MobyServiceType[] types = createServiceTypesFromXML (result);
+ for (int i = 0; i < types.length; i++) {
+ results.put (types[i].getName(),
+ types[i].getDescription());
+ }
+ return results;
+ }
+
+ //
+ protected String getServiceTypesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceTypes",
+ new Object[] {});
+ }
+
+ // but be aware that the created MobyServiceTypes are not complete
+ // - they do not have the relationship information; that's why
+ // this method is not public; the full service types are available
+ // from CentralDigest implementations
+ protected MobyServiceType[] createServiceTypesFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceType");
+ if (list == null || list.getLength() == 0)
+ return new MobyServiceType[] {};
+ MobyServiceType[] results = new MobyServiceType [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
+ st.setLSID (elem.getAttribute ("lsid"));
+ st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = st;
+ }
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <Namespaces>
+ * <Namespace name="namespace" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * <contactEmail>...</contactEmail>
+ * <authURI>...</authURI>
+ * </Namespace>
+ * ...
+ * ...
+ * </Namespaces>
+ *
+ *************************************************************************/
+ public MobyNamespace[] getFullNamespaces()
+ throws MobyException {
+
+ String result = getNamespacesAsXML();
+ return createNamespacesFromXML (result);
+ }
+
+ //
+ protected String getNamespacesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveNamespaces",
+ new Object[] {});
+ }
+
+ //
+ protected MobyNamespace[] createNamespacesFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
+ if (list == null || list.getLength() == 0) {
+ return new MobyNamespace[] {};
+ }
+ MobyNamespace[] results = new MobyNamespace [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
+ nm.setLSID (elem.getAttribute ("lsid"));
+ nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = nm;
+ }
+
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ * @deprecated Replaced by {@link #getFullNamespaces} that gives
+ * more information for the same price.
+ *************************************************************************/
+ public Map getNamespaces()
+ throws MobyException {
+
+ Map results = new TreeMap (getStringComparator());
+ MobyNamespace[] namespaces = getFullNamespaces();
+ for (int i = 0; i < namespaces.length; i++) {
+ results.put (namespaces[i].getName(),
+ namespaces[i].getDescription());
+ }
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <objectNames>
+ * <Object name="objectName" lsid="...">
+ * <Description><![CDATA[free text description here]]></Description>
+ * </Object>
+ * ...
+ * ...
+ * </objectNames>
+ *
+ *************************************************************************/
+ public Map getDataTypeNames()
+ throws MobyException {
+ String result = getDataTypeNamesAsXML();
+ return createDataTypeNamesFromXML (result, true);
+ }
+
+ //
+ protected String getDataTypeNamesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveObjectNames",
+ new Object[] {});
+ }
+
+ // if onlyNames == true
+ // Map: data type name -> description (String)
+ // else
+ // Map: data type name -> MobyDataType[]
+ // (filled with name, description, and lsid)
+ protected Map createDataTypeNamesFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Object");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ if (name == null)
+ continue; // ignore no-named data types
+ String desc = "";
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("Description")) {
+ desc = getFirstValue (children.item (j));
+ break;
+ }
+ }
+ if (onlyNames) {
+ results.put (name, desc);
+ } else {
+ MobyDataType dt = new MobyDataType (name);
+ dt.setDescription (desc);
+ dt.setLSID (elem.getAttribute ("lsid"));
+ results.put (name, dt);
+ }
+ }
+ return results;
+ }
+
+
+ /**************************************************************************
+ * Parses and imports the following XML. An example:
+ *
+ *
+ * <retrieveObjectDefinition>
+ * <objectType lsid="...">go_term</objectType>
+ * <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
+ * <authURI>http://www.illuminae.com</authURI>
+ * <contactEmail>markw at illuminae.com</contactEmail>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType articleName=''>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
+ * <objectType articleName='Term'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType articleName='Definition'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:has'>
+ * <objectType articleName='Problems'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType articleName='Issues'>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * </Relationship>
+ * </retrieveObjectDefinition>
+ *
+ *************************************************************************/
+ public MobyDataType getDataType (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ String result = getDataTypeAsXML (dataTypeName);
+ return createDataTypeFromXML (result, dataTypeName);
+ }
+
+ public MobyDataType[] getDataTypes()
+ throws MobyException, NoSuccessException {
+ Map datatypeMap = getDataTypeNames();
+ MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
+ int i = 0;
+ for(String dataTypeName: datatypeMap.keySet()){
+ datatypes[i++] = getDataType(dataTypeName);
+ }
+ return datatypes;
+ }
+
+ protected String getDataTypeAsXML (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ return (String)doCall ("retrieveObjectDefinition",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ " "
+ });
+ }
+
+ protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
+ NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
+ if (list == null || list.getLength() == 0)
+ throw new NoSuccessException ("Data Type name was not found.",
+ dataTypeName);
+ MobyDataType data = null;
+ Element elem = (Element)list.item (0);
+ NodeList children = elem.getChildNodes();
+
+ // first find the "real" (LSID-ized) data type name
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("objectType")) {
+ data = new MobyDataType (getFirstValue (children.item (j)));
+ data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
+ break;
+ }
+ }
+
+ // if not found (unprobable) use the name given by the caller
+ if (data == null)
+ data = new MobyDataType (dataTypeName);
+
+ // now fill the data type object with the rest of attributes
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ data.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("authURI")) {
+ data.setAuthority (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ data.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Relationship")) {
+ String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
+ if (relationshipType.endsWith ("isa")) {
+
+ NodeList parents = children.item (j).getChildNodes();
+ for (int k = 0; k < parents.getLength(); k++) {
+ if (parents.item (k).getNodeName().equals ("objectType")) {
+ data.addParentName (getFirstValue (parents.item (k)));
+ }
+ }
+ } else if (relationshipType.endsWith ("hasa")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ getFirstValue (belows.item (k)),
+ Central.iHASA );
+ }
+ }
+ } else if (relationshipType.endsWith ("has")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ belows.item (k).getFirstChild().getNodeValue(),
+ Central.iHAS );
+ }
+ }
+ }
+ }
+ }
+ return data;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName)
+ throws MobyException, NoSuccessException {
+
+ Map names = getServiceNames();
+
+ for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ if ( ((String)entry.getKey()).equals (serviceName) )
+ return getServiceWSDL (serviceName, (String)entry.getValue());
+ }
+
+ throw new NoSuccessException ("Service not found.", serviceName);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName, String authority)
+ throws MobyException, NoSuccessException {
+
+ String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
+ String cachedResults = (String)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("retrieveService",
+ new Object[] {
+ "" +
+ " "
+ });
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ Element service = document.getDocumentElement();
+ Node wsdl = service.getFirstChild();
+ if (wsdl == null)
+ throw new NoSuccessException ("Service not found OR WSDL is not available.",
+ serviceName + " (" + authority + ")");
+
+ String results = wsdl.getNodeValue();
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterDataTypeXML (MobyDataType dataType) {
+
+ // build the ISA tag (expressing hierarchy of data types)
+ String[] names = dataType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ // build the HASA/HAS tags (expressing containments of data types)
+ MobyRelationship[] children = dataType.getChildren();
+ StringBuffer buf2 = new StringBuffer(); // for HASA
+ StringBuffer buf3 = new StringBuffer(); // for HAS
+ for (int i = 0; i < children.length; i++) {
+ if (children[i].getRelationshipType() == Central.iHASA) {
+ buf2.append ("");
+ buf2.append (children[i].getDataTypeName());
+ buf2.append (" ");
+ } else if (children[i].getRelationshipType() == Central.iHAS) {
+ buf3.append ("");
+ buf3.append (children[i].getDataTypeName());
+ buf3.append (" ");
+ }
+ }
+
+ return
+ "" +
+ "" + dataType.getName() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ "" + new String (buf2) +
+ " " +
+ "" + new String (buf3) +
+ " " +
+ "" + dataType.getAuthority() + " " +
+ "" + dataType.getEmailContact() + " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerObjectClass",
+ new Object[] { getRegisterDataTypeXML (dataType) });
+ dataType.setId (checkRegistration (result, dataType)[0]);
+ }
+
+ /*************************************************************************
+ * B
+ *************************************************************************/
+ public void unregisterDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterObjectClass",
+ new Object[] {
+ "" +
+ "" + dataType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, dataType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
+
+ // build the ISA tag (expressing hierarchy of service types)
+ String[] names = serviceType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ return
+ "" +
+ "" + serviceType.getName() + " " +
+ "" + serviceType.getEmailContact() + " " +
+ "" + serviceType.getAuthority() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerServiceType",
+ new Object[] { getRegisterServiceTypeXML (serviceType) });
+ serviceType.setId (checkRegistration (result, serviceType)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterServiceType",
+ new Object[] {
+ "" +
+ "" + serviceType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, serviceType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterNamespaceXML (MobyNamespace namespace) {
+ return
+ "" +
+ "" + namespace.getName() + " " +
+ "" + namespace.getEmailContact() + " " +
+ "" + namespace.getAuthority() + " " +
+ "" +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("registerNamespace",
+ new Object[] { getRegisterNamespaceXML (namespace) });
+ namespace.setId (checkRegistration (result, namespace)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterNamespace",
+ new Object[] {
+ "" +
+ "" + namespace.getName() + " " +
+ " "
+ });
+ checkRegistration (result, namespace);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceXML (MobyService service) {
+ return
+ "" +
+ "" + service.getCategory() + " " +
+ "" + service.getName() + " " +
+ "" + service.getType() + " " +
+ "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
+ "" + service.getAuthority() + " " +
+ "" + escapeXML (service.getSignatureURL()) + " " +
+ "" + escapeXML (service.getURL()) + " " +
+ "" + service.getEmailContact() + " " +
+ "" + (service.isAuthoritative() ? "1" : "0") + " " +
+ "" +
+ " " +
+ buildPrimaryInputTag (service) +
+ buildSecondaryInputTag (service) +
+ buildOutputTag (service) +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerService",
+ new Object[] { getRegisterServiceXML (service) });
+ String[] registered = checkRegistration (result, service);
+ service.setId (registered [0]);
+ service.setRDF (registered [1]);
+ String pathToRDF = service.getPathToRDF();
+ if ( ! pathToRDF.equals ("") ) {
+ File fileRDF = new File (pathToRDF);
+ try {
+ PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
+ fileout.println (registered [1]);
+ fileout.close();
+ } catch (IOException e) {
+ StringBuffer buf = new StringBuffer (100);
+ buf.append ("Failed to save RDF in '");
+ buf.append (fileRDF.getAbsolutePath() + "'. ");
+ buf.append (e.toString());
+ try {
+ File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
+ PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
+ fileout.println (registered [1]);
+ fileout.close();
+ buf.append ("\nReturned RDF file was therefore stored in: ");
+ buf.append (tmpFile.getAbsolutePath());
+ } catch (IOException e2) {
+ buf.append ("\nEven saving in a temporary file failed: ");
+ buf.append (e2.toString());
+ }
+ throw new MobyException (buf.toString());
+ }
+ }
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterService",
+ new Object[] {
+ "" +
+ "" + service.getAuthority() + " " +
+ "" + service.getName() + " " +
+ " "
+ });
+ checkRegistration (result, service);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String serviceType)
+ throws MobyException {
+ if (serviceType == null)
+ return new MobyService[] {};
+ MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ pattern.setType (serviceType);
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String[] keywords)
+ throws MobyException {
+ if (keywords == null)
+ return new MobyService[] {};
+ return findService (null, keywords);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern)
+ throws MobyException {
+ if (pattern == null)
+ return new MobyService[] {};
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords)
+ throws MobyException {
+ return findService (pattern, keywords, true, true);
+ }
+
+ /**************************************************************************
+ * All 'findService' methods end up here.
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ if (pattern == null) {
+ pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ }
+
+ String result =
+ getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
+ MobyService[] services = extractServices (result);
+ return services;
+ }
+
+ // ...actually all 'findService' methods end up here
+ protected String getServicesAsXML (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ String[] query = new String[] {
+ "" +
+ buildQueryObject (pattern, keywords,
+ includeParentDataTypes,
+ includeChildrenServiceTypes,
+ false) +
+ " "
+ };
+ return (String)doCall ("findService", query);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String call (String methodName, String inputXML)
+ throws MobyException {
+ Object result;
+ if (inputXML == null || inputXML.equals (""))
+ result = doCall (methodName, new Object[] { });
+ else
+ result = doCall (methodName, new Object[] { inputXML });
+ return (String)result;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected static String resultToString (Object result)
+ throws MobyException {
+ if (result == null)
+ throw new MobyException ("Returned result is null.");
+ if (result instanceof String)
+ return (String)result;
+ if (result instanceof String[]) {
+ String[] tmp = (String[])result;
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < tmp.length; i++)
+ buf.append (tmp[i]);
+ return new String (buf);
+ }
+ if (result instanceof byte[])
+ return new String ((byte[])result);
+
+ throw new MobyException ("Unknown type of result: " + result.getClass().getName());
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean setDebug (boolean enabled) {
+ boolean oldMode = debug;
+ debug = enabled;
+ return oldMode;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
+ * <serviceType>urn:lsid:biomoby.org:servicetype:analysis</serviceType>
+ * <serviceType>urn:lsid:biomoby.org:servicetype:service</serviceType>
+ * </Relationship>
+ * </Relationships>
+ *
+ *************************************************************************/
+ public String[] getServiceTypeRelationships (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
+ return createServiceTypeRelationshipsFromXML (result);
+ }
+
+ //
+ protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ return
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + serviceTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + (expand ? "1" : "0") + " " +
+ " "
+ });
+ }
+
+ //
+ protected String[] createServiceTypeRelationshipsFromXML (String result)
+ throws MobyException {
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("serviceType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ *<Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
+ * </Relationship>
+ *</Relationships>
+ *
+ *
+ * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
+ * attributes 'lsid' and 'articleName' in <objectType> element.
+ *************************************************************************/
+ public Map getDataTypeRelationships (String dataTypeName)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName;
+ Map cachedResults = (Map)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + Central.HASA + " " +
+ "" + Central.HAS + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Map results = new HashMap();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String relType = elem.getAttribute ("relationshipType");
+ NodeList children = elem.getChildNodes();
+ Vector v = new Vector();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ String[] names = new String [v.size()];
+ v.copyInto (names);
+ results.put (relType, names);
+ }
+
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ *<Relationships>
+ * <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
+ * <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
+ * <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
+ * </Relationship>
+ *</Relationships>
+ *
+ *************************************************************************/
+ public String[] getDataTypeRelationships (String dataTypeName,
+ String relationshipType)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + relationshipType + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ // it should always be just one element in this list
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+
+ setContents (cacheId, results);
+ return results;
+ }
+
+// /**************************************************************************
+// *
+// *************************************************************************/
+// public MobyRelationship[] getRelationships (String dataTypeName)
+// throws MobyException {
+// return null;
+// }
+
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getRegistryEndpoint() {
+ return endpoint.toString();
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getRegistryNamespace() {
+ return uri;
+ }
+
+ /**************************************************************************
+ * Parses and imports the following XML.
+ *
+ * <resourceURLs>
+ * <Resource name="Service" url="..." />
+ * <Resource name="Object" url="..." />
+ * <Resource name="Namespace" url="..." />
+ * <Resource name="ServiceInstance" url="..." />
+ * <Resource name="Full" url="..." />
+ * </resourceURLs>
+ *
+ *************************************************************************/
+ public MobyResourceRef[] getResourceRefs()
+ throws MobyException {
+
+ String cacheId = "retrieveResourceURLs";
+ MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveResourceURLs",
+ new Object[] {});
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Resource");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ try {
+ v.addElement
+ (new MobyResourceRef (elem.getAttribute ("name"),
+ new URL ((String)elem.getAttribute ("url")),
+ elem.getAttribute ("type")));
+ } catch (MalformedURLException e2) {
+ if (debug)
+ System.err.println ("Bad URL: " + elem.getAttribute ("url"));
+ }
+ }
+
+ MobyResourceRef[] results = new MobyResourceRef [v.size()];
+ v.copyInto (results);
+
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
+
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public InputStream getResource (String resourceName)
+ throws MobyException {
+
+ MobyResourceRef[] resourceRefs = getResourceRefs();
+ for (int i = 0; i < resourceRefs.length; i++) {
+ if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
+ return Utils.getInputStream (resourceRefs[i].getResourceLocation());
+ }
+ }
+ throw new MobyException ("No resource found for '" + resourceName + "'.");
+ }
+
+ /**************************************************************************
+ * Return a case-insensitive comparator of Strings. It is used to
+ * create various TreeMaps where keys are strings.
+ *************************************************************************/
+ protected static Comparator getStringComparator() {
+ return new Comparator() {
+ public int compare (Object o1, Object o2) {
+ return ((String)o1).compareToIgnoreCase ((String)o2);
+ }
+ };
+ }
+
+ // cache URL/URI so we only check once
+ private static String CHECKED_URL = null;
+ private static String CHECKED_URI = null;
+
+ /**
+ * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
+ * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
+ * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+ *
+ * @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
+ */
+ public static CentralImpl getDefaultCentral() throws MobyException{
+ return getDefaultCentral(null);
+ }
+
+ public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
+ if(reg == null && defaultCentrals.containsKey("")){
+ return defaultCentrals.get("");
+ }
+ else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+ return defaultCentrals.get(reg.getEndpoint());
+ }
+
+ String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+ ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+ URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+ if(resURL != null){
+ System.err.println("Loading "+resURL);
+ try{
+ LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+ for(String line = reader.readLine(); line != null; line = reader.readLine()){
+ if(!line.trim().startsWith("#")){
+ className = line.trim();
+ break;
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Error reading " + resURL,
+ e);
+ }
+ }
+ try{
+ System.err.println("Central class is "+className);
+ Class clazz = Class.forName(className);
+ if(reg == null){ // should use default nullary c-tor
+ defaultCentrals.put("", (CentralImpl) clazz.newInstance());
+ }
+ else{ // should have (String endpoint, String namespace) c-tor
+ for(Constructor ctor: clazz.getDeclaredConstructors()){
+ Class[] params = ctor.getParameterTypes();
+ if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+ params[1].getName().equals("java.lang.String") ){
+ defaultCentrals.put(reg.getEndpoint(),
+ (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+ break;
+ }
+ }
+ if(!defaultCentrals.containsKey(reg.getEndpoint())){
+ logger.log(Level.WARNING,
+ "Could not find required (String endpoint, String namespace)" +
+ "constructor for class " + className);
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Could not load class " + className,
+ e);
+ if(reg == null){
+ defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
+ }
+ else{
+ defaultCentrals.put(reg.getEndpoint(),
+ new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+ }
+ }
+
+ return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
+ }
+
+ /**
+ *
+ * @return a String representing the Default mobycentral endpoint. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
+ * is returned.
+ */
+ public static String getDefaultURL() {
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+
+ if (check) {
+ // return the last checked url if we have done this before
+ if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
+ return CHECKED_URL;
+ }
+
+ // create a HttpClient object
+ HttpClient client = new HttpClient();
+ // set up the Head method
+ HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
+ // do not follow redirects or we will get a 411 error
+ method.setFollowRedirects(false);
+ // retry 3 times
+ method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
+ // set the user agent ... should probably make this something more reasonable
+ method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
+ try {
+ // Execute the method.
+ int statusCode = client.executeMethod(method);
+
+ if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
+ System.err.println("Method failed: "
+ + method.getStatusLine());
+ } else {
+ try {
+ String location = method.getResponseHeader("location").getValue();
+ CHECKED_URL = location;
+ try {
+ CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
+ } catch (MalformedURLException murle ) {
+ CHECKED_URI = DEFAULT_NAMESPACE;
+ }
+ return CHECKED_URL;
+ } catch (NullPointerException npe) {
+ return DEFAULT_ENDPOINT;
+ }
+ }
+ } catch (HttpException e) {
+ System.err.println("Fatal protocol violation: "
+ + e.getMessage());
+ e.printStackTrace();
+ } catch (IOException e) {
+ System.err.println("Fatal transport error: " + e.getMessage());
+ e.printStackTrace();
+ } finally {
+ // Release the connection.
+ method.releaseConnection();
+ }
+
+ } else {
+ return DEFAULT_ENDPOINT;
+ }
+ return DEFAULT_ENDPOINT;
+ }
+
+ /**
+ *
+ * @return a String representing the default mobycentral uri. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central namespace is returned, otherwise DEFAULT_NAMESPACE
+ * is returned.
+ */
+ public static String getDefaultURI() {
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+ if (check) {
+ if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
+ return CHECKED_URI;
+ }
+ // need to check ...
+ getDefaultURL();
+ return CHECKED_URI;
+ } else {
+ return DEFAULT_NAMESPACE;
+ }
+ }
+ /**************************************************************************
+ * Convert non-suitable characters in a XML string into their
+ * entity references.
+ *
+ * Adapted from jDom.
+ *
+ * @param str input to be converted
+ * @return If there were any non-suitable characters, return a new
+ * string with those characters escaped, otherwise return the
+ * unmodified input string
+ *
+ *************************************************************************/
+ public String escapeXML (String str) {
+ StringBuffer buffer = null;
+ char ch;
+ String entity;
+ for (int i = 0; i < str.length(); i++) {
+ ch = str.charAt (i);
+ switch (ch) {
+ case '<' :
+ entity = "<";
+ break;
+ case '>' :
+ entity = ">";
+ break;
+ case '&' :
+ entity = "&";
+ break;
+ default :
+ entity = null;
+ break;
+ }
+ if (buffer == null) {
+ if (entity != null) {
+ // An entity occurred, so we'll have to use StringBuffer
+ // (allocate room for it plus a few more entities).
+ buffer = new StringBuffer (str.length() + 20);
+ // Copy previous skipped characters and fall through
+ // to pickup current character
+ buffer.append (str.substring (0, i));
+ buffer.append (entity);
+ }
+ } else {
+ if (entity == null) {
+ buffer.append (ch);
+ } else {
+ buffer.append (entity);
+ }
+ }
+ }
+
+ // If there were any entities, return the escaped characters
+ // that we put in the StringBuffer. Otherwise, just return
+ // the unmodified input string.
+ return (buffer == null) ? str : buffer.toString();
+ }
+
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static String formatFault (AxisFault e, String endpoint, QName method) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ formatFault (e, new PrintStream (baos), endpoint, method);
+ return baos.toString();
+ }
+
+ /*************************************************************************
+ * Format an exception.
+ *************************************************************************/
+ public static void formatFault (AxisFault e, PrintStream out,
+ String endpoint, QName method) {
+
+ out.println ("===ERROR===");
+ out.println ("Fault details:");
+ // for some obvious errors I do not print all details (with a lenghty trace stack)
+ String faultString = e.getFaultString();
+ if ( (! faultString.startsWith ("java.net.ConnectException")) &&
+ (faultString.indexOf ("Could not find class for the service named:") == -1)
+ ) {
+ org.w3c.dom.Element[] details = e.getFaultDetails();
+ for (int i = 0; i < details.length; i++) {
+ String s = details[i].toString().replaceAll ("<", "<");
+ s = s.replaceAll (">", ">");
+ out.println (s);
+ }
+ }
+ out.println ("Fault string: " + faultString);
+ out.println ("Fault code: " + e.getFaultCode());
+ out.println ("Fault actor: " + e.getFaultActor());
+ if (endpoint != null || method != null)
+ out.println ("When calling:");
+ if (endpoint != null)
+ out.println ("\t" + endpoint);
+ if (method != null)
+ out.println ("\t" + method);
+ out.println ("===========");
+ }
+
+
+}
From groscurt at dev.open-bio.org Wed Dec 3 15:21:13 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 10:21:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031521.mB3FLDqF013719@dev.open-bio.org>
groscurt
Wed Dec 3 10:21:13 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv13676/src/main/org/biomoby/service/dashboard
Modified Files:
SimpleClientPanel.java ServiceCallerModel.java
DashboardProperties.java
Log Message:
changes made for the authentication... without formatting this time
moby-live/Java/src/main/org/biomoby/service/dashboard SimpleClientPanel.java,1.13,1.14 ServiceCallerModel.java,1.7,1.8 DashboardProperties.java,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java 2008/11/26 08:54:21 1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/SimpleClientPanel.java 2008/12/03 15:21:12 1.14
@@ -1,791 +1,838 @@
-// SimpleClientPanel.java
-//
-// Created: December 2005
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.service.dashboard;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.util.Date;
-
-import javax.swing.BorderFactory;
-import javax.swing.Box;
-import javax.swing.ButtonGroup;
-import javax.swing.Icon;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JPasswordField;
-import javax.swing.JRadioButton;
-import javax.swing.JSplitPane;
-import javax.swing.JTextField;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import org.biomoby.service.dashboard.data.DataContainer;
-import org.biomoby.service.dashboard.data.ServiceInputPanel;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.tulsoft.shared.UUtils;
-import org.tulsoft.tools.gui.AwtUtils;
-import org.tulsoft.tools.gui.JFileChooserWithHistory;
-import org.tulsoft.tools.gui.JTextFieldWithHistory;
-import org.tulsoft.tools.gui.SwingUtils;
-
-/**
- * A panel allowing to formulate input data and to call an arbitrary Biomoby service. Its interface is however not that
- * user-friendly, and it is supposed to be used more or less for testing purposes in time when a new service is being
- * created and developed.
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-public class SimpleClientPanel extends AbstractPanel {
-
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory
- .getLog( SimpleClientPanel.class );
-
- /**
- * A property name. Its value contains a name of color that will be used to display service name.
- */
- protected static final String P_S_TITLE_COLOR = "simpleclient.service.title.color";
-
- /**
- * A property name. Its value contains a name of color that will be used as background for editable console with XML
- * input.
- */
- protected static final String P_S_EDIT_BGCOLOR = "simpleclient.service.edit.bgcolor";
-
- // some texts
- protected static final String INIT_SELECT = "
Start by selecting a service \n" + " ";
- data.setData( emptyMsg );
- input.setText( emptyMsg );
- }
-
- // finally, call the service
- stopButton.setEnabled( true );
- callerModel.runIt( data );
-
- }
- catch ( MobyException e ) {
- exception = e;
-
- }
- catch ( Error e ) {
- exception = new MobyException( e.toString() );
- }
- return null; // not used here
- }
-
- // runs on the event-dispatching thread
- public void finished() {
- if ( wasCancelled ) {
- // service was interrupted by the Stop button - do
- // nothing (the whole GUI should be already in a good
- // state - the button 'Stop' took care about it)
- return;
- }
-
- if ( exception == null ) {
-
- // handle results here (using renderers...)
- if ( propertyChannel.getString( DP_INP_PING ).toLowerCase().equals( "true" ) ) {
- propertyChannel.fire( DP_STATUS_MSG, service.getName() + " isAlive." );
- }
- else {
- propertyChannel.fire( DP_STATUS_MSG, "Service invocation finished." );
- }
-
- if ( !DP_CS_NONE.equals( propertyChannel.getString( DP_CALL_SERVICE ) ) ) {
- results.updateComponent( data );
- }
-
- }
- else {
- if ( propertyChannel.getString( DP_INP_PING ).toLowerCase().equals( "true" ) ) {
- propertyChannel.fire( DP_STATUS_MSG, service.getName() + " is dead." );
- results.removeResults();
- }
- else {
- propertyChannel.fire( DP_STATUS_MSG, "Service invocation failed." );
- error( CALLER_ERROR, exception );
- }
- exception.printStackTrace();
- }
- serviceFinished();
- }
- }
-
- /*******************************************************************************************************************
- * Called when a call to a service finished.
- ******************************************************************************************************************/
- protected void serviceFinished() {
- runButton.setEnabled( true );
- stopButton.setEnabled( false );
- }
-
- /*******************************************************************************************************************
- * Called when a service is selected in a service tree (or in a 'recently used services' combo box), and also at the
- * beginning when a service name is retrieved from user preferences.
- *
- * Get selected service from a registry model and generate a new 'input data panel' to reflect input data of the
- * selected service.
- ******************************************************************************************************************/
- protected void selectService( final String serviceName ) {
- final Object source = this;
- final SwingWorker worker = new SwingWorker() {
- MobyService service;
- MobyDataType[] dataTypes;
-
- public Object construct() {
- try {
- service = registryModel.getService( serviceName );
- dataTypes = registryModel.getDataTypes( source );
- }
- catch ( MobyException e ) {
- error( ServicesTree.SERVICES_ACCESS_ERROR, e );
- }
- return service; // not used here
- }
-
- // runs on the event-dispatching thread.
- public void finished() {
- if ( service == null ) {
- deselectService();
- }
- else {
- updateInputDataPanel( service, dataTypes );
- selService.setText( service.getName() );
- // selectionAllowed = false;
- // recentServices.setText (service.getName());
- // selectionAllowed = true;
- propertyChannel.put( DP_SC_SERVICE, service );
- runButton.setEnabled( true );
-
- }
- }
- };
- worker.start();
- }
-
- /*******************************************************************************************************************
- * Called when no service is selected in order to display this fact on various places in the panel.
- ******************************************************************************************************************/
- protected void deselectService() {
- selService.setText( "" );
- updateInputDataPanel( INIT_SELECT );
- propertyChannel.remove( DP_SC_SERVICE );
- runButton.setEnabled( false );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getName() {
- return "Simple Client";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getDescription() {
- return "A panel allowing to create input data and to call an arbitrary Biomoby service. "
- + "Its purpose is mostly for the service developers to test their new services.";
- }
-
- /*******************************************************************************************************************
- *
- * Customized tree of services...
- *
- ******************************************************************************************************************/
- protected class CustomServicesTree extends ServicesTree {
-
- /***************************************************************************************************************
- * Construtor
- **************************************************************************************************************/
- public CustomServicesTree( RegistryModel model, CommonConsole console ) {
- super( model, console );
- }
-
- /***************************************************************************************************************
- *
- **************************************************************************************************************/
- protected void createPopups( String title ) {
- super.createPopups( title );
- removeFromPopups( AC_RELOAD );
- removeSeparatorAfter( AC_COLLAPSE );
- }
-
- /***************************************************************************************************************
- * Service selected in a service tree...
- **************************************************************************************************************/
- protected void selected( DefaultMutableTreeNode node ) {
- if ( node == null ) {
- // nothing selected
- deselectService();
- return;
- }
- updateInputDataPanel( "Loading..." );
- selService.setText( "" );
- final CommonNode nodeObject = ( CommonNode ) node.getUserObject();
- String currentServiceName = nodeObject.getValue();
- selectService( currentServiceName );
- setPrefValue( DP_SC_SERVICE_NAME, currentServiceName );
- }
- }
-
-}
+// SimpleClientPanel.java
+//
+// Created: December 2005
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.service.dashboard;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.util.Date;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JPasswordField;
+import javax.swing.JRadioButton;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import org.biomoby.service.dashboard.data.DataContainer;
+import org.biomoby.service.dashboard.data.ServiceInputPanel;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.tulsoft.shared.UUtils;
+import org.tulsoft.tools.gui.AwtUtils;
+import org.tulsoft.tools.gui.JFileChooserWithHistory;
+import org.tulsoft.tools.gui.JTextFieldWithHistory;
+import org.tulsoft.tools.gui.SwingUtils;
+
+/**
+ * A panel allowing to formulate input data and to call an arbitrary
+ * Biomoby service. Its interface is however not that user-friendly,
+ * and it is supposed to be used more or less for testing purposes in
+ * time when a new service is being created and developed.
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class SimpleClientPanel
+ extends AbstractPanel {
+
+ private static org.apache.commons.logging.Log log =
+ org.apache.commons.logging.LogFactory.getLog (SimpleClientPanel.class);
+
+ /** A property name. Its value contains a name of color that will
+ * be used to display service name.
+ */
+ protected static final String P_S_TITLE_COLOR = "simpleclient.service.title.color";
+
+ /** A property name. Its value contains a name of color that will
+ * be used as background for editable console with XML input.
+ */
+ protected static final String P_S_EDIT_BGCOLOR = "simpleclient.service.edit.bgcolor";
+
+ // some texts
+ protected static final String INIT_SELECT =
+ "
Start by selecting a service \n" +
+ " ";
+ data.setData(emptyMsg);
+ input.setText(emptyMsg);
+ }
+
+ // finally, call the service
+ stopButton.setEnabled (true);
+ callerModel.runIt (data);
+
+ } catch (MobyException e) {
+ exception = e;
+
+ } catch (Error e) {
+ exception = new MobyException (e.toString());
+ }
+ return null; // not used here
+ }
+
+ // runs on the event-dispatching thread
+ public void finished() {
+ if (wasCancelled) {
+ // service was interrupted by the Stop button - do
+ // nothing (the whole GUI should be already in a good
+ // state - the button 'Stop' took care about it)
+ return;
+ }
+
+ if (exception == null) {
+
+ // handle results here (using renderers...)
+ if (propertyChannel.getString(DP_INP_PING).toLowerCase().equals("true")) {
+ propertyChannel.fire (DP_STATUS_MSG, service.getName()+" isAlive.");
+ } else {
+ propertyChannel.fire (DP_STATUS_MSG, "Service invocation finished.");
+ }
+
+ if (! DP_CS_NONE.equals (propertyChannel.getString (DP_CALL_SERVICE))) {
+ results.updateComponent (data);
+ }
+
+ } else {
+ if (propertyChannel.getString(DP_INP_PING).toLowerCase().equals("true")) {
+ propertyChannel.fire (DP_STATUS_MSG, service.getName()+" is dead.");
+ results.removeResults();
+ } else {
+ propertyChannel.fire (DP_STATUS_MSG, "Service invocation failed.");
+ error (CALLER_ERROR, exception);
+ }
+ exception.printStackTrace();
+ }
+ serviceFinished();
+ }
+ }
+
+ /**************************************************************************
+ * Called when a call to a service finished.
+ **************************************************************************/
+ protected void serviceFinished() {
+ runButton.setEnabled (true);
+ stopButton.setEnabled (false);
+ }
+
+ /**************************************************************************
+ * Called when a service is selected in a service tree (or in a
+ * 'recently used services' combo box), and also at the beginning
+ * when a service name is retrieved from user preferences.
+ *
+ * Get selected service from a registry model and generate a new
+ * 'input data panel' to reflect input data of the selected
+ * service.
+ **************************************************************************/
+ protected void selectService (final String serviceName) {
+ final Object source = this;
+ final SwingWorker worker = new SwingWorker() {
+ MobyService service;
+ MobyDataType[] dataTypes;
+ public Object construct() {
+ try {
+ service = registryModel.getService (serviceName);
+ dataTypes = registryModel.getDataTypes (source);
+ } catch (MobyException e) {
+ error (ServicesTree.SERVICES_ACCESS_ERROR, e);
+ }
+ return service; // not used here
+ }
+
+ // runs on the event-dispatching thread.
+ public void finished() {
+ if (service == null) {
+ deselectService();
+ } else {
+ updateInputDataPanel (service, dataTypes);
+ selService.setText (service.getName());
+// selectionAllowed = false;
+// recentServices.setText (service.getName());
+// selectionAllowed = true;
+ propertyChannel.put (DP_SC_SERVICE, service);
+ runButton.setEnabled (true);
+
+ }
+ }
+ };
+ worker.start();
+ }
+
+ /**************************************************************************
+ * Called when no service is selected in order to display this
+ * fact on various places in the panel.
+ **************************************************************************/
+ protected void deselectService() {
+ selService.setText ("");
+ updateInputDataPanel (INIT_SELECT);
+ propertyChannel.remove (DP_SC_SERVICE);
+ runButton.setEnabled (false);
+ }
+
+ /**************************************************************************
+ *
+ **************************************************************************/
+ public String getName() {
+ return "Simple Client";
+ }
+
+ /**************************************************************************
+ *
+ **************************************************************************/
+ public String getDescription() {
+ return
+ "A panel allowing to create input data and to call an arbitrary Biomoby service. " +
+ "Its purpose is mostly for the service developers to test their new services.";
+ }
+
+ /**************************************************************************
+ *
+ * Customized tree of services...
+ *
+ **************************************************************************/
+ protected class CustomServicesTree
+ extends ServicesTree {
+
+ /*********************************************************************
+ * Construtor
+ ********************************************************************/
+ public CustomServicesTree (RegistryModel model,
+ CommonConsole console) {
+ super (model, console);
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ protected void createPopups (String title) {
+ super.createPopups (title);
+ removeFromPopups (AC_RELOAD);
+ removeSeparatorAfter (AC_COLLAPSE);
+ }
+
+ /*********************************************************************
+ * Service selected in a service tree...
+ ********************************************************************/
+ protected void selected (DefaultMutableTreeNode node) {
+ if (node == null) {
+ // nothing selected
+ deselectService();
+ return;
+ }
+ updateInputDataPanel ("Loading...");
+ selService.setText ("");
+ final CommonNode nodeObject = (CommonNode)node.getUserObject();
+ String currentServiceName = nodeObject.getValue();
+ selectService (currentServiceName);
+ setPrefValue (DP_SC_SERVICE_NAME, currentServiceName);
+ }
+ }
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java 2008/11/26 08:54:21 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceCallerModel.java 2008/12/03 15:21:13 1.8
@@ -1,168 +1,180 @@
-// ServiceCallerModel.java
-//
-// Created: February 2006
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.service.dashboard;
-
-import org.apache.axis.client.Call;
-import org.biomoby.client.ExtendedProtocolClient;
-import org.biomoby.client.ExtendedServiceLocator;
-import org.biomoby.client.MobyServiceLocator;
-import org.biomoby.service.dashboard.data.DataContainer;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.parser.MobyJob;
-import org.biomoby.shared.parser.MobyPackage;
-import org.tulsoft.shared.UUtils;
-
-/**
- * A model that achieves its task by calling (local, remote, or none) Biomoby service. It delegates the task of calling
- * a service to a true Biomoby client (that extends BaseClient ).
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-public class ServiceCallerModel extends AbstractModel {
-
- // private static org.apache.commons.logging.Log log =
- // org.apache.commons.logging.LogFactory.getLog (ServiceCallerModel.class);
-
- /*******************************************************************************************************************
- * Call a service. This is the main purpose of this model.
- *
- *
- * @param data
- * contains input data and this method replaces them by result data
- ******************************************************************************************************************/
- public void runIt( DataContainer data ) throws MobyException {
- SimpleClient worker = new SimpleClient( data );
- worker.process();
- }
-
- /*******************************************************************************************************************
- *
- * A real client - the main worker for this model..
- *
- ******************************************************************************************************************/
- protected class SimpleClient extends ExtendedProtocolClient {
-
- DataContainer data;
-
- /***************************************************************************************************************
- * Constructor.
- **************************************************************************************************************/
- public SimpleClient( DataContainer data ) {
- super();
- this.data = data;
- }
-
- /***************************************************************************************************************
- * What service to call and where to find it.
- **************************************************************************************************************/
- public MobyServiceLocator getServiceLocator() throws MobyException {
- return new MyServiceLocator();
- }
-
- /***************************************************************************************************************
- * Not used here...
- **************************************************************************************************************/
- public boolean fillRequest( MobyJob request, MobyPackage inputContext ) throws MobyException {
- return true;
- }
-
- /***************************************************************************************************************
- * Not used here...
- **************************************************************************************************************/
- public boolean useResponse( MobyJob response, MobyPackage responseContext ) throws MobyException {
- return true;
- }
-
- /***************************************************************************************************************
- * Return input XML (from a data container obtained in the constructor).
- **************************************************************************************************************/
- public String fillRequest() throws MobyException {
-
- if ( data == null ) throw new MobyException( "No input data given." );
-
- return ( String ) data.getData();
- }
-
- /**
- * Sets the authentication for the service call. If the user has checked the corresponding box in the Dashboard
- * the values are stored in the propertychannel.
- */
- protected void setAuthentication( Call call ) {
- String user = propertyChannel.getString( DashboardProperties.DP_USER_AUTHENTICATION );
- if ( !isEmpty( user ) ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, new String( ( char[] ) propertyChannel
- .get( DashboardProperties.DP_PASSWORD_AUTHENTICATION ) ) );
- }
- }
-
- /***************************************************************************************************************
- *
- **************************************************************************************************************/
- public boolean useResponse( String xmlResponse ) throws MobyException {
-
- data.setData( xmlResponse );
-
- // do nothing more if it is just an input echo
- if ( ( ( ExtendedServiceLocator ) getServiceLocator() ).isLoop() ) return false;
-
- return false;
- }
- }
-
- /*******************************************************************************************************************
- *
- * A service locator filled from the property channel.
- *
- ******************************************************************************************************************/
- protected class MyServiceLocator extends ExtendedServiceLocator {
-
- public MyServiceLocator() throws MobyException {
- super();
-
- // fill this locator by a service
- MobyService selService = ( MobyService ) propertyChannel.get( DP_SC_SERVICE );
- if ( selService == null ) throw new MobyException( "No service given." );
- MobyService clonedService = new MobyService( selService.getName(), selService.getAuthority() );
- clonedService.setURL( selService.getURL() );
- setService( clonedService );
-
- // fill how to call this service
- String howToCall = propertyChannel.getString( DP_CALL_SERVICE );
- if ( DP_CS_NEWURL.equals( howToCall ) ) {
- String sEndpoint = propertyChannel.getString( DP_ENDPOINT );
- if ( !UUtils.isEmpty( sEndpoint ) ) clonedService.setURL( sEndpoint );
-
- }
- else if ( DP_CS_REGISTRY.equals( howToCall ) ) {
- clonedService.setURL( null );
- setRegistryEndpoint( propertyChannel.getString( DP_REGISTRY_ENDPOINT ) );
- setRegistryNamespace( propertyChannel.getString( DP_REGISTRY_NAMESPACE ) );
-
- }
- else if ( DP_CS_CLASS.equals( howToCall ) ) {
- String localClass = propertyChannel.getString( DP_IMPL_CLASS );
- if ( UUtils.isEmpty( localClass ) ) throw new MobyException( "No local class given." );
- setLocalClass( localClass );
-
- }
- else if ( DP_CS_NONE.equals( howToCall ) ) {
- setLoop( true );
- }
-
- setAsBytes( propertyChannel.getBoolean( DP_INP_ASBYTES, false ) );
-
- }
- }
-
-}
+// ServiceCallerModel.java
+//
+// Created: February 2006
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.service.dashboard;
+
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.parser.MobyPackage;
+import org.biomoby.shared.parser.MobyJob;
+import org.biomoby.client.ExtendedProtocolClient;
+import org.biomoby.client.MobyServiceLocator;
+import org.biomoby.client.ExtendedServiceLocator;
+import org.biomoby.service.dashboard.data.DataContainer;
+
+import org.tulsoft.shared.UUtils;
+
+/**
+ * A model that achieves its task by calling (local, remote, or none)
+ * Biomoby service. It delegates the task of calling a service to a
+ * true Biomoby client (that extends BaseClient ).
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+public class ServiceCallerModel
+ extends AbstractModel {
+
+// private static org.apache.commons.logging.Log log =
+// org.apache.commons.logging.LogFactory.getLog (ServiceCallerModel.class);
+
+ /**************************************************************************
+ * Call a service. This is the main purpose of this model.
+ *
+ * @param data contains input data and this method replaces them
+ * by result data
+ *************************************************************************/
+ public void runIt (DataContainer data)
+ throws MobyException {
+ SimpleClient worker = new SimpleClient (data);
+ worker.process();
+ }
+
+ /**************************************************************************
+ *
+ * A real client - the main worker for this model..
+ *
+ *************************************************************************/
+ protected class SimpleClient
+ extends ExtendedProtocolClient {
+
+ DataContainer data;
+
+ /**************************************************************************
+ * Constructor.
+ *************************************************************************/
+ public SimpleClient (DataContainer data) {
+ super();
+ this.data = data;
+ }
+
+ /**************************************************************************
+ * What service to call and where to find it.
+ *************************************************************************/
+ public MobyServiceLocator getServiceLocator()
+ throws MobyException {
+ return new MyServiceLocator();
+ }
+
+ /**************************************************************************
+ * Not used here...
+ *************************************************************************/
+ public boolean fillRequest (MobyJob request, MobyPackage inputContext)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * Not used here...
+ *************************************************************************/
+ public boolean useResponse (MobyJob response,
+ MobyPackage responseContext)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * Return input XML (from a data container obtained in the
+ * constructor).
+ *************************************************************************/
+ public String fillRequest()
+ throws MobyException {
+
+ if (data == null)
+ throw new MobyException ("No input data given.");
+
+ return (String)data.getData();
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean useResponse (String xmlResponse)
+ throws MobyException {
+
+ data.setData (xmlResponse);
+
+ // do nothing more if it is just an input echo
+ if ( ((ExtendedServiceLocator)getServiceLocator()).isLoop())
+ return false;
+
+ return false;
+ }
+ }
+
+ /**************************************************************************
+ *
+ * A service locator filled from the property channel.
+ *
+ *************************************************************************/
+ protected class MyServiceLocator
+ extends ExtendedServiceLocator {
+
+ public MyServiceLocator()
+ throws MobyException {
+ super();
+
+ // fill this locator by a service
+ MobyService selService = (MobyService)propertyChannel.get (DP_SC_SERVICE);
+ if (selService == null)
+ throw new MobyException ("No service given.");
+ MobyService clonedService = new MobyService (selService.getName(), selService.getAuthority());
+ clonedService.setURL (selService.getURL());
+ setService (clonedService);
+
+ // fill how to call this service
+ String howToCall = propertyChannel.getString (DP_CALL_SERVICE);
+ if (DP_CS_NEWURL.equals (howToCall)) {
+ String sEndpoint = propertyChannel.getString (DP_ENDPOINT);
+ if (! UUtils.isEmpty (sEndpoint))
+ clonedService.setURL (sEndpoint);
+
+ } else if (DP_CS_REGISTRY.equals (howToCall)) {
+ clonedService.setURL (null);
+ setRegistryEndpoint (propertyChannel.getString (DP_REGISTRY_ENDPOINT));
+ setRegistryNamespace (propertyChannel.getString (DP_REGISTRY_NAMESPACE));
+
+ } else if (DP_CS_CLASS.equals (howToCall)) {
+ String localClass = propertyChannel.getString (DP_IMPL_CLASS);
+ if (UUtils.isEmpty (localClass))
+ throw new MobyException ("No local class given.");
+ setLocalClass (localClass);
+
+ } else if (DP_CS_NONE.equals (howToCall)) {
+ setLoop (true);
+ }
+
+ setAsBytes (propertyChannel.getBoolean (DP_INP_ASBYTES, false));
+
+ // sets the user and the password
+ // the getString method returns an empty string in case the
+ // key is not in the propertychannel, therefore the test if
+ // the value is not empty
+ String user = propertyChannel.getString(DP_USER_AUTHENTICATION);
+ if(user.length() > 0) {
+ setUser( user );
+ }
+ String password = propertyChannel.getString(DP_PASSWORD_AUTHENTICATION);
+ if(password.length() > 0) {
+ setPassword( password );
+ }
+ }
+ }
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java 2008/11/26 08:54:21 1.30
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DashboardProperties.java 2008/12/03 15:21:13 1.31
@@ -9,10 +9,10 @@
package org.biomoby.service.dashboard;
/**
- * A list of names of most/all recognized properties that can be fired by dashboard panels, and a list of names of Java
- * properties that can be used to configure the dashboard.
- *
- *
+ * A list of names of most/all recognized properties that can be fired
+ * by dashboard panels, and a list of names of Java properties that
+ * can be used to configure the dashboard.
+ *
* @author Martin Senger
* @version $Id$
*/
@@ -44,9 +44,9 @@
static final String DP_FL_BIOCASE = "biocase";
static final String DP_FL_HIBERNATE = "hibernate";
- static final String DP_SEL_SERVICES = "selectedServices"; // type: Vector with service/authority name
- static final String DP_SEL_AUTHORITIES = "selectedAuthorities"; // type: Vector with authority name
- static final String DP_DEPL_SERVICES = "servicesToDeploy"; // type: Map with serviceName => className
+ static final String DP_SEL_SERVICES = "selectedServices"; // type: Vector with service/authority name
+ static final String DP_SEL_AUTHORITIES = "selectedAuthorities"; // type: Vector with authority name
+ static final String DP_DEPL_SERVICES = "servicesToDeploy"; // type: Map with serviceName => className
static final String DP_LOCAL_DEPLOY = "use-local-deploy";
static final String DP_TOMCAT_HOME = "tomcatHome";
@@ -82,10 +82,10 @@
static final String DP_DETACH_VIEW = "detachViewers";
- // static final String DP_SC_IN_DATA = "sc-inputData";
+// static final String DP_SC_IN_DATA = "sc-inputData";
static final String DP_SC_IN_FILE = "sc-inputFromFile";
static final String DP_SC_INPUT_FILE = "sc-inputFile";
- static final String DP_SC_SERVICE = "dp-sc-service"; // type: MobyService
+ static final String DP_SC_SERVICE = "dp-sc-service"; // type: MobyService
static final String DP_SC_SERVICE_NAME = "dp-sc-service-name";
static final String DP_SC_SERVICES = "dp-sc-recent-services";
@@ -97,21 +97,21 @@
static final String DP_DATATYPE_NAME = "dp-datatype-name";
// names of properties used in property channel storage
- static final String DP_REGISTRY_MODEL = "dp-registry-model"; // type: RegistryModel
- static final String DP_ANT_MODEL = "dp-ant-model"; // type: AntModel
+ static final String DP_REGISTRY_MODEL = "dp-registry-model"; // type: RegistryModel
+ static final String DP_ANT_MODEL = "dp-ant-model"; // type: AntModel
static final String DP_REGISTRY_SYNONYM = "dp-registry-synonym";
- static final String DP_REG_INFO = "dp-reg-info"; // type: Boolean
+ static final String DP_REG_INFO = "dp-reg-info"; // type: Boolean
static final String DP_REGISTRY_ENDPOINT = "dp-registry-endpoint";
static final String DP_REGISTRY_NAMESPACE = "dp-registry-namespace";
static final String DP_CACHE_DIR = "dp-cache-dir";
- static final String DP_USE_CACHE = "dp-use-cache"; // type: Boolean
+ static final String DP_USE_CACHE = "dp-use-cache"; // type: Boolean
static final String DP_REG_DT_NAME = "dp-reg-dt-name";
static final String DP_REG_DT_AUTH = "dp-reg-dt-auth";
static final String DP_REG_DT_EMAIL = "dp-reg-dt-email";
static final String DP_REG_DT_DESC = "dp-reg-dt-desc";
- static final String DP_REG_DT_TREE = "dp-reg-dt-tree"; // type: MobyDataType
+ static final String DP_REG_DT_TREE = "dp-reg-dt-tree"; // type: MobyDataType
static final String DP_REG_NS_NAME = "dp-reg-ns-name";
static final String DP_REG_NS_AUTH = "dp-reg-ns-auth";
@@ -132,88 +132,97 @@
static final String DP_REG_S_RDF_URL = "dp-reg-s-rdf-url";
static final String DP_REG_S_RDF_PATH = "dp-reg-s-rdf-path";
static final String DP_REG_S_XML_PATH = "dp-reg-s-xml-path";
- static final String DP_USE_SIGNATURE = "dp-use-signature"; // type: Boolean
- static final String DP_USE_AUTHORITATIVE = "dp-use-auth"; // type: Boolean
+ static final String DP_USE_SIGNATURE = "dp-use-signature"; // type: Boolean
+ static final String DP_USE_AUTHORITATIVE = "dp-use-auth"; // type: Boolean
static final String DP_REG_S_TYPE = "dp-reg-s-type";
static final String DP_REG_VERBOSE = "dp-reg-verbose";
- static final String DP_S_SELECTED = "dp-s-selected"; // type: MobyService
+ static final String DP_S_SELECTED = "dp-s-selected"; // type: MobyService
- /**
- * A property name. Its value contains a title that will appear in big fonts on top of the dashboard. It may be
- * empty if property {@link #DP_TITLE_ICON} is defined; otherwise a default value will be used.
+ /** A property name. Its value contains a title that will appear
+ * in big fonts on top of the dashboard. It may be empty if
+ * property {@link #DP_TITLE_ICON} is defined; otherwise a default
+ * value will be used.
*/
static final String DP_TITLE = "dashboard.title";
- /**
- * A property name. Its value contains a filename with an icon accompanying a dashboard title (defined by property
- * {@link #DP_TITLE}. No default value used. Specify here either an absolute path (not recommended) or a relative
- * path whose beginning can be found somewhere on the CLASSPATH.
+ /** A property name. Its value contains a filename with an icon
+ * accompanying a dashboard title (defined by property {@link
+ * #DP_TITLE}. No default value used. Specify here either an
+ * absolute path (not recommended) or a relative path whose
+ * beginning can be found somewhere on the CLASSPATH.
*/
static final String DP_TITLE_ICON = "dashboard.title.icon";
- /**
- * A property name. Its value contains a filename with the main dashboard icon. Specify here either an absolute path
- * (not recommended) or a relative path whose beginning can be found somewhere on the CLASSPATH.
+ /** A property name. Its value contains a filename with the main
+ * dashboard icon. Specify here either an absolute path (not
+ * recommended) or a relative path whose beginning can be found
+ * somewhere on the CLASSPATH.
*/
static final String DP_ICON = "dashboard.icon";
- /**
- * A property name. Its value contains a color name used to paint main dashboard background. The name can be a color
- * name, or a number in various format (see GraphColours for details).
+ /** A property name. Its value contains a color name used to paint
+ * main dashboard background. The name can be a color name, or a
+ * number in various format (see GraphColours for
+ * details).
*/
static final String DP_BGCOLOR = "dashboard.bgcolor";
- /**
- * A property name. Its value contains a short description what a dashboard can do generally. Often, however, it is
- * more convenient to put the description in a file and to use property {@link #DP_DESCRIPTION_FILE}.
+ /** A property name. Its value contains a short description what a
+ dashboard can do generally. Often, however, it is more
+ convenient to put the description in a file and to use
+ property {@link #DP_DESCRIPTION_FILE}.
*/
static final String DP_DESCRIPTION = "dashboard.description";
- /**
- * A property name. Its value contains a file name with a short description what a dashboard can do generally.
+ /** A property name. Its value contains a file name with a short
+ description what a dashboard can do generally.
*/
static final String DP_DESCRIPTION_FILE = "dashboard.description.file";
- /**
- * A property name. Its value contains a short description of a project that uses this dashboard. Often, however, it
- * is more convenient to put the description in a file and to use property {@link #DP_P_DESCRIPTION_FILE}.
+ /** A property name. Its value contains a short description of a
+ project that uses this dashboard. Often, however, it is more
+ convenient to put the description in a file and to use
+ property {@link #DP_P_DESCRIPTION_FILE}.
*/
static final String DP_P_DESCRIPTION = "project.description";
- /**
- * A property name. Its value contains a file name with a short description of a project that uses this dashboard.
+ /** A property name. Its value contains a file name with a short
+ description of a project that uses this dashboard.
*/
static final String DP_P_DESCRIPTION_FILE = "project.description.file";
- /**
- * A property name. Its value contains a name of a contact person, possibly with an email address.
+ /** A property name. Its value contains a name of a contact
+ person, possibly with an email address.
*/
static final String DP_CONTACT = "dashboard.contact";
- /**
- * A property name. Its value contains a directory name with the local cache of a BiMoby Central registry.
+ /** A property name. Its value contains a directory name with the
+ * local cache of a BiMoby Central registry.
*/
static final String DP_REGISTRY_CACHE_DIR = "registry.cache.dir";
- /**
- * A property name. Its value contains a name or a comma-separated list of names of BioMoby registries that will be
- * displayed in the RegistryPanel. If this property is missing, the list is taken from the hard-coded known
- * registries in the Java source file.
- *
- *
- * The names (values of this property) are equivalent to the 'synonym' attribute of the Registry class.
+ /** A property name. Its value contains a name or a
+ * comma-separated list of names of BioMoby registries that will
+ * be displayed in the RegistryPanel. If this property is missing,
+ * the list is taken from the hard-coded known registries in the
+ * Java source file.
+ *
+ * The names (values of this property) are equivalent to the
+ * 'synonym' attribute of the Registry class.
*/
static final String DP_WANTED_REGISTRIES = "dashboard.wanted.registries";
- /**
- * A property name. Its value contains a name (synonym) of a default BioMoby registry. By default, the default
- * registry is taken either from the first element in {@link #DP_WANTED_REGISTRIES} or from
+ /** A property name. Its value contains a name (synonym) of a
+ * default BioMoby registry. By default, the default registry is
+ * taken either from the first element in {@link
+ * #DP_WANTED_REGISTRIES} or from
* Registries.DEFAULT_REGISTRY_SYNONYM .
*/
static final String DP_DEFAULT_REGISTRY = "dashboard.default.registry";
+
/**
* A property name. Its value contains the user name used for the authentication required for the servlet container
* the service is hosted at.
From groscurt at dev.open-bio.org Wed Dec 3 15:21:13 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 10:21:13 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031521.mB3FLD8Y013747@dev.open-bio.org>
groscurt
Wed Dec 3 10:21:13 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv13676/src/main/org/biomoby/client
Modified Files:
MobyRequest.java BaseClient.java MobyServiceLocator.java
Log Message:
changes made for the authentication... without formatting this time
moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.41,1.42 BaseClient.java,1.13,1.14 MobyServiceLocator.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/11/26 08:53:43 1.41
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/12/03 15:21:13 1.42
@@ -1,1028 +1,1030 @@
-
-package org.biomoby.client;
-
-import java.io.*;
-import java.util.*;
-
-import javax.xml.namespace.QName;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.rpc.Service;
-import javax.xml.transform.TransformerException;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.message.MessageElement;
-import org.apache.xml.utils.PrefixResolver;
-import org.apache.xml.utils.PrefixResolverDefault;
-import org.apache.xpath.XPath;
-import org.apache.xpath.XPathContext;
-import org.apache.xpath.objects.XNodeSet;
-import org.apache.xpath.objects.XObject;
-
-import org.biomoby.shared.*;
-import org.biomoby.shared.data.*;
-import org.biomoby.shared.parser.MobyTags; // defined the Moby XML element names
-import org.biomoby.w3c.addressing.EndpointReference;
-import org.omg.lsae.notifications.AnalysisEvent;
-
-import org.w3c.dom.*;
-
-/**
- * This class handles the WSDL transaction to request a response from a remote SOAP Web service that handles the MOBY format. It depends on having already retrieved the definition of the Web
- * service via the MOBY central registry using the jMOBY
- * API, and for now it uses the Apache Axis Web services framework,
- * as well as Apache Xalan. There are code comments for the few lines that rely on Axis classes rather than the JAX-RPC
- * interfaces.
- *
- * @author Paul Gordon gordonp at ucalgary.ca
- */
-public class MobyRequest {
-
- protected MobyService mobyService = null;
- protected MobyContentInstance inputData = null;
- protected MobyContentInstance outputData = null;
- protected Central mobyCentral = null;
- protected PrefixResolver mobyPrefixResolver = null;
-
- protected Hashtable wsdlCache = null;
- protected String lastWsdlCacheKey = null;
- protected DocumentBuilder docBuilder = null;
- protected Service service = null;
-
- protected Class stringType;
- protected static boolean debug = false;
- protected PrintStream debugPS = System.err;
- protected XPathContext xpath_context;
- protected String responseString = null;
-
- private XPath stringEncodedXPath;
- private XPath base64EncodedXPath;
- private XPath simpleChildXPath;
- private XPath collectionChildXPath;
-
- private int autoID = 0;
-
- // Used as invocation callback if MobyRequest is acting as a server,
- // or is executing services as a client asynchronously
- private Vector< MobyRequestEventHandler > eventHandlers;
-
- private String user;
- private String password;
-
- /**
- * Default constructor. You should have a Central instance around since you're going to be retrieving MobyServices
- * to pass into here. Lets reuse it.
- *
- * @param central An instance of a Moby central object so we can make requests about object types, etc.
- * @throws ParserConfigurationException if JAXP doesn't have any valid DOM-building XML parsers set up for use
- */
- public MobyRequest( Central central ) throws ParserConfigurationException {
- mobyCentral = central;
- wsdlCache = new Hashtable();
-
- eventHandlers = new Vector< MobyRequestEventHandler >();
-
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware( true );
- docBuilder = dbf.newDocumentBuilder();
-
- try {
- stringType = Class.forName( "java.lang.String" );
- }
- catch ( ClassNotFoundException classe ) {
- debugPS.println( "WARNING: Something is very wrong, could not find Class definition of String: " + classe );
- }
-
- xpath_context = new XPathContext();
- mobyPrefixResolver = new MobyPrefixResolver();
-
- // Now compile the XPath statements that will be used fetch data from the server response
- try {
- base64EncodedXPath = new XPath( "//*[starts-with(substring-after(@" + MobyPrefixResolver.XSI1999_PREFIX
- + ":type, ':'), \"base64\") or starts-with(substring-after(@" + MobyPrefixResolver.XSI2001_PREFIX
- + ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT );
- stringEncodedXPath = new XPath( "//*[substring-after(@" + MobyPrefixResolver.XSI1999_PREFIX
- + ":type, ':')=\"string\" or substring-after(@" + MobyPrefixResolver.XSI2001_PREFIX
- + ":type, ':')=\"string\"] | //" + MobyPrefixResolver.SOAP_ENC_PREFIX + ":string", null,
- mobyPrefixResolver, XPath.SELECT );
- simpleChildXPath = new XPath( "moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT );
- collectionChildXPath = new XPath( "moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT );
- }
- catch ( TransformerException te ) {
- debugPS.println( "Syntax error encountered while compiling XPath "
- + "statements for internal use (code bug?): " + te );
- }
- setDebugMode( System.getProperty( "moby.debug" ) != null );
- }
-
- /**
- * @param mode if true, debugging information is printed to the stream returned by getDebugOutputStream
- */
- public void setDebugMode(boolean mode) {
- debug = mode;
- }
-
- /**
- * Standard error is used unless this method is called.
- *
- * @param ps the OutputStream to which debugging information is sent.
- * @throws IllegalArgumentException if the stream is null
- */
- public void setDebugPrintStream(PrintStream ps) throws IllegalArgumentException {
- if ( ps == null ) {
- throw new IllegalArgumentException( "The OutputStream specified to MobyRequest was null" );
- }
- debugPS = ps;
- }
-
- /**
- * @param user the user for a possible service authentication
- * @param password the passoword for a possible service authentication
- */
- public void setAuthentication(String user, String password) {
- this.user = user;
- this.password = password;
- }
-
- /**
- * @return the instance of the class implementing Central that we are using
- */
- public Central getCentralImpl() {
- return mobyCentral;
- }
-
- /**
- * @param mobyservice the MobyService that should be executed when invokeService is called
- */
- public void setService(MobyService mobyservice) {
- if ( mobyservice == null ) {
- mobyService = null;
- }
- else if ( mobyService == null || !mobyservice.equals( mobyService ) ) {
- mobyService = mobyservice;
- }
- }
-
- /**
- * @return the MobyService that will be executed when invokeService is called
- */
- public MobyService getService() {
- return mobyService;
- }
-
- /**
- * @return the Raw MOBY XML response as a string
- */
- public String getResponseXML() {
- return responseString;
- }
-
- /**
- * Sets the input data for the MOBY service request. The length of the input array, and the number of input
- * parameters required by the service must be equal when invokeService() is called. This method strictly enforces
- * that the input be of the appropriate type for the service.
- *
- * Note that there is no requirement to use MobyDataInstance.setXmlMode() before passing in data, this class will
- * temporarily set the XML mode of the data when it is required.
- *
- * @throws IllegalArgumentException if the input does not fit the criteria of the service (e.g. wrong data type)
- */
- public void setInput(MobyContentInstance data) throws MobyException {
- inputData = data;
- }
-
- /**
- * Takes the data in the array, with their current articleNames, as input for the service
- */
- public void setInput(MobyDataInstance[] data) throws MobyException {
- MobyDataJob job = new MobyDataJob();
- for ( MobyDataInstance param : data ) {
- job.put( param.getName(), param );
- }
- inputData = new MobyContentInstance();
- inputData.put( job );
- }
-
- /**
- * Convenience method to run services that take one argument. If the service requires the input to have a name, it
- * will be automatically assigned.
- */
- public void setInput(MobyDataInstance datum) throws MobyException {
- setInput( datum, "" );
- }
-
- /**
- * Convenience method to run services that take one named argument.
- */
- public void setInput(MobyDataInstance datum, String paramName) throws MobyException {
- inputData = new MobyContentInstance( datum, paramName );
- }
-
- /**
- * @return the MobyService that will be executed when invokeService is called
- */
- public MobyContentInstance getInput() {
- return inputData;
- }
-
- /**
- * Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
- */
- public void setSecondaryInput(Collection< MobyDataSecondaryInstance > secondaryData) throws MobyException {
- setSecondaryInput( secondaryData.toArray( new MobyDataSecondaryInstance[ secondaryData.size() ] ) );
- }
-
- /**
- * This method will assign the provided secondary parameters to all primary input data currently in this object.
- * This is covenient if you are running 100 seqs through BLAST and only want to set the parameters once. If you
- * instead want to set secondary input differently for all primary inputs, you'll need to create a custom
- * MobyContentInstance as input to setInput().
- *
- * @throws MobyException if a parameter name is blank, or overrides a primary parameter
- */
- public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException {
-
- Iterator queryNames = inputData.keySet().iterator();
- // For each query
- while (queryNames.hasNext()) {
- MobyDataJob queryParams = inputData.get( queryNames.next() );
- // Set all the secondary params (overwrites any old ones)
- for ( int i = 0; i < secondaryData.length; i++ ) {
- String secName = secondaryData[ i ].getName();
- if ( secName == null || secName.length() == 0 ) {
- throw new MobyException( "A secondary parameter cannot have a blank name (array index " + i + ")" );
- }
- if ( queryParams.containsKey( secName ) && queryParams.get( secName ) instanceof MobyPrimaryData ) {
- throw new MobyException( "A secondary parameter cannot override an existing primary parameter "
- + "with the same name (" + secName + ")" );
- }
- queryParams.put( secName, secondaryData[ i ] );
- }
- }
- }
-
- /**
- * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the
- * correspondingly indexed input request.
- *
- * @throws MobyException if you try to get the results before calling InvokeService
- */
- public MobyContentInstance getOutput() throws MobyException {
- if ( outputData == null ) {
- throw new MobyException( "Trying to access MOBY service results " + "before the service is invoked" );
- }
- else {
- return outputData;
- }
- }
-
- /**
- * The main method of the class. If all of the MOBY input objects are properly defined according to the Web service
- * definition, a SOAP request will be sent to the remote server, and the method will return one or more MOBY objects
- * (synchronous). Call this method after calling setService, and setInput. If you do not call setSecondaryInput, the
- * default secondary parameter values will be used.
- *
- * @return the results of the remote Web service in response to the give input
- *
- * @throws MobyException i.e. there was something wrong with the input, output or remote service's logic
- * @throws SOAPException i.e. there was a problem with the underlying transaction/transport layer
- */
- public MobyContentInstance invokeService() throws Exception, MobyException, SOAPException, NoSuccessException {
- return mobyService.isAsynchronous()
- ? invokeService( inputData, new StringBuffer() )
- : invokeService( inputData, ( StringBuffer ) null );
- }
-
- // Used internally for asynchronous thread calls that all need the XML data
- // and can't rely on the answer from thread-insensitive getResponseXML()
- private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML) throws Exception,
- MobyException, SOAPException, NoSuccessException {
- return invokeService( inData, contentsXML, null, 0 );
- }
-
- private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML,
- MobyRequestEventHandler handler, int requestId) throws Exception, MobyException, SOAPException,
- NoSuccessException {
-
- if ( mobyService == null ) {
- throw new MobyException( "Tried to invoke null service from MobyRequest (call setService first)" );
- }
-
- Element mobyDOM = null;
- if ( mobyService.isAsynchronous() ) {
- // Async is "simpler", because it had to merge DOMs together into a single MobyContentInstance anyway
- MobyContentInstance mci = performAsyncSOAPRequest( mobyService, inData, handler, requestId );
- StringWriter writer = new StringWriter();
- MobyDataUtils.toXMLDocument( writer, mci );
- contentsXML.append( writer.toString() );
- return mci;
- }
- else {
- String mobyXML = convertMOBYDataToMOBYRequest( inData );
- Call call = getServiceFromWSDL();
- if ( user != null && password != null ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, password );
- }
- mobyDOM = performSOAPRequest( call, mobyXML, contentsXML );
- // The following parses the DOM and extracts all the appropriate jMOBY objects to represent the XML in Java
- return MobyDataUtils.fromXMLDocument( mobyDOM, mobyService.getServiceType().getRegistry() );
- }
- }
-
- protected MobyContentInstance performAsyncSOAPRequest(MobyService mservice, MobyContentInstance inData,
- MobyRequestEventHandler handler, int requestId) throws Exception {
- String mobyXML = convertMOBYDataToMOBYRequest( inData );
- EndpointReference epr = AsyncClient.sendRequest( mservice, mobyXML );
-
- // Essentially cloning, so removing ids doesn't change the
- // MobyContentInstance "data" (which we will use again later on)
- MobyContentInstance finalContents = new MobyContentInstance();
- Set< String > queryIDs = new HashSet< String >( inData.keySet() );
- try {
- // Should add some timeout here...
- while (!queryIDs.isEmpty()) {
- // todo: make this setable
- Thread.sleep( 5000 );
-
- AnalysisEvent[] events = AsyncClient.poll( epr, queryIDs );
-
- Vector< String > newDataAvailable = new Vector< String >();
- for ( AnalysisEvent event : events ) {
- if ( event != null && event.isCompleted() ) {
- queryIDs.remove( event.getQueryId() );
- newDataAvailable.add( event.getQueryId() );
- }
- }
-
- if ( newDataAvailable.size() > 0 ) {
- // Parse and merge the new data into the existing contents
- InputStream resultStream = AsyncClient.getResultStream( epr, newDataAvailable );
- Element mobyDOM = asyncSoapTextToMobyDOM( resultStream );
- MobyContentInstance newResults = MobyDataUtils.fromXMLDocument( mobyDOM,
- mservice.getServiceType()
- .getRegistry() );
- // The merge
- for ( String jobid : newResults.keySet() ) {
- finalContents.put( jobid, newResults.get( jobid ) );
- }
-
- // Inform the handler that some data has been added to the response (for incremental display?)
- if ( handler != null ) {
- MobyRequestEvent mre = new MobyRequestEvent( finalContents, this, mservice, null, requestId );
- StringWriter xmlWriter = new StringWriter();
- MobyDataUtils.toXMLDocument( xmlWriter, finalContents );
-
- mre.setContentsXML( xmlWriter.toString() );
- if ( !queryIDs.isEmpty() ) {
- // Send an update event only if we aren't finished yet.
- // If we are finished, the client is going to get this event as the
- // invocation thread finishes up (no need to double up).
- handler.processEvent( mre );
- }
- }
- }
- }
- }
- catch ( Exception e ) {
- e.printStackTrace();
- AsyncClient.destroy( epr );
- throw new Exception( "Exception occured while polling the service invocation: " + e );
- }
-
- return finalContents;
- }
-
- private Element asyncSoapTextToMobyDOM(InputStream inStream) throws Exception {
- Element soapDOM = null;
- synchronized ( docBuilder ) {
- soapDOM = docBuilder.parse( inStream ).getDocumentElement();
- }
- final boolean IS_ASYNC_SERVICE_CALL = true;
- return decodeSOAPMessage( soapDOM, null, null, IS_ASYNC_SERVICE_CALL );
- }
-
- /**
- * Asynchronous call to invokeService. A callback to the passed-in handler will be made when the response is ready,
- * or there is an exception.
- *
- * @return the id that the callback event will return from getID(), allowing a client to distinguish between
- * multiple concurrent invocation callbacks
- */
- public synchronized int invokeService(MobyRequestEventHandler handler) {
- int id = autoID++;
-
- Thread t = new InvocationThread( this, inputData, handler, id ); // see internal class definition below
- t.start();
-
- return id;
- }
-
- // This is the class that asynchronously calls the service and does a callback to
- // the handler specified in the invocation.
- class InvocationThread extends Thread {
- MobyContentInstance data;
- MobyService mservice;
- MobyRequest mobyRequest;
- MobyRequestEventHandler handler;
- int requestId;
-
- InvocationThread( MobyRequest mr, MobyContentInstance inData, MobyRequestEventHandler h, int id ) {
- data = inData;
- mobyRequest = mr;
- mservice = mobyRequest.getService();
- handler = h;
- requestId = id;
-
- // Name the thread after the service being run, mostly for ease of debugging
- setName( mservice.getName() + requestId );
- }
-
- public void run() {
- MobyRequestEvent requestEvent = new MobyRequestEvent( data, mobyRequest, mservice, null, requestId );
- // Tell the handler we're starting the request, with the given data
- handler.start( requestEvent );
-
- MobyRequestEvent responseEvent = null;
- MobyContentInstance content = null;
- StringBuffer contentsXML = new StringBuffer(); // to be filled in by the RPC call below
- try {
- content = mobyRequest.invokeService( data, contentsXML, handler, requestId ); // RPC call...
- }
- catch ( Exception e ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, e, requestId );
- }
- catch ( Error err ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, err, requestId );
- }
- if ( responseEvent == null ) {
- responseEvent = new MobyRequestEvent( content, mobyRequest, mservice, null, requestId );
- }
- // We've got the raw XML laying around, so why not provide it unmolested to the callback?
- responseEvent.setContentsXML( contentsXML.toString() );
- handler.processEvent( responseEvent );
- handler.stop( mobyRequest, requestId );
- }
- }
-
- public void addEventHandler(MobyRequestEventHandler h) {
- eventHandlers.add( h );
- }
-
- public void removeEventHandler(MobyRequestEventHandler h) {
- eventHandlers.remove( h );
- }
-
- public void sendResponse(MobyRequestEvent mre) {
- // Not yet implemented, need to conform to some web.xml specification here...
- }
-
- /**
- * This method retrieves from Moby Central a copy of the WSDL document for the service (or uses an internally cached
- * copy from a previous invocation), and sets the variables for the SOAP call appropriately so you can consequently
- * call performSOAPRequest.
- */
- protected Call getServiceFromWSDL() throws MobyException, NoSuccessException {
- // String wsdl = null;
-
- // // Since this is how we retrieve a service from Central, use the same values as the key to the hash
- // String wsdlCacheKey = mobyService.getName() + "@" + mobyService.getAuthority();
-
- // // This is the same call as last time, so we don't need to change the setup
- // if(wsdlCacheKey.equals(lastWsdlCacheKey)){
- // return setCallFromWSDL((String) wsdlCache.get(wsdlCacheKey));
- // }
- // // We haven't encountered this service yet
- // else if(!wsdlCache.containsKey(wsdlCacheKey)){
- // wsdl = mobyCentral.getServiceWSDL(mobyService.getName(), mobyService.getAuthority());
- // wsdlCache.put(wsdlCacheKey, wsdl);
- // }
- // // We've dealt with this one before
- // else{
- // wsdl = (String) wsdlCache.get(wsdlCacheKey);
- // }
-
- // lastWsdlCacheKey = wsdlCacheKey; // Keep track of the last invocation
-
- // Get ready to do SOAP
- return setCallFromWSDL( null );
- }
-
- /**
- * Creates the SOAP Call that will be invoked later. This should be based on the WSDL document and parameter
- * information from the MobyService, but these are currently not up to snuff.
- */
- protected Call setCallFromWSDL(String wsdl) throws MobyException, SOAPException {
- if ( service == null ) {
- service = new org.apache.axis.client.Service(); // AXIS SPECIFIC This acts as a factory for Calls
- }
-
- Call soapCall;
- try {
- soapCall = ( Call ) service.createCall();// create a fresh Call each time
- }
- catch ( javax.xml.rpc.ServiceException se ) {
- throw new SOAPException( "Could not instatiate call to SOAP Service: " + se );
- }
-
- // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll
- // have to do the call's info setting manually.
- // ((org.apache.axis.client.Call) soapCall).setSOAPService(soapService);
- soapCall.removeAllParameters();
- soapCall.setTargetEndpointAddress( mobyService.getURL() );
- soapCall.setPortName( new QName( "http://biomoby.org/", mobyService.getName() + "PortType" ) );
- // soapCall.setOperationName(new QName("http://biomoby.org/",
- // mobyService.getName()));
- soapCall.setSOAPActionURI( "http://biomoby.org/#" + mobyService.getName() );
- return soapCall;
- }
-
- /**
- * Calls the invoke() method of the JAX-RPC Call interface.
- */
- protected Element performSOAPRequest(Call soapCall, String mobyInputXML, StringBuffer contentsXMLOutput)
- throws SOAPException {
- // First, turn the input objects into a MOBY XML request
- String[] mobyXMLInputData = new String[ 1 ];
-
- // Setup
- mobyXMLInputData[ 0 ] = mobyInputXML;
-
- if ( debug )
- debugPS.println( "returnType just before invoke call is " + soapCall.getReturnType() );
- Object returnedObject = null;
- try {
- returnedObject = soapCall.invoke( new QName( "http://biomoby.org/", mobyService.getName() ),
- mobyXMLInputData );
- }
- catch ( Exception e ) {
- e.printStackTrace();
- // System.err.println("Input: "+mobyInputXML);
- throw new SOAPException( "While invoking SOAP Call: " + e );
- }
-
- try {
- if ( debug ) {
- debugPS.println( "SOAP Response was:\n" );
- debugPS.println( soapCall.getResponseMessage().getSOAPPart().getEnvelope() );
- }
- Element resultDom = ( ( MessageElement ) soapCall.getResponseMessage().getSOAPPart().getEnvelope() ).getAsDOM();
- return decodeSOAPMessage( resultDom, contentsXMLOutput, mobyInputXML );
- }
- catch ( Exception e ) {
- e.printStackTrace();
- throw new SOAPException( "Could not get SOAP response as DOM Element: " + e );
- }
-
- }
-
- public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML) throws SOAPException,
- MobyException {
- return decodeSOAPMessage( n, contentsXMLOutput, inputXML, false );
- }
-
- /**
- * Isolates the MOBY Data from the SOAP message returned by the remote service host.
- *
- * @throws SOAPException if the MOBY payload cannot be found in the SOAP message
- * @throws MobyException if the MOBY message is not well-formed XML
- *
- * @return The root element of the MOBY response DOM
- */
- public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML, boolean async)
- throws SOAPException, MobyException {
- if ( n == null ) {
- throw new SOAPException( "SOAP Message given to decode is null" );
- }
-
- NodeList node_list = null;
- XPath responseElementXPath = null;
- try {
- if ( async ) {
- responseElementXPath = new XPath( "//" + MobyPrefixResolver.WSRP_PREFIX + ":"
- + AsyncClient.WSRP_MULTI_PROPERTY_TAG_NAME + "Response", null, mobyPrefixResolver, XPath.SELECT );
- }
- else {
- responseElementXPath = new XPath( "//" + MobyPrefixResolver.MOBY_TRANSPORT_PREFIX + ":"
- + mobyService.getName() + "Response | //" + mobyService.getName() + "Response | " + "//"
- + MobyPrefixResolver.MOBY_TRANSPORT_PREFIX + ":" + mobyService.getName() + " | //"
- + mobyService.getName(), null, mobyPrefixResolver, XPath.SELECT );
- }
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select SOAP nodes due to exception "
- + "while compiling XPath statement (code bug?):" + te );
- }
- try {
- node_list = runXPath( responseElementXPath, n );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select SOAP nodes due to exception " + "while executing XPath statement:"
- + te );
- }
-
- if ( node_list == null || node_list.getLength() == 0 ) {
- throw new SOAPException( "Could not find a response element in SOAP payload (service "
- + mobyService.getName() + ")" );
- }
-
- if ( node_list.getLength() > 1 ) {
- throw new SOAPException( "Found more than one response element in SOAP payload, "
- + "unable to resolve ambiguity of the payload (service provider error?)" );
- }
-
- Node[] responseNodes = null;
- if ( async ) {
- Vector< Node > nodes = new Vector< Node >();
- NodeList resultNodeList = node_list.item( 0 ).getChildNodes();
- for ( int i = 0; resultNodeList != null && i < resultNodeList.getLength(); i++ ) {
- if ( ! ( resultNodeList.item( i ) instanceof Element ) ) {
- continue;
- }
- Element resultElement = ( Element ) resultNodeList.item( i );
- if ( resultElement.getLocalName().startsWith( AsyncClient.MOBY_RESULT_PROPERTY_PREFIX ) ) {
- nodes.add( resultElement );
- }
- }
- responseNodes = nodes.toArray( new Node[ nodes.size() ] );
- }
- else {
- responseNodes = new Node[]{node_list.item( 0 )};
- }
-
- Element domRoot = null; // Where the result will be put
-
- for ( Node responseNode : responseNodes ) {
- // Find base64 encoded elements in the SOAP message using XPath and
- // replace them with the real decoded contents
- node_list = null;
- try {
- node_list = runXPath( base64EncodedXPath, responseNode );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select base64 encoded SOAP nodes due to exception "
- + "while executing XPath statement:" + te );
- }
- if ( debug && node_list != null ) {
- debugPS.println( "There were " + node_list.getLength() + " base64 encoded elements in the data" );
- }
-
- // Do decoding for each base64 part found
- for ( int i = 0; node_list != null && i < node_list.getLength(); i++ ) {
- org.w3c.dom.Node change = node_list.item( i );
- /* Make sure the text data is all put into one contiguous piece for decoding */
- change.normalize();
-
- byte[] decodedBytes = org.apache.axis.encoding.Base64.decode( change.getFirstChild().getNodeValue() );
- String newText = new String( decodedBytes );
- if ( debug ) {
- debugPS.println( "New decoded text is" + newText );
- }
-
- // Swap out this node for the decoded data
- change.getParentNode().replaceChild( n.getOwnerDocument().createTextNode( new String( decodedBytes ) ),
- change );
- }
-
- // Now see if there are any strings that need decoding
- node_list = null;
- try {
- node_list = runXPath( stringEncodedXPath, responseNode );
- }
- catch ( TransformerException te ) {
- throw new SOAPException( "Cannot select string encoded SOAP nodes due to exception "
- + "while executing XPath statement:" + te );
- }
-
- // Do concatenation for each plain string part found
- for ( int i = 0; node_list != null && i < node_list.getLength(); i++ ) {
- org.w3c.dom.Node change = node_list.item( i );
- /* Make sure the text data is all put into one contiguous piece for decoding */
- change.normalize();
- String plainString = "";
- int j = 0;
- for ( NodeList children = change.getChildNodes(); children != null && j < children.getLength(); j++ ) {
- Node child = children.item( j );
- if ( child instanceof CDATASection || child instanceof Text ) {
- plainString += child.getNodeValue();
- if ( debug ) {
- debugPS.println( "Plain string is now " + plainString );
- }
- }
- }
-
- // Swap out this node for the decoded data
- change.getParentNode().replaceChild( n.getOwnerDocument().createCDATASection( plainString ), change );
- }
- if ( debug && node_list != null ) {
- debugPS.println( "There were " + node_list.getLength()
- + " XML Schema string encoded elements in the data" );
- }
-
- // Parse the MOBY XML document payload
- responseNode.normalize();
- NodeList children = responseNode.getChildNodes();
- if ( children == null ) {
- throw new MobyException( "The MOBY payload has no contents at all" );
- }
- if ( children.getLength() != 1 ) {
- if ( debug ) {
- debugPS.println( "Warning: MOBY Payload appears to have more than "
- + "just text in it, skipping the non-text sections" );
- }
- }
-
- Element predefinedDOM = null; // Choice of ripping DOM Element for moby payload out of SOAP DOM
- String localResponseString = ""; // or storing raw XML strings, to be converted to a DOM later
- for ( int j = 0; j < children.getLength(); j++ ) {
- Node child = children.item( j );
- if ( child instanceof CDATASection || child instanceof Text ) {
- // Unescape XML special characters in the string, so we can later on
- // parse the payload as regular XML.
- // Ignore whitespace-only node
- if ( child.getNodeValue().matches( "^\\s+$" ) ) {
- continue;
- }
- if ( debug ) {
- debugPS.println( "Concatenating text in response " + child.getNodeValue() );
- }
- localResponseString += child.getNodeValue();// .replaceAll("<", "<").replaceAll(">",
- // ">").replaceAll("(&|F)", "&");
- }
- if ( child instanceof Element && child.getLocalName().equals( MobyTags.MOBY ) ) {
- debugPS.println( "Warning: The MOBY contents was found as raw XML inside the SOAP response!\n"
- + "This is illegal according to the MOBY-API, please inform the service\n "
- + " provider, as parsing such text may not be supported in the future" );
- localResponseString = null;
- // Store the moby payload root element's DOM represntation, so we don't
- // have to serialize it to the localResponseString and then parse it out
- // again (that would be wasteful).
- predefinedDOM = ( Element ) child;
- break;
- }
- }
-
- if ( localResponseString != null ) {
- if ( localResponseString.length() == 0 ) {
- throw new MobyException( "The MOBY payload has no text contents at all" );
- }
- if ( Character.isWhitespace( localResponseString.charAt( 0 ) ) ) {
- localResponseString = localResponseString.trim();
- }
- }
-
- // Check if the payload is an XML document. If not, try a last ditch effort
- // by base64 decoding the contents. This is technically not allowable in the
- // MOBY spec, but we are being lenient.
- if ( localResponseString != null && !localResponseString.startsWith( "\n" + localResponseString;
- debugPS.println( "Warning: The MOBY contents was missing an XML declaration, but it is "
- + "required by the MOBY API, and may stop working in the future without it. Please "
- + "contact the client's provider to correct this." );
- }
- else {
- String oldResponse = localResponseString;
- localResponseString = new String( org.apache.axis.encoding.Base64.decode( localResponseString ) );
- if ( !localResponseString.startsWith( " entry : data.entrySet() ) {
- String queryName = entry.getKey();
- MobyDataJob query = entry.getValue();
-
- // Additionally, we check if they are MobyDataInstances below
- Map< String, MobyPrimaryData > primaryParams = new HashMap< String, MobyPrimaryData >();
- Map< String, MobySecondaryData > secondaryParams = new HashMap< String, MobySecondaryData >();
-
- // To store the primary input parameter name as given by the user,
- // in case we need it later on for parameter renaming...
- String primaryParamName = null;
-
- for ( Map.Entry< String, MobyDataInstance > subentry : query.entrySet() ) {
- String name = subentry.getKey();
- MobyDataInstance param = subentry.getValue();
- if ( param == null ) {
- throw new MobyException( "Query " + queryName + " contained a null input parameter (" + name + ")" );
- }
- else if ( param instanceof MobyPrimaryData ) {
- primaryParams.put( name, ( MobyPrimaryData ) param );
- primaryParamName = name;
- }
- else if ( param instanceof MobySecondaryData ) {
- secondaryParams.put( name, ( MobySecondaryData ) param );
- }
- else {
- System.err.println( "Input parameter " + name + " (query " + queryName
- + ") was not a MobyPrimaryData or MobySecondaryData "
- + "as expected, but rather was of class " + param.getClass().getName() );
- }
- }
-
- if ( inputs != null && inputs.length != primaryParams.size() ) {
- throw new MobyException( "Service " + mobyService.getName() + " was provided " + primaryParams.size()
- + " primary input parameter(s), but takes " + inputs.length + " (query " + queryName + ")" );
- }
- if ( secondaries != null ) {
- // If no secondaries provided, fill them in by default
- if ( secondaries.length != 0 ) {
- for ( MobySecondaryData secondary : secondaries ) {
- if ( !secondaryParams.containsKey( secondary.getName() ) ) {
- if ( debug ) {
- System.err.println( "Setting default secondary param value for missing param "
- + secondary );
- }
- query.put( secondary.getName(), new MobyDataSecondaryInstance( secondary ) );
- }
- }
- }
- if ( secondaries.length != secondaryParams.size() ) {
- throw new MobyException( "Service " + mobyService.getName() + " was provided "
- + secondaryParams.size() + " secondary input parameter(s), but takes " + secondaries.length
- + " (query " + queryName + "). Extra secondary" + " parameters must have been specified" );
- }
- }
-
- // If there was one anonymous input, assign the name automatically in
- // the case the service requires it to be named. This is the only
- // unambiguous case in which we can do this.
- if ( inputs.length == 1 ) {
- String serviceParamName = inputs[ 0 ].getName(); // name as req'd by the service
-
- // name isn't the same as required currently
- if ( serviceParamName != null && serviceParamName.length() > 0
- && !serviceParamName.equals( primaryParamName ) ) {
- // take out the old parameter
- MobyPrimaryData theInputToRename = ( MobyPrimaryData ) query.remove( primaryParamName );
-
- // Add in the same parameter, but with the appropriate name
- query.put( serviceParamName, ( MobyDataInstance ) theInputToRename );
- }
- }
- }
-
- ByteArrayOutputStream mobyRequest = new ByteArrayOutputStream();
- try {
- MobyDataUtils.toXMLDocument( mobyRequest, data );
- }
- catch ( MobyException me ) {
- throw me;
- }
- catch ( Exception e ) {
- e.printStackTrace();
- throw new MobyException( "Could not create MOBY payload XML from input data: " + e );
- }
-
- if ( debug ) {
- debugPS.println( "Input to MOBY Service is:" );
- debugPS.print( mobyRequest.toString() );
- }
-
- return mobyRequest.toString();
- }
-
- /**
- * A method that sets up the execution environment for and runs a compiled XPath statement against a DOM node You
- * should call releaseXPath when you're done with the results
- *
- * @return the list of Nodes that satisfy the XPath in this Node's context
- */
- protected NodeList runXPath(XPath xpath, Node n) throws TransformerException {
- NodeList result = null;
- int dtm_node_handle = xpath_context.getDTMHandleFromNode( n );
- PrefixResolver node_prefix_resolver = new PrefixResolverDefault( n );
- XObject xobject = xpath.execute( xpath_context, n, node_prefix_resolver );
- if ( xobject instanceof XNodeSet ) {
- result = ( ( XNodeSet ) xobject ).nodelist();
- }
- else if ( debug && xobject != null ) {
- debugPS.println( "Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName() );
- debugPS.flush();
- }
- return result;
- }
-
- protected void releaseXPath(Node n) {
- xpath_context.release( xpath_context.getDTM( xpath_context.getDTMHandleFromNode( n ) ), false );
- }
-}
+package org.biomoby.client;
+
+import java.io.*;
+import java.util.*;
+
+import javax.xml.namespace.QName;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.rpc.Service;
+import javax.xml.transform.TransformerException;
+
+import org.apache.axis.client.Call;
+import org.apache.axis.message.MessageElement;
+import org.apache.xml.utils.PrefixResolver;
+import org.apache.xml.utils.PrefixResolverDefault;
+import org.apache.xpath.XPath;
+import org.apache.xpath.XPathContext;
+import org.apache.xpath.objects.XNodeSet;
+import org.apache.xpath.objects.XObject;
+
+import org.biomoby.shared.*;
+import org.biomoby.shared.data.*;
+import org.biomoby.shared.parser.MobyTags; // defined the Moby XML element names
+import org.biomoby.w3c.addressing.EndpointReference;
+import org.omg.lsae.notifications.AnalysisEvent;
+
+import org.w3c.dom.*;
+
+/**
+ * This class handles the WSDL transaction to request a response
+ * from a remote SOAP Web service that handles the
+ * MOBY format. It depends on
+ * having already retrieved the definition of the Web service via
+ * the MOBY central registry using the
+ * jMOBY API,
+ * and for now it uses the
+ * Apache
+ * Axis Web services framework, as well as Apache Xalan. There are code comments for the
+ * few lines that rely on Axis classes rather than the JAX-RPC interfaces.
+ *
+ * @author Paul Gordon gordonp at ucalgary.ca
+ */
+public class MobyRequest{
+
+ protected MobyService mobyService = null;
+ protected MobyContentInstance inputData = null;
+ protected MobyContentInstance outputData = null;
+ protected Central mobyCentral = null;
+ protected PrefixResolver mobyPrefixResolver = null;
+
+ protected Hashtable wsdlCache = null;
+ protected String lastWsdlCacheKey = null;
+ protected DocumentBuilder docBuilder = null;
+ protected Service service = null;
+
+ protected Class stringType;
+ protected static boolean debug = false;
+ protected PrintStream debugPS = System.err;
+ protected XPathContext xpath_context;
+ protected String responseString = null;
+
+ private XPath stringEncodedXPath;
+ private XPath base64EncodedXPath;
+ private XPath simpleChildXPath;
+ private XPath collectionChildXPath;
+ private String user;
+ private String password;
+
+ private int autoID = 0;
+
+ // Used as invocation callback if MobyRequest is acting as a server,
+ // or is executing services as a client asynchronously
+ private Vector eventHandlers;
+
+ /**
+ * Default constructor. You should have a Central instance around since you're going to
+ * be retrieving MobyServices to pass into here. Lets reuse it.
+ *
+ * @param central An instance of a Moby central object so we can make requests about object types, etc.
+ * @throws ParserConfigurationException if JAXP doesn't have any valid DOM-building XML parsers set up for use
+ */
+ public MobyRequest(Central central) throws ParserConfigurationException{
+ mobyCentral = central;
+ wsdlCache = new Hashtable();
+
+ eventHandlers = new Vector();
+
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware(true);
+ docBuilder = dbf.newDocumentBuilder();
+
+ try{
+ stringType = Class.forName("java.lang.String");
+ }catch(ClassNotFoundException classe){
+ debugPS.println("WARNING: Something is very wrong, could not find Class definition of String: " + classe);
+ }
+
+ xpath_context = new XPathContext();
+ mobyPrefixResolver = new MobyPrefixResolver();
+
+ // Now compile the XPath statements that will be used fetch data from the server response
+ try{
+ base64EncodedXPath = new XPath("//*[starts-with(substring-after(@"+
+ MobyPrefixResolver.XSI1999_PREFIX+
+ ":type, ':'), \"base64\") or starts-with(substring-after(@"+
+ MobyPrefixResolver.XSI2001_PREFIX+
+ ":type, ':'), \"base64\")]", null,
+ mobyPrefixResolver, XPath.SELECT);
+ stringEncodedXPath = new XPath("//*[substring-after(@"+
+ MobyPrefixResolver.XSI1999_PREFIX+
+ ":type, ':')=\"string\" or substring-after(@"+
+ MobyPrefixResolver.XSI2001_PREFIX+
+ ":type, ':')=\"string\"] | //"+
+ MobyPrefixResolver.SOAP_ENC_PREFIX+":string", null,
+ mobyPrefixResolver, XPath.SELECT);
+ simpleChildXPath = new XPath("moby:Simple | Simple", null,
+ mobyPrefixResolver, XPath.SELECT);
+ collectionChildXPath = new XPath("moby:Collection | Collection", null,
+ mobyPrefixResolver, XPath.SELECT);
+ }
+ catch(TransformerException te){
+ debugPS.println("Syntax error encountered while compiling XPath " +
+ "statements for internal use (code bug?): " + te);
+ }
+ setDebugMode(System.getProperty("moby.debug") != null);
+ }
+
+ public void setAuthentication(String user, String password){
+ this.user = user;
+ this.password = password;
+ }
+
+ /**
+ * @param mode if true, debugging information is printed to the stream returned by getDebugOutputStream
+ */
+ public void setDebugMode(boolean mode){
+ debug = mode;
+ }
+
+ /**
+ * Standard error is used unless this method is called.
+ *
+ * @param ps the OutputStream to which debugging information is sent.
+ * @throws IllegalArgumentException if the stream is null
+ */
+ public void setDebugPrintStream(PrintStream ps) throws IllegalArgumentException{
+ if(ps == null){
+ throw new IllegalArgumentException("The OutputStream specified to MobyRequest was null");
+ }
+ debugPS = ps;
+ }
+
+ /**
+ * @return the instance of the class implementing Central that we are using
+ */
+ public Central getCentralImpl(){
+ return mobyCentral;
+ }
+
+ /**
+ * @param mobyservice the MobyService that should be executed when invokeService is called
+ */
+ public void setService(MobyService mobyservice){
+ if(mobyservice == null){
+ mobyService = null;
+ }
+ else if(mobyService == null || !mobyservice.equals(mobyService)){
+ mobyService = mobyservice;
+ }
+ }
+
+ /**
+ * @return the MobyService that will be executed when invokeService is called
+ */
+ public MobyService getService(){
+ return mobyService;
+ }
+
+ /**
+ * @return the Raw MOBY XML response as a string
+ */
+ public String getResponseXML(){
+ return responseString;
+ }
+
+ /**
+ * Sets the input data for the MOBY service request. The length of the input array, and the
+ * number of input parameters required by the service must be equal when invokeService() is called.
+ * This method strictly enforces that the input be of the appropriate type for the service.
+ *
+ * Note that there is no requirement to use MobyDataInstance.setXmlMode() before passing in
+ * data, this class will temporarily set the XML mode of the data when it is required.
+ *
+ * @throws IllegalArgumentException if the input does not fit the criteria of the service (e.g. wrong data type)
+ */
+ public void setInput(MobyContentInstance data) throws MobyException{
+ inputData = data;
+ }
+
+ /**
+ * Takes the data in the array, with their current articleNames, as input for the service
+ */
+ public void setInput(MobyDataInstance[] data) throws MobyException{
+ MobyDataJob job = new MobyDataJob();
+ for(MobyDataInstance param: data){
+ job.put(param.getName(), param);
+ }
+ inputData = new MobyContentInstance();
+ inputData.put(job);
+ }
+
+ /**
+ * Convenience method to run services that take one argument. If the service
+ * requires the input to have a name, it will be automatically assigned.
+ */
+ public void setInput(MobyDataInstance datum) throws MobyException{
+ setInput(datum, "");
+ }
+
+ /**
+ * Convenience method to run services that take one named argument.
+ */
+ public void setInput(MobyDataInstance datum, String paramName) throws MobyException{
+ inputData = new MobyContentInstance(datum, paramName);
+ }
+
+ /**
+ * @return the MobyService that will be executed when invokeService is called
+ */
+ public MobyContentInstance getInput(){
+ return inputData;
+ }
+
+ /**
+ * Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
+ */
+ public void setSecondaryInput(Collection secondaryData) throws MobyException{
+ setSecondaryInput(secondaryData.toArray(new MobyDataSecondaryInstance[secondaryData.size()]));
+ }
+
+ /**
+ * This method will assign the provided secondary parameters to all primary input data currently
+ * in this object. This is covenient if you are running 100 seqs through BLAST and only want to set
+ * the parameters once. If you instead want to set secondary input differently for all primary inputs, you'll
+ * need to create a custom MobyContentInstance as input to setInput().
+ *
+ * @throws MobyException if a parameter name is blank, or overrides a primary parameter
+ */
+ public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException{
+
+ Iterator queryNames = inputData.keySet().iterator();
+ // For each query
+ while(queryNames.hasNext()){
+ MobyDataJob queryParams = inputData.get(queryNames.next());
+ // Set all the secondary params (overwrites any old ones)
+ for(int i = 0; i < secondaryData.length; i++){
+ String secName = secondaryData[i].getName();
+ if(secName == null || secName.length() == 0){
+ throw new MobyException("A secondary parameter cannot have a blank name (array index " + i + ")");
+ }
+ if(queryParams.containsKey(secName) && queryParams.get(secName) instanceof MobyPrimaryData){
+ throw new MobyException("A secondary parameter cannot override an existing primary parameter " +
+ "with the same name (" + secName + ")");
+ }
+ queryParams.put(secName, secondaryData[i]);
+ }
+ }
+ }
+
+ /**
+ * @return a vector of MobyDataInstance[], each element of the vector is the collection of response objects for the correspondingly indexed input request.
+ *
+ * @throws MobyException if you try to get the results before calling InvokeService
+ */
+ public MobyContentInstance getOutput() throws MobyException{
+ if(outputData == null){
+ throw new MobyException("Trying to access MOBY service results " +
+ "before the service is invoked");
+ }
+ else{
+ return outputData;
+ }
+ }
+
+ /**
+ * The main method of the class. If all of the MOBY input objects
+ * are properly defined according to the Web service definition,
+ * a SOAP request will be sent to the remote server, and the method
+ * will return one or more MOBY objects (synchronous).
+ * Call this method after calling setService, and setInput. If you do not call
+ * setSecondaryInput, the default secondary parameter values will be used.
+ *
+ * @return the results of the remote Web service in response to the give input
+ *
+ * @throws MobyException i.e. there was something wrong with the input, output or remote service's logic
+ * @throws SOAPException i.e. there was a problem with the underlying transaction/transport layer
+ */
+ public MobyContentInstance invokeService() throws Exception, MobyException, SOAPException, NoSuccessException{
+ return mobyService.isAsynchronous() ? invokeService(inputData, new StringBuffer()) : invokeService(inputData, (StringBuffer) null);
+ }
+
+ // Used internally for asynchronous thread calls that all need the XML data
+ // and can't rely on the answer from thread-insensitive getResponseXML()
+ private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML)
+ throws Exception, MobyException, SOAPException, NoSuccessException{
+ return invokeService(inData, contentsXML, null, 0);
+ }
+
+ private MobyContentInstance invokeService(MobyContentInstance inData, StringBuffer contentsXML, MobyRequestEventHandler handler, int requestId)
+ throws Exception, MobyException, SOAPException, NoSuccessException{
+
+ if(mobyService == null){
+ throw new MobyException("Tried to invoke null service from MobyRequest (call setService first)");
+ }
+
+ Element mobyDOM = null;
+ if(mobyService.isAsynchronous()){
+ // Async is "simpler", because it had to merge DOMs together into a single MobyContentInstance anyway
+ MobyContentInstance mci = performAsyncSOAPRequest(mobyService, inData, handler, requestId);
+ StringWriter writer = new StringWriter();
+ MobyDataUtils.toXMLDocument(writer, mci);
+ contentsXML.append(writer.toString());
+ return mci;
+ }
+ else{
+ String mobyXML = convertMOBYDataToMOBYRequest(inData);
+ Call call = getServiceFromWSDL();
+ if(user != null && password != null) {
+ call.setProperty( Call.USERNAME_PROPERTY, user );
+ call.setProperty( Call.PASSWORD_PROPERTY, password );
+ }
+ mobyDOM = performSOAPRequest(call, mobyXML, contentsXML);
+ // The following parses the DOM and extracts all the appropriate jMOBY objects to represent the XML in Java
+ return MobyDataUtils.fromXMLDocument(mobyDOM, mobyService.getServiceType().getRegistry());
+ }
+ }
+
+ protected MobyContentInstance performAsyncSOAPRequest(MobyService mservice, MobyContentInstance inData,
+ MobyRequestEventHandler handler, int requestId)
+ throws Exception{
+ String mobyXML = convertMOBYDataToMOBYRequest(inData);
+ EndpointReference epr = AsyncClient.sendRequest(mservice, mobyXML);
+
+ // Essentially cloning, so removing ids doesn't change the
+ // MobyContentInstance "data" (which we will use again later on)
+ MobyContentInstance finalContents = new MobyContentInstance();
+ Set queryIDs = new HashSet(inData.keySet());
+ try {
+ // Should add some timeout here...
+ while(!queryIDs.isEmpty()){
+ // todo: make this setable
+ Thread.sleep(5000);
+
+ AnalysisEvent[] events =
+ AsyncClient.poll(epr, queryIDs);
+
+ Vector newDataAvailable = new Vector();
+ for(AnalysisEvent event: events){
+ if(event != null && event.isCompleted()){
+ queryIDs.remove(event.getQueryId());
+ newDataAvailable.add(event.getQueryId());
+ }
+ }
+
+ if(newDataAvailable.size() > 0){
+ // Parse and merge the new data into the existing contents
+ InputStream resultStream = AsyncClient.getResultStream(epr, newDataAvailable);
+ Element mobyDOM = asyncSoapTextToMobyDOM(resultStream);
+ MobyContentInstance newResults = MobyDataUtils.fromXMLDocument(mobyDOM, mservice.getServiceType().getRegistry());
+ // The merge
+ for(String jobid: newResults.keySet()){
+ finalContents.put(jobid, newResults.get(jobid));
+ }
+
+ // Inform the handler that some data has been added to the response (for incremental display?)
+ if(handler != null){
+ MobyRequestEvent mre = new MobyRequestEvent(finalContents, this, mservice, null, requestId);
+ StringWriter xmlWriter = new StringWriter();
+ MobyDataUtils.toXMLDocument(xmlWriter, finalContents);
+
+ mre.setContentsXML(xmlWriter.toString());
+ if(!queryIDs.isEmpty()){
+ // Send an update event only if we aren't finished yet.
+ // If we are finished, the client is going to get this event as the
+ // invocation thread finishes up (no need to double up).
+ handler.processEvent(mre);
+ }
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ AsyncClient.destroy(epr);
+ throw new Exception("Exception occured while polling the service invocation: " + e);
+ }
+
+ return finalContents;
+ }
+
+ private Element asyncSoapTextToMobyDOM(InputStream inStream) throws Exception{
+ Element soapDOM = null;
+ synchronized(docBuilder){
+ soapDOM = docBuilder.parse(inStream).getDocumentElement();
+ }
+ final boolean IS_ASYNC_SERVICE_CALL = true;
+ return decodeSOAPMessage(soapDOM, null, null, IS_ASYNC_SERVICE_CALL);
+ }
+
+ /**
+ * Asynchronous call to invokeService. A callback to the passed-in handler will be made when
+ * the response is ready, or there is an exception.
+ *
+ * @return the id that the callback event will return from getID(), allowing a client to distinguish between multiple concurrent invocation callbacks
+ */
+ public synchronized int invokeService(MobyRequestEventHandler handler){
+ int id = autoID++;
+
+ Thread t = new InvocationThread(this, inputData, handler, id); // see internal class definition below
+ t.start();
+
+ return id;
+ }
+
+ // This is the class that asynchronously calls the service and does a callback to
+ // the handler specified in the invocation.
+ class InvocationThread extends Thread {
+ MobyContentInstance data;
+ MobyService mservice;
+ MobyRequest mobyRequest;
+ MobyRequestEventHandler handler;
+ int requestId;
+
+ InvocationThread(MobyRequest mr, MobyContentInstance inData, MobyRequestEventHandler h, int id){
+ data = inData;
+ mobyRequest = mr;
+ mservice = mobyRequest.getService();
+ handler = h;
+ requestId = id;
+
+ // Name the thread after the service being run, mostly for ease of debugging
+ setName(mservice.getName()+requestId);
+ }
+
+ public void run() {
+ MobyRequestEvent requestEvent = new MobyRequestEvent(data, mobyRequest, mservice, null, requestId);
+ // Tell the handler we're starting the request, with the given data
+ handler.start(requestEvent);
+
+ MobyRequestEvent responseEvent = null;
+ MobyContentInstance content = null;
+ StringBuffer contentsXML = new StringBuffer(); //to be filled in by the RPC call below
+ try{
+ content = mobyRequest.invokeService(data, contentsXML, handler, requestId); //RPC call...
+ }
+ catch(Exception e){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, e, requestId);
+ }
+ catch(Error err){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, err, requestId);
+ }
+ if(responseEvent == null){
+ responseEvent = new MobyRequestEvent(content, mobyRequest, mservice, null, requestId);
+ }
+ // We've got the raw XML laying around, so why not provide it unmolested to the callback?
+ responseEvent.setContentsXML(contentsXML.toString());
+ handler.processEvent(responseEvent);
+ handler.stop(mobyRequest, requestId);
+ }
+ }
+
+ public void addEventHandler(MobyRequestEventHandler h){
+ eventHandlers.add(h);
+ }
+
+ public void removeEventHandler(MobyRequestEventHandler h){
+ eventHandlers.remove(h);
+ }
+
+ public void sendResponse(MobyRequestEvent mre){
+ // Not yet implemented, need to conform to some web.xml specification here...
+ }
+
+ /**
+ * This method retrieves from Moby Central a copy of the WSDL document for the service
+ * (or uses an internally cached copy from a previous invocation), and sets the variables for the
+ * SOAP call appropriately so you can consequently call performSOAPRequest.
+ */
+ protected Call getServiceFromWSDL() throws MobyException, NoSuccessException{
+// String wsdl = null;
+
+// // Since this is how we retrieve a service from Central, use the same values as the key to the hash
+// String wsdlCacheKey = mobyService.getName() + "@" + mobyService.getAuthority();
+
+// // This is the same call as last time, so we don't need to change the setup
+// if(wsdlCacheKey.equals(lastWsdlCacheKey)){
+// return setCallFromWSDL((String) wsdlCache.get(wsdlCacheKey));
+// }
+// // We haven't encountered this service yet
+// else if(!wsdlCache.containsKey(wsdlCacheKey)){
+// wsdl = mobyCentral.getServiceWSDL(mobyService.getName(), mobyService.getAuthority());
+// wsdlCache.put(wsdlCacheKey, wsdl);
+// }
+// // We've dealt with this one before
+// else{
+// wsdl = (String) wsdlCache.get(wsdlCacheKey);
+// }
+
+// lastWsdlCacheKey = wsdlCacheKey; // Keep track of the last invocation
+
+ // Get ready to do SOAP
+ return setCallFromWSDL(null);
+ }
+
+ /**
+ * Creates the SOAP Call that will be invoked later. This should be based on the WSDL document
+ * and parameter information from the MobyService, but these are currently not up to snuff.
+ */
+ protected Call setCallFromWSDL(String wsdl) throws MobyException, SOAPException{
+ if(service == null){
+ service = new org.apache.axis.client.Service(); // AXIS SPECIFIC This acts as a factory for Calls
+ }
+
+ Call soapCall;
+ try{
+ soapCall = (Call) service.createCall();//create a fresh Call each time
+ }catch(javax.xml.rpc.ServiceException se){
+ throw new SOAPException("Could not instatiate call to SOAP Service: " + se);
+ }
+
+ // Should initialize endpoint, etc. This call is AXIS SPECIFIC, otherwise you'll
+ // have to do the call's info setting manually.
+ //((org.apache.axis.client.Call) soapCall).setSOAPService(soapService);
+ soapCall.removeAllParameters();
+ soapCall.setTargetEndpointAddress(mobyService.getURL());
+ soapCall.setPortName(new QName("http://biomoby.org/",
+ mobyService.getName() + "PortType"));
+ //soapCall.setOperationName(new QName("http://biomoby.org/",
+ // mobyService.getName()));
+ soapCall.setSOAPActionURI("http://biomoby.org/#" + mobyService.getName());
+ return soapCall;
+ }
+
+ /**
+ * Calls the invoke() method of the JAX-RPC Call interface.
+ */
+ protected Element performSOAPRequest(Call soapCall, String mobyInputXML, StringBuffer contentsXMLOutput) throws SOAPException{
+ // First, turn the input objects into a MOBY XML request
+ String[] mobyXMLInputData = new String[1];
+
+ //Setup
+ mobyXMLInputData[0] = mobyInputXML;
+
+ if(debug)
+ debugPS.println("returnType just before invoke call is " + soapCall.getReturnType());
+ Object returnedObject = null;
+ try{
+ returnedObject = soapCall.invoke(new QName("http://biomoby.org/",
+ mobyService.getName()), mobyXMLInputData);
+ }
+ catch(Exception e){
+ e.printStackTrace();
+ //System.err.println("Input: "+mobyInputXML);
+ throw new SOAPException("While invoking SOAP Call: " + e);
+ }
+
+ try{
+ if(debug){
+ debugPS.println("SOAP Response was:\n");
+ debugPS.println(soapCall.getResponseMessage().getSOAPPart().getEnvelope());
+ }
+ Element resultDom = ((MessageElement) soapCall.getResponseMessage().getSOAPPart().getEnvelope()).getAsDOM();
+ return decodeSOAPMessage(resultDom, contentsXMLOutput, mobyInputXML);
+ } catch(Exception e){
+ e.printStackTrace();
+ throw new SOAPException("Could not get SOAP response as DOM Element: "+ e);
+ }
+
+ }
+
+ public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML)
+ throws SOAPException, MobyException{
+ return decodeSOAPMessage(n, contentsXMLOutput, inputXML, false);
+ }
+
+ /**
+ * Isolates the MOBY Data from the SOAP message returned by the remote service host.
+ *
+ * @throws SOAPException if the MOBY payload cannot be found in the SOAP message
+ * @throws MobyException if the MOBY message is not well-formed XML
+ *
+ * @return The root element of the MOBY response DOM
+ */
+ public Element decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML, boolean async)
+ throws SOAPException, MobyException{
+ if(n == null){
+ throw new SOAPException("SOAP Message given to decode is null");
+ }
+
+ NodeList node_list = null;
+ XPath responseElementXPath = null;
+ try{
+ if(async){
+ responseElementXPath = new XPath("//"+MobyPrefixResolver.WSRP_PREFIX +
+ ":"+AsyncClient.WSRP_MULTI_PROPERTY_TAG_NAME+"Response",
+ null, mobyPrefixResolver, XPath.SELECT);
+ }
+ else{
+ responseElementXPath = new XPath("//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+
+ ":"+mobyService.getName()+"Response | //" +
+ mobyService.getName()+"Response | " +
+ "//"+ MobyPrefixResolver.MOBY_TRANSPORT_PREFIX+
+ ":"+mobyService.getName() + " | //" +
+ mobyService.getName(),
+ null, mobyPrefixResolver, XPath.SELECT);
+ }
+ }catch(TransformerException te){
+ throw new SOAPException("Cannot select SOAP nodes due to exception "+
+ "while compiling XPath statement (code bug?):" +te);
+ }
+ try{
+ node_list = runXPath(responseElementXPath, n);
+ }catch(TransformerException te){
+ throw new SOAPException("Cannot select SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+
+ if(node_list == null || node_list.getLength() == 0){
+ throw new SOAPException("Could not find a response element in SOAP payload (service " +
+ mobyService.getName() + ")");
+ }
+
+ if(node_list.getLength() > 1){
+ throw new SOAPException("Found more than one response element in SOAP payload, " +
+ "unable to resolve ambiguity of the payload (service provider error?)");
+ }
+
+ Node[] responseNodes = null;
+ if(async){
+ Vector nodes = new Vector();
+ NodeList resultNodeList = node_list.item(0).getChildNodes();
+ for(int i = 0; resultNodeList != null && i < resultNodeList.getLength(); i++){
+ if(!(resultNodeList.item(i) instanceof Element)){
+ continue;
+ }
+ Element resultElement = (Element) resultNodeList.item(i);
+ if(resultElement.getLocalName().startsWith(AsyncClient.MOBY_RESULT_PROPERTY_PREFIX)){
+ nodes.add(resultElement);
+ }
+ }
+ responseNodes = nodes.toArray(new Node[nodes.size()]);
+ }
+ else{
+ responseNodes = new Node[]{node_list.item(0)};
+ }
+
+ Element domRoot = null; // Where the result will be put
+
+ for(Node responseNode: responseNodes){
+ // Find base64 encoded elements in the SOAP message using XPath and
+ // replace them with the real decoded contents
+ node_list = null;
+ try{
+ node_list = runXPath(base64EncodedXPath, responseNode);
+ }
+ catch(TransformerException te){
+ throw new SOAPException("Cannot select base64 encoded SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+ if(debug && node_list != null){
+ debugPS.println("There were " + node_list.getLength() +
+ " base64 encoded elements in the data");
+ }
+
+ // Do decoding for each base64 part found
+ for(int i = 0; node_list != null && i < node_list.getLength(); i++){
+ org.w3c.dom.Node change = node_list.item(i);
+ /* Make sure the text data is all put into one contiguous piece for decoding*/
+ change.normalize();
+
+ byte[] decodedBytes = org.apache.axis.encoding.Base64.decode(change.getFirstChild().getNodeValue());
+ String newText = new String(decodedBytes);
+ if(debug){
+ debugPS.println("New decoded text is" + newText);
+ }
+
+ // Swap out this node for the decoded data
+ change.getParentNode().replaceChild(n.getOwnerDocument().createTextNode(new String(decodedBytes)),
+ change);
+ }
+
+ // Now see if there are any strings that need decoding
+ node_list = null;
+ try{
+ node_list = runXPath(stringEncodedXPath, responseNode);
+ }
+ catch(TransformerException te){
+ throw new SOAPException("Cannot select string encoded SOAP nodes due to exception "+
+ "while executing XPath statement:" +te);
+ }
+
+ // Do concatenation for each plain string part found
+ for(int i = 0; node_list != null && i < node_list.getLength(); i++){
+ org.w3c.dom.Node change = node_list.item(i);
+ /* Make sure the text data is all put into one contiguous piece for decoding*/
+ change.normalize();
+ String plainString = "";
+ int j = 0;
+ for(NodeList children = change.getChildNodes();
+ children != null && j < children.getLength();
+ j++){
+ Node child = children.item(j);
+ if(child instanceof CDATASection || child instanceof Text){
+ plainString += child.getNodeValue();
+ if(debug){
+ debugPS.println("Plain string is now " + plainString);
+ }
+ }
+ }
+
+ // Swap out this node for the decoded data
+ change.getParentNode().replaceChild(n.getOwnerDocument().createCDATASection(plainString), change);
+ }
+ if(debug && node_list != null){
+ debugPS.println("There were " + node_list.getLength() +
+ " XML Schema string encoded elements in the data");
+ }
+
+ // Parse the MOBY XML document payload
+ responseNode.normalize();
+ NodeList children = responseNode.getChildNodes();
+ if(children == null){
+ throw new MobyException("The MOBY payload has no contents at all");
+ }
+ if(children.getLength() != 1){
+ if(debug){
+ debugPS.println("Warning: MOBY Payload appears to have more than " +
+ "just text in it, skipping the non-text sections");
+ }
+ }
+
+ Element predefinedDOM = null; // Choice of ripping DOM Element for moby payload out of SOAP DOM
+ String localResponseString = ""; // or storing raw XML strings, to be converted to a DOM later
+ for(int j = 0; j < children.getLength(); j++){
+ Node child = children.item(j);
+ if(child instanceof CDATASection || child instanceof Text){
+ // Unescape XML special characters in the string, so we can later on
+ // parse the payload as regular XML.
+ // Ignore whitespace-only node
+ if(child.getNodeValue().matches("^\\s+$")){
+ continue;
+ }
+ if(debug){
+ debugPS.println("Concatenating text in response " + child.getNodeValue());
+ }
+ localResponseString += child.getNodeValue();//.replaceAll("<", "<").replaceAll(">", ">").replaceAll("(&|F)", "&");
+ }
+ if(child instanceof Element && child.getLocalName().equals(MobyTags.MOBY)){
+ debugPS.println("Warning: The MOBY contents was found as raw XML inside the SOAP response!\n" +
+ "This is illegal according to the MOBY-API, please inform the service\n " +
+ " provider, as parsing such text may not be supported in the future");
+ localResponseString = null;
+ // Store the moby payload root element's DOM represntation, so we don't
+ // have to serialize it to the localResponseString and then parse it out
+ // again (that would be wasteful).
+ predefinedDOM = (Element) child;
+ break;
+ }
+ }
+
+ if(localResponseString != null){
+ if(localResponseString.length() == 0){
+ throw new MobyException("The MOBY payload has no text contents at all");
+ }
+ if(Character.isWhitespace(localResponseString.charAt(0))){
+ localResponseString = localResponseString.trim();
+ }
+ }
+
+ // Check if the payload is an XML document. If not, try a last ditch effort
+ // by base64 decoding the contents. This is technically not allowable in the
+ // MOBY spec, but we are being lenient.
+ if(localResponseString != null && !localResponseString.startsWith("\n"+localResponseString;
+ debugPS.println("Warning: The MOBY contents was missing an XML declaration, but it is " +
+ "required by the MOBY API, and may stop working in the future without it. Please " +
+ "contact the client's provider to correct this.");
+ }
+ else{
+ String oldResponse = localResponseString;
+ localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString));
+ if(!localResponseString.startsWith(" entry: data.entrySet()){
+ String queryName = entry.getKey();
+ MobyDataJob query = entry.getValue();
+
+ // Additionally, we check if they are MobyDataInstances below
+ Map primaryParams = new HashMap();
+ Map secondaryParams = new HashMap();
+
+ // To store the primary input parameter name as given by the user,
+ // in case we need it later on for parameter renaming...
+ String primaryParamName = null;
+
+ for(Map.Entry subentry: query.entrySet()){
+ String name = subentry.getKey();
+ MobyDataInstance param = subentry.getValue();
+ if(param == null){
+ throw new MobyException("Query " + queryName +
+ " contained a null input parameter (" + name + ")");
+ }
+ else if(param instanceof MobyPrimaryData){
+ primaryParams.put(name, (MobyPrimaryData) param);
+ primaryParamName = name;
+ }
+ else if(param instanceof MobySecondaryData){
+ secondaryParams.put(name, (MobySecondaryData) param);
+ }
+ else{
+ System.err.println("Input parameter " + name + " (query " + queryName +
+ ") was not a MobyPrimaryData or MobySecondaryData " +
+ "as expected, but rather was of class " + param.getClass().getName());
+ }
+ }
+
+ if(inputs != null && inputs.length != primaryParams.size()){
+ throw new MobyException("Service " + mobyService.getName() + " was provided " +
+ primaryParams.size() +
+ " primary input parameter(s), but takes " + inputs.length +
+ " (query " + queryName + ")");
+ }
+ if(secondaries != null){
+ // If no secondaries provided, fill them in by default
+ if(secondaries.length != 0){
+ for(MobySecondaryData secondary: secondaries){
+ if(!secondaryParams.containsKey(secondary.getName())){
+ if(debug){
+ System.err.println("Setting default secondary param value for missing param " + secondary);
+ }
+ query.put(secondary.getName(), new MobyDataSecondaryInstance(secondary));
+ }
+ }
+ }
+ if(secondaries.length != secondaryParams.size()){
+ throw new MobyException("Service " + mobyService.getName() + " was provided " +
+ secondaryParams.size() +
+ " secondary input parameter(s), but takes " + secondaries.length +
+ " (query " + queryName + "). Extra secondary" +
+ " parameters must have been specified");
+ }
+ }
+
+ // If there was one anonymous input, assign the name automatically in
+ // the case the service requires it to be named. This is the only
+ // unambiguous case in which we can do this.
+ if(inputs.length == 1){
+ String serviceParamName = inputs[0].getName(); // name as req'd by the service
+
+ // name isn't the same as required currently
+ if(serviceParamName != null && serviceParamName.length() > 0 &&
+ !serviceParamName.equals(primaryParamName)){
+ // take out the old parameter
+ MobyPrimaryData theInputToRename = (MobyPrimaryData) query.remove(primaryParamName);
+
+ // Add in the same parameter, but with the appropriate name
+ query.put(serviceParamName, (MobyDataInstance) theInputToRename);
+ }
+ }
+ }
+
+ ByteArrayOutputStream mobyRequest = new ByteArrayOutputStream();
+ try{
+ MobyDataUtils.toXMLDocument(mobyRequest, data);
+ }
+ catch(MobyException me){
+ throw me;
+ }
+ catch(Exception e){
+ e.printStackTrace();
+ throw new MobyException("Could not create MOBY payload XML from input data: " +e);
+ }
+
+ if(debug){
+ debugPS.println("Input to MOBY Service is:");
+ debugPS.print(mobyRequest.toString());
+ }
+
+ return mobyRequest.toString();
+ }
+
+ /**
+ * A method that sets up the execution environment for and runs a compiled XPath statement against a DOM node
+ * You should call releaseXPath when you're done with the results
+ * @return the list of Nodes that satisfy the XPath in this Node's context
+ */
+ protected NodeList runXPath(XPath xpath, Node n) throws TransformerException{
+ NodeList result = null;
+ int dtm_node_handle = xpath_context.getDTMHandleFromNode(n);
+ PrefixResolver node_prefix_resolver = new PrefixResolverDefault(n);
+ XObject xobject = xpath.execute(xpath_context, n, node_prefix_resolver);
+ if(xobject instanceof XNodeSet){
+ result = ((XNodeSet) xobject).nodelist();
+ }
+ else if(debug && xobject != null){
+ debugPS.println("Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName());
+ debugPS.flush();
+ }
+ return result;
+ }
+
+ protected void releaseXPath(Node n){
+ xpath_context.release(xpath_context.getDTM(xpath_context.getDTMHandleFromNode(n)), false);
+ }
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2008/11/26 08:53:43 1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseClient.java 2008/12/03 15:21:13 1.14
@@ -1,429 +1,487 @@
-// BaseClient.java
-//
-// Created: August 2005
-//
-// This file is a component of the BioMoby project.
-// Copyright Martin Senger (martin.senger at gmail.com).
-//
-
-package org.biomoby.client;
-
-import java.io.StringReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-
-import org.apache.axis.client.Call;
-import org.apache.commons.lang.StringUtils;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.parser.JDOMUtils;
-import org.biomoby.shared.parser.MobyJob;
-import org.biomoby.shared.parser.MobyPackage;
-import org.biomoby.shared.parser.MobyTags;
-import org.biomoby.shared.parser.ServiceException;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-import org.tulsoft.shared.GException;
-import org.tulsoft.tools.soap.axis.AxisCall;
-
-/**
- * This is a base class for Biomoby clients. It takes care about converting user input into Biomoby XML, sending it in a
- * SOAP message to a Biomoby service, waiting for the response and parsing it from Biomoby XML. It also divides requests
- * and responses into so-called jobs - each of them corresponds to a Biomoby query (a Biomoby single network
- * request may contain more queries/jobs).
- *
- *
- * Any client can override various methods - but the ones she/he must override in a subclass are those
- * telling what service to call ({@link #getServiceLocator}), what data to put in a request ({@link #fillRequest(MobyJob,MobyPackage) fillRequest}),
- * and what to do with a response ({@link #useResponse(MobyJob,MobyPackage) useResponse}.
- *
- *
- * @author Martin Senger
- * @version $Id$
- */
-
-abstract public class BaseClient {
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog( BaseClient.class );
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- static protected boolean notEmpty(String value) {
- return StringUtils.isNotBlank( value );
- }
- static protected boolean isEmpty(String value) {
- return StringUtils.isBlank( value );
- }
-
- /*******************************************************************************************************************
- * The main method that packs input data, invokes a BioMoby service and uses its response. Use this method if the
- * input data should have just one job (which is a usual case) - otherwise use method {@link #process(int)}.
- *
- *
- * @throws MobyException if (a) a sub-class throws it during the filling data or using response, or (b) a Biomoby
- * service invocation fails
- ******************************************************************************************************************/
- public void process() throws MobyException {
- process( 1 );
- }
-
- /*******************************************************************************************************************
- * The main method that packs input data, invokes a BioMoby service and uses its response. The input data may
- * consist from more than one job (query) - the 'jobCount' is a suggestion how many jobs will be included, but this
- * can be changed by the implementing sub-class.
- *
- *
- * Usually a client developer does not need to overwrite this method. She or he makes the real input data filling in
- * the {@link #fillRequest} method, and uses the response in the {@link #useResponse} method.
- *
- *
- * @throws MobyException if (a) a sub-class throws it during the filling data or using response, or (b) a Biomoby
- * service invocation fails
- ******************************************************************************************************************/
- public void process(int jobCount) throws MobyException {
-
- String xmlResponse = null;
-
- // input: raw-level processing
- String xmlInput = fillRequest();
- if ( xmlInput != null ) {
- if ( ( xmlInput = interceptRequest( xmlInput ) ) == null )
- return;
- }
-
- // input: usual processing (i.e. collect XML in iterations)
- else {
- MobyPackage mobyInput = new MobyPackage();
- if ( !fillRequest( mobyInput, jobCount ) )
- return;
- xmlInput = mobyInput.toXML();
- if ( ( xmlInput = interceptRequest( xmlInput ) ) == null )
- return;
- }
-
- // calling service
- xmlResponse = callRemoteService( xmlInput );
-
- // output: raw-level processing
- if ( !useResponse( xmlResponse ) )
- return;
-
- // output: usual processing (again by iterations)
- MobyPackage mobyResponse = MobyPackage.createFromXML( xmlResponse );
- useResponse( mobyResponse );
- }
-
- public String interceptRequest(String xmlInput) throws MobyException {
- return xmlInput;
- }
-
- /*******************************************************************************************************************
- * Create raw XML input. Override this method if you have already an input XML, or you want to create it yourself.
- *
- *
- * @return a full XML input for a Biomoby service (in this case no other fillRequest methods will
- * called); return null if no XML was created and a usual process to gather it will be used
- *
- * @throws MobyException if an XML cannot be created
- ******************************************************************************************************************/
- public String fillRequest() throws MobyException {
- return null;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected String filterMobyResponseType(Object result) throws MobyException {
- if ( result instanceof String )
- return ( String ) result;
- else if ( result instanceof byte[] )
- return new String( ( byte[] ) result );
- else
- throw new MobyException(
- "The Biomoby data should be sent/received either as type String or base64/byte[]. "
- + "But they are of type '" + result.getClass().getName() + "'." );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected String callBiomobyService(MobyServiceLocator locator, String xmlInput) throws MobyException {
-
- MobyService service = locator.getService();
- String serviceName = service.getName();
- boolean asBytes = locator.isAsBytes();
- String serviceEndpoint = service.getURL();
- int timeout = locator.getSuggestedTimeout();
-
- try {
- URL target = new URL( serviceEndpoint );
- AxisCall call = new AxisCall( target, timeout );
- // to allow service calls which need authentication
- setAuthentication( call.getCall() );
- call.getCall().setSOAPActionURI( MobyService.BIOMOBY_SERVICE_URI + "#" + serviceName );
-
- return filterMobyResponseType( call.doCall( MobyService.BIOMOBY_SERVICE_URI, serviceName,
- new Object[]{sendingFilter( xmlInput, asBytes )} ) );
- }
- catch ( MalformedURLException e ) {
- throw new MobyException( "Service endpoint '" + serviceEndpoint + "' is not a valid URL." );
- }
- catch ( GException e ) {
- throw new MobyException( e.getMessage(), e );
- }
- }
-
- /**
- * Sets the authentication for the call. The default implementation does not do anything !
- *
- * @param call
- */
- protected void setAuthentication(Call call) {
- return;
- }
-
- //
- protected Object sendingFilter(String input, boolean asBytes) {
- if ( asBytes ) {
- log.debug( "Data sent as a byte array" );
- return input.getBytes();
- }
- else {
- return input;
- }
- }
-
- /*******************************************************************************************************************
- * Call a SOAP-based BioMoby service. In order to find what service to call and what are its characteristics (such
- * as its endpoint) it will call method {@link #getServiceLocator} that should be implemented by a sub-class.
- *
- *
- * Once it has the service locator, this class does one of the following, in this order:
- *
- *
- * The locator must contain at least a service name. If it does not, an exception is raised.
- *
- * If the locator contains a service endpoint, a call is made to this endpoint, using also the service name as
- * a method name.
- *
- * If the locator has a registry endpoint, an enquiry to the registry is made to find an endpoint of a service
- * corresponding with the given service name. Once found, the service is called.
- *
- * The same as the previous one but using a default registry.
- *
- * @param xmlInput data will be sent to the called Biomoby service
- *
- * @return service response (still in XML)
- *
- * @throws MobyException (a) if service call (or a call to registry; for example because the registry does not know
- * given service) fails, or (b) if the used {@link MobyServiceLocator} does not contain a service name.
- *
- ******************************************************************************************************************/
- public String callRemoteService(String xmlInput) throws MobyException {
-
- // 1) service name is a must
- MobyServiceLocator locator = getServiceLocator();
- MobyService service = locator.getService();
- if ( service == null )
- throw new MobyException( "MobyService locator returned an empty service object.\n"
- + "I do not know what service to call..." );
- String serviceName = service.getName();
- if ( isEmpty( serviceName ) || MobyService.DUMMY_NAME.equals( serviceName ) )
- throw new MobyException( "MobyService locator returned an empty service name.\n"
- + "I do not know what service to call..." );
-
- // 2) try service endpoint
- String serviceEndpoint = service.getURL();
- if ( notEmpty( serviceEndpoint ) )
- return callBiomobyService( locator, xmlInput );
-
- // 3) find service endpoint in a Biomoby registry
- Central worker = new CentralImpl( locator.getRegistryEndpoint(), locator.getRegistryNamespace() );
- MobyService[] services = worker.findService( service );
- if ( services == null || services.length == 0 )
- throw new MobyException( "Service " + service.toShortString() + " is not known in Biomoby registry: \n"
- + "\t" + worker.getRegistryEndpoint() + "\n" + "\t" + worker.getRegistryNamespace() );
- // ...and call the service
- serviceEndpoint = services[ 0 ].getURL();
- if ( notEmpty( serviceEndpoint ) ) {
- service.setURL( serviceEndpoint );
- return callBiomobyService( locator, xmlInput );
- }
-
- // what else can I do?
- throw new MobyException( "Registry has not returned any URL for service " + service.toShortString() );
- }
-
- /*******************************************************************************************************************
- * Fill the whole 'mobyInput' - put there any number of jobs (queries) as you wish (you do not need to follow the
- * 'jobCount' hint suggesting how many jobs should be put there).
- *
- *
- * Usually there is not need to overwrite this method. It serves as an inter-mediator between the main
- * {@link #process} method and the individual request fillings (done by a sub-class in method
- * {@link #fillRequest(MobyJob,MobyPackage)}).
- *
- *
- * @return false if you wish to cancel whole request (nothing will be sent to a Biomoby service); otherwise return
- * true.
- *
- * @param mobyInput is an empty shell that you are supposed to fill with the input data for a Biomoby service
- * execution
- *
- * @param jobCount is only a suggestion how many requests/job should be created (it comes from the {@link #process}
- * method) - but it does not need to be obeyed
- *
- ******************************************************************************************************************/
- public boolean fillRequest(MobyPackage mobyInput, int jobCount) throws MobyException {
-
- if ( jobCount < 0 )
- jobCount = 0;
- for ( int i = 0; i < jobCount; i++ ) {
- MobyJob request = new MobyJob( "job_" + i );
- if ( !fillRequest( request, mobyInput ) )
- break;
- mobyInput.addJob( request );
- }
- return ( mobyInput.size() > 0 );
- }
-
- /*******************************************************************************************************************
- * A raw-level processing. Use it if you need access to raw XML coming from a service.
- *
- *
- * @param xmlResponse is a raw XML response returned from a BioMoby service
- *
- * @return false if the response should be considered fully processed (in this case no other 'useResponse' will be
- * called); true indicates that normal processing of the response will follow; by default, this class (BaseClient )
- * returns true
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'mobyResponse' is broken
- ******************************************************************************************************************/
- public boolean useResponse(String xmlResponse) throws MobyException {
- return true;
- }
-
- /*******************************************************************************************************************
- * A high-level processing. Use it if you need access to all jobs (queries) - that returned from a service - in the
- * same time. Otherwise use the processing on the job level (method {@link #useResponse(MobyJob,MobyPackage)}.
- *
- *
- * @param mobyResponse is a full response returned from a BioMoby service
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'mobyResponse' is broken
- ******************************************************************************************************************/
- public void useResponse(MobyPackage mobyResponse) throws MobyException {
-
- // iterate over all input jobs
- for ( int i = 0; i < mobyResponse.size(); i++ ) {
- if ( !useResponse( mobyResponse.getJob( i ), mobyResponse ) )
- return;
- }
- }
-
- /*******************************************************************************************************************
- * Extracts errors from a raw service response. It is iseful when one does not want to create a whole
- * MobyPackage from a response, but just find whether a response is good or bad.
- *
- *
- * @param xmlResponse is a full response returned from a BioMoby service
- *
- * @return a slightly formatted list of exceptions (of severity error ) extracted from the response; or
- * null if there are no errors there
- ******************************************************************************************************************/
- public String errorsInResponse(String xmlResponse) {
- try {
- StringBuffer buf = new StringBuffer();
- SAXBuilder builder = new SAXBuilder();
- Document doc = builder.build( new StringReader( xmlResponse ) );
- Element root = doc.getRootElement();
- Element mobyContent = JDOMUtils.getChild( root, MobyTags.MOBYCONTENT );
- Element serviceNotes = JDOMUtils.getChild( mobyContent, MobyTags.SERVICENOTES );
- ServiceException[] exceptions = ServiceException.extractExceptions( serviceNotes );
- for ( int i = 0; i < exceptions.length; i++ ) {
- if ( exceptions[ i ].getSeverity() != ServiceException.ERROR )
- continue;
- if ( buf.length() > 0 )
- buf.append( "\n" );
- buf.append( exceptions[ i ].getErrorCodeAsString() );
- buf.append( ": " );
- buf.append( exceptions[ i ].getMessage() );
- }
- return ( buf.length() == 0 ? null : new String( buf ) );
-
- }
- catch ( Exception e ) {
- return e.toString();
- }
- }
-
- //
- // Abstract methods
- //
-
- /*******************************************************************************************************************
- * Return characteristics of a BioMoby service that will be called, and that reveal where to find such service.
- *
- *
- * @see #callRemoteService
- *
- * @return an object defining a location of a BioMoby service
- * @throws MobyException if service locator cannot be returned/created (e.g. because there is not enough information
- * about what service to call)
- ******************************************************************************************************************/
- abstract public MobyServiceLocator getServiceLocator() throws MobyException;
-
- /*******************************************************************************************************************
- * Crate data (fill them into 'request') for one Moby job (query). The request will be sent within given
- * 'inputContext' - but it is not yet there (because you may wish not to put it there - see the return value), and
- * it is not the task of this method to put it there (just fill the 'request').
- *
- *
- * This is a method that should be implemented by a client developer, and it is the place where the client's
- * business logic sits.
- *
- *
- * @return true if this request should be included into the input data (package) that will be sent to a biomoby
- * service; or return false if you do not wish to create any more requests for this particular package (also
- * this 'request' will not be used)
- *
- * @param request is an object that you are supposed to fill with input data for one service invocation; it already
- * has a name (so called 'query id' in the BioMoby speak) but you are free to change it
- *
- * @param inputContext is an envelope where all requests will be stored and sent to a Biomoby service; you do not
- * need to do anything with it here unless you wish; note that all already created requests are there,
- * but not the one you are just creating in this method
- *
- * @throws MobyException if you need so (from whatever reason in your business logic); if thrown then nothing will
- * be sent to a Biomoby service
- *
- ******************************************************************************************************************/
- abstract public boolean fillRequest(MobyJob request, MobyPackage inputContext) throws MobyException;
-
- /*******************************************************************************************************************
- * Process a single job returned from a BioMoby service.
- *
- *
- * This is a method that should be implemented by a client developer, and it is the place where the client's
- * business logic using the response sits.
- *
- *
- * @param response is an object that you are supposed to use
- *
- * @param responseContext is an envelope where the full response (all its jobs) is located; you do not need to do
- * anything with it here unless you wish (e.g. it gives you knowledge about how many jobs are in the full
- * response, or it gives you access to the so-called 'service notes')
- *
- * @return false if you do not wish to get any more responses/jobs; otherwise return true
- *
- * @throws MobyException if you are not satisfied with a response data, or from whatever reasons; it also throws
- * this exception if the 'response' is broken
- *
- ******************************************************************************************************************/
- abstract public boolean useResponse(MobyJob response, MobyPackage responseContext) throws MobyException;
-
-}
+// BaseClient.java
+//
+// Created: August 2005
+//
+// This file is a component of the BioMoby project.
+// Copyright Martin Senger (martin.senger at gmail.com).
+//
+
+package org.biomoby.client;
+
+import org.biomoby.shared.MobyException;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.parser.JDOMUtils;
+import org.biomoby.shared.Central;
+import org.biomoby.client.CentralImpl;
+import org.biomoby.shared.parser.MobyPackage;
+import org.biomoby.shared.parser.MobyJob;
+import org.biomoby.shared.parser.ServiceException;
+import org.biomoby.shared.parser.MobyTags;
+
+import org.tulsoft.tools.soap.axis.AxisCall;
+import org.tulsoft.shared.GException;
+
+import org.apache.axis.client.Call;
+import org.apache.commons.lang.StringUtils;
+
+import org.jdom.input.SAXBuilder;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.Namespace;
+
+import java.net.URL;
+import java.net.MalformedURLException;
+import java.io.StringReader;
+
+/**
+ * This is a base class for Biomoby clients. It takes care about
+ * converting user input into Biomoby XML, sending it in a SOAP
+ * message to a Biomoby service, waiting for the response and parsing
+ * it from Biomoby XML. It also divides requests and responses into
+ * so-called jobs - each of them corresponds to a Biomoby
+ * query (a Biomoby single network request may contain more
+ * queries/jobs).
+ *
+ * Any client can override various methods - but the ones she/he
+ * must override in a subclass are those telling what service
+ * to call ({@link #getServiceLocator}), what data to put in a request
+ * ({@link #fillRequest(MobyJob,MobyPackage) fillRequest}), and what
+ * to do with a response ({@link #useResponse(MobyJob,MobyPackage)
+ * useResponse}.
+ *
+ * @author Martin Senger
+ * @version $Id$
+ */
+
+abstract public class BaseClient {
+
+ private static org.apache.commons.logging.Log log =
+ org.apache.commons.logging.LogFactory.getLog (BaseClient.class);
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ static protected boolean notEmpty (String value) {
+ return StringUtils.isNotBlank (value);
+ }
+ static protected boolean isEmpty (String value) {
+ return StringUtils.isBlank (value);
+ }
+
+ /**************************************************************************
+ * The main method that packs input data, invokes a BioMoby
+ * service and uses its response. Use this method if the input
+ * data should have just one job (which is a usual case) -
+ * otherwise use method {@link #process(int)}.
+ *
+ * @throws MobyException if (a) a sub-class throws it during the
+ * filling data or using response, or (b) a Biomoby service
+ * invocation fails
+ *************************************************************************/
+ public void process()
+ throws MobyException {
+ process (1);
+ }
+
+ /**************************************************************************
+ * The main method that packs input data, invokes a BioMoby
+ * service and uses its response. The input data may consist from
+ * more than one job (query) - the 'jobCount' is a suggestion how
+ * many jobs will be included, but this can be changed by the
+ * implementing sub-class.
+ *
+ * Usually a client developer does not need to overwrite this
+ * method. She or he makes the real input data filling in the
+ * {@link #fillRequest} method, and uses the response in the
+ * {@link #useResponse} method.
+ *
+ * @throws MobyException if (a) a sub-class throws it during the
+ * filling data or using response, or (b) a Biomoby service
+ * invocation fails
+ *************************************************************************/
+ public void process (int jobCount)
+ throws MobyException {
+
+ String xmlResponse = null;
+
+ // input: raw-level processing
+ String xmlInput = fillRequest();
+ if (xmlInput != null) {
+ if ( (xmlInput = interceptRequest (xmlInput)) == null )
+ return;
+ }
+
+ // input: usual processing (i.e. collect XML in iterations)
+ else {
+ MobyPackage mobyInput = new MobyPackage();
+ if (! fillRequest (mobyInput, jobCount)) return;
+ xmlInput = mobyInput.toXML();
+ if ( (xmlInput = interceptRequest (xmlInput)) == null )
+ return;
+ }
+
+ // calling service
+ xmlResponse = callRemoteService (xmlInput);
+
+ // output: raw-level processing
+ if (! useResponse (xmlResponse)) return;
+
+ // output: usual processing (again by iterations)
+ MobyPackage mobyResponse = MobyPackage.createFromXML (xmlResponse);
+ useResponse (mobyResponse);
+ }
+
+ public String interceptRequest (String xmlInput)
+ throws MobyException {
+ return xmlInput;
+ }
+
+ /**************************************************************************
+ * Create raw XML input. Override this method if you have already
+ * an input XML, or you want to create it yourself.
+ *
+ * @return a full XML input for a Biomoby service (in this case no
+ * other fillRequest methods will called); return null if
+ * no XML was created and a usual process to gather it will be used
+ *
+ * @throws MobyException if an XML cannot be created
+ *************************************************************************/
+ public String fillRequest()
+ throws MobyException {
+ return null;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected String filterMobyResponseType (Object result)
+ throws MobyException {
+ if (result instanceof String)
+ return (String)result;
+ else if (result instanceof byte[])
+ return new String ((byte[])result);
+ else
+ throw new MobyException
+ ("The Biomoby data should be sent/received either as type String or base64/byte[]. " +
+ "But they are of type '" + result.getClass().getName() + "'.");
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected String callBiomobyService (MobyServiceLocator locator,
+ String xmlInput)
+ throws MobyException {
+
+
+ MobyService service = locator.getService();
+ String serviceName = service.getName();
+ boolean asBytes = locator.isAsBytes();
+ String serviceEndpoint = service.getURL();
+ int timeout = locator.getSuggestedTimeout();
+
+ try {
+ URL target = new URL (serviceEndpoint);
+ AxisCall call = new AxisCall (target, timeout);
+ // if the locator has authentication information.
+ if(locator.hasAuthentication()) {
+ call.getCall().setProperty( Call.USERNAME_PROPERTY, locator.getUser() );
+ call.getCall().setProperty( Call.PASSWORD_PROPERTY, locator.getPassword() );
+ }
+ call.getCall().setSOAPActionURI (MobyService.BIOMOBY_SERVICE_URI + "#" + serviceName);
+ return filterMobyResponseType
+ (call.doCall (MobyService.BIOMOBY_SERVICE_URI,
+ serviceName,
+ new Object[] { sendingFilter (xmlInput, asBytes) }));
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Service endpoint '" + serviceEndpoint +
+ "' is not a valid URL.");
+ } catch (GException e) {
+ throw new MobyException (e.getMessage(), e);
+ }
+ }
+
+ //
+ protected Object sendingFilter (String input, boolean asBytes) {
+ if (asBytes) {
+ log.debug ("Data sent as a byte array");
+ return input.getBytes();
+ } else {
+ return input;
+ }
+ }
+
+ /**************************************************************************
+ * Call a SOAP-based BioMoby service. In order to find what
+ * service to call and what are its characteristics (such as its
+ * endpoint) it will call method {@link #getServiceLocator} that
+ * should be implemented by a sub-class.
+ *
+ * Once it has the service locator, this class does one of the
+ * following, in this order:
+ *
+ * The locator must contain at least a service name. If it
+ * does not, an exception is raised.
+ *
+ * If the locator contains a service endpoint, a call is
+ * made to this endpoint, using also the service name as a
+ * method name.
+ *
+ * If the locator has a registry endpoint, an enquiry to
+ * the registry is made to find an endpoint of a service
+ * corresponding with the given service name. Once found, the
+ * service is called.
+ *
+ * The same as the previous one but using a default
+ * registry.
+ *
+ * @param xmlInput data will be sent to the called Biomoby service
+ *
+ * @return service response (still in XML)
+ *
+ * @throws MobyException (a) if service call (or a call to
+ * registry; for example because the registry does not know given
+ * service) fails, or (b) if the used {@link MobyServiceLocator}
+ * does not contain a service name.
+ *
+ *************************************************************************/
+ public String callRemoteService (String xmlInput)
+ throws MobyException {
+
+ // 1) service name is a must
+ MobyServiceLocator locator = getServiceLocator();
+ MobyService service = locator.getService();
+ if (service == null)
+ throw new MobyException ("MobyService locator returned an empty service object.\n" +
+ "I do not know what service to call...");
+ String serviceName = service.getName();
+ if (isEmpty (serviceName) ||
+ MobyService.DUMMY_NAME.equals (serviceName))
+ throw new MobyException ("MobyService locator returned an empty service name.\n" +
+ "I do not know what service to call...");
+
+ // 2) try service endpoint
+ String serviceEndpoint = service.getURL();
+ if (notEmpty (serviceEndpoint))
+ return callBiomobyService (locator, xmlInput);
+
+ // 3) find service endpoint in a Biomoby registry
+ Central worker = new CentralImpl (locator.getRegistryEndpoint(),
+ locator.getRegistryNamespace());
+ MobyService[] services = worker.findService (service);
+ if (services == null || services.length == 0)
+ throw new MobyException ("Service " + service.toShortString() +
+ " is not known in Biomoby registry: \n" +
+ "\t" + worker.getRegistryEndpoint() + "\n" +
+ "\t" + worker.getRegistryNamespace());
+ // ...and call the service
+ serviceEndpoint = services[0].getURL();
+ if (notEmpty (serviceEndpoint)) {
+ service.setURL (serviceEndpoint);
+ return callBiomobyService (locator, xmlInput);
+ }
+
+ // what else can I do?
+ throw new MobyException ("Registry has not returned any URL for service " +
+ service.toShortString());
+ }
+
+ /**************************************************************************
+ * Fill the whole 'mobyInput' - put there any number of jobs
+ * (queries) as you wish (you do not need to follow the 'jobCount'
+ * hint suggesting how many jobs should be put there).
+ *
+ * Usually there is not need to overwrite this method. It serves
+ * as an inter-mediator between the main {@link #process} method
+ * and the individual request fillings (done by a sub-class in
+ * method {@link #fillRequest(MobyJob,MobyPackage)}).
+ *
+ * @return false if you wish to cancel whole request (nothing will
+ * be sent to a Biomoby service); otherwise return true.
+ *
+ * @param mobyInput is an empty shell that you are supposed to
+ * fill with the input data for a Biomoby service execution
+ *
+ * @param jobCount is only a suggestion how many requests/job
+ * should be created (it comes from the {@link #process} method) -
+ * but it does not need to be obeyed
+ *
+ *************************************************************************/
+ public boolean fillRequest (MobyPackage mobyInput, int jobCount)
+ throws MobyException {
+
+ if (jobCount < 0) jobCount = 0;
+ for (int i = 0; i < jobCount; i++) {
+ MobyJob request = new MobyJob ("job_" + i);
+ if (! fillRequest (request, mobyInput))
+ break;
+ mobyInput.addJob (request);
+ }
+ return (mobyInput.size() > 0);
+ }
+
+ /**************************************************************************
+ * A raw-level processing. Use it if you need access to raw XML
+ * coming from a service.
+ *
+ * @param xmlResponse is a raw XML response returned from a
+ * BioMoby service
+ *
+ * @return false if the response should be considered fully
+ * processed (in this case no other 'useResponse' will be called);
+ * true indicates that normal processing of the response will
+ * follow; by default, this class (BaseClient ) returns true
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'mobyResponse' is broken
+ *************************************************************************/
+ public boolean useResponse (String xmlResponse)
+ throws MobyException {
+ return true;
+ }
+
+ /**************************************************************************
+ * A high-level processing. Use it if you need access to all jobs
+ * (queries) - that returned from a service - in the same time.
+ * Otherwise use the processing on the job level (method {@link
+ * #useResponse(MobyJob,MobyPackage)}.
+ *
+ * @param mobyResponse is a full response returned from a BioMoby
+ * service
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'mobyResponse' is broken
+ *************************************************************************/
+ public void useResponse (MobyPackage mobyResponse)
+ throws MobyException {
+
+ // iterate over all input jobs
+ for (int i = 0; i < mobyResponse.size(); i++) {
+ if (! useResponse (mobyResponse.getJob (i),
+ mobyResponse))
+ return;
+ }
+ }
+
+ /**************************************************************************
+ * Extracts errors from a raw service response. It is iseful when
+ * one does not want to create a whole MobyPackage from a
+ * response, but just find whether a response is good or bad.
+ *
+ * @param xmlResponse is a full response returned from a BioMoby
+ * service
+ *
+ * @return a slightly formatted list of exceptions (of severity
+ * error ) extracted from the response; or null if there
+ * are no errors there
+ *************************************************************************/
+ public String errorsInResponse (String xmlResponse) {
+ try {
+ StringBuffer buf = new StringBuffer();
+ SAXBuilder builder = new SAXBuilder();
+ Document doc =
+ builder.build (new StringReader (xmlResponse));
+ Element root = doc.getRootElement();
+ Element mobyContent = JDOMUtils.getChild (root, MobyTags.MOBYCONTENT);
+ Element serviceNotes = JDOMUtils.getChild (mobyContent, MobyTags.SERVICENOTES);
+ ServiceException[] exceptions =
+ ServiceException.extractExceptions (serviceNotes);
+ for (int i = 0; i < exceptions.length; i++) {
+ if (exceptions[i].getSeverity() != ServiceException.ERROR)
+ continue;
+ if (buf.length() > 0)
+ buf.append ("\n");
+ buf.append (exceptions[i].getErrorCodeAsString());
+ buf.append (": ");
+ buf.append (exceptions[i].getMessage());
+ }
+ return (buf.length() == 0 ? null : new String (buf));
+
+ } catch (Exception e) {
+ return e.toString();
+ }
+ }
+
+
+ //
+ // Abstract methods
+ //
+
+ /**************************************************************************
+ * Return characteristics of a BioMoby service that will be
+ * called, and that reveal where to find such service.
+ *
+ * @see #callRemoteService
+ *
+ * @return an object defining a location of a BioMoby service
+ * @throws MobyException if service locator cannot be
+ * returned/created (e.g. because there is not enough information
+ * about what service to call)
+ *************************************************************************/
+ abstract public MobyServiceLocator getServiceLocator()
+ throws MobyException;
+
+ /**************************************************************************
+ * Crate data (fill them into 'request') for one Moby job
+ * (query). The request will be sent within given 'inputContext' -
+ * but it is not yet there (because you may wish not to put it
+ * there - see the return value), and it is not the task of this
+ * method to put it there (just fill the 'request').
+ *
+ * This is a method that should be implemented by a client
+ * developer, and it is the place where the client's business
+ * logic sits.
+ *
+ * @return true if this request should be included into the input
+ * data (package) that will be sent to a biomoby service; or
+ * return false if you do not wish to create any more requests for
+ * this particular package (also this 'request' will not be used)
+ *
+ * @param request is an object that you are supposed to fill with
+ * input data for one service invocation; it already has a name
+ * (so called 'query id' in the BioMoby speak) but you are free to change it
+ *
+ * @param inputContext is an envelope where all requests will be
+ * stored and sent to a Biomoby service; you do not need to do
+ * anything with it here unless you wish; note that all already
+ * created requests are there, but not the one you are just
+ * creating in this method
+ *
+ * @throws MobyException if you need so (from whatever reason in
+ * your business logic); if thrown then nothing will be sent to a
+ * Biomoby service
+ *
+ *************************************************************************/
+ abstract public boolean fillRequest (MobyJob request, MobyPackage inputContext)
+ throws MobyException;
+
+ /**************************************************************************
+ * Process a single job returned from a BioMoby service.
+ *
+ * This is a method that should be implemented by a client
+ * developer, and it is the place where the client's business
+ * logic using the response sits.
+ *
+ * @param response is an object that you are supposed to use
+ *
+ * @param responseContext is an envelope where the full response
+ * (all its jobs) is located; you do not need to do anything with
+ * it here unless you wish (e.g. it gives you knowledge about how
+ * many jobs are in the full response, or it gives you access to
+ * the so-called 'service notes')
+ *
+ * @return false if you do not wish to get any more
+ * responses/jobs; otherwise return true
+ *
+ * @throws MobyException if you are not satisfied with a response
+ * data, or from whatever reasons; it also throws this exception
+ * if the 'response' is broken
+ *
+ *************************************************************************/
+ abstract public boolean useResponse (MobyJob response,
+ MobyPackage responseContext)
+ throws MobyException;
+
+}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2006/02/19 18:42:55 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/03 15:21:13 1.5
@@ -33,6 +33,8 @@
protected String registryNamespace;
protected boolean asBytes = false;
protected int timeout = 0;
+ protected String user;
+ protected String password;
/**************************************************************************
* Default constructor.
@@ -131,6 +133,44 @@
public void setAsBytes (boolean enabled) {
asBytes = enabled;
}
-
-
+
+ /*****************************************
+ * Sets the user for authentication
+ * @param user
+ ***************************************/
+ public void setUser(String user) {
+ this.user = user;
+ }
+
+ /***************************************
+ * Sets the password for authentication
+ * @param password
+ ***************************************/
+ public void setPassword(String password) {
+ this.password = password;
+ }
+
+ /******************************************
+ * Returns the user for the authentication
+ * @return user
+ ******************************************/
+ public String getUser() {
+ return user;
+ }
+
+ /**********************************************
+ * Returns the password for the authentication
+ * @return password
+ **********************************************/
+ public String getPassword() {
+ return password;
+ }
+
+ /***************************************************
+ * Returns true if the user AND the password is set
+ * @return
+ ***************************************************/
+ public boolean hasAuthentication() {
+ return user != null && password != null;
+ }
}
From groscurt at dev.open-bio.org Wed Dec 3 12:09:41 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 3 Dec 2008 07:09:41 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812031209.mB3C9f1X011972@dev.open-bio.org>
groscurt
Wed Dec 3 07:09:40 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv11937/src/main/org/biomoby/client
Modified Files:
CentralImpl.java
Log Message:
reformatted it to the original version and removed the System.properties for the service authentication
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.58,1.59
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/11/26 08:53:43 1.58
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2008/12/03 12:09:40 1.59
@@ -69,50 +69,53 @@
import java.util.logging.*;
/**
- * A default implementation of the interface {@link org.biomoby.shared.Central Central} allowing access to a Moby
- * registry.
- *
- * This class is supposed to be used by all other clients that wish to communicate with the Moby Registry, but do not
- * want to know about all XML details that are necessary for talking with the Moby Central directly. This is an example
- * of a client program:
- *
- *
+ * A default implementation of the
+ * interface {@link org.biomoby.shared.Central Central}
+ * allowing access to a Moby registry.
+ *
+ * This class is supposed to be used by all other clients that wish
+ * to communicate with the Moby Registry, but do not want to know
+ * about all XML details that are necessary for talking with the Moby Central
+ * directly. This is an example of a client program:
+ *
* import org.biomoby.shared.Central;
* import org.biomoby.shared.MobyException;
* import org.biomoby.client.CentralImpl;
* import java.util.Map;
* import java.util.Iterator;
- *
+ *
* public class Test {
- *
- * public static void main( String[] args ) throws MobyException {
- *
- * Central worker = new CentralImpl();
- * Map authorities = worker.getServiceNamesByAuthority();
- *
- * for ( Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
- * Map.Entry entry = ( Map.Entry ) it.next();
- * System.out.println( entry.getKey() );
- * String[] names = ( String[] ) entry.getValue();
- * for ( int i = 0; i < names.length; i++ )
- * System.out.println( "\t" + names[ i ] );
- * }
- * }
+ *
+ * public static void main (String[] args)
+ * throws MobyException {
+ *
+ * Central worker = new CentralImpl();
+ * Map authorities = worker.getServiceNamesByAuthority();
+ *
+ * for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
+ * Map.Entry entry = (Map.Entry)it.next();
+ * System.out.println (entry.getKey());
+ * String[] names = (String[])entry.getValue();
+ * for (int i = 0; i < names.length; i++)
+ * System.out.println ("\t" + names[i]);
+ * }
+ * }
* }
- *
- *
+ *
+ *
* @author Martin Senger
* @version $Id$
*/
-public class CentralImpl implements Central, SimpleCache {
+public class CentralImpl
+ implements Central, SimpleCache {
private URL endpoint;
private String uri;
protected boolean debug = false;
/** Common central used to if getDefaultCentral() is called */
- protected static Map< String, CentralImpl > defaultCentrals = new HashMap< String, CentralImpl >();
+ protected static Map defaultCentrals = new HashMap();
/** Default location (endpoint) of a Moby registry. */
public static final String DEFAULT_ENDPOINT = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
@@ -121,322 +124,368 @@
public static final String DEFAULT_NAMESPACE = "http://moby.ucalgary.ca/MOBY/Central";
/**
- * The META-INF resource file that will be checked to determine what default class should be instantiated in order
- * to create a Central Implementation when getDefaultCentral() is called.
+ * The META-INF resource file that will be checked to determine what
+ * default class should be instantiated in order to create a Central Implementation
+ * when getDefaultCentral() is called.
*/
public static final String CENTRAL_IMPL_RESOURCE_NAME = "org.biomoby.shared.CentralDefaultImpl";
/** The class to use for getDefaultCentral if all else fails */
public static final String DEFAULT_CENTRAL_IMPL_CLASSNAME = "org.biomoby.client.CentralDigestCachedImpl";
- private static Logger logger = Logger.getLogger( "org.biomoby.client.CentralImpl" );
+ private static Logger logger = Logger.getLogger("org.biomoby.client.CentralImpl");
- /**
- * Thread local that gives each thread its own DocumentBuilderFactory (since it is not thread-safe). Code taken from
- * Apache's JaxpUtils.
- */
- public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
- protected synchronized Object initialValue() {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware( true );
- return dbf;
- }
- };
-
- /*******************************************************************************************************************
- * Default constructor. It connects to a default Moby registry (as defined in {@link #DEFAULT_ENDPOINT}) using a
- * default namespace (as defined int {@link #DEFAULT_NAMESPACE}).
- ******************************************************************************************************************/
- public CentralImpl() throws MobyException {
- this( DEFAULT_ENDPOINT, DEFAULT_NAMESPACE );
+ /**
+ * Thread local that gives each thread its own
+ * DocumentBuilderFactory (since it is not thread-safe). Code taken
+ * from Apache's JaxpUtils.
+ */
+ public static ThreadLocal DOCUMENT_BUILDER_FACTORIES = new ThreadLocal() {
+ protected synchronized Object initialValue() {
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ dbf.setNamespaceAware (true);
+ return dbf;
+ }
+ };
+
+
+ /*************************************************************************
+ * Default constructor. It connects to a default Moby registry
+ * (as defined in {@link #DEFAULT_ENDPOINT}) using a default namespace
+ * (as defined int {@link #DEFAULT_NAMESPACE}).
+ *************************************************************************/
+ public CentralImpl()
+ throws MobyException {
+ this (DEFAULT_ENDPOINT, DEFAULT_NAMESPACE);
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Constructor allowing to specify which Moby Registry to use.
- *
- * @throws MobyException
- * if 'endpoint' is not a valid URL, or if no DOM parser is available
- ******************************************************************************************************************/
- public CentralImpl( String endpoint ) throws MobyException {
- this( endpoint, DEFAULT_NAMESPACE );
- }
-
- /*******************************************************************************************************************
- * Constructor allowing to specify which Moby Registry and what namespace to use. If any of the parameters is null,
- * its default value is used instead.
- *
- *
- * @throws MobyException
- * if 'endpoint' is not a valid URL, or if no DOM parser was found
- ******************************************************************************************************************/
- public CentralImpl( String endpoint, String namespace ) throws MobyException {
-
- if ( endpoint == null || "".equals( endpoint.trim() ) ) endpoint = DEFAULT_ENDPOINT;
- if ( namespace == null || "".equals( namespace.trim() ) ) namespace = DEFAULT_NAMESPACE;
-
- try {
- this.endpoint = new URL( endpoint );
- }
- catch ( MalformedURLException e ) {
- throw new MobyException( "Bad URL: " + endpoint );
- }
- this.uri = namespace;
-
- cache = new Hashtable< String, Object >();
- useCache = true;
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser is available
+ *************************************************************************/
+ public CentralImpl (String endpoint)
+ throws MobyException {
+ this (endpoint, DEFAULT_NAMESPACE);
+ }
+
+ /*************************************************************************
+ * Constructor allowing to specify which Moby Registry and what
+ * namespace to use. If any of the parameters is null, its default
+ * value is used instead.
+ *
+ * @throws MobyException if 'endpoint' is not a valid URL, or if no
+ * DOM parser was found
+ *************************************************************************/
+ public CentralImpl (String endpoint, String namespace)
+ throws MobyException {
+
+ if (endpoint == null || "".equals (endpoint.trim()))
+ endpoint = DEFAULT_ENDPOINT;
+ if (namespace == null || "".equals (namespace.trim()))
+ namespace = DEFAULT_NAMESPACE;
+
+ try {
+ this.endpoint = new URL (endpoint);
+ } catch (MalformedURLException e) {
+ throw new MobyException ("Bad URL: " + endpoint);
+ }
+ this.uri = namespace;
+
+ cache = new Hashtable();
+ useCache = true;
+ }
+
+ /*************************************************************************
+ * Loads a DOM Document from an InputStream. Uses thread-safe
+ * mechanism.
+ *************************************************************************/
+ public static Document loadDocument (InputStream input)
+ throws MobyException {
+ try {
+ DocumentBuilderFactory dbf
+ = (DocumentBuilderFactory)DOCUMENT_BUILDER_FACTORIES.get();
+ DocumentBuilder db = dbf.newDocumentBuilder();
+ return (db.parse (input));
+ } catch (Exception e) {
+ throw new MobyException ("Problem with reading XML input: " + e.toString(), e);
}
-
- /*******************************************************************************************************************
- * Loads a DOM Document from an InputStream. Uses thread-safe mechanism.
- ******************************************************************************************************************/
- public static Document loadDocument( InputStream input ) throws MobyException {
- try {
- DocumentBuilderFactory dbf = ( DocumentBuilderFactory ) DOCUMENT_BUILDER_FACTORIES.get();
- DocumentBuilder db = dbf.newDocumentBuilder();
- return ( db.parse( input ) );
- }
- catch ( Exception e ) {
- throw new MobyException( "Problem with reading XML input: " + e.toString(), e );
- }
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Call 'method' with 'parameters' and return its result.
- ******************************************************************************************************************/
- protected Object doCall( String method, Object[] parameters ) throws MobyException {
-
- Call call = null;
- try {
- Service service = new Service();
- call = ( Call ) service.createCall();
- call.setTargetEndpointAddress( endpoint );
- call.setTimeout( new Integer( 0 ) );
-
- String user = System.getProperty( "user" );
- String password = System.getProperty( "password" );
-
- if ( user != null && password != null ) {
- call.setProperty( Call.USERNAME_PROPERTY, user );
- call.setProperty( Call.PASSWORD_PROPERTY, password );
- }
-
- call.setSOAPActionURI( uri + "#" + method );
-
- if ( debug ) {
- System.err.println( "METHOD CALL: " + method );
- System.err.println( "------------" );
- if ( parameters.length > 0 ) System.err.println( parameters[ 0 ] + "\n" );
- System.err.println( "------------\n" );
-
- Object result = call.invoke( uri, method, parameters );
-
- System.err.println( "METHOD RETURN:" );
- System.err.println( "------------" );
- if ( result != null ) System.err.println( result + "\n" );
- System.err.println( "------------\n" );
-
- return resultToString( result );
-
- }
- else {
- return resultToString( call.invoke( uri, method, parameters ) );
- }
-
- }
- catch ( AxisFault e ) {
- throw new MobyException( formatFault( e, endpoint.toString(), ( call == null ? null : call
- .getOperationName() ) ), e );
- // (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
-
- }
- catch ( Exception e ) {
- throw new MobyException( e.toString(), e );
- // e.printStackTrace();
- }
- }
-
- /*******************************************************************************************************************
- * Parse the given XML sniplet to find tag 'success'. If it has value '1' look further for tag 'id' and return it
- * back (or return an empty string if ID is not there). Otherwise raise an exception with the 'culprit' and with the
- * message from the tag 'message'.
- *
- *
- * The return value is a two-element long array. The first element is the ID (given by BioMobe registry), and the
- * second element is RDF corresponding with the registered object (BioMoby returns this only for service instances,
- * so for other objects this will be null).
- *
- *
- * This is how the XML is supposed to look:
- *
- * Success takes the value "1" to indicate success, "0" to indicate failure, and "-1" to indicate "Pending
- * Curation".
- ******************************************************************************************************************/
- protected String[] checkRegistration( String xml, Object culprit ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String id = "", success = "0", message = "", rdf = "";
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( xml.getBytes() ) );
- Element root = document.getDocumentElement();
-
- NodeList children = root.getChildNodes();
- for ( int i = 0; i < children.getLength(); i++ ) {
- if ( children.item( i ).getNodeType() != Node.ELEMENT_NODE ) continue;
- Element elem = ( Element ) children.item( i );
- if ( elem.getNodeName().equals( "id" ) ) {
- if ( elem.getFirstChild() != null ) id = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "success" ) ) {
- if ( elem.getFirstChild() != null ) success = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "message" ) ) {
- if ( elem.getFirstChild() != null ) message = elem.getFirstChild().getNodeValue();
- }
- else if ( elem.getNodeName().equals( "RDF" ) ) {
- if ( elem.getFirstChild() != null ) rdf = elem.getFirstChild().getNodeValue();
- }
- }
-
- if ( success.equals( "0" ) )
- throw new NoSuccessException( message, culprit );
- else if ( success.equals( "-1" ) ) throw new PendingCurationException();
- return new String[] { id, rdf };
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML created from the definitions representing input data types and their usage in the given
- * service. Only data considered primary are included. Note that the main job of converting to XML is done by
- * instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- ******************************************************************************************************************/
- protected String buildSecondaryInputTag( MobyService service ) {
- StringBuffer buf = new StringBuffer();
- MobyData[] secInputs = service.getSecondaryInputs();
- buf.append( "\n" );
- for ( int i = 0; i < secInputs.length; i++ ) {
- buf.append( secInputs[ i ].toXML() );
- }
- buf.append( " \n" );
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML created from the definitions representing output data types and their usage in the given
- * service. Only data considered primary are included. Note that the main job of converting to XML is done by
- * instances of MobyPrimaryData.
- *
- * The returned XML looks like this:
- *
- *
- ******************************************************************************************************************/
- protected String buildOutputTag( MobyService service ) {
- StringBuffer buf = new StringBuffer();
- MobyData[] primaryOutputs = service.getPrimaryOutputs();
- buf.append( "\n" );
- for ( int i = 0; i < primaryOutputs.length; i++ )
- buf.append( primaryOutputs[ i ].toXML() );
- buf.append( " \n" );
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Return a piece of XML represented a query object (an object used to find a service).
- *
+ *************************************************************************/
+ protected Object doCall (String method, Object[] parameters)
+ throws MobyException {
+
+ Call call = null;
+ try {
+ Service service = new Service();
+ call = (Call) service.createCall();
+ call.setTargetEndpointAddress (endpoint);
+ call.setTimeout (new Integer (0));
+
+ call.setSOAPActionURI (uri + "#" + method);
+
+ if (debug) {
+ System.err.println ("METHOD CALL: " + method);
+ System.err.println ("------------");
+ if (parameters.length > 0)
+ System.err.println (parameters[0] + "\n");
+ System.err.println ("------------\n");
+
+ Object result = call.invoke (uri, method, parameters);
+
+ System.err.println ("METHOD RETURN:");
+ System.err.println ("------------");
+ if (result != null)
+ System.err.println (result + "\n");
+ System.err.println ("------------\n");
+
+ return resultToString (result);
+
+ } else {
+ return resultToString (call.invoke (uri, method, parameters));
+ }
+
+ } catch (AxisFault e) {
+ throw new MobyException
+ (formatFault (e,
+ endpoint.toString(),
+ (call == null ? null : call.getOperationName())),
+ e);
+// (endpoint.toString()+(call == null ? "" : call.getOperationName()), e);
+
+ } catch (Exception e) {
+ throw new MobyException (e.toString(), e);
+// e.printStackTrace();
+ }
+ }
+
+
+ /**************************************************************************
+ * Parse the given XML sniplet to find tag 'success'. If it has value '1'
+ * look further for tag 'id' and return it back (or return an empty string
+ * if ID is not there). Otherwise raise an exception with the 'culprit'
+ * and with the message from the tag 'message'.
+ *
+ * The return value is a two-element long array. The first element
+ * is the ID (given by BioMobe registry), and the second element
+ * is RDF corresponding with the registered object (BioMoby
+ * returns this only for service instances, so for other objects
+ * this will be null).
+ *
+ * This is how the XML is supposed to look:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * Success takes the value "1" to indicate success, "0" to
+ * indicate failure, and "-1" to indicate "Pending Curation".
+ *************************************************************************/
+ protected String[] checkRegistration (String xml, Object culprit)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String id = "", success = "0", message = "", rdf = "";
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ Element root = document.getDocumentElement();
+
+ NodeList children = root.getChildNodes();
+ for (int i = 0; i < children.getLength(); i++) {
+ if (children.item (i).getNodeType() != Node.ELEMENT_NODE)
+ continue;
+ Element elem = (Element)children.item (i);
+ if (elem.getNodeName().equals ("id")) {
+ if (elem.getFirstChild() != null)
+ id = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals("success")) {
+ if (elem.getFirstChild() != null)
+ success = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("message")) {
+ if (elem.getFirstChild() != null)
+ message = elem.getFirstChild().getNodeValue();
+ } else if (elem.getNodeName().equals ("RDF")) {
+ if (elem.getFirstChild() != null)
+ rdf = elem.getFirstChild().getNodeValue();
+ }
+ }
+
+ if (success.equals ("0"))
+ throw new NoSuccessException (message, culprit);
+ else if (success.equals ("-1"))
+ throw new PendingCurationException();
+ return new String[] { id, rdf };
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing input
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
* The returned XML looks like this:
- *
- *
- *
- * ServiceTypeTerm ServiceName moby
- * http://desired.service.provider ; 1|0 1|0
- * 1|0 something .... ....
- ******************************************************************************************************************/
- protected String buildQueryObject( MobyService service, String[] keywords, boolean expandObjects,
- boolean expandServices, boolean authoritative ) {
- if ( service == null ) {
- service = new MobyService( "dummy" );
- service.setCategory( "" );
- }
- StringBuffer buf = new StringBuffer();
-
- buf.append( "\n \n" );
-
- buf.append( "\n\n" );
- MobyData[] po = service.getPrimaryOutputs();
- if ( po.length > 0 ) {
- for ( int i = 0; i < po.length; i++ )
- buf.append( po[ i ].toXML() );
- }
- buf.append( " \n \n" );
-
- buf.append( "" + service.getType() + " \n" );
-
- String name = service.getName();
- if ( !name.equals( "" ) && !name.equals( "dummy" ) && !name.equals( MobyService.DUMMY_NAME ) )
- buf.append( "" + service.getName() + " \n" );
-
- String sigURL = service.getSignatureURL();
- if ( !sigURL.equals( "" ) ) buf.append( "" + sigURL + " \n" );
-
- buf.append( "" + service.getCategory() + " \n" );
- buf.append( "" + service.getAuthority() + " \n" );
-
- buf.append( "" );
- buf.append( expandObjects ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "" );
- buf.append( expandServices ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "" );
- buf.append( authoritative ? "1" : "0" );
- buf.append( " \n" );
-
- buf.append( "\n" );
- if ( keywords != null && keywords.length > 0 ) {
- for ( int i = 0; i < keywords.length; i++ ) {
- buf.append( "" );
- buf.append( keywords[ i ] );
- buf.append( " \n" );
- }
- }
- buf.append( " \n" );
-
- return new String( buf );
- }
-
- /*******************************************************************************************************************
- * Extract one or more MobyService objects from the given XML piece. The XML should look like this:
- *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildSecondaryInputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] secInputs = service.getSecondaryInputs();
+ buf.append ("\n");
+ for (int i = 0; i < secInputs.length; i++) {
+ buf.append (secInputs[i].toXML());
+ }
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML created from the definitions representing output
+ * data types and their usage in the given service. Only data considered
+ * primary are included. Note that the main job of converting to XML is
+ * done by instances of MobyPrimaryData.
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *************************************************************************/
+ protected String buildOutputTag (MobyService service) {
+ StringBuffer buf = new StringBuffer();
+ MobyData[] primaryOutputs = service.getPrimaryOutputs();
+ buf.append ("\n");
+ for (int i = 0; i < primaryOutputs.length; i++)
+ buf.append (primaryOutputs[i].toXML());
+ buf.append (" \n");
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Return a piece of XML represented a query object (an object used
+ * to find a service).
+ *
+ * The returned XML looks like this:
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ *
+ * ServiceTypeTerm
+ * ServiceName
+ * moby
+ * http://desired.service.provider ;
+ * 1|0
+ * 1|0
+ * 1|0
+ *
+ * something
+ * ....
+ * ....
+ *
+ *************************************************************************/
+ protected String buildQueryObject (MobyService service,
+ String[] keywords,
+ boolean expandObjects,
+ boolean expandServices,
+ boolean authoritative) {
+ if (service == null) {
+ service = new MobyService ("dummy");
+ service.setCategory ("");
+ }
+ StringBuffer buf = new StringBuffer();
+
+ buf.append ("\n \n");
+
+ buf.append ("\n\n");
+ MobyData[] po = service.getPrimaryOutputs();
+ if (po.length > 0) {
+ for (int i = 0; i < po.length; i++)
+ buf.append (po[i].toXML());
+ }
+ buf.append (" \n \n");
+
+ buf.append ("" + service.getType() + " \n");
+
+ String name = service.getName();
+ if (!name.equals ("") && !name.equals ("dummy") && !name.equals (MobyService.DUMMY_NAME))
+ buf.append ("" + service.getName() + " \n");
+
+ String sigURL = service.getSignatureURL();
+ if (!sigURL.equals (""))
+ buf.append ("" + sigURL + " \n");
+
+ buf.append ("" + service.getCategory() + " \n");
+ buf.append ("" + service.getAuthority() + " \n");
+
+ buf.append ("");
+ buf.append (expandObjects ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (expandServices ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("");
+ buf.append (authoritative ? "1" : "0");
+ buf.append (" \n");
+
+ buf.append ("\n");
+ if (keywords != null && keywords.length > 0) {
+ for (int i = 0; i < keywords.length; i++) {
+ buf.append ("");
+ buf.append (keywords[i]);
+ buf.append (" \n");
+ }
+ }
+ buf.append (" \n");
+
+ return new String (buf);
+ }
+
+ /**************************************************************************
+ * Extract one or more MobyService objects from the given XML piece.
+ * The XML should look like this:
*
* <Services>
- * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
+ * <Service authURI="authority.URI.here" lsid="..." serviceName="MyService">
* <serviceType>Service_Ontology_Term</serviceType>
* <Category>moby</Category> <!-- or 'cgi' or 'soap' -->
* <contactEmail>your at email.addy.here</contactEmail>
@@ -459,359 +508,359 @@
* ...
* </Services>
*
- *
- * @throws MobyException
- * if the XML document is invalid
- ******************************************************************************************************************/
- public MobyService[] extractServices( String xml ) throws MobyException {
-
- Document document = loadDocument( new ByteArrayInputStream( xml.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Service" );
- MobyService[] results = new MobyService[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyService service = new MobyService( elem.getAttribute( "serviceName" ) );
- service.setAuthority( elem.getAttribute( "authURI" ) );
- service.setLSID( elem.getAttribute( "lsid" ) );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "Description" ) ) {
- service.setDescription( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "Category" ) ) {
- service.setCategory( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "URL" ) ) {
- service.setURL( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "signatureURL" ) ) {
- service.setSignatureURL( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "contactEmail" ) ) {
- service.setEmailContact( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "serviceType" ) ) {
- service.setType( getFirstValue( children.item( j ) ) );
- MobyServiceType mst = new MobyServiceType( service.getType() );
- NamedNodeMap map = ( children.item( j ).getAttributes() );
- if ( map != null ) {
- Node node = map.getNamedItemNS( children.item( j ).getNamespaceURI(), "lsid" );
- if ( node != null ) mst.setLSID( node.getNodeValue() );
- }
- service.setServiceType( mst );
- }
- else if ( nodeName.equals( "authoritative" ) ) {
- String authoritative = getFirstValue( children.item( j ) );
- service.setAuthoritative( authoritative.equals( "1" ) ? true : false );
- }
- else if ( nodeName.equals( "Input" ) ) {
- //
- // ...
- //
- //
- // ......
- // ......
- //
- //
- NodeList inputs = children.item( j ).getChildNodes();
- for ( int k = 0; k < inputs.getLength(); k++ ) {
- if ( inputs.item( k ).getNodeName().equals( "Simple" ) ) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple( ( Element ) inputs.item( k ) );
- service.addInput( data );
- }
- else if ( inputs.item( k ).getNodeName().equals( "Collection" ) ) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet( ( Element ) inputs.item( k ) );
- service.addInput( data );
- }
- }
- }
- else if ( nodeName.equals( "Output" ) ) {
- //
- //
- //
- NodeList inputs = children.item( j ).getChildNodes();
- for ( int k = 0; k < inputs.getLength(); k++ ) {
- if ( inputs.item( k ).getNodeName().equals( "Simple" ) ) {
- MobyPrimaryDataSimple data = new MobyPrimaryDataSimple( ( Element ) inputs.item( k ) );
- service.addOutput( data );
- }
- else if ( inputs.item( k ).getNodeName().equals( "Collection" ) ) {
- MobyPrimaryDataSet data = new MobyPrimaryDataSet( ( Element ) inputs.item( k ) );
- service.addOutput( data );
- }
- }
-
- }
- else if ( nodeName.equals( "secondaryArticles" ) ) {
- //
- // ...
- //
- NodeList parameters = children.item( j ).getChildNodes();
- for ( int k = 0; k < parameters.getLength(); k++ ) {
- if ( parameters.item( k ).getNodeName().equals( "Parameter" ) ) {
- MobySecondaryData data = new MobySecondaryData( ( Element ) parameters.item( k ) );
- service.addInput( data );
- }
- }
- }
+ * @throws MobyException if the XML document is invalid
+ *************************************************************************/
+ public MobyService[] extractServices (String xml)
+ throws MobyException {
+
+ Document document = loadDocument (new ByteArrayInputStream (xml.getBytes()));
+ NodeList list = document.getElementsByTagName ("Service");
+ MobyService[] results = new MobyService [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyService service = new MobyService (elem.getAttribute ("serviceName"));
+ service.setAuthority (elem.getAttribute ("authURI"));
+ service.setLSID (elem.getAttribute ("lsid"));
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ service.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Category")) {
+ service.setCategory (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("URL")) {
+ service.setURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("signatureURL")) {
+ service.setSignatureURL (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ service.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("serviceType")) {
+ service.setType (getFirstValue (children.item (j)));
+ MobyServiceType mst = new MobyServiceType(service.getType());
+ NamedNodeMap map = (children.item (j).getAttributes());
+ if (map != null) {
+ Node node = map.getNamedItemNS(children.item(j).getNamespaceURI(),"lsid");
+ if (node != null)
+ mst.setLSID(node.getNodeValue());
+ }
+ service.setServiceType(mst);
+ } else if (nodeName.equals ("authoritative")) {
+ String authoritative = getFirstValue (children.item (j));
+ service.setAuthoritative (authoritative.equals ("1") ? true : false);
+ } else if (nodeName.equals ("Input")) {
+ //
+ // ...
+ //
+ //
+ // ......
+ // ......
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addInput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addInput (data);
+ }
+ }
+ } else if (nodeName.equals ("Output")) {
+ //
+ //
+ //
+ NodeList inputs = children.item (j).getChildNodes();
+ for (int k = 0; k < inputs.getLength(); k++) {
+ if (inputs.item (k).getNodeName().equals ("Simple")) {
+ MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ((Element)inputs.item (k));
+ service.addOutput (data);
+ } else if (inputs.item (k).getNodeName().equals ("Collection")) {
+ MobyPrimaryDataSet data = new MobyPrimaryDataSet ((Element)inputs.item (k));
+ service.addOutput (data);
+ }
+ }
+
+ } else if (nodeName.equals ("secondaryArticles")) {
+ //
+ // ...
+ //
+ NodeList parameters = children.item (j).getChildNodes();
+ for (int k = 0; k < parameters.getLength(); k++) {
+ if (parameters.item (k).getNodeName().equals ("Parameter")) {
+ MobySecondaryData data = new MobySecondaryData ((Element)parameters.item (k));
+ service.addInput (data);
+ }
}
- results[ i ] = service;
}
- return results;
+ }
+ results [i] = service;
+ }
+ return results;
}
// protect against null values
- protected String getFirstValue( Node child ) {
- Node node = child.getFirstChild();
- if ( node == null ) return "";
- String value = node.getNodeValue();
- if ( value == null ) return "";
- return value;
+ protected String getFirstValue (Node child) {
+ Node node = child.getFirstChild();
+ if (node == null) return "";
+ String value = node.getNodeValue();
+ if (value == null) return "";
+ return value;
+ }
+
+ protected String getFirstValue (NodeList children) {
+ if (children.item(0) != null && children.item(0).hasChildNodes()) {
+ children.item(0).normalize();
+ return getFirstValue (children.item(0));
}
-
- protected String getFirstValue( NodeList children ) {
- if ( children.item( 0 ) != null && children.item( 0 ).hasChildNodes() ) {
- children.item( 0 ).normalize();
- return getFirstValue( children.item( 0 ) );
- }
- return "";
+ return "";
}
- /*******************************************************************************************************************
+ /**************************************************************************
*
* Implementing SimpleCache interface.
- *
- * Why to have an interface for such trivial thing? Well, because I needed to overwrite the caching mechanism in the
- * subclasses so I needed to have all caching functions as separate methods - that's why I have collect them in an
- * interface.
- *
- ******************************************************************************************************************/
- private Hashtable< String, Object > cache; // this is the cache itself
- private boolean useCache; // this signal that we are actually caching things
+ *
+ * Why to have an interface for such trivial thing? Well, because
+ * I needed to overwrite the caching mechanism in the subclasses
+ * so I needed to have all caching functions as separate methods -
+ * that's why I have collect them in an interface.
+ *
+ *************************************************************************/
+ private Hashtable cache; // this is the cache itself
+ private boolean useCache; // this signal that we are actually caching things
// not used here
- public String createId( String rootName, String semanticType, String syntaxType, long lastModified, Properties props ) {
- return ""; // not used here
+ public String createId (String rootName,
+ String semanticType, String syntaxType,
+ long lastModified,
+ Properties props) {
+ return ""; // not used here
}
// check existence of a cached object
- public boolean existsInCache( String id ) {
- synchronized ( cache ) {
- if ( useCache )
- return cache.containsKey( id );
- else
- return false;
- }
+ public boolean existsInCache (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.containsKey (id);
+ else return false;
+ }
}
// retrieve from cache
- public Object getContents( String id ) {
- synchronized ( cache ) {
- if ( useCache )
- return cache.get( id );
- else
- return null;
- }
+ public Object getContents (String id) {
+ synchronized (cache) {
+ if (useCache) return cache.get (id);
+ else return null;
+ }
}
// cache an object
- public void setContents( String id, java.lang.Object data ) {
- synchronized ( cache ) {
- if ( useCache ) cache.put( id, data );
- }
+ public void setContents (String id, java.lang.Object data) {
+ synchronized (cache) {
+ if (useCache) cache.put (id, data);
+ }
}
// in this implementation, it clears the whole cache, regardless
// what 'id' is passed
- public void removeFromCache( String id ) {
- cache.clear();
+ public void removeFromCache (String id) {
+ cache.clear();
}
- /*******************************************************************************************************************
- *
- * And the other methods related to caching (but not part of the SimpleCache interface).
- *
- ******************************************************************************************************************/
-
- /*******************************************************************************************************************
- * By default, caching is enabled to reduce network traffic. Setting this to false will clear the cache, and not
- * cache any further calls unless it is set to true again.
- *
- *
- * @param shouldCache
- * whether retrieveXXX call results should be cached in case they are called again (i.e. don't request
- * MobyCentral every time)
- ******************************************************************************************************************/
- public void setCacheMode( boolean shouldCache ) {
- useCache = shouldCache;
- if ( !useCache ) removeFromCache( null );
+ /**************************************************************************
+ *
+ * And the other methods related to caching (but not part of the
+ * SimpleCache interface).
+ *
+ **************************************************************************/
+
+ /**************************************************************************
+ * By default, caching is enabled to reduce network traffic.
+ * Setting this to false will clear the cache, and not cache any
+ * further calls unless it is set to true again.
+ *
+ * @param shouldCache whether retrieveXXX call results should be
+ * cached in case they are called again (i.e. don't request
+ * MobyCentral every time)
+ **************************************************************************/
+ public void setCacheMode (boolean shouldCache) {
+ useCache = shouldCache;
+ if (! useCache)
+ removeFromCache (null);
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Find if caching is currently enabled.
- *
+ *
* @return true if caching is enabled
- ******************************************************************************************************************/
- public boolean getCacheMode() {
- return useCache;
+ **************************************************************************/
+ public boolean getCacheMode(){
+ return useCache;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceNames>
- * <serviceName name="serviceName" authURI='authority.info.here'/>
+ * <serviceName name="serviceName" authURI='authority.info.here'/>
* ...
* ...
* </serviceNames>
*
- *
- * @deprecated Replaced by {@link #getServiceNamesByAuthority}. The reason is that this method returns a random
- * result if there are more services with the same name but belonging to different authorities.
- *
- *
- ******************************************************************************************************************/
- public Map< String, String > getServiceNames() throws MobyException {
-
- String result = ( String ) doCall( "retrieveServiceNames", new Object[] {} );
- // parse returned XML
- Map< String, String > results = new TreeMap< String, String >( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceName" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- results.put( elem.getAttribute( "name" ), elem.getAttribute( "authURI" ) );
- }
+ *
+ * @deprecated Replaced by {@link
+ * #getServiceNamesByAuthority}. The reason is that this method
+ * returns a random result if there are more services with the
+ * same name but belonging to different authorities.
+ *
+ *************************************************************************/
+ public Map getServiceNames()
+ throws MobyException {
+
+ String result = (String)doCall ("retrieveServiceNames",
+ new Object[] {});
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ results.put (elem.getAttribute ("name"),
+ elem.getAttribute ("authURI"));
+ }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceNames>
- * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
+ * <serviceName name="serviceName" lsid="..." authURI='authority.info.here'/>
* ...
* ...
* </serviceNames>
*
- *
- * @return a Map which has authorities as keys, and String arrays with service names as a values.
- ******************************************************************************************************************/
- public Map getServiceNamesByAuthority() throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML( result, true );
- }
-
- /*******************************************************************************************************************
- * Similar to {@link #getServiceNamesByAuthority} but the resulting Map contains slightly more.
- *
- *
- * @return a Map which has authorities as keys, and arrays of MobyServices as a values. Each MobyService is filled
- * with its name, authority and LSID.
- ******************************************************************************************************************/
- public Map getServicesByAuthority() throws MobyException {
- String result = getServiceNamesByAuthorityAsXML();
- return createServicesByAuthorityFromXML( result, false );
+ *
+ * @return a Map which has authorities as keys, and String arrays
+ * with service names as a values.
+ *************************************************************************/
+ public Map getServiceNamesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, true);
+ }
+
+ /**************************************************************************
+ * Similar to {@link #getServiceNamesByAuthority} but the
+ * resulting Map contains slightly more.
+ *
+ * @return a Map which has authorities as keys, and arrays of
+ * MobyServices as a values. Each MobyService is filled with its
+ * name, authority and LSID.
+ *************************************************************************/
+ public Map getServicesByAuthority()
+ throws MobyException {
+ String result = getServiceNamesByAuthorityAsXML();
+ return createServicesByAuthorityFromXML (result, false);
}
//
- protected String getServiceNamesByAuthorityAsXML() throws MobyException {
- return ( String ) doCall( "retrieveServiceNames", new Object[] {} );
+ protected String getServiceNamesByAuthorityAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceNames",
+ new Object[] {});
}
// if onlyNames == true
- // Map: authority name -> String[]
- // (filled with service namea)
+ // Map: authority name -> String[]
+ // (filled with service namea)
// else
- // Map: authority name -> MobyService[]
- // (filled with service name, authority and lsid)
- protected Map createServicesByAuthorityFromXML( String result, boolean onlyNames ) throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceName" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String name = elem.getAttribute( "name" );
- String auth = elem.getAttribute( "authURI" );
- Vector< Object > v = ( results.containsKey( auth ) ? ( Vector ) results.get( auth )
- : new Vector< Object >() );
- if ( onlyNames ) {
- v.addElement( name );
- }
- else {
- MobyService ms = new MobyService( name );
- ms.setAuthority( auth );
- ms.setLSID( elem.getAttribute( "lsid" ) );
- v.addElement( ms );
- }
- results.put( auth, v );
- }
-
- // change values of type Vector to MobyService[] or String[]
- for ( Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = ( Map.Entry ) it.next();
- Vector v = ( Vector ) entry.getValue();
- if ( onlyNames ) {
- String[] sNames = new String[ v.size() ];
- v.copyInto( sNames );
- entry.setValue( sNames );
- }
- else {
- MobyService[] mss = new MobyService[ v.size() ];
- v.copyInto( mss );
- entry.setValue( mss );
- }
+ // Map: authority name -> MobyService[]
+ // (filled with service name, authority and lsid)
+ protected Map createServicesByAuthorityFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceName");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ String auth = elem.getAttribute ("authURI");
+ Vector v =
+ (results.containsKey (auth) ? (Vector)results.get (auth) : new Vector());
+ if (onlyNames) {
+ v.addElement (name);
+ } else {
+ MobyService ms = new MobyService (name);
+ ms.setAuthority (auth);
+ ms.setLSID (elem.getAttribute ("lsid"));
+ v.addElement (ms);
+ }
+ results.put (auth, v);
+ }
+
+ // change values of type Vector to MobyService[] or String[]
+ for (Iterator it = results.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ Vector v = (Vector)entry.getValue();
+ if (onlyNames) {
+ String[] sNames = new String [v.size()];
+ v.copyInto (sNames);
+ entry.setValue (sNames);
+ } else {
+ MobyService[] mss = new MobyService [v.size()];
+ v.copyInto (mss);
+ entry.setValue (mss);
}
+ }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceProviders>
- * <serviceProvider name="authority.URI.here"/>
+ * <serviceProvider name="authority.URI.here"/>
* ...
* ...
* </serviceProviders>
*
- ******************************************************************************************************************/
- public String[] getProviders() throws MobyException {
+ *************************************************************************/
+ public String[] getProviders()
+ throws MobyException {
- String cacheId = "retrieveServiceProviders";
- String[] cachedResults = ( String[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
+ String cacheId = "retrieveServiceProviders";
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
- String result = ( String ) doCall( "retrieveServiceProviders", new Object[] {} );
+ String result = (String)doCall ("retrieveServiceProviders",
+ new Object[] {});
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceProvider" );
- String[] results = new String[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ )
- results[ i ] = ( ( Element ) list.item( i ) ).getAttribute( "name" );
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceProvider");
+ String[] results = new String [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++)
+ results[i] = ((Element)list.item (i)).getAttribute ("name");
- // Add this data to the cache in case we get called again
- setContents( cacheId, results );
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <serviceTypes>
- * <serviceType name="serviceName" lsid="...">
+ * <serviceType name="serviceName" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* <contactEmail>...</contactEmail>
* <authURI>...</authURI>
@@ -820,52 +869,57 @@
* ...
* </serviceTypes>
*
- ******************************************************************************************************************/
- public Map getServiceTypes() throws MobyException {
- String result = getServiceTypesAsXML();
- Map results = new TreeMap( getStringComparator() );
- MobyServiceType[] types = createServiceTypesFromXML( result );
- for ( int i = 0; i < types.length; i++ ) {
- results.put( types[ i ].getName(), types[ i ].getDescription() );
- }
- return results;
+ *************************************************************************/
+ public Map getServiceTypes()
+ throws MobyException {
+ String result = getServiceTypesAsXML();
+ Map results = new TreeMap (getStringComparator());
+ MobyServiceType[] types = createServiceTypesFromXML (result);
+ for (int i = 0; i < types.length; i++) {
+ results.put (types[i].getName(),
+ types[i].getDescription());
+ }
+ return results;
}
//
- protected String getServiceTypesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveServiceTypes", new Object[] {} );
+ protected String getServiceTypesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveServiceTypes",
+ new Object[] {});
}
// but be aware that the created MobyServiceTypes are not complete
// - they do not have the relationship information; that's why
// this method is not public; the full service types are available
// from CentralDigest implementations
- protected MobyServiceType[] createServiceTypesFromXML( String result ) throws MobyException {
+ protected MobyServiceType[] createServiceTypesFromXML (String result)
+ throws MobyException {
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "serviceType" );
- if ( list == null || list.getLength() == 0 ) return new MobyServiceType[] {};
- MobyServiceType[] results = new MobyServiceType[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyServiceType st = new MobyServiceType( elem.getAttribute( "name" ) );
- st.setLSID( elem.getAttribute( "lsid" ) );
- st.setDescription( getFirstValue( elem.getElementsByTagName( "Description" ) ) );
- st.setEmailContact( getFirstValue( elem.getElementsByTagName( "contactEmail" ) ) );
- st.setAuthority( getFirstValue( elem.getElementsByTagName( "authURI" ) ) );
- results[ i ] = st;
- }
- java.util.Arrays.sort( results );
- return results;
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("serviceType");
+ if (list == null || list.getLength() == 0)
+ return new MobyServiceType[] {};
+ MobyServiceType[] results = new MobyServiceType [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyServiceType st = new MobyServiceType (elem.getAttribute ("name"));
+ st.setLSID (elem.getAttribute ("lsid"));
+ st.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ st.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ st.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = st;
+ }
+ java.util.Arrays.sort (results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <Namespaces>
- * <Namespace name="namespace" lsid="...">
+ * <Namespace name="namespace" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* <contactEmail>...</contactEmail>
* <authURI>...</authURI>
@@ -874,122 +928,133 @@
* ...
* </Namespaces>
*
- ******************************************************************************************************************/
- public MobyNamespace[] getFullNamespaces() throws MobyException {
+ *************************************************************************/
+ public MobyNamespace[] getFullNamespaces()
+ throws MobyException {
- String result = getNamespacesAsXML();
- return createNamespacesFromXML( result );
+ String result = getNamespacesAsXML();
+ return createNamespacesFromXML (result);
}
//
- protected String getNamespacesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveNamespaces", new Object[] {} );
+ protected String getNamespacesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveNamespaces",
+ new Object[] {});
}
//
- protected MobyNamespace[] createNamespacesFromXML( String result ) throws MobyException {
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getDocumentElement().getElementsByTagName( "Namespace" );
- if ( list == null || list.getLength() == 0 ) {
- return new MobyNamespace[] {};
- }
- MobyNamespace[] results = new MobyNamespace[ list.getLength() ];
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- MobyNamespace nm = new MobyNamespace( elem.getAttribute( "name" ) );
- nm.setLSID( elem.getAttribute( "lsid" ) );
- nm.setDescription( getFirstValue( elem.getElementsByTagName( "Description" ) ) );
- nm.setEmailContact( getFirstValue( elem.getElementsByTagName( "contactEmail" ) ) );
- nm.setAuthority( getFirstValue( elem.getElementsByTagName( "authURI" ) ) );
- results[ i ] = nm;
- }
+ protected MobyNamespace[] createNamespacesFromXML (String result)
+ throws MobyException {
- java.util.Arrays.sort( results );
- return results;
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
+ if (list == null || list.getLength() == 0) {
+ return new MobyNamespace[] {};
+ }
+ MobyNamespace[] results = new MobyNamespace [list.getLength()];
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ MobyNamespace nm = new MobyNamespace (elem.getAttribute ("name"));
+ nm.setLSID (elem.getAttribute ("lsid"));
+ nm.setDescription (getFirstValue (elem.getElementsByTagName ("Description")));
+ nm.setEmailContact (getFirstValue (elem.getElementsByTagName ("contactEmail")));
+ nm.setAuthority (getFirstValue (elem.getElementsByTagName ("authURI")));
+ results[i] = nm;
+ }
+
+ java.util.Arrays.sort (results);
+ return results;
+ }
+
+ /**************************************************************************
+ *
+ * @deprecated Replaced by {@link #getFullNamespaces} that gives
+ * more information for the same price.
+ *************************************************************************/
+ public Map getNamespaces()
+ throws MobyException {
+
+ Map results = new TreeMap (getStringComparator());
+ MobyNamespace[] namespaces = getFullNamespaces();
+ for (int i = 0; i < namespaces.length; i++) {
+ results.put (namespaces[i].getName(),
+ namespaces[i].getDescription());
}
-
- /*******************************************************************************************************************
- *
- * @deprecated Replaced by {@link #getFullNamespaces} that gives more information for the same price.
- *
- ******************************************************************************************************************/
- public Map getNamespaces() throws MobyException {
-
- Map results = new TreeMap( getStringComparator() );
- MobyNamespace[] namespaces = getFullNamespaces();
- for ( int i = 0; i < namespaces.length; i++ ) {
- results.put( namespaces[ i ].getName(), namespaces[ i ].getDescription() );
- }
- return results;
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <objectNames>
- * <Object name="objectName" lsid="...">
+ * <Object name="objectName" lsid="...">
* <Description><![CDATA[free text description here]]></Description>
* </Object>
* ...
* ...
* </objectNames>
*
- ******************************************************************************************************************/
- public Map getDataTypeNames() throws MobyException {
- String result = getDataTypeNamesAsXML();
- return createDataTypeNamesFromXML( result, true );
+ *************************************************************************/
+ public Map getDataTypeNames()
+ throws MobyException {
+ String result = getDataTypeNamesAsXML();
+ return createDataTypeNamesFromXML (result, true);
}
//
- protected String getDataTypeNamesAsXML() throws MobyException {
- return ( String ) doCall( "retrieveObjectNames", new Object[] {} );
+ protected String getDataTypeNamesAsXML()
+ throws MobyException {
+ return (String)doCall ("retrieveObjectNames",
+ new Object[] {});
}
// if onlyNames == true
- // Map: data type name -> description (String)
+ // Map: data type name -> description (String)
// else
- // Map: data type name -> MobyDataType[]
- // (filled with name, description, and lsid)
- protected Map createDataTypeNamesFromXML( String result, boolean onlyNames ) throws MobyException {
-
- // parse returned XML
- Map results = new TreeMap( getStringComparator() );
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Object" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String name = elem.getAttribute( "name" );
- if ( name == null ) continue; // ignore no-named data types
- String desc = "";
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "Description" ) ) {
- desc = getFirstValue( children.item( j ) );
- break;
- }
- }
- if ( onlyNames ) {
- results.put( name, desc );
- }
- else {
- MobyDataType dt = new MobyDataType( name );
- dt.setDescription( desc );
- dt.setLSID( elem.getAttribute( "lsid" ) );
- results.put( name, dt );
- }
+ // Map: data type name -> MobyDataType[]
+ // (filled with name, description, and lsid)
+ protected Map createDataTypeNamesFromXML (String result,
+ boolean onlyNames)
+ throws MobyException {
+
+ // parse returned XML
+ Map results = new TreeMap (getStringComparator());
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Object");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String name = elem.getAttribute ("name");
+ if (name == null)
+ continue; // ignore no-named data types
+ String desc = "";
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("Description")) {
+ desc = getFirstValue (children.item (j));
+ break;
}
- return results;
+ }
+ if (onlyNames) {
+ results.put (name, desc);
+ } else {
+ MobyDataType dt = new MobyDataType (name);
+ dt.setDescription (desc);
+ dt.setLSID (elem.getAttribute ("lsid"));
+ results.put (name, dt);
+ }
+ }
+ return results;
}
- /*******************************************************************************************************************
+
+ /**************************************************************************
* Parses and imports the following XML. An example:
- *
+ *
*
* <retrieveObjectDefinition>
- * <objectType lsid="...">go_term</objectType>
+ * <objectType lsid="...">go_term</objectType>
* <Description><![CDATA[A very lightweight object holding a GO term name and its definition]]></Description>
* <authURI>http://www.illuminae.com</authURI>
* <contactEmail>markw at illuminae.com</contactEmail>
@@ -1006,448 +1071,529 @@
* </Relationship>
* </retrieveObjectDefinition>
*
- ******************************************************************************************************************/
- public MobyDataType getDataType( String dataTypeName ) throws MobyException, NoSuccessException {
-
- String result = getDataTypeAsXML( dataTypeName );
- return createDataTypeFromXML( result, dataTypeName );
- }
-
- public MobyDataType[] getDataTypes() throws MobyException, NoSuccessException {
- Map< String, String > datatypeMap = getDataTypeNames();
- MobyDataType[] datatypes = new MobyDataType[ datatypeMap.size() ];
- int i = 0;
- for ( String dataTypeName : datatypeMap.keySet() ) {
- datatypes[ i++ ] = getDataType( dataTypeName );
- }
- return datatypes;
- }
-
- protected String getDataTypeAsXML( String dataTypeName ) throws MobyException, NoSuccessException {
-
- return ( String ) doCall( "retrieveObjectDefinition", new Object[] { ""
- + "" + dataTypeName + " " + " " } );
- }
-
- protected MobyDataType createDataTypeFromXML( String xmlSource, String dataTypeName ) throws MobyException,
- NoSuccessException {
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( xmlSource.getBytes() ) );
- NodeList list = document.getElementsByTagName( "retrieveObjectDefinition" );
- if ( list == null || list.getLength() == 0 )
- throw new NoSuccessException( "Data Type name was not found.", dataTypeName );
- MobyDataType data = null;
- Element elem = ( Element ) list.item( 0 );
- NodeList children = elem.getChildNodes();
-
- // first find the "real" (LSID-ized) data type name
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "objectType" ) ) {
- data = new MobyDataType( getFirstValue( children.item( j ) ) );
- data.setLSID( ( ( Element ) children.item( j ) ).getAttribute( "lsid" ) );
- break;
- }
- }
-
- // if not found (unprobable) use the name given by the caller
- if ( data == null ) data = new MobyDataType( dataTypeName );
-
- // now fill the data type object with the rest of attributes
- for ( int j = 0; j < children.getLength(); j++ ) {
- String nodeName = children.item( j ).getNodeName();
- if ( nodeName.equals( "Description" ) ) {
- data.setDescription( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "authURI" ) ) {
- data.setAuthority( getFirstValue( children.item( j ) ) );
+ *************************************************************************/
+ public MobyDataType getDataType (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ String result = getDataTypeAsXML (dataTypeName);
+ return createDataTypeFromXML (result, dataTypeName);
+ }
+
+ public MobyDataType[] getDataTypes()
+ throws MobyException, NoSuccessException {
+ Map datatypeMap = getDataTypeNames();
+ MobyDataType[] datatypes = new MobyDataType[datatypeMap.size()];
+ int i = 0;
+ for(String dataTypeName: datatypeMap.keySet()){
+ datatypes[i++] = getDataType(dataTypeName);
+ }
+ return datatypes;
+ }
+
+ protected String getDataTypeAsXML (String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ return (String)doCall ("retrieveObjectDefinition",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ " "
+ });
+ }
+
+ protected MobyDataType createDataTypeFromXML (String xmlSource, String dataTypeName)
+ throws MobyException, NoSuccessException {
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (xmlSource.getBytes()));
+ NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
+ if (list == null || list.getLength() == 0)
+ throw new NoSuccessException ("Data Type name was not found.",
+ dataTypeName);
+ MobyDataType data = null;
+ Element elem = (Element)list.item (0);
+ NodeList children = elem.getChildNodes();
+
+ // first find the "real" (LSID-ized) data type name
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("objectType")) {
+ data = new MobyDataType (getFirstValue (children.item (j)));
+ data.setLSID ( ((Element)children.item (j) ).getAttribute ("lsid"));
+ break;
+ }
+ }
+
+ // if not found (unprobable) use the name given by the caller
+ if (data == null)
+ data = new MobyDataType (dataTypeName);
+
+ // now fill the data type object with the rest of attributes
+ for (int j = 0; j < children.getLength(); j++) {
+ String nodeName = children.item (j).getNodeName();
+ if (nodeName.equals ("Description")) {
+ data.setDescription (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("authURI")) {
+ data.setAuthority (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("contactEmail")) {
+ data.setEmailContact (getFirstValue (children.item (j)));
+ } else if (nodeName.equals ("Relationship")) {
+ String relationshipType = ((Element)children.item (j)).getAttribute ("relationshipType");
+ if (relationshipType.endsWith ("isa")) {
+
+ NodeList parents = children.item (j).getChildNodes();
+ for (int k = 0; k < parents.getLength(); k++) {
+ if (parents.item (k).getNodeName().equals ("objectType")) {
+ data.addParentName (getFirstValue (parents.item (k)));
+ }
+ }
+ } else if (relationshipType.endsWith ("hasa")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ getFirstValue (belows.item (k)),
+ Central.iHASA );
+ }
+ }
+ } else if (relationshipType.endsWith ("has")) {
+
+ NodeList belows = children.item (j).getChildNodes();
+ for (int k = 0; k < belows.getLength(); k++) {
+ if (belows.item (k).getNodeName().equals ("objectType")) {
+ data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"),
+ belows.item (k).getFirstChild().getNodeValue(),
+ Central.iHAS );
}
- else if ( nodeName.equals( "contactEmail" ) ) {
- data.setEmailContact( getFirstValue( children.item( j ) ) );
- }
- else if ( nodeName.equals( "Relationship" ) ) {
- String relationshipType = ( ( Element ) children.item( j ) ).getAttribute( "relationshipType" );
- if ( relationshipType.endsWith( "isa" ) ) {
-
- NodeList parents = children.item( j ).getChildNodes();
- for ( int k = 0; k < parents.getLength(); k++ ) {
- if ( parents.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addParentName( getFirstValue( parents.item( k ) ) );
- }
- }
- }
- else if ( relationshipType.endsWith( "hasa" ) ) {
-
- NodeList belows = children.item( j ).getChildNodes();
- for ( int k = 0; k < belows.getLength(); k++ ) {
- if ( belows.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addChild( ( ( Element ) belows.item( k ) ).getAttribute( "articleName" ),
- getFirstValue( belows.item( k ) ), Central.iHASA );
- }
- }
- }
- else if ( relationshipType.endsWith( "has" ) ) {
-
- NodeList belows = children.item( j ).getChildNodes();
- for ( int k = 0; k < belows.getLength(); k++ ) {
- if ( belows.item( k ).getNodeName().equals( "objectType" ) ) {
- data.addChild( ( ( Element ) belows.item( k ) ).getAttribute( "articleName" ), belows.item(
- k ).getFirstChild().getNodeValue(), Central.iHAS );
- }
- }
- }
}
}
- return data;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getServiceWSDL( String serviceName ) throws MobyException, NoSuccessException {
-
- Map names = getServiceNames();
-
- for ( Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
- Map.Entry entry = ( Map.Entry ) it.next();
- if ( ( ( String ) entry.getKey() ).equals( serviceName ) )
- return getServiceWSDL( serviceName, ( String ) entry.getValue() );
- }
-
- throw new NoSuccessException( "Service not found.", serviceName );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getServiceWSDL( String serviceName, String authority ) throws MobyException, NoSuccessException {
-
- String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
- String cachedResults = ( String ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "retrieveService",
- new Object[] { "" + " " } );
-
- // parse returned XML
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- Element service = document.getDocumentElement();
- Node wsdl = service.getFirstChild();
- if ( wsdl == null )
- throw new NoSuccessException( "Service not found OR WSDL is not available.", serviceName + " (" + authority
- + ")" );
-
- String results = wsdl.getNodeValue();
- setContents( cacheId, results );
- return results;
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterDataTypeXML( MobyDataType dataType ) {
-
- // build the ISA tag (expressing hierarchy of data types)
- String[] names = dataType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < names.length; i++ ) {
- buf.append( "" );
- buf.append( names[ i ] );
- buf.append( " " );
- buf.append( "\n" );
- }
-
- // build the HASA/HAS tags (expressing containments of data types)
- MobyRelationship[] children = dataType.getChildren();
- StringBuffer buf2 = new StringBuffer(); // for HASA
- StringBuffer buf3 = new StringBuffer(); // for HAS
- for ( int i = 0; i < children.length; i++ ) {
- if ( children[ i ].getRelationshipType() == Central.iHASA ) {
- buf2.append( "" );
- buf2.append( children[ i ].getDataTypeName() );
- buf2.append( " " );
- }
- else if ( children[ i ].getRelationshipType() == Central.iHAS ) {
- buf3.append( "" );
- buf3.append( children[ i ].getDataTypeName() );
- buf3.append( " " );
- }
}
-
- return "" + "" + dataType.getName() + " "
- + "" + " "
- + "" + new String( buf ) + " "
- + "" + new String( buf2 ) + " "
- + "" + new String( buf3 ) + " " + ""
- + dataType.getAuthority() + " " + "" + dataType.getEmailContact()
- + " " + " ";
}
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerDataType( MobyDataType dataType ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerObjectClass", new Object[] { getRegisterDataTypeXML( dataType ) } );
- dataType.setId( checkRegistration( result, dataType )[ 0 ] );
+ return data;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName)
+ throws MobyException, NoSuccessException {
+
+ Map names = getServiceNames();
+
+ for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ if ( ((String)entry.getKey()).equals (serviceName) )
+ return getServiceWSDL (serviceName, (String)entry.getValue());
+ }
+
+ throw new NoSuccessException ("Service not found.", serviceName);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String getServiceWSDL (String serviceName, String authority)
+ throws MobyException, NoSuccessException {
+
+ String cacheId = "getServiceWSDL" + serviceName + ":" + authority;
+ String cachedResults = (String)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("retrieveService",
+ new Object[] {
+ "" +
+ " "
+ });
+
+ // parse returned XML
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ Element service = document.getDocumentElement();
+ Node wsdl = service.getFirstChild();
+ if (wsdl == null)
+ throw new NoSuccessException ("Service not found OR WSDL is not available.",
+ serviceName + " (" + authority + ")");
+
+ String results = wsdl.getNodeValue();
+ setContents (cacheId, results);
+ return results;
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterDataTypeXML (MobyDataType dataType) {
+
+ // build the ISA tag (expressing hierarchy of data types)
+ String[] names = dataType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ // build the HASA/HAS tags (expressing containments of data types)
+ MobyRelationship[] children = dataType.getChildren();
+ StringBuffer buf2 = new StringBuffer(); // for HASA
+ StringBuffer buf3 = new StringBuffer(); // for HAS
+ for (int i = 0; i < children.length; i++) {
+ if (children[i].getRelationshipType() == Central.iHASA) {
+ buf2.append ("");
+ buf2.append (children[i].getDataTypeName());
+ buf2.append (" ");
+ } else if (children[i].getRelationshipType() == Central.iHAS) {
+ buf3.append ("");
+ buf3.append (children[i].getDataTypeName());
+ buf3.append (" ");
+ }
+ }
+
+ return
+ "" +
+ "" + dataType.getName() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ "" + new String (buf2) +
+ " " +
+ "" + new String (buf3) +
+ " " +
+ "" + dataType.getAuthority() + " " +
+ "" + dataType.getEmailContact() + " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerObjectClass",
+ new Object[] { getRegisterDataTypeXML (dataType) });
+ dataType.setId (checkRegistration (result, dataType)[0]);
}
- /*******************************************************************************************************************
+ /*************************************************************************
* B
- ******************************************************************************************************************/
- public void unregisterDataType( MobyDataType dataType ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterObjectClass", new Object[] { ""
- + "" + dataType.getName() + " " + " " } );
- checkRegistration( result, dataType );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterServiceTypeXML( MobyServiceType serviceType ) {
-
- // build the ISA tag (expressing hierarchy of service types)
- String[] names = serviceType.getParentNames();
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < names.length; i++ ) {
- buf.append( "" );
- buf.append( names[ i ] );
- buf.append( " " );
- buf.append( "\n" );
- }
-
- return "" + "" + serviceType.getName() + " " + ""
- + serviceType.getEmailContact() + " " + "" + serviceType.getAuthority()
- + " " + "" + " "
- + "" + new String( buf ) + " "
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerServiceType( MobyServiceType serviceType ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerServiceType",
- new Object[] { getRegisterServiceTypeXML( serviceType ) } );
- serviceType.setId( checkRegistration( result, serviceType )[ 0 ] );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterServiceType( MobyServiceType serviceType ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterServiceType", new Object[] { ""
- + "" + serviceType.getName() + " " + " " } );
- checkRegistration( result, serviceType );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterNamespaceXML( MobyNamespace namespace ) {
- return "" + "" + namespace.getName() + " " + ""
- + namespace.getEmailContact() + " " + "" + namespace.getAuthority()
- + " " + "" + " "
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerNamespace( MobyNamespace namespace ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "registerNamespace", new Object[] { getRegisterNamespaceXML( namespace ) } );
- namespace.setId( checkRegistration( result, namespace )[ 0 ] );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterNamespace( MobyNamespace namespace ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterNamespace", new Object[] { ""
- + "" + namespace.getName() + " " + " " } );
- checkRegistration( result, namespace );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String getRegisterServiceXML( MobyService service ) {
- return "" + "" + service.getCategory() + " " + ""
- + service.getName() + " " + "" + service.getType() + " "
- + "" + ( service.getLSID() == null ? "" : service.getLSID().trim() ) + " "
- + "" + service.getAuthority() + " " + ""
- + escapeXML( service.getSignatureURL() ) + " " + "" + escapeXML( service.getURL() )
- + " " + "" + service.getEmailContact() + " "
- + "" + ( service.isAuthoritative() ? "1" : "0" ) + " "
- + "" + " "
- + buildPrimaryInputTag( service ) + buildSecondaryInputTag( service ) + buildOutputTag( service )
- + " ";
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void registerService( MobyService service ) throws MobyException, NoSuccessException,
- PendingCurationException {
-
- String result = ( String ) doCall( "registerService", new Object[] { getRegisterServiceXML( service ) } );
- String[] registered = checkRegistration( result, service );
- service.setId( registered[ 0 ] );
- service.setRDF( registered[ 1 ] );
- String pathToRDF = service.getPathToRDF();
- if ( !pathToRDF.equals( "" ) ) {
- File fileRDF = new File( pathToRDF );
- try {
- PrintStream fileout = new PrintStream( new FileOutputStream( fileRDF ) );
- fileout.println( registered[ 1 ] );
- fileout.close();
- }
- catch ( IOException e ) {
- StringBuffer buf = new StringBuffer( 100 );
- buf.append( "Failed to save RDF in '" );
- buf.append( fileRDF.getAbsolutePath() + "'. " );
- buf.append( e.toString() );
- try {
- File tmpFile = File.createTempFile( service.getName() + "-", ".rdf" );
- PrintStream fileout = new PrintStream( new FileOutputStream( tmpFile ) );
- fileout.println( registered[ 1 ] );
- fileout.close();
- buf.append( "\nReturned RDF file was therefore stored in: " );
- buf.append( tmpFile.getAbsolutePath() );
- }
- catch ( IOException e2 ) {
- buf.append( "\nEven saving in a temporary file failed: " );
- buf.append( e2.toString() );
- }
- throw new MobyException( buf.toString() );
- }
- }
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public void unregisterService( MobyService service ) throws MobyException, NoSuccessException,
- PendingCurationException {
- String result = ( String ) doCall( "deregisterService", new Object[] { "" + ""
- + service.getAuthority() + " " + "" + service.getName() + " "
- + " " } );
- checkRegistration( result, service );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( String serviceType ) throws MobyException {
- if ( serviceType == null ) return new MobyService[] {};
- MobyService pattern = new MobyService( "dummy" );
- pattern.setCategory( "" );
- pattern.setType( serviceType );
- return findService( pattern, null );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( String[] keywords ) throws MobyException {
- if ( keywords == null ) return new MobyService[] {};
- return findService( null, keywords );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern ) throws MobyException {
- if ( pattern == null ) return new MobyService[] {};
- return findService( pattern, null );
- }
-
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern, String[] keywords ) throws MobyException {
- return findService( pattern, keywords, true, true );
+ *************************************************************************/
+ public void unregisterDataType (MobyDataType dataType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterObjectClass",
+ new Object[] {
+ "" +
+ "" + dataType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, dataType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceTypeXML (MobyServiceType serviceType) {
+
+ // build the ISA tag (expressing hierarchy of service types)
+ String[] names = serviceType.getParentNames();
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < names.length; i++) {
+ buf.append ("");
+ buf.append (names[i]);
+ buf.append (" ");
+ buf.append ("\n");
+ }
+
+ return
+ "" +
+ "" + serviceType.getName() + " " +
+ "" + serviceType.getEmailContact() + " " +
+ "" + serviceType.getAuthority() + " " +
+ "" +
+ " " +
+ "" + new String (buf) +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerServiceType",
+ new Object[] { getRegisterServiceTypeXML (serviceType) });
+ serviceType.setId (checkRegistration (result, serviceType)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterServiceType (MobyServiceType serviceType)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterServiceType",
+ new Object[] {
+ "" +
+ "" + serviceType.getName() + " " +
+ " "
+ });
+ checkRegistration (result, serviceType);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterNamespaceXML (MobyNamespace namespace) {
+ return
+ "" +
+ "" + namespace.getName() + " " +
+ "" + namespace.getEmailContact() + " " +
+ "" + namespace.getAuthority() + " " +
+ "" +
+ " " +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("registerNamespace",
+ new Object[] { getRegisterNamespaceXML (namespace) });
+ namespace.setId (checkRegistration (result, namespace)[0]);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterNamespace (MobyNamespace namespace)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterNamespace",
+ new Object[] {
+ "" +
+ "" + namespace.getName() + " " +
+ " "
+ });
+ checkRegistration (result, namespace);
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public String getRegisterServiceXML (MobyService service) {
+ return
+ "" +
+ "" + service.getCategory() + " " +
+ "" + service.getName() + " " +
+ "" + service.getType() + " " +
+ "" + (service.getLSID() == null ? "" : service.getLSID().trim() )+ " " +
+ "" + service.getAuthority() + " " +
+ "" + escapeXML (service.getSignatureURL()) + " " +
+ "" + escapeXML (service.getURL()) + " " +
+ "" + service.getEmailContact() + " " +
+ "" + (service.isAuthoritative() ? "1" : "0") + " " +
+ "" +
+ " " +
+ buildPrimaryInputTag (service) +
+ buildSecondaryInputTag (service) +
+ buildOutputTag (service) +
+ " ";
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void registerService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+
+ String result =
+ (String)doCall ("registerService",
+ new Object[] { getRegisterServiceXML (service) });
+ String[] registered = checkRegistration (result, service);
+ service.setId (registered [0]);
+ service.setRDF (registered [1]);
+ String pathToRDF = service.getPathToRDF();
+ if ( ! pathToRDF.equals ("") ) {
+ File fileRDF = new File (pathToRDF);
+ try {
+ PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF));
+ fileout.println (registered [1]);
+ fileout.close();
+ } catch (IOException e) {
+ StringBuffer buf = new StringBuffer (100);
+ buf.append ("Failed to save RDF in '");
+ buf.append (fileRDF.getAbsolutePath() + "'. ");
+ buf.append (e.toString());
+ try {
+ File tmpFile = File.createTempFile (service.getName() + "-", ".rdf");
+ PrintStream fileout = new PrintStream (new FileOutputStream (tmpFile));
+ fileout.println (registered [1]);
+ fileout.close();
+ buf.append ("\nReturned RDF file was therefore stored in: ");
+ buf.append (tmpFile.getAbsolutePath());
+ } catch (IOException e2) {
+ buf.append ("\nEven saving in a temporary file failed: ");
+ buf.append (e2.toString());
+ }
+ throw new MobyException (buf.toString());
+ }
+ }
+ }
+
+ /*************************************************************************
+ *
+ *************************************************************************/
+ public void unregisterService (MobyService service)
+ throws MobyException, NoSuccessException, PendingCurationException {
+ String result =
+ (String)doCall ("deregisterService",
+ new Object[] {
+ "" +
+ "" + service.getAuthority() + " " +
+ "" + service.getName() + " " +
+ " "
+ });
+ checkRegistration (result, service);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String serviceType)
+ throws MobyException {
+ if (serviceType == null)
+ return new MobyService[] {};
+ MobyService pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ pattern.setType (serviceType);
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (String[] keywords)
+ throws MobyException {
+ if (keywords == null)
+ return new MobyService[] {};
+ return findService (null, keywords);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern)
+ throws MobyException {
+ if (pattern == null)
+ return new MobyService[] {};
+ return findService (pattern, null);
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords)
+ throws MobyException {
+ return findService (pattern, keywords, true, true);
}
- /*******************************************************************************************************************
+ /**************************************************************************
* All 'findService' methods end up here.
- ******************************************************************************************************************/
- public MobyService[] findService( MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes ) throws MobyException {
- if ( pattern == null ) {
- pattern = new MobyService( "dummy" );
- pattern.setCategory( "" );
- }
+ *************************************************************************/
+ public MobyService[] findService (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ if (pattern == null) {
+ pattern = new MobyService ("dummy");
+ pattern.setCategory ("");
+ }
- String result = getServicesAsXML( pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes );
- MobyService[] services = extractServices( result );
- return services;
+ String result =
+ getServicesAsXML (pattern, keywords, includeChildrenServiceTypes, includeParentDataTypes);
+ MobyService[] services = extractServices (result);
+ return services;
}
// ...actually all 'findService' methods end up here
- protected String getServicesAsXML( MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes,
- boolean includeParentDataTypes ) throws MobyException {
- String[] query = new String[] { ""
- + buildQueryObject( pattern, keywords, includeParentDataTypes, includeChildrenServiceTypes, false )
- + " " };
- return ( String ) doCall( "findService", query );
+ protected String getServicesAsXML (MobyService pattern, String[] keywords,
+ boolean includeChildrenServiceTypes,
+ boolean includeParentDataTypes)
+ throws MobyException {
+ String[] query = new String[] {
+ "" +
+ buildQueryObject (pattern, keywords,
+ includeParentDataTypes,
+ includeChildrenServiceTypes,
+ false) +
+ " "
+ };
+ return (String)doCall ("findService", query);
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public String call( String methodName, String inputXML ) throws MobyException {
- Object result;
- if ( inputXML == null || inputXML.equals( "" ) )
- result = doCall( methodName, new Object[] {} );
- else
- result = doCall( methodName, new Object[] { inputXML } );
- return ( String ) result;
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public String call (String methodName, String inputXML)
+ throws MobyException {
+ Object result;
+ if (inputXML == null || inputXML.equals (""))
+ result = doCall (methodName, new Object[] { });
+ else
+ result = doCall (methodName, new Object[] { inputXML });
+ return (String)result;
+ }
+
+ /**************************************************************************
+ *
+ *************************************************************************/
+ protected static String resultToString (Object result)
+ throws MobyException {
+ if (result == null)
+ throw new MobyException ("Returned result is null.");
+ if (result instanceof String)
+ return (String)result;
+ if (result instanceof String[]) {
+ String[] tmp = (String[])result;
+ StringBuffer buf = new StringBuffer();
+ for (int i = 0; i < tmp.length; i++)
+ buf.append (tmp[i]);
+ return new String (buf);
}
+ if (result instanceof byte[])
+ return new String ((byte[])result);
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- protected static String resultToString( Object result ) throws MobyException {
- if ( result == null ) throw new MobyException( "Returned result is null." );
- if ( result instanceof String ) return ( String ) result;
- if ( result instanceof String[] ) {
- String[] tmp = ( String[] ) result;
- StringBuffer buf = new StringBuffer();
- for ( int i = 0; i < tmp.length; i++ )
- buf.append( tmp[ i ] );
- return new String( buf );
- }
- if ( result instanceof byte[] ) return new String( ( byte[] ) result );
-
- throw new MobyException( "Unknown type of result: " + result.getClass().getName() );
+ throw new MobyException ("Unknown type of result: " + result.getClass().getName());
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public boolean setDebug( boolean enabled ) {
- boolean oldMode = debug;
- debug = enabled;
- return oldMode;
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public boolean setDebug (boolean enabled) {
+ boolean oldMode = debug;
+ debug = enabled;
+ return oldMode;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:servicerelation:isa'>
@@ -1456,45 +1602,55 @@
* </Relationship>
* </Relationships>
*
- ******************************************************************************************************************/
- public String[] getServiceTypeRelationships( String serviceTypeName, boolean expand ) throws MobyException {
- String result = getServiceTypeRelationshipsAsXML( serviceTypeName, expand );
- return createServiceTypeRelationshipsFromXML( result );
+ *************************************************************************/
+ public String[] getServiceTypeRelationships (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ String result = getServiceTypeRelationshipsAsXML (serviceTypeName, expand);
+ return createServiceTypeRelationshipsFromXML (result);
}
//
- protected String getServiceTypeRelationshipsAsXML( String serviceTypeName, boolean expand ) throws MobyException {
- return ( String ) doCall( "Relationships", new Object[] { "" + "" + serviceTypeName
- + " " + "" + Central.ISA + " "
- + "" + ( expand ? "1" : "0" ) + " " + " " } );
+ protected String getServiceTypeRelationshipsAsXML (String serviceTypeName,
+ boolean expand)
+ throws MobyException {
+ return
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + serviceTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + (expand ? "1" : "0") + " " +
+ " "
+ });
}
//
- protected String[] createServiceTypeRelationshipsFromXML( String result ) throws MobyException {
+ protected String[] createServiceTypeRelationshipsFromXML (String result)
+ throws MobyException {
- // parse returned XML
- Vector< String > v = new Vector< String >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "serviceType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("serviceType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
}
- String[] results = new String[ v.size() ];
- v.copyInto( results );
- return results;
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
- * lt;Relationships>
+ *<Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
* <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
@@ -1503,411 +1659,431 @@
* <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:integer</objectType>
* </Relationship>
- * lt;/Relationships>
+ *</Relationships>
*
- *
- * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an attributes 'lsid' and 'articleName' in
- * <objectType> element.
- ******************************************************************************************************************/
- public Map getDataTypeRelationships( String dataTypeName ) throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName;
- Map cachedResults = ( Map ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "Relationships", new Object[] { "" + ""
- + dataTypeName + " " + "" + Central.ISA + " "
- + "" + Central.HASA + " " + "" + Central.HAS
- + " " + "1 " + " " } );
-
- // parse returned XML
- Map results = new HashMap();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
-
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- String relType = elem.getAttribute( "relationshipType" );
- NodeList children = elem.getChildNodes();
- Vector< String > v = new Vector< String >();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "objectType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
- String[] names = new String[ v.size() ];
- v.copyInto( names );
- results.put( relType, names );
+ *
+ * Added at Sun Feb 19 19:32:31 PHT 2006: it recognizes also an
+ * attributes 'lsid' and 'articleName' in <objectType> element.
+ *************************************************************************/
+ public Map getDataTypeRelationships (String dataTypeName)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName;
+ Map cachedResults = (Map)getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + Central.ISA + " " +
+ "" + Central.HASA + " " +
+ "" + Central.HAS + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Map results = new HashMap();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ String relType = elem.getAttribute ("relationshipType");
+ NodeList children = elem.getChildNodes();
+ Vector v = new Vector();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
+ }
}
+ String[] names = new String [v.size()];
+ v.copyInto (names);
+ results.put (relType, names);
+ }
- setContents( cacheId, results );
- return results;
+ setContents (cacheId, results);
+ return results;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
- * lt;Relationships>
+ *<Relationships>
* <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
* <objectType>urn:lsid:biomoby.org:objectclass:virtualsequence</objectType>
* <objectType>urn:lsid:biomoby.org:objectclass:object</objectType>
* </Relationship>
- * lt;/Relationships>
+ *</Relationships>
*
- ******************************************************************************************************************/
- public String[] getDataTypeRelationships( String dataTypeName, String relationshipType ) throws MobyException {
-
- String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
- String[] cachedResults = ( String[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "Relationships", new Object[] { "" + ""
- + dataTypeName + " " + "" + relationshipType + " "
- + "1 " + " " } );
-
- // parse returned XML
- Vector< String > v = new Vector< String >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Relationship" );
-
- // it should always be just one element in this list
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- NodeList children = elem.getChildNodes();
- for ( int j = 0; j < children.getLength(); j++ ) {
- if ( children.item( j ).getNodeName().equals( "objectType" ) ) {
- v.addElement( getFirstValue( children.item( j ) ) );
- }
- }
+ *************************************************************************/
+ public String[] getDataTypeRelationships (String dataTypeName,
+ String relationshipType)
+ throws MobyException {
+
+ String cacheId = "getDataTypeRelationships_" + dataTypeName + ":" + relationshipType;
+ String[] cachedResults = (String[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result =
+ (String)doCall ("Relationships",
+ new Object[] {
+ "" +
+ "" + dataTypeName + " " +
+ "" + relationshipType + " " +
+ "1 " +
+ " "
+ });
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Relationship");
+
+ // it should always be just one element in this list
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ NodeList children = elem.getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item (j).getNodeName().equals ("objectType")) {
+ v.addElement (getFirstValue (children.item (j)));
}
- String[] results = new String[ v.size() ];
- v.copyInto( results );
+ }
+ }
+ String[] results = new String [v.size()];
+ v.copyInto (results);
- setContents( cacheId, results );
- return results;
+ setContents (cacheId, results);
+ return results;
}
- // /**************************************************************************
- // *
- // *************************************************************************/
- // public MobyRelationship[] getRelationships (String dataTypeName)
- // throws MobyException {
- // return null;
- // }
+// /**************************************************************************
+// *
+// *************************************************************************/
+// public MobyRelationship[] getRelationships (String dataTypeName)
+// throws MobyException {
+// return null;
+// }
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
+
+ /**************************************************************************
+ *
+ *************************************************************************/
public String getRegistryEndpoint() {
- return endpoint.toString();
+ return endpoint.toString();
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
+ /**************************************************************************
+ *
+ *************************************************************************/
public String getRegistryNamespace() {
- return uri;
+ return uri;
}
- /*******************************************************************************************************************
+ /**************************************************************************
* Parses and imports the following XML.
- *
*
* <resourceURLs>
- * <Resource name="Service" url="..." />
- * <Resource name="Object" url="..." />
- * <Resource name="Namespace" url="..." />
- * <Resource name="ServiceInstance" url="..." />
- * <Resource name="Full" url="..." />
+ * <Resource name="Service" url="..." />
+ * <Resource name="Object" url="..." />
+ * <Resource name="Namespace" url="..." />
+ * <Resource name="ServiceInstance" url="..." />
+ * <Resource name="Full" url="..." />
* </resourceURLs>
*
- ******************************************************************************************************************/
- public MobyResourceRef[] getResourceRefs() throws MobyException {
-
- String cacheId = "retrieveResourceURLs";
- MobyResourceRef[] cachedResults = ( MobyResourceRef[] ) getContents( cacheId );
- if ( cachedResults != null ) return cachedResults;
-
- String result = ( String ) doCall( "retrieveResourceURLs", new Object[] {} );
-
- // parse returned XML
- Vector< MobyResourceRef > v = new Vector< MobyResourceRef >();
- Document document = loadDocument( new ByteArrayInputStream( result.getBytes() ) );
- NodeList list = document.getElementsByTagName( "Resource" );
- for ( int i = 0; i < list.getLength(); i++ ) {
- Element elem = ( Element ) list.item( i );
- try {
- v.addElement( new MobyResourceRef( elem.getAttribute( "name" ), new URL( ( String ) elem
- .getAttribute( "url" ) ), elem.getAttribute( "type" ) ) );
- }
- catch ( MalformedURLException e2 ) {
- if ( debug ) System.err.println( "Bad URL: " + elem.getAttribute( "url" ) );
- }
+ *************************************************************************/
+ public MobyResourceRef[] getResourceRefs()
+ throws MobyException {
+
+ String cacheId = "retrieveResourceURLs";
+ MobyResourceRef[] cachedResults = (MobyResourceRef[])getContents (cacheId);
+ if (cachedResults != null)
+ return cachedResults;
+
+ String result = (String)doCall ("retrieveResourceURLs",
+ new Object[] {});
+
+ // parse returned XML
+ Vector v = new Vector();
+ Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
+ NodeList list = document.getElementsByTagName ("Resource");
+ for (int i = 0; i < list.getLength(); i++) {
+ Element elem = (Element)list.item (i);
+ try {
+ v.addElement
+ (new MobyResourceRef (elem.getAttribute ("name"),
+ new URL ((String)elem.getAttribute ("url")),
+ elem.getAttribute ("type")));
+ } catch (MalformedURLException e2) {
+ if (debug)
+ System.err.println ("Bad URL: " + elem.getAttribute ("url"));
}
+ }
- MobyResourceRef[] results = new MobyResourceRef[ v.size() ];
- v.copyInto( results );
+ MobyResourceRef[] results = new MobyResourceRef [v.size()];
+ v.copyInto (results);
- // Add this data to the cache in case we get called again
- setContents( cacheId, results );
+ // Add this data to the cache in case we get called again
+ setContents (cacheId, results);
- return results;
+ return results;
}
- /*******************************************************************************************************************
- *
- ******************************************************************************************************************/
- public InputStream getResource( String resourceName ) throws MobyException {
+ /**************************************************************************
+ *
+ *************************************************************************/
+ public InputStream getResource (String resourceName)
+ throws MobyException {
- MobyResourceRef[] resourceRefs = getResourceRefs();
- for ( int i = 0; i < resourceRefs.length; i++ ) {
- if ( resourceName.equalsIgnoreCase( resourceRefs[ i ].getResourceName() ) ) {
- return Utils.getInputStream( resourceRefs[ i ].getResourceLocation() );
- }
+ MobyResourceRef[] resourceRefs = getResourceRefs();
+ for (int i = 0; i < resourceRefs.length; i++) {
+ if (resourceName.equalsIgnoreCase (resourceRefs[i].getResourceName())) {
+ return Utils.getInputStream (resourceRefs[i].getResourceLocation());
}
- throw new MobyException( "No resource found for '" + resourceName + "'." );
+ }
+ throw new MobyException ("No resource found for '" + resourceName + "'.");
}
- /*******************************************************************************************************************
- * Return a case-insensitive comparator of Strings. It is used to create various TreeMaps where keys are strings.
- ******************************************************************************************************************/
+ /**************************************************************************
+ * Return a case-insensitive comparator of Strings. It is used to
+ * create various TreeMaps where keys are strings.
+ *************************************************************************/
protected static Comparator getStringComparator() {
- return new Comparator() {
- public int compare( Object o1, Object o2 ) {
- return ( ( String ) o1 ).compareToIgnoreCase( ( String ) o2 );
- }
+ return new Comparator() {
+ public int compare (Object o1, Object o2) {
+ return ((String)o1).compareToIgnoreCase ((String)o2);
+ }
};
}
-
- // cache URL/URI so we only check once
+
+ // cache URL/URI so we only check once
private static String CHECKED_URL = null;
private static String CHECKED_URI = null;
-
+
/**
- * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared class hierarchy
- * that implicitly check the registry will use the same cache. Otherwise, methods such as
- * MobyNamespace.getNamespace() must be passed a Central object parameter as well.
- *
+ * Using this method to get a Central object will ensure that other parts of the org.biomoby.shared
+ * class hierarchy that implicitly check the registry will use the same cache. Otherwise, methods
+ * such as MobyNamespace.getNamespace() must be passed a Central object parameter as well.
+ *
* @return a CentralImpl using the default Central URI, and currently a class implementing a caching mechanism
*/
- public static CentralImpl getDefaultCentral() throws MobyException {
- return getDefaultCentral( null );
+ public static CentralImpl getDefaultCentral() throws MobyException{
+ return getDefaultCentral(null);
}
- public static CentralImpl getDefaultCentral( Registry reg ) throws MobyException {
- if ( reg == null && defaultCentrals.containsKey( "" ) ) {
- return defaultCentrals.get( "" );
- }
- else if ( reg != null && defaultCentrals.containsKey( reg.getEndpoint() ) ) {
- return defaultCentrals.get( reg.getEndpoint() );
- }
+ public static CentralImpl getDefaultCentral(Registry reg) throws MobyException{
+ if(reg == null && defaultCentrals.containsKey("")){
+ return defaultCentrals.get("");
+ }
+ else if(reg != null && defaultCentrals.containsKey(reg.getEndpoint())){
+ return defaultCentrals.get(reg.getEndpoint());
+ }
- String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
- ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
- URL resURL = classLoader.getResource( "META-INF/" + CENTRAL_IMPL_RESOURCE_NAME );
- if ( resURL != null ) {
- System.err.println( "Loading " + resURL );
- try {
- LineNumberReader reader = new LineNumberReader( new InputStreamReader( resURL.openStream() ) );
- for ( String line = reader.readLine(); line != null; line = reader.readLine() ) {
- if ( !line.trim().startsWith( "#" ) ) {
- className = line.trim();
- break;
- }
- }
- }
- catch ( Exception e ) {
- logger.log( Level.WARNING, "Error reading " + resURL, e );
+ String className = DEFAULT_CENTRAL_IMPL_CLASSNAME;
+ ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+ URL resURL = classLoader.getResource("META-INF/"+CENTRAL_IMPL_RESOURCE_NAME);
+ if(resURL != null){
+ System.err.println("Loading "+resURL);
+ try{
+ LineNumberReader reader = new LineNumberReader(new InputStreamReader(resURL.openStream()));
+ for(String line = reader.readLine(); line != null; line = reader.readLine()){
+ if(!line.trim().startsWith("#")){
+ className = line.trim();
+ break;
}
}
- try {
- System.err.println( "Central class is " + className );
- Class clazz = Class.forName( className );
- if ( reg == null ) { // should use default nullary c-tor
- defaultCentrals.put( "", ( CentralImpl ) clazz.newInstance() );
- }
- else { // should have (String endpoint, String namespace) c-tor
- for ( Constructor ctor : clazz.getDeclaredConstructors() ) {
- Class[] params = ctor.getParameterTypes();
- if ( params.length == 2 && params[ 0 ].getName().equals( "java.lang.String" )
- && params[ 1 ].getName().equals( "java.lang.String" ) ) {
- defaultCentrals.put( reg.getEndpoint(), ( CentralImpl ) ctor.newInstance( reg.getEndpoint(),
- reg.getNamespace() ) );
- break;
- }
- }
- if ( !defaultCentrals.containsKey( reg.getEndpoint() ) ) {
- logger.log( Level.WARNING, "Could not find required (String endpoint, String namespace)"
- + "constructor for class " + className );
- }
- }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Error reading " + resURL,
+ e);
}
- catch ( Exception e ) {
- logger.log( Level.WARNING, "Could not load class " + className, e );
- if ( reg == null ) {
- defaultCentrals.put( "", new CentralImpl() ); // fallback to this class, no caching, etc.
- }
- else {
- defaultCentrals.put( reg.getEndpoint(), new CentralImpl( reg.getEndpoint(), reg.getNamespace() ) );
+ }
+ try{
+ System.err.println("Central class is "+className);
+ Class clazz = Class.forName(className);
+ if(reg == null){ // should use default nullary c-tor
+ defaultCentrals.put("", (CentralImpl) clazz.newInstance());
+ }
+ else{ // should have (String endpoint, String namespace) c-tor
+ for(Constructor ctor: clazz.getDeclaredConstructors()){
+ Class[] params = ctor.getParameterTypes();
+ if(params.length == 2 && params[0].getName().equals("java.lang.String") &&
+ params[1].getName().equals("java.lang.String") ){
+ defaultCentrals.put(reg.getEndpoint(),
+ (CentralImpl) ctor.newInstance(reg.getEndpoint(), reg.getNamespace()));
+ break;
}
}
+ if(!defaultCentrals.containsKey(reg.getEndpoint())){
+ logger.log(Level.WARNING,
+ "Could not find required (String endpoint, String namespace)" +
+ "constructor for class " + className);
+ }
+ }
+ } catch(Exception e){
+ logger.log(Level.WARNING,
+ "Could not load class " + className,
+ e);
+ if(reg == null){
+ defaultCentrals.put("", new CentralImpl()); //fallback to this class, no caching, etc.
+ }
+ else{
+ defaultCentrals.put(reg.getEndpoint(),
+ new CentralImpl(reg.getEndpoint(), reg.getNamespace()));
+ }
+ }
- return defaultCentrals.get( reg == null ? "" : reg.getEndpoint() );
+ return defaultCentrals.get(reg == null ? "" : reg.getEndpoint());
}
/**
*
- * @return a String representing the Default mobycentral endpoint. If the system property 'moby.check.default'
- * exists and is set to true, then the URL http://biomoby.org/mobycentral is queried and the default central
- * endpoint is returned, otherwise DEFAULT_ENDPOINT is returned.
+ * @return a String representing the Default mobycentral endpoint. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central endpoint is returned, otherwise DEFAULT_ENDPOINT
+ * is returned.
*/
public static String getDefaultURL() {
- boolean check = false;
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+
+ if (check) {
+ // return the last checked url if we have done this before
+ if (CHECKED_URL != null && CHECKED_URL.trim() != "") {
+ return CHECKED_URL;
+ }
+
+ // create a HttpClient object
+ HttpClient client = new HttpClient();
+ // set up the Head method
+ HeadMethod method = new HeadMethod("http://biomoby.org/mobycentral");
+ // do not follow redirects or we will get a 411 error
+ method.setFollowRedirects(false);
+ // retry 3 times
+ method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,new DefaultHttpMethodRetryHandler(3, false));
+ // set the user agent ... should probably make this something more reasonable
+ method.getParams().setParameter(HttpMethodParams.USER_AGENT,"jMoby/1.0");
try {
- check = Boolean.getBoolean( "moby.check.default" );
- }
- catch ( Exception e ) {
-
- }
+ // Execute the method.
+ int statusCode = client.executeMethod(method);
- if ( check ) {
- // return the last checked url if we have done this before
- if ( CHECKED_URL != null && CHECKED_URL.trim() != "" ) {
- return CHECKED_URL;
- }
-
- // create a HttpClient object
- HttpClient client = new HttpClient();
- // set up the Head method
- HeadMethod method = new HeadMethod( "http://biomoby.org/mobycentral" );
- // do not follow redirects or we will get a 411 error
- method.setFollowRedirects( false );
- // retry 3 times
- method.getParams().setParameter( HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler( 3, false ) );
- // set the user agent ... should probably make this something more reasonable
- method.getParams().setParameter( HttpMethodParams.USER_AGENT, "jMoby/1.0" );
+ if (statusCode != HttpStatus.SC_MOVED_PERMANENTLY) {
+ System.err.println("Method failed: "
+ + method.getStatusLine());
+ } else {
try {
- // Execute the method.
- int statusCode = client.executeMethod( method );
-
- if ( statusCode != HttpStatus.SC_MOVED_PERMANENTLY ) {
- System.err.println( "Method failed: " + method.getStatusLine() );
- }
- else {
- try {
- String location = method.getResponseHeader( "location" ).getValue();
- CHECKED_URL = location;
- try {
- CHECKED_URI = "http://" + ( new URL( CHECKED_URL ).getAuthority() ) + "/MOBY/Central";
- }
- catch ( MalformedURLException murle ) {
- CHECKED_URI = DEFAULT_NAMESPACE;
- }
- return CHECKED_URL;
- }
- catch ( NullPointerException npe ) {
- return DEFAULT_ENDPOINT;
- }
- }
- }
- catch ( HttpException e ) {
- System.err.println( "Fatal protocol violation: " + e.getMessage() );
- e.printStackTrace();
- }
- catch ( IOException e ) {
- System.err.println( "Fatal transport error: " + e.getMessage() );
- e.printStackTrace();
- }
- finally {
- // Release the connection.
- method.releaseConnection();
+ String location = method.getResponseHeader("location").getValue();
+ CHECKED_URL = location;
+ try {
+ CHECKED_URI = "http://" + (new URL(CHECKED_URL).getAuthority()) + "/MOBY/Central";
+ } catch (MalformedURLException murle ) {
+ CHECKED_URI = DEFAULT_NAMESPACE;
}
-
- }
- else {
+ return CHECKED_URL;
+ } catch (NullPointerException npe) {
return DEFAULT_ENDPOINT;
+ }
}
+ } catch (HttpException e) {
+ System.err.println("Fatal protocol violation: "
+ + e.getMessage());
+ e.printStackTrace();
+ } catch (IOException e) {
+ System.err.println("Fatal transport error: " + e.getMessage());
+ e.printStackTrace();
+ } finally {
+ // Release the connection.
+ method.releaseConnection();
+ }
+
+ } else {
return DEFAULT_ENDPOINT;
}
-
+ return DEFAULT_ENDPOINT;
+ }
+
/**
*
- * @return a String representing the default mobycentral uri. If the system property 'moby.check.default' exists and
- * is set to true, then the URL http://biomoby.org/mobycentral is queried and the default central namespace
- * is returned, otherwise DEFAULT_NAMESPACE is returned.
+ * @return a String representing the default mobycentral uri. If the
+ * system property 'moby.check.default' exists and is set to true,
+ * then the URL http://biomoby.org/mobycentral is queried and the
+ * default central namespace is returned, otherwise DEFAULT_NAMESPACE
+ * is returned.
*/
public static String getDefaultURI() {
- boolean check = false;
- try {
- check = Boolean.getBoolean( "moby.check.default" );
- }
- catch ( Exception e ) {
-
- }
- if ( check ) {
- if ( CHECKED_URI != null && CHECKED_URI.trim() != "" ) {
- return CHECKED_URI;
- }
- // need to check ...
- getDefaultURL();
- return CHECKED_URI;
- }
- else {
- return DEFAULT_NAMESPACE;
- }
- }
-
- /*******************************************************************************************************************
- * Convert non-suitable characters in a XML string into their entity references.
- *
- *
+ boolean check = false;
+ try {
+ check = Boolean.getBoolean("moby.check.default");
+ } catch (Exception e) {
+
+ }
+ if (check) {
+ if (CHECKED_URI != null && CHECKED_URI.trim() != "") {
+ return CHECKED_URI;
+ }
+ // need to check ...
+ getDefaultURL();
+ return CHECKED_URI;
+ } else {
+ return DEFAULT_NAMESPACE;
+ }
+ }
+ /**************************************************************************
+ * Convert non-suitable characters in a XML string into their
+ * entity references.
+ *
* Adapted from jDom.
- *
- * @param str
- * input to be converted
- * @return If there were any non-suitable characters, return a new string with those characters escaped, otherwise
- * return the unmodified input string
- *
- ******************************************************************************************************************/
- public String escapeXML( String str ) {
+ *
+ * @param str input to be converted
+ * @return If there were any non-suitable characters, return a new
+ * string with those characters escaped, otherwise return the
+ * unmodified input string
+ *
+ *************************************************************************/
+ public String escapeXML (String str) {
StringBuffer buffer = null;
char ch;
String entity;
- for ( int i = 0; i < str.length(); i++ ) {
- ch = str.charAt( i );
- switch ( ch ) {
- case '<':
- entity = "<";
- break;
- case '>':
- entity = ">";
- break;
- case '&':
- entity = "&";
- break;
- default:
- entity = null;
- break;
+ for (int i = 0; i < str.length(); i++) {
+ ch = str.charAt (i);
+ switch (ch) {
+ case '<' :
+ entity = "<";
+ break;
+ case '>' :
+ entity = ">";
+ break;
+ case '&' :
+ entity = "&";
+ break;
+ default :
+ entity = null;
+ break;
}
- if ( buffer == null ) {
- if ( entity != null ) {
+ if (buffer == null) {
+ if (entity != null) {
// An entity occurred, so we'll have to use StringBuffer
// (allocate room for it plus a few more entities).
- buffer = new StringBuffer( str.length() + 20 );
+ buffer = new StringBuffer (str.length() + 20);
// Copy previous skipped characters and fall through
// to pickup current character
- buffer.append( str.substring( 0, i ) );
- buffer.append( entity );
- }
- }
- else {
- if ( entity == null ) {
- buffer.append( ch );
+ buffer.append (str.substring (0, i));
+ buffer.append (entity);
}
- else {
- buffer.append( entity );
+ } else {
+ if (entity == null) {
+ buffer.append (ch);
+ } else {
+ buffer.append (entity);
}
}
}
@@ -1915,43 +2091,49 @@
// If there were any entities, return the escaped characters
// that we put in the StringBuffer. Otherwise, just return
// the unmodified input string.
- return ( buffer == null ) ? str : buffer.toString();
+ return (buffer == null) ? str : buffer.toString();
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Format an exception.
- ******************************************************************************************************************/
- public static String formatFault( AxisFault e, String endpoint, QName method ) {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- formatFault( e, new PrintStream( baos ), endpoint, method );
- return baos.toString();
+ *************************************************************************/
+ public static String formatFault (AxisFault e, String endpoint, QName method) {
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ formatFault (e, new PrintStream (baos), endpoint, method);
+ return baos.toString();
}
- /*******************************************************************************************************************
+ /*************************************************************************
* Format an exception.
- ******************************************************************************************************************/
- public static void formatFault( AxisFault e, PrintStream out, String endpoint, QName method ) {
-
- out.println( "===ERROR===" );
- out.println( "Fault details:" );
- // for some obvious errors I do not print all details (with a lenghty trace stack)
- String faultString = e.getFaultString();
- if ( ( !faultString.startsWith( "java.net.ConnectException" ) )
- && ( faultString.indexOf( "Could not find class for the service named:" ) == -1 ) ) {
- org.w3c.dom.Element[] details = e.getFaultDetails();
- for ( int i = 0; i < details.length; i++ ) {
- String s = details[ i ].toString().replaceAll( "<", "<" );
- s = s.replaceAll( ">", ">" );
- out.println( s );
- }
- }
- out.println( "Fault string: " + faultString );
- out.println( "Fault code: " + e.getFaultCode() );
- out.println( "Fault actor: " + e.getFaultActor() );
- if ( endpoint != null || method != null ) out.println( "When calling:" );
- if ( endpoint != null ) out.println( "\t" + endpoint );
- if ( method != null ) out.println( "\t" + method );
- out.println( "===========" );
+ *************************************************************************/
+ public static void formatFault (AxisFault e, PrintStream out,
+ String endpoint, QName method) {
+
+ out.println ("===ERROR===");
+ out.println ("Fault details:");
+ // for some obvious errors I do not print all details (with a lenghty trace stack)
+ String faultString = e.getFaultString();
+ if ( (! faultString.startsWith ("java.net.ConnectException")) &&
+ (faultString.indexOf ("Could not find class for the service named:") == -1)
+ ) {
+ org.w3c.dom.Element[] details = e.getFaultDetails();
+ for (int i = 0; i < details.length; i++) {
+ String s = details[i].toString().replaceAll ("<", "<");
+ s = s.replaceAll (">", ">");
+ out.println (s);
+ }
+ }
+ out.println ("Fault string: " + faultString);
+ out.println ("Fault code: " + e.getFaultCode());
+ out.println ("Fault actor: " + e.getFaultActor());
+ if (endpoint != null || method != null)
+ out.println ("When calling:");
+ if (endpoint != null)
+ out.println ("\t" + endpoint);
+ if (method != null)
+ out.println ("\t" + method);
+ out.println ("===========");
}
+
}
From kawas at dev.open-bio.org Thu Dec 4 15:31:27 2008
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 4 Dec 2008 10:31:27 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812041531.mB4FVRR8016254@dev.open-bio.org>
kawas
Thu Dec 4 10:31:27 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv16218/Perl/MOBY-Server
Modified Files:
MANIFEST
Log Message:
added share/cgi/service_unit_tester.pl to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST 2008/11/20 19:40:41 1.9
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST 2008/12/04 15:31:26 1.10
@@ -97,6 +97,7 @@
share/cgi/OntologyServer.cgi
share/cgi/RESOURCES
share/cgi/service_tester.pl
+share/cgi/service_unit_tester.pl
share/cgi/ServicePingerValidator
share/cgi/ValidateService
share/config/mobycentral.config.template
From groscurt at dev.open-bio.org Wed Dec 17 10:21:57 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 05:21:57 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171021.mBHALvuv005113@dev.open-bio.org>
groscurt
Wed Dec 17 05:21:57 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test
In directory dev.open-bio.org:/tmp/cvs-serv5054/src/main/de/mpg/mpiz_koeln/featureClient/test
Modified Files:
SimpleSingleCall.java SingleCallWithParameters.java
MultiCallWithParameters.java MultiCallByDefinition.java
ComplexSingleCall.java SimpleMultiCall.java
SingleMultiServiceCall.java
Log Message:
moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test SimpleSingleCall.java,1.1,1.2 SingleCallWithParameters.java,1.1,1.2 MultiCallWithParameters.java,1.1,1.2 MultiCallByDefinition.java,1.1,1.2 ComplexSingleCall.java,1.1,1.2 SimpleMultiCall.java,1.1,1.2 SingleMultiServiceCall.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.MobyObject;
@@ -19,7 +18,7 @@
client.setTimeout( 45 );
client.addService( "mpiz-koeln.mpg.de", "ID2IDs" );
client.setServiceInputSingleCall( "", "NP_176539.1" );
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
Collection< MobyObject > collection = mobyServiceResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.AminoAcidSequence;
@@ -38,7 +37,7 @@
client.setServiceInputSingleCall( organism, sequence, geneName );
- List< FeatureClientResult > result = client.call();
+ Collection < FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
Collection< FASTA_AA > fastas = mobyServiceResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -79,7 +78,7 @@
client.addServiceInputMultiCall( "gene2", organism, sequence, geneName );
// the service is called
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// the map stores for each identifier given the list of results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -34,7 +33,7 @@
client.addServiceInputMultiCall( "AGI_LocusCode", "AT1G12000" );
// call the service, which will be found
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// as we have called the service multiple times we get back for each identifier the returned results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 10:21:56 1.2
@@ -34,7 +34,7 @@
client.setServiceInputSingleCall( sequence );
// start the call and retrieve the results
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult featureClientResult : result ) {
// as the service was called once we get back the result for this service call
Collection< AminoAcidSequence > sequences = featureClientResult.getSingleCallResult();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import java.util.Map;
import org.biomoby.shared.MobyException;
@@ -29,7 +28,7 @@
client.addServiceInputMultiCall( "GO", "0004396" );
// call the service
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// the map stores for each id of the input object a list of results
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 10:21:56 1.2
@@ -1,7 +1,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.MobyService;
@@ -27,7 +26,7 @@
client.setServiceInputSingleCall( "AGI_LocusCode", "AT1G12000" );
// call the service
- List< FeatureClientResult > result = client.call();
+ Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
// you can get which service returned the current result
From groscurt at dev.open-bio.org Wed Dec 17 14:07:17 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:07:17 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171407.mBHE7H6U005665@dev.open-bio.org>
groscurt
Wed Dec 17 09:07:16 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv5630/src/main/org/biomoby/shared
Modified Files:
MobyService.java
Log Message:
added hashCode method, based on the uniquename as used in the equals method
moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/10/21 16:38:44 1.25
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/12/17 14:07:16 1.26
@@ -102,6 +102,10 @@
if (obj == null) return false;
return getUniqueName().equals ( ((MobyService)obj).getUniqueName() );
}
+
+ public int hashCode() {
+ return getUniqueName().hashCode();
+ }
/**************************************************************************
* Default constructor.
From groscurt at dev.open-bio.org Wed Dec 17 14:09:00 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:09:00 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171409.mBHE90wZ005705@dev.open-bio.org>
groscurt
Wed Dec 17 09:09:00 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv5670/src/main/org/biomoby/client
Modified Files:
MobyServiceLocator.java
Log Message:
javadoc had a warning...
moby-live/Java/src/main/org/biomoby/client MobyServiceLocator.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/03 15:21:13 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyServiceLocator.java 2008/12/17 14:09:00 1.6
@@ -168,7 +168,7 @@
/***************************************************
* Returns true if the user AND the password is set
- * @return
+ * @return if authentication shall be used
***************************************************/
public boolean hasAuthentication() {
return user != null && password != null;
From groscurt at dev.open-bio.org Wed Dec 17 14:09:54 2008
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Wed, 17 Dec 2008 09:09:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200812171409.mBHE9sdL005791@dev.open-bio.org>
groscurt
Wed Dec 17 09:09:54 EST 2008
Update of /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test
In directory dev.open-bio.org:/tmp/cvs-serv5728/src/main/de/mpg/mpiz_koeln/featureClient/test
Modified Files:
SingleCallDefinition.java SingleCallWithParameters.java
ComplexSingleCall.java SingleMultiServiceCall.java
MultiCallWithParameters.java SimpleSingleCall.java
SimpleMultiCall.java MultiCallByDefinition.java
Log Message:
minor changes
moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test SingleCallDefinition.java,1.1,1.2 SingleCallWithParameters.java,1.2,1.3 ComplexSingleCall.java,1.2,1.3 SingleMultiServiceCall.java,1.2,1.3 MultiCallWithParameters.java,1.2,1.3 SimpleSingleCall.java,1.2,1.3 SimpleMultiCall.java,1.2,1.3 MultiCallByDefinition.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java 2008/11/26 08:52:20 1.1
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallDefinition.java 2008/12/17 14:09:54 1.2
@@ -9,14 +9,14 @@
import de.mpg.mpiz_koeln.featureClient.FeatureClientException;
import de.mpg.mpiz_koeln.featureClient.FeatureClientResult;
-public class SingleCallDefinition {
+class SingleCallDefinition {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.addOutput( "Object", "PMID" );
client.setTimeout( 45 );
client.add2Filter( "Locus2GeneAliases", "getCor", "getGeneticElementNameByFreeText", "getGoTermAssociations",
"getConservedDomainLabelFromDomainId", "ExplodeOutCrossReferences" );
- client.setServiceInputSingleCall( "", "Q9SZW4" );
+ client.setSingleCallInput( "", "Q9SZW4" );
Collection< FeatureClientResult > collection = client.call();
for ( FeatureClientResult mobyServiceResult : collection ) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleCallWithParameters.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
import de.mpg.mpiz_koeln.featureClient.FeatureClientException;
import de.mpg.mpiz_koeln.featureClient.FeatureClientResult;
-public class SingleCallWithParameters {
+class SingleCallWithParameters {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 120 );
@@ -35,7 +35,7 @@
geneName.setId( "my_gene" );
geneName.setName( "gene_name" );
- client.setServiceInputSingleCall( organism, sequence, geneName );
+ client.setSingleCallInput( organism, sequence, geneName );
Collection < FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/ComplexSingleCall.java 2008/12/17 14:09:54 1.3
@@ -2,7 +2,6 @@
package de.mpg.mpiz_koeln.featureClient.test;
import java.util.Collection;
-import java.util.List;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.datatypes.AminoAcidSequence;
@@ -18,7 +17,7 @@
* This examples shows how to use the client to call a web service once which consumes a complex data type, such as
* AminoAcidSequence.
*/
-public class ComplexSingleCall {
+class ComplexSingleCall {
public static void main(String[] args) throws MobyException, FeatureClientException {
FeatureClient client = new FeatureClient();
// timeout of the calls is set to 45 seconds
@@ -31,7 +30,7 @@
sequence.set_SequenceString( new MobyString( "MQPVKVYADRRSQPSRAVIIFCRVNQIDFEEVTVDLFKSQHLTPEFRKVNPMGQVPAIVDGR" ) );
sequence.set_Length( new MobyInteger( 50 ) );
// set the input to the client
- client.setServiceInputSingleCall( sequence );
+ client.setSingleCallInput( sequence );
// start the call and retrieve the results
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SingleMultiServiceCall.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
/**
* This example shows how to call more service one with one input.
*/
-public class SingleMultiServiceCall {
+class SingleMultiServiceCall {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 30 );
@@ -23,7 +23,7 @@
client.addService( "Locus2Publications" );
// set the input of the service
- client.setServiceInputSingleCall( "AGI_LocusCode", "AT1G12000" );
+ client.setSingleCallInput( "AGI_LocusCode", "AT1G12000" );
// call the service
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallWithParameters.java 2008/12/17 14:09:54 1.3
@@ -18,7 +18,7 @@
* This example shows how to call a service multiple times which consumes more than one input. It also shows the mixture
* of a simple object input and a complex data type input.
*/
-public class MultiCallWithParameters {
+class MultiCallWithParameters {
public static void main( String[] args ) throws MobyException, FeatureClientException {
FeatureClient client = new FeatureClient();
// the service might take longer, so we set the timeout to 120 seconds
@@ -55,7 +55,7 @@
// adds the inputs to the client and give it an identifier, so that you are able to distinguish the several
// calls later. This identifier is completely free to choice !
- client.addServiceInputMultiCall( "gene1", organism, sequence, geneName );
+ client.addMultipleCallInput( "gene1", organism, sequence, geneName );
// we want to call the same service a second time so we build again some input values
organism = new MobyObject();
@@ -75,7 +75,7 @@
geneName.setName( "gene_name" );
// adds the inputs to the client for the second call with a different identifier as before
- client.addServiceInputMultiCall( "gene2", organism, sequence, geneName );
+ client.addMultipleCallInput( "gene2", organism, sequence, geneName );
// the service is called
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleSingleCall.java 2008/12/17 14:09:54 1.3
@@ -12,12 +12,12 @@
/**
* This example shows how to call a service once with a simple object input.
*/
-public class SimpleSingleCall {
+class SimpleSingleCall {
public static void main( String[] args ) throws FeatureClientException, MobyException {
FeatureClient client = new FeatureClient();
client.setTimeout( 45 );
client.addService( "mpiz-koeln.mpg.de", "ID2IDs" );
- client.setServiceInputSingleCall( "", "NP_176539.1" );
+ client.setSingleCallInput( "", "NP_176539.1" );
Collection< FeatureClientResult > result = client.call();
for ( FeatureClientResult mobyServiceResult : result ) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/SimpleMultiCall.java 2008/12/17 14:09:54 1.3
@@ -13,7 +13,7 @@
/**
* This example shows how to call a web service multiple times with a simple object input.
*/
-public class SimpleMultiCall {
+class SimpleMultiCall {
public static void main( String[] args ) throws MobyException, FeatureClientException {
// the client queries the default central if no given otherwise
FeatureClient client = new FeatureClient();
@@ -23,9 +23,9 @@
client.addService( "mpiz-koeln.mpg.de", "get_go_information_by_go_term" );
// the three different inputs for the three service calls
- client.addServiceInputMultiCall( "GO", "0044408" );
- client.addServiceInputMultiCall( "GO", "0020015" );
- client.addServiceInputMultiCall( "GO", "0004396" );
+ client.addMultipleCallInput( "GO", "0044408" );
+ client.addMultipleCallInput( "GO", "0020015" );
+ client.addMultipleCallInput( "GO", "0004396" );
// call the service
Collection< FeatureClientResult > result = client.call();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 10:21:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/de/mpg/mpiz_koeln/featureClient/test/MultiCallByDefinition.java 2008/12/17 14:09:54 1.3
@@ -18,7 +18,7 @@
*
* It also shows how to filter out services or authorities which shall be not called at all.
*/
-public class MultiCallByDefinition {
+class MultiCallByDefinition {
public static void main( String[] args ) throws MobyException, FeatureClientException {
// create a client to the default moby central in calgary with a timeout of 30 seconds
FeatureClient client = new FeatureClient();
@@ -28,9 +28,9 @@
// exclude services identified by service name or authority
client.add2Filter( "Locus2GeneAliases", "getCor", "bioinfo.icapture.ubc.ca" );
// input for the first call -> it also defines now we search for service which consumes an AGI code
- client.addServiceInputMultiCall( "AGI_LocusCode", "AT4G30110" );
+ client.addMultipleCallInput( "AGI_LocusCode", "AT4G30110" );
// input for the second call
- client.addServiceInputMultiCall( "AGI_LocusCode", "AT1G12000" );
+ client.addMultipleCallInput( "AGI_LocusCode", "AT1G12000" );
// call the service, which will be found
Collection< FeatureClientResult > result = client.call();