[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Sun Nov 20 12:30:51 UTC 2005
senger
Sun Nov 20 07:30:51 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv4966/src/main/org/biomoby/client
Modified Files:
BaseCmdLineClient.java CentralDigestCachedImpl.java
CentralImpl.java GraphsServlet.java ServicesEdge.java
Log Message:
moby-live/Java/src/main/org/biomoby/client BaseCmdLineClient.java,1.4,1.5 CentralDigestCachedImpl.java,1.14,1.15 CentralImpl.java,1.35,1.36 GraphsServlet.java,1.14,1.15 ServicesEdge.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseCmdLineClient.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/BaseCmdLineClient.java 2005/10/12 11:36:59 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseCmdLineClient.java 2005/11/20 12:30:51 1.5
@@ -297,12 +297,12 @@
}
}
- protected MobyObject createInstance (MobyObject obj)
+ protected MobyObject createInstance (MobyObject mobj)
throws MobyException {
try {
- return (MobyObject)obj.getClass().newInstance();
+ return (MobyObject)mobj.getClass().newInstance();
} catch (Exception e) {
- throw new MobyException ("Cannot instantiate data type '" + obj.getClass().getName() + "'.");
+ throw new MobyException ("Cannot instantiate data type '" + mobj.getClass().getName() + "'.");
}
}
@@ -351,14 +351,14 @@
/**************************************************************************
*
*************************************************************************/
- protected boolean createChildren (MobyObject obj)
+ protected boolean createChildren (MobyObject mobj)
throws MobyException {
boolean someChildrenCreated = false;
try {
HashMap methodsAndArticleNames = new HashMap();
HashMap methodsAndChildTypes = new HashMap();
HashMap methodNamesAndHowManyTimes = new HashMap();
- Class myClass = obj.getClass();
+ Class myClass = mobj.getClass();
Field[] fields = myClass.getFields();
for (int i = 0; i < fields.length; i++) {
String fieldName = fields[i].getName();
@@ -392,20 +392,20 @@
Class childType = (Class)entry.getValue();
int count = ( ((Integer)methodNamesAndHowManyTimes.get (method.getName())).intValue() );
while (count-- > 0) {
- if (createOneChild (obj, method, childType, (String)methodsAndArticleNames.get (method)))
+ if (createOneChild (mobj, method, childType, (String)methodsAndArticleNames.get (method)))
someChildrenCreated = true;
}
}
} else {
// this is a leaf that does not have any children...
- if (obj.isPrimitiveType()) {
+ if (mobj.isPrimitiveType()) {
// ...if it is a primitive type, we may ignore it if there is no more values
- return setPrimitiveValue (obj, articleName);
+ return setPrimitiveValue (mobj, articleName);
} else {
// ...if it is an Object leaf, we always keep it
// but id and namespaces are here like values for
// primitives so filltem
- setIdAndNamespace (obj);
+ setIdAndNamespace (mobj);
return true;
}
}
@@ -422,12 +422,12 @@
/**************************************************************************
*
*************************************************************************/
- boolean createOneChild (MobyObject parent, Method setMethod, Class childType, String articleName)
+ boolean createOneChild (MobyObject parent, Method setMethod, Class childType, String artName)
throws MobyException {
try {
MobyObject child = createInstance (childType);
if (child.isPrimitiveType()) {
- if (setPrimitiveValue (child, articleName)) {
+ if (setPrimitiveValue (child, artName)) {
setMethod.invoke (parent, new Object[] { child });
return true;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2005/11/12 16:43:47 1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2005/11/20 12:30:51 1.15
@@ -215,7 +215,7 @@
/**
- * Create a cache directory from 'cacheDir' and 'registryId' if it
+ * Create a cache directory from 'cacheDirectory' and 'registryId' if it
* does not exist yet. Make sure that it is writable. Return a
* File representing created directory.
*
@@ -223,11 +223,11 @@
* cache is going to be created for. If null, an endpoint of a
* default Moby registry is used.
*/
- protected File createCacheDir (String cacheDir, String registryId)
+ protected File createCacheDir (String cacheDirectory, String registryId)
throws MobyException {
if (registryId == null || registryId.equals (""))
registryId = CentralImpl.DEFAULT_ENDPOINT;
- File cache = new File (cacheDir + fileSeparator + clean (registryId));
+ File cache = new File (cacheDirectory + fileSeparator + clean (registryId));
try {
if (! cache.exists())
if (! cache.mkdirs())
@@ -246,11 +246,13 @@
* Remove cache and all (but given in 'subCacheDirNames') its
* subdirectories.
*/
- protected void removeCacheDir (String cacheDir, String registryId, String[] subCacheDirNames)
+ protected void removeCacheDir (String cacheDirectory,
+ String registryId,
+ String[] subCacheDirNames)
throws MobyException {
if (registryId == null || registryId.equals (""))
registryId = CentralImpl.DEFAULT_ENDPOINT;
- File cache = new File (cacheDir + fileSeparator + clean (registryId));
+ File cache = new File (cacheDirectory + fileSeparator + clean (registryId));
try {
if (! cache.exists()) return;
if (! cache.isDirectory())
@@ -263,7 +265,8 @@
for (int f = 0; f < files.length; f++) {
if (files[f].isDirectory())
throw new MobyException ("Found a directory '" + files[f].getAbsolutePath() + "' where no directory should be");
- files[f].delete();
+ if (! files[f].delete())
+ log.error ("Can't delete file '" + files[f] + "'.");
}
cacheSubDir.delete();
}
@@ -673,7 +676,8 @@
if (ignored (list[i])) continue;
v.addElement (createDataTypeFromXML (load (list[i]), "-dummy-"));
} catch (NoSuccessException e) {
- System.err.println (MSG_CACHE_BAD_FILE (list[i], e));
+ log.error (MSG_CACHE_BAD_FILE (list[i], e));
+ //System.err.println (MSG_CACHE_BAD_FILE (list[i], e));
}
}
MobyDataType[] result = new MobyDataType [v.size()];
@@ -736,7 +740,7 @@
v.addElement (servs[j]);
}
} catch (MobyException e) {
- System.err.println (MSG_CACHE_BAD_FILE (list[i], e));
+ log.error (MSG_CACHE_BAD_FILE (list[i], e));
}
}
MobyService[] result = new MobyService [v.size()];
@@ -799,6 +803,7 @@
try {
types[i].setParentNames (createServiceTypeRelationshipsFromXML (load (file)));
} catch (MobyException e) {
+ log.error (MSG_CACHE_BAD_FILE (file, e));
System.err.println (MSG_CACHE_BAD_FILE (file, e));
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.35
retrieving revision 1.36
diff -u -r1.35 -r1.36
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2005/11/12 16:43:47 1.35
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2005/11/20 12:30:51 1.36
@@ -154,7 +154,7 @@
dbf.setNamespaceAware(true);
docBuilder = dbf.newDocumentBuilder();
} catch (Exception e) {
- throw new MobyException ("Could not configure an XML parser: " + e);
+ throw new MobyException ("Could not configure an XML parser: " + e, e);
}
cache = new Hashtable();
@@ -241,7 +241,7 @@
try {
document=docBuilder.parse(new ByteArrayInputStream(xml.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
Element root = document.getDocumentElement();
@@ -465,12 +465,13 @@
*************************************************************************/
public MobyService[] extractServices (String xml)
throws MobyException {
-
+// if (xmk == null)
+// throw new MobyException ()
Document document = null;
try {
document = docBuilder.parse(new ByteArrayInputStream(xml.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("Service");
@@ -677,7 +678,7 @@
try {
document = docBuilder.parse(new ByteArrayInputStream(result.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("serviceName");
@@ -723,7 +724,7 @@
try {
document = docBuilder.parse (new ByteArrayInputStream (result.getBytes()));
} catch (Exception e) {
- throw new MobyException (e.toString());
+ throw new MobyException (e.toString(), e);
}
NodeList list = document.getElementsByTagName ("serviceName");
@@ -774,7 +775,7 @@
try {
document = docBuilder.parse(new ByteArrayInputStream(result.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("serviceProvider");
@@ -832,7 +833,8 @@
Document document = null;
try {
document = docBuilder.parse(new ByteArrayInputStream(result.getBytes()));}
- catch(Exception e){throw new MobyException(e.toString());}
+ catch(Exception e){throw new MobyException(e.toString(), e);
+ }
NodeList list = document.getElementsByTagName ("serviceType");
if (list == null || list.getLength() == 0)
@@ -888,7 +890,7 @@
try {
document = docBuilder.parse(new ByteArrayInputStream(result.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace");
@@ -960,7 +962,7 @@
try {
document = docBuilder.parse(new ByteArrayInputStream(result.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("Object");
@@ -1027,7 +1029,7 @@
try {
document = docBuilder.parse(new ByteArrayInputStream (xmlSource.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("retrieveObjectDefinition");
@@ -1135,7 +1137,7 @@
// parse returned XML
Document document = null;
try{document=docBuilder.parse(new ByteArrayInputStream(result.getBytes()));}
- catch(Exception e){throw new MobyException(e.toString());}
+ catch(Exception e){throw new MobyException(e.toString(), e);}
Element service = document.getDocumentElement();
Node wsdl = service.getFirstChild();
@@ -1555,7 +1557,7 @@
Vector v = new Vector();
Document document = null;
try{document=docBuilder.parse(new ByteArrayInputStream(result.getBytes()));}
- catch(Exception e){throw new MobyException(e.toString());}
+ catch(Exception e){throw new MobyException(e.toString(), e);}
NodeList list = document.getElementsByTagName ("Relationship");
for (int i = 0; i < list.getLength(); i++) {
@@ -1611,7 +1613,7 @@
Map results = new HashMap();
Document document = null;
try{document=docBuilder.parse(new ByteArrayInputStream(result.getBytes()));}
- catch(Exception e){throw new MobyException(e.toString());}
+ catch(Exception e){throw new MobyException(e.toString(), e);}
NodeList list = document.getElementsByTagName ("Relationship");
@@ -1668,7 +1670,7 @@
Vector v = new Vector();
Document document = null;
try{document=docBuilder.parse(new ByteArrayInputStream(result.getBytes()));}
- catch(Exception e){throw new MobyException(e.toString());}
+ catch(Exception e){throw new MobyException(e.toString(), e);}
NodeList list = document.getElementsByTagName ("Relationship");
@@ -1732,7 +1734,7 @@
try {
document = docBuilder.parse (new ByteArrayInputStream (result.getBytes()));
} catch (Exception e) {
- throw new MobyException(e.toString());
+ throw new MobyException(e.toString(), e);
}
NodeList list = document.getElementsByTagName ("Resource");
@@ -1771,7 +1773,7 @@
try {
return url.openStream();
} catch (java.io.IOException e2) {
- throw new MobyException (e2.toString());
+ throw new MobyException (e2.toString(), e2);
}
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/11/06 16:47:10 1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/11/20 12:30:51 1.15
@@ -1759,11 +1759,11 @@
* cached files starting from CACHE_DIR directory, otherwise we
* store them inside this servlet context on the 'contextPath'.
********************************************************************/
- protected SimpleFileCache initCache (ServletContext context,
+ protected SimpleFileCache initCache (ServletContext sContext,
String contextPath) {
String cacheDir = (String)initParams.get (CACHE_DIR);
if (UUtils.isEmpty (cacheDir)) {
- return new ServletFileCache (context, contextPath);
+ return new ServletFileCache (sContext, contextPath);
} else {
String cacheURL = (String)initParams.get (CACHE_URL);
return new FileCache (cacheDir, cacheURL);
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServicesEdge.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServicesEdge.java 2005/07/19 12:39:59 1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ServicesEdge.java 2005/11/20 12:30:51 1.7
@@ -219,9 +219,9 @@
/*************************************************************************
* Checks if the given connection type is known.
*************************************************************************/
- private boolean checkConnectionType (int connectionType) {
- return (connectionType >= MIN_CONNECTION_TYPE &&
- connectionType <= MAX_CONNECTION_TYPE);
+ private boolean checkConnectionType (int conType) {
+ return (conType >= MIN_CONNECTION_TYPE &&
+ conType <= MAX_CONNECTION_TYPE);
}
}
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