[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Wed Oct 11 01:54:51 UTC 2006
kawas
Tue Oct 10 21:54:51 EDT 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources
In directory dev.open-bio.org:/tmp/cvs-serv25229/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources
Modified Files:
RESOURCE.java
Log Message:
moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2006/09/15 21:50:21 1.22
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2006/10/11 01:54:51 1.23
@@ -14,8 +14,6 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.naming.Context;
-import javax.naming.InitialContext;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
@@ -24,18 +22,15 @@
import org.apache.commons.discovery.tools.DiscoverSingleton;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
-import org.biomoby.client.CentralDigestImpl;
import org.biomoby.client.CentralImpl;
import org.biomoby.client.rdf.builder.ServiceInstanceRDF;
import org.biomoby.client.rdf.vocabulary.DC_PROTEGE;
import org.biomoby.client.rdf.vocabulary.Predicates;
+import org.biomoby.client.ui.graphical.servlet.utilities.ContextLoader;
import org.biomoby.registry.definitions.types.JNamespacesSqlImpl;
import org.biomoby.registry.definitions.types.JObjectsSqlImpl;
import org.biomoby.registry.definitions.types.JServicesSqlImpl;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.CentralDigest;
import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyResourceRef;
import org.biomoby.shared.MobyService;
import org.w3c.rdf.model.ModelException;
@@ -94,189 +89,44 @@
* the following used to be final, but on error, i would like to ensure that
* i dont waste time trying to perform caching operations
*/
- private static boolean isCachableServiceInstances;
+ private static boolean isCachableServiceInstances = false;
- private static boolean isCachableNamespaces;
+ private static boolean isCachableNamespaces = false;
- private static boolean isCachableServiceTypes;
+ private static boolean isCachableServiceTypes = false;
- private static boolean isCachableObjects;
-
- /* the individual caching classes */
- private static RDFCache ServiceInstanceCache = null;
-
- private static RDFCache ServiceTypesCache = null;
-
- private static RDFCache ObjectsCache = null;
-
- private static RDFCache NamespaceCache = null;
+ private static boolean isCachableObjects = false;
private static boolean RUN_MAIN = false;
-
+ private static ContextLoader cLoader = null;
+
static {
- boolean __success = false;
- log.info("init(setting environment variables)");
try {
- Object className;
- Context c = new InitialContext();
- try {
- log.info("Checking for caching classes ...");
- className = c.lookup("java:comp/env/ServiceInstancesCachingClass");
- if (className != null && className instanceof String) {
- try {
- ServiceInstanceCache = (RDFCache) DiscoverSingleton.find(Class.forName((String) className), Class.forName((String) className).getName());
- log.info((ServiceInstanceCache == null ? "Caching of service instances not enabled."
- : "Caching of service instances enabled."));
- } catch (Exception e) {
- ServiceInstanceCache = null;
- log.info("Caching of service instances not enabled\n" + e);
- }
- }
- } catch (Exception e) {
- log
- .info("Caching of service instances not enabled. Caching file was not specified.\n"
- + e);
- }
- try {
- className = c.lookup("java:comp/env/ServiceTypesCachingClass");
- if (className != null && className instanceof String) {
- try {
- ServiceTypesCache = (RDFCache) DiscoverSingleton.find(Class.forName((String) className), Class.forName((String) className).getName());
- log
- .info((ServiceTypesCache == null ? "Caching of service types not enabled."
- : "Caching of service types enabled."));
- } catch (Exception e) {
- ServiceTypesCache = null;
- log.info("Caching of service types not enabled\n" + e);
- }
- }
- } catch (Exception e) {
- log.info("Caching of service types not enabled. Caching file was not specified.\n"
- + e);
- }
- try {
- className = c.lookup("java:comp/env/ObjectsCachingClass");
- if (className != null && className instanceof String) {
- try {
- ObjectsCache = (RDFCache) DiscoverSingleton.find(Class.forName((String) className), Class.forName((String) className).getName());
- log.info((ObjectsCache == null ? "Caching of datatypes not enabled."
- : "Caching of datatypes enabled."));
- } catch (Exception e) {
- ObjectsCache = null;
- log.info("Caching of datatypes not enabled\n" + e);
- }
- }
- } catch (Exception e) {
- log.info("Caching of datatypes not enabled. Caching file was not specified.\n" + e);
- }
- try {
- className = c.lookup("java:comp/env/NamespacesCachingClass");
- if (className != null && className instanceof String) {
- try {
- NamespaceCache = (RDFCache) DiscoverSingleton.find(Class.forName((String) className), Class.forName((String) className).getName());
- log.info((NamespaceCache == null ? "Caching of namespaces not enabled."
- : "Caching of namespaces enabled."));
- } catch (Exception e) {
- NamespaceCache = null;
- log.info("Caching of namespaces not enabled\n" + e);
- }
- }
- } catch (Exception e) {
- log.info("Caching of service types not enabled. Caching file was not specified.\n"
- + e);
- }
+ cLoader = (ContextLoader) DiscoverSingleton.find(Class
+ .forName((String) ContextLoader.class.getCanonicalName()), Class.forName(
+ (String) ContextLoader.class.getCanonicalName()).getName());
+ log
+ .info((cLoader == null ? "ContextLoader is null and is therefore not loaded. This is BAD!"
+ : "ContextLoader has loaded successfully."));
} catch (Exception e) {
- log.info("Caching is not enabled for any ontology.\n" + e);
+ log.warn("ContextLoader is null and is therefore not loaded. This is BAD!"
+ + System.getProperty("line.separator") + e.getMessage());
}
- // caching variables
- isCachableNamespaces = (NamespaceCache == null ? false : true);
- isCachableServiceTypes = (ServiceTypesCache == null ? false : true);
- isCachableObjects = (ObjectsCache == null ? false : true);
- isCachableServiceInstances = (ServiceInstanceCache == null ? false : true);
-
-
- log.info("getting mobycentral registry properties ...");
- try {
- Context c = new InitialContext();
- try {
- String MOBY_CENTRAL_CONFIG = null;
- MOBY_CENTRAL_CONFIG = (String) c.lookup("java:comp/env/MOBY_CENTRAL_CONFIG");
- if (MOBY_CENTRAL_CONFIG != null && !MOBY_CENTRAL_CONFIG.equals("")) {
- // set MOBY_CENTRAL_CONFIG
- log.info("init(setting MOBY_CENTRAL_CONFIG)");
- System.setProperty("MOBY_CENTRAL_CONFIG", MOBY_CENTRAL_CONFIG);
- }
- } catch (Exception ex) {
- }
- try {
- String MOBY_SERVER = null;
- MOBY_SERVER = (String) c.lookup("java:comp/env/MOBY_SERVER");
- if (MOBY_SERVER != null && !MOBY_SERVER.equals("")) {
- // set MOBY_SERVER
- log.info("init(setting MOBY_SERVER)");
- System.setProperty("MOBY_SERVER", MOBY_SERVER);
- if (!__success)
- try {
- Central central = new CentralImpl(MOBY_SERVER);
- MobyResourceRef[] refs = central.getResourceRefs();
- for (int i = 0; i < refs.length; i++) {
- String url = refs[i].getResourceLocation().toExternalForm();
- if (url.lastIndexOf("#") < 0)
- url = url + "#";
- URI_MAP.put(refs[i].getResourceName(), url);
- }
- __success = true;
- } catch (Exception ex) {
-
- }
- }
- } catch (Exception ex) {
- }
-
- try {
- String MOBY_URI = null;
- MOBY_URI = (String) c.lookup("java:comp/env/MOBY_URI");
- if (MOBY_URI != null && !MOBY_URI.equals("")) {
- // set MOBY_URI
- log.info("init(setting MOBY_URI)");
- System.setProperty("MOBY_URI", MOBY_URI);
- }
- } catch (Exception ex) {
- }
- } catch (Exception ex) {
+ // attempt to load caching classes
+ if (cLoader != null) {
+ isCachableNamespaces = (cLoader.getNamespaceCache() == null ? false : true);
+ isCachableServiceTypes = (cLoader.getServiceTypesCache() == null ? false : true);
+ isCachableObjects = (cLoader.getObjectsCache() == null ? false : true);
+ isCachableServiceInstances = (cLoader.getServiceInstanceCache() == null ? false : true);
}
- if (!__success)
- try {
- // default to mobycentral
- log.warn("Defaulting to default mobycentral.");
- Central central = new CentralImpl();
- MobyResourceRef[] refs = central.getResourceRefs();
- for (int i = 0; i < refs.length; i++) {
- String url = refs[i].getResourceLocation().toExternalForm();
- if (url.lastIndexOf("#") < 0)
- url = url + "#";
- URI_MAP.put(refs[i].getResourceName(), url);
- }
- } catch (Exception ex) {
- // some defaults if nothing else works
- URI_MAP.put("Object", "http://biomoby.org/RESOURCES/MOBY-S/Objects#");
-
- URI_MAP.put("Service", "http://biomoby.org/RESOURCES/MOBY-S/Services#");
-
- URI_MAP.put("Namespace", "http://biomoby.org/RESOURCES/MOBY-S/Namespaces#");
-
- URI_MAP.put("ServiceInstance",
- "http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#");
- }
-
- OBJ = (String) URI_MAP.get("Object");
- SRV = (String) URI_MAP.get("Service");
- NS = (String) URI_MAP.get("Namespace");
+ OBJ = (String) cLoader.getURI_MAP().get("Object");
+ SRV = (String) cLoader.getURI_MAP().get("Service");
+ NS = (String) cLoader.getURI_MAP().get("Namespace");
PRED = "http://biomoby.org/RESOURCES/MOBY-S/Predicates#";
- SI = (String) URI_MAP.get("ServiceInstance");
+ SI = (String) cLoader.getURI_MAP().get("ServiceInstance");
}
/*
@@ -292,11 +142,11 @@
throws ServletException, IOException {
PrintWriter out = response.getWriter();
String path = request.getPathInfo();
- if (path == null ) {
+ if (path == null) {
out
.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\"> <html><head><meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\"><title>not MOBY-S</title></head><body><h2>not MOBY-S </h2></body></html>");
return;
- }
+ }
Pattern p = Pattern.compile("/MOBY\\-S/(\\S+)");
Matcher m = p.matcher(path);
if (!m.matches()) {
@@ -317,7 +167,7 @@
} catch (MobyException e) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST,
"Could not get Objects");
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return;
}
if (model == null) {
@@ -337,7 +187,7 @@
} catch (MobyException e) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST,
"Could not get Namespaces");
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return;
}
if (model == null) {
@@ -357,7 +207,7 @@
} catch (MobyException e) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST,
"Could not get Services");
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return;
}
if (model == null) {
@@ -377,8 +227,8 @@
response.setHeader("Content-Disposition",
"attachment;filename=ServiceInstances");
if (isCachableServiceInstances) {
- if (ServiceInstanceCache.isCachedMostRecent()) {
- out.write(ServiceInstanceCache.getCachedRDF());
+ if (cLoader.getServiceInstanceCache().isCachedMostRecent()) {
+ out.write(cLoader.getServiceInstanceCache().getCachedRDF());
return;
} else {
try {
@@ -401,9 +251,9 @@
writer.setProperty("showXmlDeclaration", "false");
writer.setProperty("tab", "5");
writer.write(model, stream, null);
- if (!ServiceInstanceCache.isCachedMostRecent())
- ServiceInstanceCache.cacheRDF(stream.getOutput(),
- ServiceInstanceCache.getLatestCriteria());
+ if (!cLoader.getServiceInstanceCache().isCachedMostRecent())
+ cLoader.getServiceInstanceCache().cacheRDF(stream.getOutput(),
+ cLoader.getServiceInstanceCache().getLatestCriteria());
stream = null;
// now output the RDF
writer = model.getWriter("RDF/XML-ABBREV");
@@ -417,7 +267,7 @@
} catch (Exception e) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST,
"Could not get ServiceInstances");
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return;
}
if (model == null) {
@@ -448,7 +298,7 @@
model = getAll(model);
} catch (Exception e) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Could not get All");
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return;
}
if (model == null) {
@@ -492,7 +342,7 @@
try {
model = getServiceInstances(model);
} catch (ModelException e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return null;
}
return model;
@@ -513,7 +363,7 @@
createNsMap(model);
}
- CentralDigest central = null;
+ CentralImpl central = null;
MobyService[] services = null;
try {
String registryURL;
@@ -524,26 +374,26 @@
log.info("System vars: " + registryURL + ", " + registryNamespace);
if (registryURL == null) {
// use default registry, since we dont have a local one
- central = new CentralDigestImpl();
+ central = new CentralImpl();
} else if (registryNamespace == null) {
// use default namespace since one isnt defined
- central = new CentralDigestImpl(registryURL);
+ central = new CentralImpl(registryURL);
} else {
// use defined url and namespacce
- central = new CentralDigestImpl(registryURL, registryNamespace);
+ central = new CentralImpl(registryURL, registryNamespace);
}
} else {
// use default registry since we cant determine if local one
// exists
- central = new CentralDigestImpl();
+ central = new CentralImpl();
}
- services = central.getServices();
+ services = central.findService(new MobyService(""));
} catch (MobyException e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
}
if (central == null || services == null)
throw new MobyException(
- "Could not retrieve useful information from CentralDigestImpl().getServices(String)");
+ "Could not retrieve useful information from CentralImpl().findService(String)");
return ServiceInstanceRDF.createRDFModel(model, services, true);
}
@@ -762,7 +612,7 @@
}
/*
- *
+ *
*/
private final Resource _addClassResource(Model model, String uri, String label, String lsid,
String def, String authority, String email) {
@@ -788,19 +638,19 @@
try {
return new JObjectsSqlImpl().getFullObjectsAsArray();
} catch (Exception e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
}
} else if (type.equalsIgnoreCase("services")) {
try {
return new JServicesSqlImpl().getFullServicesAsArray();
} catch (Exception e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
}
} else if (type.equalsIgnoreCase("namespaces")) {
try {
return new JNamespacesSqlImpl().getFullNamespacesAsArray();
} catch (Exception e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
}
}
return null;
@@ -858,7 +708,7 @@
try {
model = getServiceInstances(model);
} catch (Exception e) {
- e.printStackTrace();
+ log.error("Exception thrown: " + e.getMessage());
return "";
}
RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
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