[MOBY-guts] biomoby commit

[Martin Senger]

senger
Mon Sep 19 04:08:32 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv29075/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedImpl.java CentralImpl.java 
Log Message:
caching also namespaces

moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.5,1.6 CentralImpl.java,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.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/CentralDigestCachedImpl.java	2005/08/26 06:27:04	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java	2005/09/19 08:08:32	1.6
@@ -50,6 +50,7 @@
     private String cacheDir;        // as defined in the constructor
     protected File dataTypesCache;
     protected File servicesCache;
+    protected File namespacesCache;
 
     // cache age
     private long cacheAge = -1;
@@ -95,11 +96,15 @@
 	    long dataTypesCacheAge = (isCacheEmpty (dataTypesCache) ? -1 : dataTypesCache.lastModified());
 	    servicesCache  = createSubCacheDir (cache, "services");
 	    long servicesCacheAge = (isCacheEmpty (servicesCache) ? -1 : servicesCache.lastModified());
+	    namespacesCache = createSubCacheDir (cache, "namespaces");
+	    long namespacesCacheAge = (isCacheEmpty (namespacesCache) ? -1 : namespacesCache.lastModified());
 
-	    if (dataTypesCacheAge > -1 && servicesCacheAge > -1)
-		cacheAge = Math.min (dataTypesCacheAge, servicesCacheAge);
+	    if (dataTypesCacheAge > -1 && servicesCacheAge > -1 && namespacesCacheAge > -1)
+		cacheAge = Math.min (Math.min (dataTypesCacheAge, servicesCacheAge),
+				     namespacesCacheAge);
 	    else
-		cacheAge = Math.max (dataTypesCacheAge, servicesCacheAge);
+		cacheAge = Math.max (Math.max (dataTypesCacheAge, servicesCacheAge),
+				     namespacesCacheAge);
 	}
     }
 
@@ -318,6 +323,20 @@
 	}
     }
 
+    //
+    protected void fillNamespacesCache()
+	throws MobyException {
+	try {
+	    String xml = getNamespacesAsXML();
+	    store (namespacesCache, "all_namespaces_in_one_go", xml);
+	    if (cacheAge <= 0)
+		cacheAge = namespacesCache.lastModified();
+
+	} catch (Exception e) {
+	    throw new MobyException (formatException (e));
+	}
+    }
+
     // read all data types
     public MobyDataType[] getDataTypes()
 	throws MobyException {
@@ -375,6 +394,35 @@
 	}
     }
 
+//     public MobyNamespace[] getNamespaces()
+    public Map getNamespaces()
+	throws MobyException {
+	if (namespacesCache == null)
+	    return super.getNamespaces();
+	synchronized (namespacesCache) {
+	    if (isCacheEmpty (namespacesCache)) {
+		initCache();
+		fillNamespacesCache();
+	    }
+	    File[] list = namespacesCache.listFiles();
+	    if (list == null)
+		throw new MobyException
+		    ("Surprisingly, '" + namespacesCache.getAbsolutePath() + "' is not a directory. Strange...");
+	    for (int i = 0; i < list.length; i++) {
+		try {
+		    if (list[i].getPath().endsWith ("~"))
+			continue;   // ignore some files
+		    return createNamespacesFromXML (load (list[i]));
+		} catch (MobyException e) {
+		    System.err.println ("Ignoring '" + list[i].getPath() +
+					"'. It should not be in the cache directory:" +
+					e.getMessage());
+		}
+	    }
+	}
+	return null;
+    }
+
     /**************************************************************************
      * It always (if it functions as a cache which is when 'cacheDir'
      * was given) disables caching in the parent (so no memory caching

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.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/client/CentralImpl.java	2005/09/04 13:45:37	1.25
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2005/09/19 08:08:32	1.26
@@ -848,14 +848,26 @@
     public Map getNamespaces()
 	throws MobyException {
 
+	String result = getNamespacesAsXML();
+	return createNamespacesFromXML (result);
+    }
+
+    //
+    protected String getNamespacesAsXML()
+	throws MobyException {
+	return (String)doCall ("retrieveNamespaces",
+			       new Object[] {});
+    }
+
+    //
+    protected Map createNamespacesFromXML (String result)
+	throws MobyException {
+
 	String cacheId = "retrieveNamespaces";
 	Map cachedResults = (Map)getContents (cacheId);
 	if (cachedResults != null)
 	    return cachedResults;
 
-	String result = (String)doCall ("retrieveNamespaces",
-					new Object[] {});
-
 	// parse returned XML
 	Map results = new HashMap();
 	Document document = null;