Changeset 402

Timestamp:

06/10/10 13:16:51 (20 months ago)

Author:

martijn

Message:

Fixed failed test in synergizer by not supporting xrefExists anymore.
This means that xrefExists is now officially an optional operation

Location:

trunk

Files:

• org.bridgedb.webservice.synergizer/src/org/bridgedb/webservice/synergizer/IDMapperSynergizer.java (modified) (1 diff)
• org.bridgedb.webservice.synergizer/src/org/bridgedb/webservice/synergizer/SynergizerStub.java (modified) (1 diff)
• org.bridgedb.webservice.synergizer/test/org/bridgedb/webservice/synergizer/Test.java (modified) (1 diff)
• org.bridgedb/src/org/bridgedb/IDMapper.java (modified) (1 diff)

trunk/org.bridgedb.webservice.synergizer/src/org/bridgedb/webservice/synergizer/IDMapperSynergizer.java

@@ -311 +311 @@
      * {@inheritDoc}
      */
-    public boolean xrefExists(Xref xref) throws IDMapperException {
-        if (xref==null)
-            return false;
-
-        DataSource ds = xref.getDataSource();
-        if (!supportedSrcDs.contains(ds))
-            return false;
-
-        String src = ds.getFullName();
-        String id = xref.getId();
-        return stub.idExist(authority, species, src, id);
+    public boolean xrefExists(Xref xref) throws IDMapperException 
+    {
+        throw new UnsupportedOperationException ("xrefExists operation not supported for synergizer");
     }
 }

trunk/org.bridgedb.webservice.synergizer/src/org/bridgedb/webservice/synergizer/SynergizerStub.java

@@ -258 +258 @@
     }
 
-    public boolean idExist(final String authority, final String species,
-            final String domain, final String id) throws IDMapperException {
-        String range = domain; // bug: client now complains that domain==range!
-        Set<String> ids = new HashSet(1);
-        ids.add(id);
-
-        SynergizerClient.TranslateResult res;
-        try {
-             res = client.translate(authority, species, domain, range, ids);
-        } catch (IOException e) {
-            throw new IDMapperException(e);
-        } catch (JSONException e) {
-            throw new IDMapperException(e);
-        }
-
-        return res.foundSourceIDsWithFoundTargetIDs().contains(id)
-                || res.foundSourceIDsWithUnfoundTargetIDs().contains(id);
-    }
 }

trunk/org.bridgedb.webservice.synergizer/test/org/bridgedb/webservice/synergizer/Test.java

@@ -72 +72 @@
             IDMapper mapper = BridgeDb.connect("idmapper-synergizer:?authority=ensembl&species=Homo sapiens");
             DataSource srcDs = DataSource.getByFullName("hgnc_symbol");
-            assertTrue(mapper.xrefExists(new Xref("snph", srcDs)));
+            
+            try
+            {
+                mapper.xrefExists(new Xref("snph", srcDs));
+                fail ("Expected UnsupportedOperationException after calling xrefExists");
+            }
+            catch (UnsupportedOperationException ex)
+            {
+                // ok.
+            }
 
             Set<Xref> srcXrefs = new HashSet();

trunk/org.bridgedb/src/org/bridgedb/IDMapper.java

@@ -54 +54 @@
         
     /**
-     * Check whether an Xref exists.
+     * Check whether an Xref is known by the given mapping source. This is an optionally supported operation.
      * @param xref reference to check
      * @return if the reference exists, false if not
-     * @throws IDMapperException if failed
+     * @throws IDMapperException if failed, UnsupportedOperationException if it's not supported by the Driver.
      */
     public boolean xrefExists(Xref xref) throws IDMapperException;