Changeset 400 for trunk/org.bridgedb.webservice.synergizer

Timestamp:

06/04/10 17:09:53 (2 years ago)

Author:

rodche

Message:

mavenized ..webservice.synergizer (test fails due to the org.bridgedb.webservice.synergizer.SynergizerStub??.idExist(SynergizerStub??.java:268) is error or outdated; probably the service changed...)

Location:

trunk/org.bridgedb.webservice.synergizer

Files:

• . (modified) (1 prop)
• pom.xml (added)
• resources (added)
• src/org/bridgedb/webservice/synergizer/SynergizerStub.java (modified) (1 diff)
• test/org/bridgedb/webservice/synergizer/Test.java (modified) (1 diff)

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

@@ -260 +260 @@
     public boolean idExist(final String authority, final String species,
             final String domain, final String id) throws IDMapperException {
-        String range = domain;
+        String range = domain; // bug: client now complains that domain==range!
         Set<String> ids = new HashSet(1);
         ids.add(id);

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

@@ -50 +50 @@
 
         public void testIDMapperSynergizer() throws IOException, IDMapperException {
-//            SynergizerStub client = SynergizerStub.getInstance();
-//            for (String auth : client.availableAuthorities()) {
-//                System.out.println("Authority: "+auth);
-//                for (String species : client.availableSpecies(auth)) {
-//                    System.out.println("  Species: "+species);
-//                    IDMapperSynergizer mapper = new IDMapperSynergizer(auth, species);
-//                    System.out.println("    Supported source data sources:");
-//                    for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources()) {
-//                        System.out.println("      "+ds.getFullName());
-//                    }
-//                    System.out.println("    Supported target data sources:");
-//                    for (DataSource ds : mapper.getCapabilities().getSupportedTgtDataSources()) {
-//                        System.out.println("      "+ds.getFullName());
-//                    }
-//                }
-//            }
+                
+            SynergizerStub client = SynergizerStub.getInstance();
+            for (String auth : client.availableAuthorities()) {
+                System.out.println("Authority: "+auth);
+                for (String species : client.availableSpecies(auth)) {
+                    System.out.println("  Species: "+species);
+                    IDMapperSynergizer mapper = new IDMapperSynergizer(auth, species);
+                    System.out.println("    Supported source data sources:");
+                    for (DataSource ds : mapper.getCapabilities().getSupportedSrcDataSources()) {
+                        System.out.println("      "+ds.getFullName());
+                    }
+                    System.out.println("    Supported target data sources:");
+                    for (DataSource ds : mapper.getCapabilities().getSupportedTgtDataSources()) {
+                        System.out.println("      "+ds.getFullName());
+                    }
+                    break; // one is enough for now
+                }
+                break; // one is enough for now
+            }
 
             IDMapper mapper = BridgeDb.connect("idmapper-synergizer:?authority=ensembl&species=Homo sapiens");
-
             DataSource srcDs = DataSource.getByFullName("hgnc_symbol");
-            assertTrue(mapper.xrefExists(new Xref("pja1", srcDs)));
+            assertTrue(mapper.xrefExists(new Xref("snph", srcDs)));
 
             Set<Xref> srcXrefs = new HashSet();