Added a method to get a MDL molfile by compound URI (and unit tests f…

…or both methods
bioclipse · Aug 11, 2012 · 58fdac0 · 58fdac0
1 parent af85e45
commit 58fdac0
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Showing 3 changed files with 38 additions and 6 deletions.
diff --git a/...oclipse.opentox.test/src/net/bioclipse/opentox/test/AbstractOpentoxManagerPluginTest.java b/...oclipse.opentox.test/src/net/bioclipse/opentox/test/AbstractOpentoxManagerPluginTest.java
@@ -211,6 +211,22 @@ CDKMolecule.INCHI_OBJECT, new InChI(
     	Assert.assertNotSame(0, compounds.size());
     }
 
+    @Test public void testDownloadAsMDLMolfile() throws Exception {
+    	String mdlMolfile = opentox.downloadCompoundAsMDLMolfile(
+    		TEST_SERVER_OT, "http://apps.ideaconsult.net:8080/ambit2/dataset/2", 1
+    	);
+    	Assert.assertNotNull(mdlMolfile);
+    	Assert.assertTrue(mdlMolfile.contains("V2000"));
+    }
+
+    @Test public void testDownloadAsMDLMolfileFromURI() throws Exception {
+    	String mdlMolfile = opentox.downloadCompoundAsMDLMolfile(
+    		"http://apps.ideaconsult.net:8080/ambit2/dataset/2/compound/1"
+    	);
+    	Assert.assertNotNull(mdlMolfile);
+    	Assert.assertTrue(mdlMolfile.contains("V2000"));
+    }
+
     @Test public void testCreateDataSetFromSet() throws Exception {
     	List<ICDKMolecule> molecules = cdk.createMoleculeList();
     	molecules.add(cdk.fromSMILES("COC"));

diff --git a/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/business/IOpentoxManager.java b/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/business/IOpentoxManager.java
@@ -317,6 +317,15 @@ public interface IOpentoxManager extends IBioclipseManager {
     public String downloadCompoundAsMDLMolfile(String service, String dataSet,
         Integer compound) throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary=
+            "Downloads a compound and returns it as a MDL molfile formated " +
+            "String.",
+        params="String compoundURI"
+    )
+    public String downloadCompoundAsMDLMolfile(String compoundURI) throws BioclipseException;
+
     @Recorded
     @PublishedMethod(
         methodSummary=

diff --git a/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/business/OpentoxManager.java b/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/business/OpentoxManager.java
@@ -470,14 +470,17 @@ public List<Integer> listCompounds(String dataSet,
             monitor.worked(1);
 
             // query the downloaded RDF
+            System.out.println(rdf.dump(store));
             IStringMatrix results = rdf.sparql(store, QUERY_COMPOUNDS);
             monitor.worked(1);
 
             // return the data set identifiers
-            for (String compound : results.getColumn("compound")) {
-                compounds.add(
-                    Integer.valueOf(compound.substring(compound.lastIndexOf('/')+1))
-                );
+            if (results.getRowCount() > 0) {
+                for (String compound : results.getColumn("compound")) {
+                    compounds.add(
+                        Integer.valueOf(compound.substring(compound.lastIndexOf('/')+1))
+                    );
+                }
             }
             monitor.worked(1);
         } catch (BioclipseException exception) {
@@ -496,14 +499,18 @@ public List<Integer> listCompounds(String dataSet,
     public String downloadCompoundAsMDLMolfile(String service, String dataSet,
             Integer compound, IProgressMonitor monitor)
         throws BioclipseException {
+        return downloadCompoundAsMDLMolfile(dataSet + "/compound/" + compound, monitor);
+    }
+
+    public String downloadCompoundAsMDLMolfile(String compoundURI, IProgressMonitor monitor)
+        throws BioclipseException {
 
         if (monitor == null) monitor = new NullProgressMonitor();
 
         monitor.beginTask("Downloading compound...", 1);
 
-        String url = dataSet + "/compound/" + compound;
         String result = bioclipse.download(
-            url, "chemical/x-mdl-molfile", monitor
+            compoundURI, "chemical/x-mdl-molfile", monitor
         );
         monitor.done();