Added a new method: opentox.listFeatures(otServer)

bioclipse · Aug 11, 2012 · 3977f97 · 3977f97
1 parent 62b3893
commit 3977f97
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diff --git a/...oclipse.opentox.test/src/net/bioclipse/opentox/test/AbstractOpentoxManagerPluginTest.java b/...oclipse.opentox.test/src/net/bioclipse/opentox/test/AbstractOpentoxManagerPluginTest.java
@@ -157,6 +157,13 @@ CDKMolecule.INCHI_OBJECT, new InChI(
     	Assert.assertNotSame(0, models.size());
     }
 
+    @Test public void testListFeatures() throws Exception {
+    	List<String> features = opentox.listFeatures(TEST_SERVER_OT);
+    	Assert.assertNotNull(features);
+    	// expect at least one hit:
+    	Assert.assertNotSame(0, features.size());
+    }
+
     @Test public void testCreateEmptyDataSet() throws Exception {
     	String uriString = opentox.createDataset(TEST_SERVER_OT);
     	Assert.assertNotNull(uriString);

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
@@ -186,6 +186,13 @@ public interface IOpentoxManager extends IBioclipseManager {
     )
     public List<String> listDataSets(String service) throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary="Lists the features available from the given service.",
+        params="String service"
+    )
+    public List<String> listFeatures(String service) 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
@@ -78,6 +78,11 @@ public class OpentoxManager implements IBioclipseManager {
         "  ?set a <http://www.opentox.org/api/1.1#Dataset> ." +
         "}";
 
+    private final static String QUERY_FEATURES =
+        "SELECT ?feature WHERE {" +
+        "  ?feature a <http://www.opentox.org/api/1.1#Feature> ." +
+        "}";
+
     private final static String QUERY_COMPOUNDS =
         "SELECT ?compound ?id WHERE {" +
         "  ?set a <http://www.opentox.org/api/1.1#Compound> ." +
@@ -226,6 +231,46 @@ public List<String> listDataSets(String service, IProgressMonitor monitor)
         return dataSets;
     }
 
+    public List<String> listFeatures(String service, IProgressMonitor monitor)
+    throws BioclipseException {
+    	if (monitor == null) monitor = new NullProgressMonitor();
+    	monitor.beginTask("Requesting available features...", 3);
+
+    	IRDFStore store = rdf.createInMemoryStore();
+    	List<String> dataSets = Collections.emptyList();
+    	Map<String, String> extraHeaders = new HashMap<String, String>();
+    	String token = Activator.getToken();
+    	if (token != null) {
+    		extraHeaders.put("subjectid", Activator.getToken());
+    	}
+    	try {
+    		// download the list of data sets as RDF
+    		rdf.importURL(store, service + "feature", extraHeaders, monitor);
+    		String dump = rdf.asRDFN3(store);
+    		System.out.println("RDF: " + dump);
+    		monitor.worked(1);
+
+    		// query the downloaded RDF
+    		IStringMatrix results = rdf.sparql(store, QUERY_FEATURES);
+    		monitor.worked(1);
+
+    		if (results.getRowCount() > 0) {
+    			dataSets = results.getColumn("feature");
+    		}
+    		monitor.worked(1);
+    	} catch (BioclipseException exception) {
+    		throw exception;
+    	} catch (Exception exception) {
+    		throw new BioclipseException(
+    			"Error while accessing RDF API of service: " + exception.getMessage(),
+    			exception
+    		);
+    	}
+
+    	monitor.done();
+    	return dataSets;
+    }
+
     public IStringMatrix searchDataSets(String ontologyServer, String query, IProgressMonitor monitor)
     throws BioclipseException {
         if (monitor == null) monitor = new NullProgressMonitor();