[Cdk-commits] SF.net SVN: cdk:[12123] cdk-taverna/trunk/src/test/java/org/openscience/cdk /applications/taverna/database/pgchem/InsertQSARResultsIntoDBTest.java

[<tho...@us...>]

Revision: 12123
          http://cdk.svn.sourceforge.net/cdk/?rev=12123&view=rev
Author:   thomaskuhn
Date:     2008-08-28 14:01:20 +0000 (Thu, 28 Aug 2008)

Log Message:
-----------
Deletes the old qsar vectors within the database before inserting the new ones. add some comment

Modified Paths:
--------------
    cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/database/pgchem/InsertQSARResultsIntoDBTest.java

Modified: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/database/pgchem/InsertQSARResultsIntoDBTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/database/pgchem/InsertQSARResultsIntoDBTest.java	2008-08-28 14:00:32 UTC (rev 12122)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/database/pgchem/InsertQSARResultsIntoDBTest.java	2008-08-28 14:01:20 UTC (rev 12123)
@@ -25,6 +25,8 @@
  */
 package org.openscience.cdk.applications.taverna.database.pgchem;
 
+import java.sql.PreparedStatement;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -33,6 +35,7 @@
 import junit.framework.TestSuite;
 
 import org.embl.ebi.escience.baclava.DataThing;
+import org.openscience.cdk.applications.taverna.CDKTavernaConfig;
 import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
 import org.openscience.cdk.applications.taverna.CMLChemFile;
 import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper;
@@ -78,29 +81,46 @@
 			if (QSARRegistry.getMoleculeIDs().size() > 0) {
 				QSARRegistry.removeAllMoleculeIDs();
 			}
-			
+			// Get some Molecules
 			Map<String, DataThing> input = new HashMap<String, DataThing>();
 			Map<String, DataThing> resultMap = worker.execute(input);
 			List<CMLChemFile> molecules = (List<CMLChemFile>)((DataThing)resultMap.get(worker.outputNames()[0])).getDataObject();
 			assertEquals(10, molecules.size());
+			
+			//Get the moleculeID's for the molecules from the database
+			List<Integer> moleculeIDs = new ArrayList<Integer>();
+			for (CMLChemFile chemFile : molecules) {
+				moleculeIDs.add((Integer)chemFile.getProperty(CDKTavernaConfig.DATABASEID));
+			}
+			// Remove the "old" qsar values for these molecules from the database
+			connector.setSqlStatement("DELETE FROM qsarresults WHERE moleculeid = ?");
+			PreparedStatement statement = connector.getConnectedPreparedStatement();
+			for (Integer id : moleculeIDs) {
+				statement.setInt(1, id);
+				statement.execute();
+			}
+			statement.close();
+			connector.closePrepareStatement();
+			connector.closeConnection();
+			// Tag the molecules
 			TagMolecules tagger = new TagMolecules();
 			
 			input = new HashMap<String, DataThing>();
 			input.put(tagger.inputNames()[0], new DataThing(molecules));
 			tagger.execute(input);
-			
+			// Calculate the qsar values for the molecules
 			QSARDescriptor qsar = new QSARDescriptor();
 			qsar.setSelectedDescriptors(QSARRegistry.getDescriptorNames().subList(0, 16));
 			resultMap = qsar.execute(input);
 			List<CMLChemFile> resultList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(resultMap
 					.get(qsar.outputNames()[0]));
-			
+			// Get a qsar vector from the molecules and the calculated qsar values
 			VectorGeneratorForDBInput vg = new VectorGeneratorForDBInput();
 			Map<String, DataThing> inputMap = new HashMap<String, DataThing>();
 			inputMap.put(vg.inputNames()[0],new DataThing(resultList));
 			Map<String, DataThing> result = vg.execute(inputMap);
 			Map<Integer, Map<String, Object>> resultVector = (Map<Integer, Map<String, Object>>) ((DataThing) (result.get(vg.outputNames()[0]))).getDataObject();
-			
+			// Insert the qsar vector into the database
 			InsertQSARResultsIntoDB insertWorker = new InsertQSARResultsIntoDB();
 			inputMap.clear();
 			inputMap.put(insertWorker.inputNames()[0], new DataThing(resultVector));


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.