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[Cdk-commits] SF.net SVN: cdk: [8449] trunk/cdk-taverna/src/test/java/org/openscience/cdk /applications/taverna/qsar/descriptors
|
From: <tho...@us...> - 2007-06-28 15:10:15
|
Revision: 8449
http://svn.sourceforge.net/cdk/?rev=8449&view=rev
Author: thomaskuhn
Date: 2007-06-28 08:10:10 -0700 (Thu, 28 Jun 2007)
Log Message:
-----------
Further refactoring of the qsar junit tests
Modified Paths:
--------------
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/IPBondTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APolTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AtomCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPolTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BondCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSATest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderOneTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderZeroTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiClusterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPathClusterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPathTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/EccentricConnectivityIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/GravitationalIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondAcceptorCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondDonorCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/IPMolecularTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/KappaShapeIndicesTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestPiSystemTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LengthOverBreadthTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LongestAliphaticChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MDETest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MomentOfInertiaTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanNumberTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanShapeIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/RotatableBondsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TPSATest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TaeAminoAcidTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/VAdjMaTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderOneTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderZeroTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WHIMTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WeightTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WeightedPathTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WienerNumbersTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/XLogPTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ZagrebIndexTest.java
Added Paths:
-----------
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java
Removed Paths:
-------------
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiChargeTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiChargeTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiChargeTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaChargeTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaChargeTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaChargeTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTChargeTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTChargeTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTChargeTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativityTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativityTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativityTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/IPBondTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/IPBondTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/IPBondTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveChargeTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveChargeTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveChargeTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -29,7 +29,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegreeTest;
import org.openscience.cdk.exception.CDKException;
/**
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APolTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APolTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APolTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,92 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.APol;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class APolTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "APol_Descriptor";
- public APolTest() {}
-
+public class APolTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private APol processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public APolTest() {
+ processor = new APol();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(APolTest.class);
}
- public void test_LocalWorkerAPol()throws CDKException, Exception{
- APol test = new APol();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
-
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("APolDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
+ }
+
}
Deleted: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -1,116 +0,0 @@
-/* $RCSfile$
- * $Author: thomaskuhn $
- * $Date: 2006-01-20 08:21:14 +0100 (Fr, 20 Jan 2006) $
- * $Revision: 5602 $
- *
- * Copyright (C) 2006 - 2007 by Thomas Kuhn <tho...@un...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AminoAcidCount;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.exception.CDKException;
-
-/**
- * Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
- */
-public class AminoAcidCountTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "AminoAcidCount_Descriptor";
- public AminoAcidCountTest() {}
-
- public static Test suite() {
- return new TestSuite(AminoAcidCountTest.class);
- }
-
- public void test_LocalWorkerAminoAcidCount()throws CDKException, Exception{
- AminoAcidCount test = new AminoAcidCount();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put("inputStructures", new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get("calculatedStructures"))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get("NOTCalculatedStructures"))).getDataObject();
- DescriptorValue = (List)((DataThing)(resultMap.get("Comment"))).getDataObject();
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("AminoAcidCountDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
- }
-
-}
Added: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java (rev 0)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -0,0 +1,85 @@
+/* $RCSfile$
+ * $Author: thomaskuhn $
+ * $Date: 2006-01-20 08:21:14 +0100 (Fr, 20 Jan 2006) $
+ * $Revision: 5602 $
+ *
+ * Copyright (C) 2006 - 2007 by Thomas Kuhn <tho...@un...>
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
+
+import junit.framework.Test;
+import junit.framework.TestSuite;
+
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
+import org.openscience.cdk.exception.CDKException;
+
+/**
+ * Class with contains JUnit-Tests for the CDK-Taverna Project
+ *
+ * @author Thomas Kuhn
+ *
+ */
+public class AminoAcidCountTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private AminoAcidCount processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public AminoAcidCountTest() {
+ processor = new AminoAcidCount();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
+ public static Test suite() {
+ return new TestSuite(AminoAcidCountTest.class);
+ }
+
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
+ }
+
+}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCountTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,92 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AromaticAtomsCount;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class AromaticAtomsCountTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "AromaticAtomsCount_Descriptor";
- public AromaticAtomsCountTest() {}
-
+public class AromaticAtomsCountTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private AromaticBondsCount processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public AromaticAtomsCountTest() {
+ processor = new AromaticBondsCount();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(AromaticAtomsCountTest.class);
}
- public void test_LocalWorkerAromaticAtomsCount()throws CDKException, Exception{
- AromaticAtomsCount test = new AromaticAtomsCount();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
-
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("AromaticAtomsCountDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
+ }
+
}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCountTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,92 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AromaticBondsCount;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class AromaticBondsCountTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "AromaticBondsCount_Descriptor";
- public AromaticBondsCountTest() {}
-
+public class AromaticBondsCountTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private AromaticBondsCount processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public AromaticBondsCountTest() {
+ processor = new AromaticBondsCount();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(AromaticBondsCountTest.class);
}
- public void test_LocalWorkerAromaticBondsCount()throws CDKException, Exception{
- AromaticBondsCount test = new AromaticBondsCount();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
+ }
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("AromaticBondsCountDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
}
}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AtomCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AtomCountTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AtomCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,90 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
-
-
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class AtomCountTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "AtomCount";
- public AtomCountTest() {}
-
+public class AtomCountTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private AtomCount processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public AtomCountTest() {
+ processor = new AtomCount();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(AtomCountTest.class);
}
-
- public void test_LocalWorkerAtomCount()throws CDKException, Exception{
- AtomCount test = new AtomCount();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures = (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures = (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures, descriptorName + "Problem.txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures, descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- System.out.println((String)fileName.get(0));
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("AtomCountDescriptor")) {
- hasFileNameAnError = true;
- System.out.println((String)fileName.get(fileName.size()-1));
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
}
-
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
+ }
+
}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,91 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class BCUTTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "BCUT_Descriptor";
- public BCUTTest() {}
+public class BCUTTest extends AbstractDescriptorTestCase {
+ /**
+ * Instance of the tested processor
+ */
+ private BCUT processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public BCUTTest() {
+ processor = new BCUT();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(BCUTTest.class);
}
- public void test_LocalWorkerBCUT()throws CDKException, Exception{
- BCUT test = new BCUT();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
+ }
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("BCUTDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
}
-}
+}
\ No newline at end of file
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPolTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPolTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPolTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,92 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BPol;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class BPolTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "BPol_Descriptor";
- public BPolTest() {}
-
+public class BPolTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private BPol processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public BPolTest() {
+ processor = new BPol();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(BPolTest.class);
}
- public void test_LocalWorkerBPol()throws CDKException, Exception{
- BPol test = new BPol();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put(test.inputNames()[0], new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[0]))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get(test.outputNames()[1]))).getDataObject();
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
+ }
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("BPolDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
}
}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BondCountTest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BondCountTest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BondCountTest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,92 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AminoAcidCount;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class BondCountTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List inputList = null;
- // map for the local worker input
- private Map inputMap = null;
- // map for the local worker result
- private Map resultMap = null;
- // List which contains the calculated results of the local worker
- private List resultListCalculatedStructures = null;
- // List which contains the NOT calculated results of the local worker
- private List resultListNOTCalculatedStructures = null;
- private List DescriptorValue = null;
- private String descriptorName = "AminoAcidCount_Descriptor";
- public BondCountTest() {}
-
+public class BondCountTest extends AbstractDescriptorTestCase {
+
+ /**
+ * Instance of the tested processor
+ */
+ private BondCount processor;
+
+ /**
+ * Constructor which instantiate the testing processor
+ */
+ public BondCountTest() {
+ processor = new BondCount();
+ processorInputNames = processor.inputNames();
+ processorOutputNames = processor.outputNames();
+ processorName = processor.getClass().getSimpleName();
+ }
+
+ /**
+ * Method which returns a test suit with the name of this class
+ *
+ * @return TestSuite
+ */
public static Test suite() {
return new TestSuite(BondCountTest.class);
}
- public void test_LocalWorkerAminoAcidCount()throws CDKException, Exception{
- AminoAcidCount test = new AminoAcidCount();
- inputList = new ArrayList();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- inputMap = new HashMap();
- inputMap.put("inputStructures", new DataThing(inputList));
- resultMap = test.execute(inputMap);
- resultListCalculatedStructures =
- (List)((DataThing)(resultMap.get("calculatedStructures"))).getDataObject();
- resultListNOTCalculatedStructures =
- (List)((DataThing)(resultMap.get("NOTCalculatedStructures"))).getDataObject();
- DescriptorValue = (List)((DataThing)(resultMap.get("Comment"))).getDataObject();
- boolean notCalculatedResults = false;
- if(resultListNOTCalculatedStructures.size()!= 0) {
- notCalculatedResults = true;
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListNOTCalculatedStructures,
- "Error_" + descriptorName + ".txt",
- CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- if(resultListCalculatedStructures.size() != 0 && CDKTavernaTests.writeResultsToFile) {
- CDKIOFileWriter.writeListOfCMLChemFilesToFile(resultListCalculatedStructures,
- descriptorName + ".txt", CDKTavernaTestData.getPathForWritingFilesOfUnitTests());
- }
- boolean hasFileNameAnError = false;
- if(resultListCalculatedStructures.size() != 0) {
- for (Iterator iter = resultListCalculatedStructures.iterator(); iter.hasNext();) {
- CMLChemFile cmlChemFile = (CMLChemFile) iter.next();
- List<String> fileName = (List<String>)cmlChemFile.getProperty(FileNameGenerator.FILENAME);
- if (!((String)fileName.get(0)).equalsIgnoreCase("JunitTesting")) {
- hasFileNameAnError = true;
- }
- if (!((String)fileName.get(fileName.size()-1)).equalsIgnoreCase("AminoAcidCountDescriptor")) {
- hasFileNameAnError = true;
- }
- }
- }
- assertEquals(false, hasFileNameAnError);
- assertEquals(false, notCalculatedResults);
+ /**
+ * Method which executes the test
+ *
+ * @throws CDKException
+ * @throws Exception
+ */
+ public void test_LocalWorker() throws CDKException, Exception {
+ executeTest();
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AbstractAtomicDescriptorTestCase#executeProcessor()
+ */
+ protected void executeProcessor() throws Exception {
+ resultMap = processor.execute(inputMap);
+ }
+
}
Modified: trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSATest.java
===================================================================
--- trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSATest.java 2007-06-28 14:38:30 UTC (rev 8448)
+++ trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSATest.java 2007-06-28 15:10:10 UTC (rev 8449)
@@ -25,84 +25,61 @@
*/
package org.openscience.cdk.applications.taverna.qsar.descriptors.molecular;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
import junit.framework.Test;
import junit.framework.TestSuite;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CDKTavernaTests;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
+import org.openscience.cdk.applications.taverna.qsar.AbstractDescriptorTestCase;
import org.openscience.cdk.exception.CDKException;
/**
* Class with contains JUnit-Tests for the CDK-Taverna Project
- * @author Thomas
- *
+ *
+ * @author Thomas Kuhn
+ *
*/
-public class CPSATest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculaton of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private...
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