Updated for refactored runWarningTest taking IBioObject as input as i…

…mplemented in bioclipse.ds branch 'nm'.
bioclipse · Sep 30, 2013 · aa201ad · aa201ad
1 parent f19ebd1
commit aa201ad
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Showing 6 changed files with 49 additions and 14 deletions.
diff --git a/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/LogPTest.java b/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/LogPTest.java
@@ -27,6 +27,8 @@
 
 import net.bioclipse.cdk.business.Activator;
 import net.bioclipse.cdk.domain.ICDKMolecule;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.ds.model.AbstractDSMolModel;
 import net.bioclipse.ds.model.AbstractDSTest;
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.ITestResult;
@@ -36,7 +38,7 @@
  * @author ola
  *
  */
-public class LogPTest extends AbstractDSTest{
+public class LogPTest extends AbstractDSMolModel{
 
     private static final Logger logger = Logger.getLogger(LogPTest.class);
 
@@ -46,8 +48,12 @@ public void initialize( IProgressMonitor monitor ) throws DSException {
 
 
     @Override
-    protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
-                                                     IProgressMonitor monitor ){
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
+			IProgressMonitor monitor) {
+
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule cdkmol = (ICDKMolecule) input;
 
 //    	monitor.beginTask(getName(), IProgressMonitor.UNKNOWN);
 

diff --git a/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/RuleOfFiveTest.java b/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/RuleOfFiveTest.java
@@ -22,13 +22,15 @@
 import org.openscience.cdk.qsar.result.IntegerResult;
 
 import net.bioclipse.cdk.domain.ICDKMolecule;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.ds.model.AbstractDSMolModel;
 import net.bioclipse.ds.model.AbstractDSTest;
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.ITestResult;
 import net.bioclipse.ds.model.result.SimpleResult;
 
 
-public class RuleOfFiveTest extends AbstractDSTest{
+public class RuleOfFiveTest extends AbstractDSMolModel{
 
     private static final Logger logger = Logger.getLogger(RuleOfFiveTest.class);
 
@@ -38,8 +40,12 @@ public void initialize( IProgressMonitor monitor ) throws DSException {
 
 
     @Override
-    protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
-                                                     IProgressMonitor monitor ) {
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
+			IProgressMonitor monitor) {
+
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule cdkmol = (ICDKMolecule) input;
 
 //    	monitor.beginTask(getName(), IProgressMonitor.UNKNOWN);
 

diff --git a/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/TPSATest.java b/plugins/net.bioclipse.ds.models.adme/src/net/bioclipse/ds/adme/impl/TPSATest.java
@@ -22,6 +22,8 @@
 import org.openscience.cdk.qsar.result.DoubleResult;
 
 import net.bioclipse.cdk.domain.ICDKMolecule;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.ds.model.AbstractDSMolModel;
 import net.bioclipse.ds.model.AbstractDSTest;
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.ITestResult;
@@ -32,7 +34,7 @@
  * @author ola
  *
  */
-public class TPSATest extends AbstractDSTest{
+public class TPSATest extends AbstractDSMolModel{
 
     private static final Logger logger = Logger.getLogger(TPSATest.class);
 
@@ -42,8 +44,12 @@ public void initialize( IProgressMonitor monitor ) throws DSException {
 
 
     @Override
-    protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
-                                                     IProgressMonitor monitor ) {
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
+			IProgressMonitor monitor) {
+
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule cdkmol = (ICDKMolecule) input;
 
 //    	monitor.beginTask(getName(), IProgressMonitor.UNKNOWN);
 

diff --git a/....models.chemspider/src/net/bioclipse/ds/chemspider/CopyOfSimilaritySearchChEMBLModel.java b/....models.chemspider/src/net/bioclipse/ds/chemspider/CopyOfSimilaritySearchChEMBLModel.java
@@ -14,6 +14,8 @@
 import net.bioclipse.chemspider.Activator;
 import net.bioclipse.chemspider.business.IChemspiderManager;
 import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.ds.model.AbstractDSMolModel;
 import net.bioclipse.ds.model.AbstractDSTest;
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.ITestResult;
@@ -25,7 +27,7 @@
  * @author Ola Spjuth
  *
  */
-public class CopyOfSimilaritySearchChEMBLModel extends AbstractDSTest{
+public class CopyOfSimilaritySearchChEMBLModel extends AbstractDSMolModel{
 
 	private static final String TANIMOTO_DISTANCE = "distance.tanimoto";
 	private static final int MAX_NEIGHBORS = 15;
@@ -54,8 +56,12 @@ public void initialize(IProgressMonitor monitor) throws DSException {
 
 
 	@Override
-	protected List<? extends ITestResult> doRunTest(ICDKMolecule molecule,
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
 			IProgressMonitor monitor) {
+
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule molecule = (ICDKMolecule) input;
 
 		//Managers we need
 		IChemspiderManager chemspider = Activator.getDefault().getJavaChemspiderManager();

diff --git a/...pse.ds.models.chemspider/src/net/bioclipse/ds/chemspider/SimilaritySearchChEMBLModel.java b/...pse.ds.models.chemspider/src/net/bioclipse/ds/chemspider/SimilaritySearchChEMBLModel.java
@@ -10,6 +10,7 @@
 
 import net.bioclipse.cdk.domain.ICDKMolecule;
 import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IBioObject;
 import net.bioclipse.ds.model.ITestResult;
 import net.bioclipse.ds.model.result.ExternalMoleculeMatch;
 
@@ -25,9 +26,13 @@ public class SimilaritySearchChEMBLModel extends SimilaritySearchModel{
 	private static final Logger logger = Logger.getLogger(SimilaritySearchChEMBLModel.class);
 
 	@Override
-	protected List<? extends ITestResult> doRunTest(ICDKMolecule molecule,
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
 			IProgressMonitor monitor) {
 
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule molecule = (ICDKMolecule) input;
+
 		List<? extends ITestResult> matches = super.doRunTest(molecule, monitor);
 		List<ExternalMoleculeMatch> toRemove = new ArrayList<ExternalMoleculeMatch>();
 

diff --git a/...bioclipse.ds.models.chemspider/src/net/bioclipse/ds/chemspider/SimilaritySearchModel.java b/...bioclipse.ds.models.chemspider/src/net/bioclipse/ds/chemspider/SimilaritySearchModel.java
@@ -14,6 +14,8 @@
 import net.bioclipse.chemspider.Activator;
 import net.bioclipse.chemspider.business.IChemspiderManager;
 import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.ds.model.AbstractDSMolModel;
 import net.bioclipse.ds.model.AbstractDSTest;
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.ITestResult;
@@ -25,7 +27,7 @@
  * @author Ola Spjuth
  *
  */
-public class SimilaritySearchModel extends AbstractDSTest{
+public class SimilaritySearchModel extends AbstractDSMolModel{
 
 	private static final String TANIMOTO_DISTANCE = "distance.tanimoto";
 	private static final int MAX_NEIGHBORS = 15;
@@ -54,8 +56,12 @@ public void initialize(IProgressMonitor monitor) throws DSException {
 
 
 	@Override
-	protected List<? extends ITestResult> doRunTest(ICDKMolecule molecule,
+	protected List<? extends ITestResult> doRunTest(IBioObject input,
 			IProgressMonitor monitor) {
+
+		if (!(input instanceof ICDKMolecule))
+			return returnError("Input is not a Molecule", "");
+		ICDKMolecule molecule = (ICDKMolecule) input;
 
 		//Managers we need
 		IChemspiderManager chemspider = Activator.getDefault().getJavaChemspiderManager();