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allow DescriptorEngine to load the two descriptors that require an IC…
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…hemObjectBuilder injection. DescriptorTest was updated and generiffied to allow testing of the modified descriptors.
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@johnmay @egonw
johnmay authored and egonw committed Mar 19, 2013
1 parent 9b736ad commit f30e2b2
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Showing 5 changed files with 74 additions and 38 deletions.
40 changes: 32 additions & 8 deletions src/main/org/openscience/cdk/qsar/DescriptorEngine.java
View file
Expand Up @@ -33,11 +33,14 @@
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

import java.io.File;
import java.io.IOException;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -94,6 +97,7 @@ public class DescriptorEngine {
private List<IImplementationSpecification> speclist = null;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(DescriptorEngine.class);
private final IChemObjectBuilder builder;

/**
* Instantiates the DescriptorEngine.
Expand All @@ -118,8 +122,9 @@ public class DescriptorEngine {
* This approach allows one to use find classes using the interface based approach ({@link #getDescriptorClassNameByInterface(String, String[])}.
* If you use this method it is preferable to specify the jar files to examine
*/
public DescriptorEngine(List<String> classNames) {
public DescriptorEngine(List<String> classNames, IChemObjectBuilder builder) {
this.classNames = classNames;
this.builder = builder;
descriptors = instantiateDescriptors(classNames);
speclist = initializeSpecifications(descriptors);

Expand All @@ -139,8 +144,8 @@ public DescriptorEngine(List<String> classNames) {
* are DescriptorEngine.ATOMIC or DescriptorEngine.MOLECULAR
*/
@TestMethod(value="testConstructor")
public DescriptorEngine(int type) {
this(type, null);
public DescriptorEngine(int type, IChemObjectBuilder builder) {
this(type, null, builder);
}

/**
Expand All @@ -157,7 +162,7 @@ public DescriptorEngine(int type) {
* situations where the system classpath is not available or is modified such as in an application
* container.
*/
public DescriptorEngine(int type, String[] jarFileNames) {
public DescriptorEngine(int type, String[] jarFileNames, IChemObjectBuilder builder) {
switch (type) {
case ATOMIC:
classNames = getDescriptorClassNameByPackage("org.openscience.cdk.qsar.descriptors.atomic", jarFileNames);
Expand All @@ -172,6 +177,7 @@ public DescriptorEngine(int type, String[] jarFileNames) {
classNames = getDescriptorClassNameByPackage("org.openscience.cdk.qsar.descriptors.atompair", jarFileNames);
break;
}
this.builder = builder;
descriptors = instantiateDescriptors(classNames);
speclist = initializeSpecifications(descriptors);
logger.debug("Found #descriptors: ", classNames.size());
Expand Down Expand Up @@ -692,12 +698,13 @@ public static List<String> getDescriptorClassNameByPackage(String packageName, S
}

public List<IDescriptor> instantiateDescriptors(List<String> descriptorClassNames) {
List<IDescriptor> descriptors;
descriptors = new ArrayList<IDescriptor>();
List<IDescriptor> descriptors = new ArrayList<IDescriptor>();
ClassLoader classLoader = getClass().getClassLoader();
for (String descriptorName : descriptorClassNames) {
try {
IDescriptor descriptor = (IDescriptor) this.getClass().getClassLoader().loadClass(descriptorName).newInstance();
descriptors.add(descriptor);
@SuppressWarnings("unchecked")
Class<? extends IDescriptor> c = (Class<? extends IDescriptor>) classLoader.loadClass(descriptorName);
descriptors.add(instantiate(c));
logger.info("Loaded descriptor: ", descriptorName);
} catch (NoClassDefFoundError error) {
logger.error("Could not find this Descriptor: ", descriptorName);
Expand All @@ -713,6 +720,23 @@ public List<IDescriptor> instantiateDescriptors(List<String> descriptorClassName
return descriptors;
}

private IDescriptor instantiate(Class<? extends IDescriptor> c) throws
IllegalAccessException,
InvocationTargetException,
InstantiationException {
for(Constructor constructor : c.getConstructors()){
Class<?>[] params = constructor.getParameterTypes();
System.out.println(c.getSimpleName() + Arrays.toString(params));
if(params.length == 0){
return (IDescriptor) constructor.newInstance();
} else if(params.length == 1
&& params[0].equals(IChemObjectBuilder.class)){
return (IDescriptor) constructor.newInstance(builder);
}
}
throw new IllegalStateException("descriptor " + c.getSimpleName() + " has no usable constructors");
}

public List<IImplementationSpecification> initializeSpecifications(List<IDescriptor> descriptors) {
List<IImplementationSpecification> speclist = new ArrayList<IImplementationSpecification>();
for (IDescriptor descriptor : descriptors) {
Expand Down
29 changes: 19 additions & 10 deletions src/test/org/openscience/cdk/qsar/DescriptorEngineTest.java
View file
Expand Up @@ -37,20 +37,22 @@
*
* @cdk.module test-qsarmolecular
*/
public class DescriptorEngineTest extends CDKTestCase {
public class DescriptorEngineTest extends CDKTestCase {

public DescriptorEngineTest() {
}

@Test
public void testConstructor() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(engine);
}

@Test
public void testLoadingOfMolecularDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertTrue("Could not load any descriptors", 0 != loadedDescriptors);
Expand All @@ -60,7 +62,8 @@ public void testLoadingOfMolecularDescriptors() {

@Test
public void testLoadingOfAtomicDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.ATOMIC);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.ATOMIC,
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertNotSame(0, loadedDescriptors);
Expand All @@ -70,7 +73,8 @@ public void testLoadingOfAtomicDescriptors() {

@Test
public void testLoadingOfBondDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.BOND);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.BOND,
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertNotSame(0, loadedDescriptors);
Expand All @@ -80,7 +84,8 @@ public void testLoadingOfBondDescriptors() {

@Test
public void testDictionaryType() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());

String className = "org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor";
DescriptorSpecification specRef = new DescriptorSpecification(
Expand All @@ -95,7 +100,8 @@ public void testDictionaryType() {

@Test
public void testDictionaryClass() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());

String className = "org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor";
DescriptorSpecification specRef = new DescriptorSpecification(
Expand All @@ -117,7 +123,8 @@ public void testDictionaryClass() {

@Test
public void testAvailableClass() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());
String[] availClasses = engine.getAvailableDictionaryClasses();
Assert.assertEquals(5, availClasses.length);
}
Expand All @@ -136,15 +143,17 @@ public void testjunk() throws Exception {
TemplateHandler3D template = TemplateHandler3D.getInstance();
ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template, "mm2");
molecule = mb3d.generate3DCoordinates(molecule, true);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());

engine.process(molecule);

}

@Test
public void testLoadingOfAtomPairDescriptors() {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.ATOMPAIR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.ATOMPAIR,
DefaultChemObjectBuilder.getInstance());
Assert.assertNotNull(engine);
int loadedDescriptors = engine.getDescriptorInstances().size();
Assert.assertNotSame(0, loadedDescriptors);
Expand Down
4 changes: 3 additions & 1 deletion src/test/org/openscience/cdk/qsar/DescriptorNamesTest.java
View file
Expand Up @@ -28,6 +28,7 @@
import org.junit.Test;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.IImplementationSpecification;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.ISimpleChemObjectReader;
Expand All @@ -50,7 +51,8 @@ public DescriptorNamesTest() {

@Test
public void checkUniqueMolecularDescriptorNames() throws Exception {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,
DefaultChemObjectBuilder.getInstance());
List<IImplementationSpecification> specs = engine.getDescriptorSpecifications();

// we work with a simple molecule with 3D coordinates
Expand Down
19 changes: 15 additions & 4 deletions src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java
View file
Expand Up @@ -23,24 +23,35 @@
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.IImplementationSpecification;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.IDescriptor;

import java.lang.reflect.Constructor;

/**
* Tests for molecular descriptors.
*
* @cdk.module test-qsar
*/
public abstract class DescriptorTest extends CDKTestCase {
public abstract class DescriptorTest<T extends IDescriptor> extends CDKTestCase {

protected IDescriptor descriptor;
protected T descriptor;

public DescriptorTest() {}

public void setDescriptor(Class<? extends IDescriptor> descriptorClass) throws Exception {
public void setDescriptor(Class<? extends T> descriptorClass) throws Exception {
if (descriptor == null) {
this.descriptor = descriptorClass.newInstance();
try {
Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor();
this.descriptor = defaultConstructor.newInstance();
} catch (NoSuchMethodException ex) {
// no default constructor, try with an IChemObjectBuilder...
Constructor<? extends T> builderConstructor = descriptorClass.getConstructor(IChemObjectBuilder.class);
this.descriptor = builderConstructor.newInstance(DefaultChemObjectBuilder.getInstance());
}
}
}

Expand Down
20 changes: 5 additions & 15 deletions src/test/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java
View file
Expand Up @@ -39,6 +39,7 @@
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.IDescriptor;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
Expand All @@ -52,32 +53,21 @@
import org.openscience.cdk.tools.diff.AtomContainerDiff;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import java.lang.reflect.Constructor;

/**
* Tests for molecular descriptors.
*
* @cdk.module test-qsarmolecular
*/
public abstract class MolecularDescriptorTest extends DescriptorTest {

protected IMolecularDescriptor descriptor;
public abstract class MolecularDescriptorTest extends DescriptorTest<IMolecularDescriptor> {

private static DictionaryDatabase dictDB = new DictionaryDatabase();
private static Dictionary dict = dictDB.getDictionary("descriptor-algorithms");

public MolecularDescriptorTest() {}

public void setDescriptor(Class descriptorClass) throws Exception {
if (descriptor == null) {
Object descriptor = descriptorClass.newInstance();
if (!(descriptor instanceof IMolecularDescriptor)) {
throw new CDKException("The passed descriptor class must be a IMolecularDescriptor");
}
this.descriptor = (IMolecularDescriptor)descriptor;
}
super.setDescriptor(descriptorClass);
}

@Test
@Test
public void testDescriptorIdentifierExistsInOntology() {
Entry ontologyEntry = dict.getEntry(
descriptor.getSpecification().getSpecificationReference()
Expand Down

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