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Separated test-libiocml's dependance on test-qsar* by creating 'test-…
…qsarcml' - this now tests the preexisting module 'qsarcml' Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,15 @@ | ||
| cdk-test.jar | ||
| cdk-test.jar | ||
| cdk-log4j.jar | ||
| cdk-annotation.jar | ||
| cdk-interfaces.jar | ||
| cdk-qsarcml.jar | ||
| cdk-io.jar | ||
| cdk-testdata.jar | ||
| cdk-libiocml.jar | ||
| cdk-test-libiocml.jar | ||
| cdk-qsar.jar | ||
| cdk-qsarmolecular.jar | ||
| cdk-data.jar | ||
| cdk-test-data.jar | ||
| cdk-core.jar | ||
| cdk-standard.jar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| junit-4.10.jar | ||
| junit-4.11.jar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| vecmath*.jar | ||
| log4j*.jar | ||
| cmlxom-2.5-b1.jar | ||
| xom*.jar |
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113 changes: 113 additions & 0 deletions
113
src/test/org/openscience/cdk/io/cml/QSARCMLRoundTripTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| /* | ||
| * Copyright (c) 2013. John May <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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 U | ||
| */ | ||
|
|
||
| package org.openscience.cdk.io.cml; | ||
|
|
||
| import org.junit.Assert; | ||
| import org.junit.BeforeClass; | ||
| import org.junit.Test; | ||
| import org.openscience.cdk.interfaces.IAtomContainer; | ||
| import org.openscience.cdk.io.CMLWriter; | ||
| import org.openscience.cdk.libio.cml.Convertor; | ||
| import org.openscience.cdk.libio.cml.QSARCustomizer; | ||
| import org.openscience.cdk.qsar.DescriptorSpecification; | ||
| import org.openscience.cdk.qsar.DescriptorValue; | ||
| import org.openscience.cdk.qsar.IMolecularDescriptor; | ||
| import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor; | ||
| import org.openscience.cdk.templates.TestMoleculeFactory; | ||
| import org.openscience.cdk.tools.ILoggingTool; | ||
| import org.openscience.cdk.tools.LoggingToolFactory; | ||
|
|
||
| import java.io.StringWriter; | ||
|
|
||
| /** | ||
| * @author John May | ||
| * @cdk.module test-qsarcml | ||
| */ | ||
| public class QSARCMLRoundTripTest { | ||
|
|
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| private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(QSARCMLRoundTripTest.class); | ||
|
|
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| private static Convertor convertor; | ||
|
|
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| @BeforeClass public static void setup() { | ||
| convertor = new Convertor(false, ""); | ||
| convertor.registerCustomizer(new QSARCustomizer()); | ||
| } | ||
|
|
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| @Test public void testDescriptorValue_QSAR() throws Exception { | ||
| IAtomContainer molecule = TestMoleculeFactory.makeBenzene(); | ||
| IMolecularDescriptor descriptor = new WeightDescriptor(); | ||
|
|
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| DescriptorValue originalValue = null; | ||
| originalValue = descriptor.calculate(molecule); | ||
| molecule.setProperty(originalValue.getSpecification(), originalValue); | ||
| IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, molecule); | ||
|
|
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| Assert.assertEquals(1, roundTrippedMol.getProperties().size()); | ||
| System.out.println("" + roundTrippedMol.getProperties().keySet()); | ||
| Object object = roundTrippedMol.getProperties().keySet().toArray()[0]; | ||
| System.out.println("" + object); | ||
| Assert.assertTrue(object instanceof DescriptorSpecification); | ||
| DescriptorSpecification spec = (DescriptorSpecification)object; | ||
| Assert.assertEquals(descriptor.getSpecification().getSpecificationReference(), | ||
| spec.getSpecificationReference()); | ||
| Assert.assertEquals(descriptor.getSpecification().getImplementationIdentifier(), | ||
| spec.getImplementationIdentifier()); | ||
| Assert.assertEquals(descriptor.getSpecification().getImplementationTitle(), | ||
| spec.getImplementationTitle()); | ||
| Assert.assertEquals(descriptor.getSpecification().getImplementationVendor(), | ||
| spec.getImplementationVendor()); | ||
|
|
||
| Object value = roundTrippedMol.getProperty(spec); | ||
| Assert.assertNotNull(value); | ||
| Assert.assertTrue(value instanceof DescriptorValue); | ||
| DescriptorValue descriptorResult = (DescriptorValue)value; | ||
| Assert.assertEquals(originalValue.getClass().getName(), | ||
| descriptorResult.getClass().getName()); | ||
| Assert.assertEquals(originalValue.getValue().toString(), | ||
| descriptorResult.getValue().toString()); | ||
| } | ||
|
|
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| @Test public void testQSARCustomization() throws Exception { | ||
| StringWriter writer = new StringWriter(); | ||
| IAtomContainer molecule = TestMoleculeFactory.makeBenzene(); | ||
| IMolecularDescriptor descriptor = new WeightDescriptor(); | ||
|
|
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| CMLWriter cmlWriter = new CMLWriter(writer); | ||
| cmlWriter.registerCustomizer(new QSARCustomizer()); | ||
| DescriptorValue value = descriptor.calculate(molecule); | ||
| molecule.setProperty(value.getSpecification(), value); | ||
|
|
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| cmlWriter.write(molecule); | ||
| String cmlContent = writer.toString(); | ||
| logger.debug("****************************** testQSARCustomization()"); | ||
| logger.debug(cmlContent); | ||
| logger.debug("******************************"); | ||
| Assert.assertTrue(cmlContent.indexOf("<property") != -1 && | ||
| cmlContent.indexOf("xmlns:qsar") != -1); | ||
| Assert.assertTrue(cmlContent.indexOf("#weight\"") != -1); | ||
| } | ||
|
|
||
| } |
40 changes: 40 additions & 0 deletions
40
src/test/org/openscience/cdk/modulesuites/MqsarcmlTests.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| /* | ||
| * Copyright (c) 2013. John May <jwmay@users.sf.net> | ||
| * | ||
| * Contact: cdk-devel@lists.sourceforge.net | ||
| * | ||
| * 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 U | ||
| */ | ||
| package org.openscience.cdk.modulesuites; | ||
|
|
||
| import org.junit.runner.RunWith; | ||
| import org.junit.runners.Suite; | ||
| import org.junit.runners.Suite.SuiteClasses; | ||
| import org.openscience.cdk.io.cml.QSARCMLRoundTripTest; | ||
|
|
||
| /** | ||
| * test suite for qsarcml module | ||
| * | ||
| * @cdk.module test-qsarcml | ||
| */ | ||
| @RunWith(value=Suite.class) | ||
| @SuiteClasses(value={ | ||
| QSARCMLRoundTripTest.class | ||
| }) | ||
| public class MqsarcmlTests {} |