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[Cdk-commits] SF.net SVN: cdk: [11498] cdk/trunk/src/test/org/openscience/cdk
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From: <eg...@us...> - 2008-07-04 08:23:17
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Revision: 11498
http://cdk.svn.sourceforge.net/cdk/?rev=11498&view=rev
Author: egonw
Date: 2008-07-04 01:22:58 -0700 (Fri, 04 Jul 2008)
Log Message:
-----------
More conversion to JUnit4
Modified Paths:
--------------
cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java
cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java
cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java
Modified: cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/CDKSourceCodeWriterTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -27,6 +27,7 @@
import java.io.StringWriter;
import org.junit.Assert;
+import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
@@ -41,10 +42,13 @@
*/
public class CDKSourceCodeWriterTest extends ChemObjectIOTest {
+ @BeforeClass public static void setup() {
+ setChemObjectIO(new CDKSourceCodeWriter());
+ }
+
@Test public void testAccepts() throws Exception {
- CDKSourceCodeWriter reader = new CDKSourceCodeWriter();
- Assert.assertTrue(reader.accepts(Molecule.class));
- Assert.assertTrue(reader.accepts(AtomContainer.class));
+ Assert.assertTrue(chemObjectIO.accepts(Molecule.class));
+ Assert.assertTrue(chemObjectIO.accepts(AtomContainer.class));
}
@Test public void testOutput() throws Exception {
Modified: cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/CTXReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,9 +29,9 @@
import java.io.InputStream;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
@@ -40,8 +40,6 @@
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMoleculeSet;
-import org.openscience.cdk.io.CTXReader;
-import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -51,51 +49,47 @@
*
* @see org.openscience.cdk.io.CrystClustReader
*/
-public class CTXReaderTest extends CDKTestCase {
+public class CTXReaderTest extends ChemObjectIOTest {
- private LoggingTool logger;
+ private static LoggingTool logger;
- public CTXReaderTest(String name) {
- super(name);
- logger = new LoggingTool(this);
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(CTXReaderTest.class);
+ setChemObjectIO(new CTXReader());
}
- public static Test suite() {
- return new TestSuite(CTXReaderTest.class);
- }
-
- public void testAccepts() {
+ @Test public void testAccepts() {
CTXReader reader = new CTXReader();
- assertTrue(reader.accepts(ChemFile.class));
+ Assert.assertTrue(reader.accepts(ChemFile.class));
}
- public void testMethanol() throws Exception {
+ @Test public void testMethanol() throws Exception {
String filename = "data/ctx/methanol_with_descriptors.ctx";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CTXReader reader = new CTXReader(ins);
IChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
IMoleculeSet moleculeSet = model.getMoleculeSet();
- assertNotNull(moleculeSet);
- assertEquals(1, moleculeSet.getAtomContainerCount());
+ Assert.assertNotNull(moleculeSet);
+ Assert.assertEquals(1, moleculeSet.getAtomContainerCount());
IAtomContainer container = moleculeSet.getAtomContainer(0);
- assertNotNull(container);
- assertEquals("Incorrect atom count.", 6, container.getAtomCount());
- assertEquals(5, container.getBondCount());
+ Assert.assertNotNull(container);
+ Assert.assertEquals("Incorrect atom count.", 6, container.getAtomCount());
+ Assert.assertEquals(5, container.getBondCount());
- assertEquals("Petra", container.getID());
+ Assert.assertEquals("Petra", container.getID());
- assertNotNull(container.getProperty(CDKConstants.TITLE));
- assertEquals("CH4O", container.getProperty(CDKConstants.TITLE));
+ Assert.assertNotNull(container.getProperty(CDKConstants.TITLE));
+ Assert.assertEquals("CH4O", container.getProperty(CDKConstants.TITLE));
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/ChemObjectIOTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -36,10 +36,10 @@
*/
public abstract class ChemObjectIOTest extends NewCDKTestCase {
- private IChemObjectIO chemObjectIO;
+ protected static IChemObjectIO chemObjectIO;
- public void setChemFormat(IChemObjectIO chemObjectIO) {
- this.chemObjectIO = chemObjectIO;
+ public static void setChemObjectIO(IChemObjectIO aChemObjectIO) {
+ chemObjectIO = aChemObjectIO;
}
@Test public void testChemObjectIOSet() {
Modified: cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/CrystClustReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -31,13 +31,12 @@
import javax.vecmath.Vector3d;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
-import org.openscience.cdk.io.CrystClustReader;
-import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -47,62 +46,58 @@
*
* @see org.openscience.cdk.io.CrystClustReader
*/
-public class CrystClustReaderTest extends CDKTestCase {
+public class CrystClustReaderTest extends ChemObjectIOTest {
- private org.openscience.cdk.tools.LoggingTool logger;
-
- public CrystClustReaderTest(String name) {
- super(name);
- logger = new LoggingTool(this);
+ private static LoggingTool logger;
+
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(CrystClustReaderTest.class);
+ setChemObjectIO(new CrystClustReader());
}
- public static Test suite() {
- return new TestSuite(CrystClustReaderTest.class);
+ @Test public void testAccepts() {
+ Assert.assertTrue(chemObjectIO.accepts(ChemFile.class));
+ Assert.assertFalse(chemObjectIO.accepts(AtomContainer.class));
}
-
- public void testAccepts() {
- CrystClustReader reader = new CrystClustReader();
- assertTrue(reader.accepts(ChemFile.class));
- }
- public void testEstrone() throws Exception {
+ @Test public void testEstrone() throws Exception {
String filename = "data/crystclust/estron.crystclust";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CrystClustReader reader = new CrystClustReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(2, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(2, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.ICrystal crystal = model.getCrystal();
- assertNotNull(crystal);
- assertEquals(42, crystal.getAtomCount());
- assertEquals(1, crystal.getZ().intValue());
+ Assert.assertNotNull(crystal);
+ Assert.assertEquals(42, crystal.getAtomCount());
+ Assert.assertEquals(1, crystal.getZ().intValue());
// test reading of partial charges
org.openscience.cdk.interfaces.IAtom atom = crystal.getAtom(0);
- assertNotNull(atom);
- assertEquals("O", atom.getSymbol());
- assertEquals(-0.68264902, atom.getCharge(), 0.00000001);
+ Assert.assertNotNull(atom);
+ Assert.assertEquals("O", atom.getSymbol());
+ Assert.assertEquals(-0.68264902, atom.getCharge(), 0.00000001);
// test unit cell axes
Vector3d a = crystal.getA();
- assertEquals(7.971030, a.x, 0.000001);
- assertEquals(0.0, a.y, 0.000001);
- assertEquals(0.0, a.z, 0.000001);
+ Assert.assertEquals(7.971030, a.x, 0.000001);
+ Assert.assertEquals(0.0, a.y, 0.000001);
+ Assert.assertEquals(0.0, a.z, 0.000001);
Vector3d b = crystal.getB();
- assertEquals(0.0, b.x, 0.000001);
- assertEquals(18.772200, b.y, 0.000001);
- assertEquals(0.0, b.z, 0.000001);
+ Assert.assertEquals(0.0, b.x, 0.000001);
+ Assert.assertEquals(18.772200, b.y, 0.000001);
+ Assert.assertEquals(0.0, b.z, 0.000001);
Vector3d c = crystal.getC();
- assertEquals(0.0, c.x, 0.000001);
- assertEquals(0.0, c.y, 0.000001);
- assertEquals(10.262220, c.z, 0.000001);
+ Assert.assertEquals(0.0, c.x, 0.000001);
+ Assert.assertEquals(0.0, c.y, 0.000001);
+ Assert.assertEquals(10.262220, c.z, 0.000001);
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/Gaussian98ReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -6,14 +6,12 @@
import java.util.Iterator;
import java.util.List;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.io.Gaussian98Reader;
-import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
@@ -23,40 +21,17 @@
*
* @author Christoph Steinbeck
*/
+public class Gaussian98ReaderTest extends ChemObjectIOTest {
-public class Gaussian98ReaderTest extends CDKTestCase {
-
- static boolean standAlone = false;
- /**
- * Test suite.
- *
- * <p><b>Performed tests</b>:
- * <ul>
- * <li>Gaussian98Reader general tests.</li>
- * </ul>
- *
- * @return A test suite for Gaussian98Reader class.
- */
- public static Test suite() {
- return new TestSuite(Gaussian98ReaderTest.class);
- }
-
- /**
- * Constructs a new "Gaussian98ReaderTest" object given the test case's name.
- *
- * @param name The test case name.
- */
- public Gaussian98ReaderTest(String name) {
- super(name);
- }
-
-
- public void testAccepts() {
- Gaussian98Reader reader = new Gaussian98Reader();
- assertTrue(reader.accepts(ChemFile.class));
+ @BeforeClass public static void setup() {
+ setChemObjectIO(new Gaussian98Reader());
}
- public void testNMRReading() throws Exception
+ @Test public void testAccepts() {
+ Assert.assertTrue(chemObjectIO.accepts(ChemFile.class));
+ }
+
+ @Test public void testNMRReading() throws Exception
{
IAtomContainer atomContainer = null;
//boolean foundOneShieldingEntry = false;
@@ -69,8 +44,8 @@
Gaussian98Reader g98Reader = new Gaussian98Reader(inputReader);
ChemFile chemFile = (ChemFile)g98Reader.read(new ChemFile());
List atomContainersList = ChemFileManipulator.getAllAtomContainers(chemFile);
- assertNotNull(atomContainersList);
- assertTrue(atomContainersList.size() == 54);
+ Assert.assertNotNull(atomContainersList);
+ Assert.assertTrue(atomContainersList.size() == 54);
//logger.debug("Found " + atomContainers.length + " atomContainers");
Iterator iterator = atomContainersList.iterator();
int counter = 0;
@@ -88,8 +63,8 @@
shieldingCounter ++;
}
}
- if (counter < 53) assertTrue(shieldingCounter == 0);
- else assertTrue(shieldingCounter == ac.getAtomCount());
+ if (counter < 53) Assert.assertTrue(shieldingCounter == 0);
+ else Assert.assertTrue(shieldingCounter == ac.getAtomCount());
//logger.debug("AtomContainer " + (f + 1) + " has " + atomContainers[f].getAtomCount() + " atoms and " + shieldingCounter + " shielding entries");
counter++;
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/GhemicalReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,13 +29,11 @@
import java.io.StringReader;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
-import org.openscience.cdk.io.GhemicalMMReader;
-import org.openscience.cdk.CDKTestCase;
/**
* TestCase for the reading Ghemical molecular dynamics files using one test file.
@@ -44,22 +42,17 @@
*
* @see org.openscience.cdk.io.GhemicalReader
*/
-public class GhemicalReaderTest extends CDKTestCase {
+public class GhemicalReaderTest extends ChemObjectIOTest {
- public GhemicalReaderTest(String name) {
- super(name);
+ @BeforeClass public static void setup() {
+ setChemObjectIO(new GhemicalMMReader());
}
- public static Test suite() {
- return new TestSuite(GhemicalReaderTest.class);
+ @Test public void testAccepts() {
+ Assert.assertTrue(chemObjectIO.accepts(ChemModel.class));
}
- public void testAccepts() {
- GhemicalMMReader reader = new GhemicalMMReader();
- assertTrue(reader.accepts(ChemModel.class));
- }
-
- public void testExample() throws Exception {
+ @Test public void testExample() throws Exception {
String testfile =
"!Header mm1gp 100\n" +
"!Info 1\n" +
@@ -95,22 +88,22 @@
GhemicalMMReader reader = new GhemicalMMReader(stringReader);
ChemModel model = (ChemModel)reader.read((ChemObject)new ChemModel());
- assertNotNull(model);
- assertNotNull(model.getMoleculeSet());
+ Assert.assertNotNull(model);
+ Assert.assertNotNull(model.getMoleculeSet());
org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
- assertNotNull(som);
- assertEquals(1, som.getMoleculeCount());
+ Assert.assertNotNull(som);
+ Assert.assertEquals(1, som.getMoleculeCount());
org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
- assertNotNull(m);
- assertEquals(6, m.getAtomCount());
- assertEquals(5, m.getBondCount());
+ Assert.assertNotNull(m);
+ Assert.assertEquals(6, m.getAtomCount());
+ Assert.assertEquals(5, m.getBondCount());
// test reading of formal charges
org.openscience.cdk.interfaces.IAtom a = m.getAtom(0);
- assertNotNull(a);
- assertEquals(6, a.getAtomicNumber().intValue());
- assertEquals(-0.2, a.getCharge(), 0.01);
- assertEquals(0.06677, a.getPoint3d().x, 0.01);
+ Assert.assertNotNull(a);
+ Assert.assertEquals(6, a.getAtomicNumber().intValue());
+ Assert.assertEquals(-0.2, a.getCharge(), 0.01);
+ Assert.assertEquals(0.06677, a.getPoint3d().x, 0.01);
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/HINReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,13 +29,12 @@
import java.io.InputStream;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
-import org.openscience.cdk.io.HINReader;
-import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.tools.LoggingTool;
/**
* TestCase for the reading HIN mol files using one test file.
@@ -44,90 +43,85 @@
*
* @see org.openscience.cdk.io.HINReader
*/
-public class HINReaderTest extends CDKTestCase {
+public class HINReaderTest extends ChemObjectIOTest {
- private org.openscience.cdk.tools.LoggingTool logger;
-
- public HINReaderTest(String name) {
- super(name);
- logger = new org.openscience.cdk.tools.LoggingTool(this);
+ private static LoggingTool logger;
+
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(HINReaderTest.class);
+ setChemObjectIO(new HINReader());
}
- public static Test suite() {
- return new TestSuite(HINReaderTest.class);
+ @Test public void testAccepts() {
+ Assert.assertTrue(chemObjectIO.accepts(ChemFile.class));
}
- public void testAccepts() {
- HINReader reader = new HINReader();
- assertTrue(reader.accepts(ChemFile.class));
- }
-
- public void testBenzene() throws Exception {
+ @Test public void testBenzene() throws Exception {
String filename = "data/hin/benzene.hin";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
HINReader reader = new HINReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
- assertNotNull(som);
- assertEquals(1, som.getMoleculeCount());
+ Assert.assertNotNull(som);
+ Assert.assertEquals(1, som.getMoleculeCount());
org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
- assertNotNull(m);
- assertEquals(12, m.getAtomCount());
+ Assert.assertNotNull(m);
+ Assert.assertEquals(12, m.getAtomCount());
// assertEquals(?, m.getBondCount());
}
- public void testMoleculeTwo() throws Exception {
+ @Test public void testMoleculeTwo() throws Exception {
String filename = "data/hin/molecule2.hin";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
HINReader reader = new HINReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
- assertNotNull(som);
- assertEquals(1, som.getMoleculeCount());
+ Assert.assertNotNull(som);
+ Assert.assertEquals(1, som.getMoleculeCount());
org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
- assertNotNull(m);
- assertEquals(37, m.getAtomCount());
+ Assert.assertNotNull(m);
+ Assert.assertEquals(37, m.getAtomCount());
// assertEquals(?, m.getBondCount());
}
- public void testMultiple() throws Exception {
+ @Test public void testMultiple() throws Exception {
String filename = "data/hin/multiple.hin";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
HINReader reader = new HINReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
- assertNotNull(som);
- assertEquals(3, som.getMoleculeCount());
+ Assert.assertNotNull(som);
+ Assert.assertEquals(3, som.getMoleculeCount());
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,13 +29,11 @@
import java.io.InputStream;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
-import org.openscience.cdk.io.INChIPlainTextReader;
-import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -46,49 +44,45 @@
* @see org.openscience.cdk.io.INChIReader
* @cdk.require java1.4+
*/
-public class INChIPlainTextReaderTest extends CDKTestCase {
+public class INChIPlainTextReaderTest extends ChemObjectIOTest {
- private LoggingTool logger;
+ private static LoggingTool logger;
- public INChIPlainTextReaderTest(String name) {
- super(name);
- logger = new LoggingTool(this);
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(INChIPlainTextReaderTest.class);
+ setChemObjectIO(new INChIPlainTextReader());
}
- public static Test suite() {
- return new TestSuite(INChIPlainTextReaderTest.class);
- }
-
- public void testAccepts() {
+ @Test public void testAccepts() {
INChIPlainTextReader reader = new INChIPlainTextReader();
- assertTrue(reader.accepts(ChemFile.class));
+ Assert.assertTrue(reader.accepts(ChemFile.class));
}
/**
* Test a INChI 1.12Beta file containing the two tautomers
* of guanine.
*/
- public void testGuanine() throws Exception {
+ @Test public void testGuanine() throws Exception {
String filename = "data/inchi/guanine.inchi";
logger.info("Testing: ", filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
INChIPlainTextReader reader = new INChIPlainTextReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
- assertNotNull(moleculeSet);
+ Assert.assertNotNull(moleculeSet);
org.openscience.cdk.interfaces.IMolecule molecule = moleculeSet.getMolecule(0);
- assertNotNull(molecule);
+ Assert.assertNotNull(molecule);
- assertEquals(11, molecule.getAtomCount());
- assertEquals(12, molecule.getBondCount());
+ Assert.assertEquals(11, molecule.getAtomCount());
+ Assert.assertEquals(12, molecule.getBondCount());
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/INChIReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,13 +29,11 @@
import java.io.InputStream;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
-import org.openscience.cdk.io.INChIReader;
-import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -46,49 +44,44 @@
* @see org.openscience.cdk.io.INChIReader
* @cdk.require java1.4+
*/
-public class INChIReaderTest extends CDKTestCase {
+public class INChIReaderTest extends ChemObjectIOTest {
- private LoggingTool logger;
+ private static LoggingTool logger;
- public INChIReaderTest(String name) {
- super(name);
- logger = new LoggingTool(this);
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(INChIReaderTest.class);
+ setChemObjectIO(new INChIReader());
}
-
- public static Test suite() {
- return new TestSuite(INChIReaderTest.class);
+
+ @Test public void testAccepts() {
+ Assert.assertTrue(chemObjectIO.accepts(ChemFile.class));
}
- public void testAccepts() {
- INChIReader reader = new INChIReader();
- assertTrue(reader.accepts(ChemFile.class));
- }
-
/**
* Test a INChI 1.1Beta file containing the two tautomers
* of guanine.
*/
- public void testGuanine() throws Exception {
+ @Test public void testGuanine() throws Exception {
String filename = "data/inchi/guanine.inchi.xml";
logger.info("Testing: ", filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
INChIReader reader = new INChIReader(ins);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
- assertNotNull(moleculeSet);
+ Assert.assertNotNull(moleculeSet);
org.openscience.cdk.interfaces.IMolecule molecule = moleculeSet.getMolecule(0);
- assertNotNull(molecule);
+ Assert.assertNotNull(molecule);
- assertEquals(11, molecule.getAtomCount());
- assertEquals(12, molecule.getBondCount());
+ Assert.assertEquals(11, molecule.getAtomCount());
+ Assert.assertEquals(12, molecule.getBondCount());
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/io/MDLReaderTest.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -28,10 +28,9 @@
import java.io.StringReader;
import java.util.List;
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.openscience.cdk.CDKTestCase;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
@@ -41,6 +40,7 @@
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.IChemObjectReader.Mode;
import org.openscience.cdk.nonotify.NNMolecule;
+import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
@@ -52,28 +52,24 @@
* @see org.openscience.cdk.io.MDLReader
* @see org.openscience.cdk.io.SDFReaderTest
*/
-public class MDLReaderTest extends CDKTestCase {
+public class MDLReaderTest extends ChemObjectIOTest {
- private org.openscience.cdk.tools.LoggingTool logger;
+ private static LoggingTool logger;
- public MDLReaderTest(String name) {
- super(name);
- logger = new org.openscience.cdk.tools.LoggingTool(this);
+ @BeforeClass public static void setup() {
+ logger = new LoggingTool(MDLReaderTest.class);
+ setChemObjectIO(new MDLReader());
}
- public static Test suite() {
- return new TestSuite(MDLReaderTest.class);
- }
-
- public void testAccepts() {
+ @Test public void testAccepts() {
MDLReader reader = new MDLReader();
reader.setReaderMode(Mode.STRICT);
- assertTrue(reader.accepts(ChemFile.class));
- assertTrue(reader.accepts(ChemModel.class));
- assertTrue(reader.accepts(Molecule.class));
+ Assert.assertTrue(reader.accepts(ChemFile.class));
+ Assert.assertTrue(reader.accepts(ChemModel.class));
+ Assert.assertTrue(reader.accepts(Molecule.class));
}
- public void testReadFromStringReader() throws Exception {
+ @Test public void testReadFromStringReader() throws Exception {
String mdl =
"cyclopropane.mol\n" +
"\n" +
@@ -99,40 +95,40 @@
" 3 9 1 0 0 0\n";
MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT);
ChemFile chemFile = (ChemFile) reader.read(new ChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ Assert.assertNotNull(chemFile);
+ Assert.assertEquals(1, chemFile.getChemSequenceCount());
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
+ Assert.assertNotNull(seq);
+ Assert.assertEquals(1, seq.getChemModelCount());
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
+ Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
- assertNotNull(som);
- assertEquals(1, som.getMoleculeCount());
+ Assert.assertNotNull(som);
+ Assert.assertEquals(1, som.getMoleculeCount());
org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
- assertNotNull(m);
- assertEquals(9, m.getAtomCount());
- assertEquals(9, m.getBondCount());
+ Assert.assertNotNull(m);
+ Assert.assertEquals(9, m.getAtomCount());
+ Assert.assertEquals(9, m.getBondCount());
}
/**
* @cdk.bug 1542467
*/
- public void testBug1542467() throws Exception {
+ @Test public void testBug1542467() throws Exception {
String filename = "data/mdl/Strychnine_nichtOK.mol";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLReader reader = new MDLReader(ins, Mode.STRICT);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
+ Assert.assertNotNull(chemFile);
List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
- assertEquals(1, containersList.size());
- assertTrue((containersList.get(0)).getAtomCount() > 0);
- assertTrue((containersList.get(0)).getBondCount() > 0);
+ Assert.assertEquals(1, containersList.size());
+ Assert.assertTrue((containersList.get(0)).getAtomCount() > 0);
+ Assert.assertTrue((containersList.get(0)).getBondCount() > 0);
}
- public void testReadProton() throws Exception {
+ @Test public void testReadProton() throws Exception {
String mdl =
"proton.mol\n" +
"\n" +
@@ -141,36 +137,36 @@
" -0.0073 -0.5272 0.9655 H 0 3 0 0 0\n";
MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT);
Molecule mol = (Molecule)reader.read(new Molecule());
- assertNotNull(mol);
- assertEquals(1, mol.getAtomCount());
- assertEquals(0, mol.getBondCount());
+ Assert.assertNotNull(mol);
+ Assert.assertEquals(1, mol.getAtomCount());
+ Assert.assertEquals(0, mol.getBondCount());
IAtom atom = mol.getAtom(0);
- assertEquals(1, atom.getFormalCharge().intValue());
+ Assert.assertEquals(1, atom.getFormalCharge().intValue());
}
/**
* The corrupt file is really ok; it is just not V2000 material.
*/
- public void testSDF() throws Exception {
+ @Test public void testSDF() throws Exception {
String filename = "data/mdl/prev2000.sd";
logger.info("Testing: " + filename);
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLReader reader = new MDLReader(ins, Mode.STRICT);
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
- assertNotNull(chemFile);
+ Assert.assertNotNull(chemFile);
List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
- assertEquals(2, containersList.size());
- assertEquals(39, (containersList.get(0)).getAtomCount());
- assertEquals(41, (containersList.get(0)).getBondCount());
- assertEquals(29, (containersList.get(1)).getAtomCount());
- assertEquals(28, (containersList.get(1)).getBondCount());
+ Assert.assertEquals(2, containersList.size());
+ Assert.assertEquals(39, (containersList.get(0)).getAtomCount());
+ Assert.assertEquals(41, (containersList.get(0)).getBondCount());
+ Assert.assertEquals(29, (containersList.get(1)).getAtomCount());
+ Assert.assertEquals(28, (containersList.get(1)).getBondCount());
}
- public void testEmptyString() throws Exception {
+ @Test public void testEmptyString() throws Exception {
String emptyString = "";
MDLReader reader = new MDLReader(new StringReader(emptyString), Mode.STRICT);
IMolecule mol = (IMolecule)reader.read(new NNMolecule());
- assertNull(mol);
+ Assert.assertNull(mol);
}
}
Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-04 06:55:28 UTC (rev 11497)
+++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java 2008-07-04 08:22:58 UTC (rev 11498)
@@ -29,6 +29,7 @@
import org.openscience.cdk.IoCoverageTest;
import org.openscience.cdk.io.CDKSourceCodeWriterTest;
+import org.openscience.cdk.io.CTXReaderTest;
import org.openscience.cdk.io.ChemObjectIOInstantionTests;
import org.openscience.cdk.io.CrystClustReaderTest;
import org.openscience.cdk.io.GamessReaderTest;
@@ -161,16 +162,16 @@
suite.addTest(IoCoverageTest.suite());
suite.addTest(CMLIOTests.suite());
- suite.addTest(CrystClustReaderTest.suite());
+ suite.addTest(new JUnit4TestAdapter(CrystClustReaderTest.class));
suite.addTest(new JUnit4TestAdapter(CDKSourceCodeWriterTest.class));
+ suite.addTest(new JUnit4TestAdapter(CTXReaderTest.class));
suite.addTest(GamessReaderTest.suite());
- suite.addTest(Gaussian98ReaderTest.suite());
- suite.addTest(GhemicalReaderTest.suite());
- suite.addTest(HINReaderTest.suite());
- //suite.addTest(IChIReaderTest.suite());
- suite.addTest(INChIReaderTest.suite());
- suite.addTest(INChIPlainTextReaderTest.suite());
- suite.addTest(MDLReaderTest.suite());
+ suite.addTest(new JUnit4TestAdapter(Gaussian98ReaderTest.class));
+ suite.addTest(new JUnit4TestAdapter(GhemicalReaderTest.class));
+ suite.addTest(new JUnit4TestAdapter(HINReaderTest.class));
+ suite.addTest(new JUnit4TestAdapter(INChIReaderTest.class));
+ suite.addTest(new JUnit4TestAdapter(INChIPlainTextReaderTest.class));
+ suite.addTest(new JUnit4TestAdapter(MDLReaderTest.class));
suite.addTest(MDLV2000ReaderTest.suite());
suite.addTest(MDLV3000ReaderTest.suite());
suite.addTest(SDFReaderTest.suite());
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