Separating out reader factory tests

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

src/test/org/openscience/cdk/io/AbstractReaderFactoryTest.java

@@ -0,0 +1,165 @@
+/*
+ * 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;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.ChemFile;
+import org.openscience.cdk.ChemModel;
+import org.openscience.cdk.Reaction;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IChemModel;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.io.formats.CMLFormat;
+import org.openscience.cdk.io.formats.CTXFormat;
+import org.openscience.cdk.io.formats.GamessFormat;
+import org.openscience.cdk.io.formats.Gaussian98Format;
+import org.openscience.cdk.io.formats.GhemicalSPMFormat;
+import org.openscience.cdk.io.formats.IChemFormat;
+import org.openscience.cdk.io.formats.IChemFormatMatcher;
+import org.openscience.cdk.io.formats.INChIFormat;
+import org.openscience.cdk.io.formats.INChIPlainTextFormat;
+import org.openscience.cdk.io.formats.IResourceFormat;
+import org.openscience.cdk.io.formats.MDLFormat;
+import org.openscience.cdk.io.formats.MDLV2000Format;
+import org.openscience.cdk.io.formats.MDLV3000Format;
+import org.openscience.cdk.io.formats.Mol2Format;
+import org.openscience.cdk.io.formats.PDBFormat;
+import org.openscience.cdk.io.formats.PubChemASNFormat;
+import org.openscience.cdk.io.formats.PubChemCompoundXMLFormat;
+import org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat;
+import org.openscience.cdk.io.formats.ShelXFormat;
+import org.openscience.cdk.io.formats.VASPFormat;
+import org.openscience.cdk.io.formats.XYZFormat;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
+import org.openscience.cdk.tools.manipulator.ReactionManipulator;
+
+import java.io.BufferedInputStream;
+import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
+
+/**
+ * TestCase for the instantiation and functionality of the {@link org.openscience.cdk.io.ReaderFactory}.
+ *
+ * @cdk.module test-io
+ */
+public class AbstractReaderFactoryTest {
+
+    private ReaderFactory factory = new ReaderFactory();
+
+    void expectReader(String filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount) throws Exception {
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        Assert.assertNotNull("Cannot find file: " + filename, ins);
+        if (expectedFormat instanceof IChemFormatMatcher) {
+        	factory.registerFormat((IChemFormatMatcher)expectedFormat);
+        }
+        ISimpleChemObjectReader reader = factory.createReader(ins);
+        Assert.assertNotNull(reader);
+        Assert.assertEquals(
+            ((IChemFormat)expectedFormat).getReaderClassName(),
+            reader.getClass().getName()
+        );
+        // now try reading something from it
+        IChemObject[] objects = { 
+        		new ChemFile(), new ChemModel(), new AtomContainer(),
+        		new Reaction()
+        };
+        boolean read = false;
+        for (int i=0; (i<objects.length && !read); i++) {
+        	if (reader.accepts(objects[i].getClass())) {
+                IChemObject chemObject = reader.read(objects[i]);
+                Assert.assertNotNull("Reader accepted a " +
+                    objects[i].getClass().getName() + " but failed to read it",
+                    chemObject
+                );
+                assertAtomCount(expectedAtomCount, chemObject);
+                assertBondCount(expectedBondCount, chemObject);
+        		read = true;
+        	}
+        }
+        if (read) {
+        	// ok, reseting worked
+        } else {
+        	Assert.fail("Reading an IChemObject from the Reader did not work properly.");
+        }
+    }
+
+    void assertBondCount(int expectedBondCount, IChemObject chemObject) {
+        if (expectedBondCount != -1) {
+            if (chemObject instanceof IChemFile) {
+                Assert.assertEquals(
+                    expectedBondCount,
+                    ChemFileManipulator.getBondCount((IChemFile)chemObject)
+                );
+            } else if (chemObject instanceof IChemModel) {
+                Assert.assertEquals(
+                    expectedBondCount,
+                    ChemModelManipulator.getBondCount((IChemModel)chemObject)
+                );
+            } else if (chemObject instanceof IAtomContainer) {
+                Assert.assertEquals(
+                    expectedBondCount,
+                    ((IAtomContainer)chemObject).getBondCount()
+                );
+            } else if (chemObject instanceof IReaction) {
+                Assert.assertEquals(
+                    expectedBondCount,
+                    ReactionManipulator.getBondCount((IReaction)chemObject)
+                );
+            }
+        }
+    }
+
+    void assertAtomCount(int expectedAtomCount, IChemObject chemObject) {
+        if (expectedAtomCount != -1) {
+            if (chemObject instanceof IChemFile) {
+                Assert.assertEquals(
+                    expectedAtomCount,
+                    ChemFileManipulator.getAtomCount((IChemFile)chemObject)
+                );
+            } else if (chemObject instanceof IChemModel) {
+                Assert.assertEquals(
+                    expectedAtomCount,
+                    ChemModelManipulator.getAtomCount((IChemModel)chemObject)
+                );
+            } else if (chemObject instanceof IAtomContainer) {
+                Assert.assertEquals(
+                    expectedAtomCount,
+                    ((IAtomContainer)chemObject).getAtomCount()
+                );
+            } else if (chemObject instanceof IReaction) {
+                Assert.assertEquals(
+                    expectedAtomCount,
+                    ReactionManipulator.getAtomCount((IReaction)chemObject)
+                );
+            }
+        }
+    }
+
+}

src/test/org/openscience/cdk/io/PDBReaderFactoryTest.java

@@ -0,0 +1,74 @@
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
+ * 
+ * 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 USA.
+ *  */
+package org.openscience.cdk.io;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.ChemFile;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.io.formats.CMLFormat;
+import org.openscience.cdk.io.formats.CTXFormat;
+import org.openscience.cdk.io.formats.GamessFormat;
+import org.openscience.cdk.io.formats.Gaussian98Format;
+import org.openscience.cdk.io.formats.GhemicalSPMFormat;
+import org.openscience.cdk.io.formats.IChemFormat;
+import org.openscience.cdk.io.formats.IChemFormatMatcher;
+import org.openscience.cdk.io.formats.INChIFormat;
+import org.openscience.cdk.io.formats.INChIPlainTextFormat;
+import org.openscience.cdk.io.formats.MDLFormat;
+import org.openscience.cdk.io.formats.MDLV2000Format;
+import org.openscience.cdk.io.formats.MDLV3000Format;
+import org.openscience.cdk.io.formats.Mol2Format;
+import org.openscience.cdk.io.formats.PDBFormat;
+import org.openscience.cdk.io.formats.PubChemASNFormat;
+import org.openscience.cdk.io.formats.PubChemCompoundXMLFormat;
+import org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat;
+import org.openscience.cdk.io.formats.ShelXFormat;
+import org.openscience.cdk.io.formats.VASPFormat;
+import org.openscience.cdk.io.formats.XYZFormat;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+
+import java.io.BufferedInputStream;
+import java.io.InputStream;
+import java.util.zip.GZIPInputStream;
+
+/**
+ * TestCase for the instantiation and functionality of the {@link org.openscience.cdk.io.ReaderFactory}.
+ *
+ * @cdk.module test-pdb
+ */
+public class PDBReaderFactoryTest extends AbstractReaderFactoryTest {
+
+    private ReaderFactory factory = new ReaderFactory();
+
+    @Test public void testPDB() throws Exception {
+        expectReader("data/pdb/coffeine.pdb", PDBFormat.getInstance(), -1, -1);
+    }
+}

src/test/org/openscience/cdk/io/ReaderFactoryTest.java

@@ -32,6 +32,7 @@
 import java.util.zip.GZIPInputStream;
 
 import org.junit.Assert;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.CDKTestCase;
@@ -73,7 +74,7 @@
  *
  * @cdk.module test-io
  */
-public class ReaderFactoryTest extends CDKTestCase {
+public class ReaderFactoryTest extends AbstractReaderFactoryTest {
 
     private ReaderFactory factory = new ReaderFactory();
 
@@ -83,6 +84,7 @@ public class ReaderFactoryTest extends CDKTestCase {
         Assert.assertNotNull(reader);
         Assert.assertEquals(format.getFormatName(), reader.getFormat().getFormatName());
     }
+
     @Test public void testGaussian98() throws Exception {
         expectReader("data/gaussian/g98.out", Gaussian98Format.getInstance(), -1, -1);
     }
@@ -135,10 +137,11 @@ public class ReaderFactoryTest extends CDKTestCase {
         expectReader("data/mdl/molV3000.mol", MDLV3000Format.getInstance(), -1, -1);
     }
 
-    @Test public void testPDB() throws Exception {
+    @Ignore("test moved to cdk-test-pdb/PDBReaderFactoryTest")
+    public void testPDB() throws Exception {
         expectReader("data/pdb/coffeine.pdb", PDBFormat.getInstance(), -1, -1);
     }
-    
+
     @Test public void testMol2() throws Exception {
     	expectReader("data/mol2/fromWebsite.mol2", Mol2Format.getInstance(), -1, -1);
     }
@@ -165,95 +168,6 @@ public class ReaderFactoryTest extends CDKTestCase {
         Assert.assertNull(reader);
     }
 
-    private void expectReader(String filename, IResourceFormat expectedFormat, int expectedAtomCount, int expectedBondCount) throws Exception {
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
-        Assert.assertNotNull("Cannot find file: " + filename, ins);
-        if (expectedFormat instanceof IChemFormatMatcher) {
-        	factory.registerFormat((IChemFormatMatcher)expectedFormat);
-        }
-        ISimpleChemObjectReader reader = factory.createReader(ins);
-        Assert.assertNotNull(reader);
-        Assert.assertEquals(
-            ((IChemFormat)expectedFormat).getReaderClassName(),
-            reader.getClass().getName()
-        );
-        // now try reading something from it
-        IChemObject[] objects = { 
-        		new ChemFile(), new ChemModel(), new AtomContainer(),
-        		new Reaction()
-        };
-        boolean read = false;
-        for (int i=0; (i<objects.length && !read); i++) {
-        	if (reader.accepts(objects[i].getClass())) {
-                IChemObject chemObject = reader.read(objects[i]);
-                Assert.assertNotNull("Reader accepted a " +
-                    objects[i].getClass().getName() + " but failed to read it",
-                    chemObject
-                );
-                assertAtomCount(expectedAtomCount, chemObject);
-                assertBondCount(expectedBondCount, chemObject);
-        		read = true;
-        	}
-        }
-        if (read) {
-        	// ok, reseting worked
-        } else {
-        	Assert.fail("Reading an IChemObject from the Reader did not work properly.");
-        }
-    }
-
-    private void assertBondCount(int expectedBondCount, IChemObject chemObject) {
-        if (expectedBondCount != -1) {
-            if (chemObject instanceof IChemFile) {
-                Assert.assertEquals(
-                    expectedBondCount,
-                    ChemFileManipulator.getBondCount((IChemFile)chemObject)
-                );
-            } else if (chemObject instanceof IChemModel) {
-                Assert.assertEquals(
-                    expectedBondCount,
-                    ChemModelManipulator.getBondCount((IChemModel)chemObject)
-                );
-            } else if (chemObject instanceof IAtomContainer) {
-                Assert.assertEquals(
-                    expectedBondCount,
-                    ((IAtomContainer)chemObject).getBondCount()
-                );
-            } else if (chemObject instanceof IReaction) {
-                Assert.assertEquals(
-                    expectedBondCount,
-                    ReactionManipulator.getBondCount((IReaction)chemObject)
-                );
-            }
-        }
-    }
-
-    private void assertAtomCount(int expectedAtomCount, IChemObject chemObject) {
-        if (expectedAtomCount != -1) {
-            if (chemObject instanceof IChemFile) {
-                Assert.assertEquals(
-                    expectedAtomCount,
-                    ChemFileManipulator.getAtomCount((IChemFile)chemObject)
-                );
-            } else if (chemObject instanceof IChemModel) {
-                Assert.assertEquals(
-                    expectedAtomCount,
-                    ChemModelManipulator.getAtomCount((IChemModel)chemObject)
-                );
-            } else if (chemObject instanceof IAtomContainer) {
-                Assert.assertEquals(
-                    expectedAtomCount,
-                    ((IAtomContainer)chemObject).getAtomCount()
-                );
-            } else if (chemObject instanceof IReaction) {
-                Assert.assertEquals(
-                    expectedAtomCount,
-                    ReactionManipulator.getAtomCount((IReaction)chemObject)
-                );
-            }
-        }
-    }
-
     /**
      * @cdk.bug 2153298
      */

src/test/org/openscience/cdk/modulesuites/MpdbTests.java

@@ -27,6 +27,7 @@
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 import org.openscience.cdk.coverage.PdbCoverageTest;
+import org.openscience.cdk.io.PDBReaderFactoryTest;
 import org.openscience.cdk.io.PDBReaderTest;
 import org.openscience.cdk.io.PDBWriterTest;
 import org.openscience.cdk.templates.AminoAcidsTest;
@@ -43,6 +44,7 @@
     AminoAcidsTest.class,
     PDBReaderTest.class,
     PDBWriterTest.class,
-    ProteinBuilderToolTest.class
+    ProteinBuilderToolTest.class,
+    PDBReaderFactoryTest.class
 })
 public class MpdbTests {}