Duplicate the expectReader test from the FormatFactory.

johnmay · egonw · commit 1fb1a62f9801 · 2021-12-24T09:03:56.000+01:00
diff --git a/base/test/src/test/java/org/openscience/cdk/io/ChemObjectIOTest.java b/base/test/src/test/java/org/openscience/cdk/io/ChemObjectIOTest.java
diff --git a/base/test/src/test/java/org/openscience/cdk/io/ChemObjectReaderTest.java b/base/test/src/test/java/org/openscience/cdk/io/ChemObjectReaderTest.java
diff --git a/base/test/src/test/java/org/openscience/cdk/io/ChemObjectWriterTest.java b/base/test/src/test/java/org/openscience/cdk/io/ChemObjectWriterTest.java
diff --git a/base/test/src/test/java/org/openscience/cdk/io/SimpleChemObjectReaderTest.java b/base/test/src/test/java/org/openscience/cdk/io/SimpleChemObjectReaderTest.java
diff --git a/misc/extra/pom.xml b/misc/extra/pom.xml
@@ -11,6 +11,7 @@
     </parent>
 
     <artifactId>cdk-extra</artifactId>
+    <name>cdk-extra</name>
     
     <dependencies>
         <dependency>
@@ -82,8 +83,4 @@
             <version>${project.parent.version}</version>
         </dependency>
     </dependencies>
-
-
-    <name>cdk-extra</name>
-    
 </project>
diff --git a/misc/test-extra/pom.xml b/misc/test-extra/pom.xml
@@ -87,13 +87,6 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-io</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-ioformats</artifactId>
diff --git a/misc/test-extra/src/test/java/org/openscience/cdk/io/ExtraReaderFactoryTest.java b/misc/test-extra/src/test/java/org/openscience/cdk/io/ExtraReaderFactoryTest.java
@@ -22,40 +22,76 @@
  *  */
 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.ChemModel;
+import org.openscience.cdk.Reaction;
+import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.io.formats.GamessFormat;
+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.VASPFormat;
 
+import java.io.InputStream;
+
 /**
  * TestCase for the instantiation and functionality of the {@link ReaderFactory} for
  * io classes currently in 'cdk-extra'.
  *
  * @cdk.module test-extra
  */
-public class ExtraReaderFactoryTest extends AbstractReaderFactoryTest {
+public class ExtraReaderFactoryTest {
 
     private ReaderFactory factory = new ReaderFactory();
 
+    void expectReader(String filename,
+                      IResourceFormat expectedFormat)
+            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);
+                read = true;
+            }
+        }
+        Assert.assertTrue("Reading an IChemObject from the Reader did not work properly.", read);
+    }
+
     @Test
     public void testINChI() throws Exception {
-        expectReader("data/inchi/guanine.inchi.xml", INChIFormat.getInstance(), -1, -1);
+        expectReader("data/inchi/guanine.inchi.xml", INChIFormat.getInstance());
     }
 
     @Test
     public void testINChIPlainText() throws Exception {
-        expectReader("data/inchi/guanine.inchi", INChIPlainTextFormat.getInstance(), -1, -1);
+        expectReader("data/inchi/guanine.inchi", INChIPlainTextFormat.getInstance());
     }
 
     @Test
     public void testVASP() throws Exception {
-        expectReader("data/vasp/LiMoS2_optimisation_ISIF3.vasp", VASPFormat.getInstance(), -1, -1);
+        expectReader("data/vasp/LiMoS2_optimisation_ISIF3.vasp", VASPFormat.getInstance());
     }
 
     @Test
     public void testGamess() throws Exception {
-        expectReader("data/gamess/ch3oh_gam.out", GamessFormat.getInstance(), -1, -1);
+        expectReader("data/gamess/ch3oh_gam.out", GamessFormat.getInstance());
     }
 
 }
diff --git a/storage/iordf/pom.xml b/storage/iordf/pom.xml
@@ -100,13 +100,6 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-io</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-test</artifactId>
diff --git a/storage/libiocml/pom.xml b/storage/libiocml/pom.xml
@@ -99,13 +99,6 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-io</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-test</artifactId>
diff --git a/storage/pdb/pom.xml b/storage/pdb/pom.xml
@@ -77,13 +77,6 @@
             <type>test-jar</type>
             <scope>test</scope>            
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-io</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-testdata</artifactId>
diff --git a/storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderFactoryTest.java b/storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderFactoryTest.java
@@ -22,20 +22,56 @@
  *  */
 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.ChemModel;
+import org.openscience.cdk.Reaction;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.io.formats.IChemFormat;
+import org.openscience.cdk.io.formats.IChemFormatMatcher;
+import org.openscience.cdk.io.formats.IResourceFormat;
 import org.openscience.cdk.io.formats.PDBFormat;
 
+import java.io.InputStream;
+
 /**
  * TestCase for the instantiation and functionality of the {@link org.openscience.cdk.io.ReaderFactory}.
  *
  * @cdk.module test-pdb
  */
-public class PDBReaderFactoryTest extends AbstractReaderFactoryTest {
+public class PDBReaderFactoryTest {
 
     private ReaderFactory factory = new ReaderFactory();
 
+    void expectReader(String filename,
+                      IResourceFormat expectedFormat)
+            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);
+                read = true;
+            }
+        }
+        Assert.assertTrue("Reading an IChemObject from the Reader did not work properly.", read);
+    }
+
     @Test
     public void testPDB() throws Exception {
-        expectReader("data/pdb/coffeine.pdb", PDBFormat.getInstance(), -1, -1);
+        expectReader("data/pdb/coffeine.pdb", PDBFormat.getInstance());
     }
 }
diff --git a/storage/smiles/pom.xml b/storage/smiles/pom.xml
@@ -118,13 +118,6 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-io</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-testdata</artifactId>
