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Added test data and setUp method for manager tests

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1 parent 4ecbc16 commit 05e7cce5fcfa590a39bd117265ecc4c7d607eeae egonw committed with egonw May 29, 2009
@@ -15,4 +15,6 @@ Require-Bundle: net.bioclipse.core;bundle-version="2.0.0",
net.bioclipse.structuredb.rdf;bundle-version="2.0.0",
net.bioclipse.structuredb;bundle-version="2.0.0",
org.eclipse.ui;bundle-version="3.4.2",
- org.junit4;bundle-version="4.3.1"
+ org.junit4;bundle-version="4.3.1",
+ net.bioclipse.cdk.business;bundle-version="2.0.0",
+ net.bioclipse.ui;bundle-version="2.0.0"
@@ -1,5 +1,6 @@
/*******************************************************************************
* Copyright (c) 2009 Egon Willighagen <egonw@users.sf.net>
+ * 2008 Jonathan Alverson
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
@@ -10,15 +11,38 @@
******************************************************************************/
package net.bioclipse.structuredb.rdf.business.tests;
-import org.junit.Assert;
-import org.junit.Test;
+import java.util.List;
+import net.bioclipse.cdk.business.CDKManager;
+import net.bioclipse.cdk.business.ICDKManager;
+import net.bioclipse.cdk.domain.ICDKMolecule;
+import net.bioclipse.core.MockIFile;
import net.bioclipse.core.business.IBioclipseManager;
import net.bioclipse.core.tests.AbstractManagerTest;
+import net.bioclipse.structuredb.business.IStructuredbManager;
+import net.bioclipse.structuredb.domain.DBMolecule;
import net.bioclipse.structuredb.rdf.business.StructureRDFManager;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
public class StructureRDFManagerTest extends AbstractManagerTest {
+ private static IStructuredbManager manager;
+ private final static String database1 = "database1";
+ private final static String database2 = "database2";
+
+ private ICDKManager cdk = new CDKManager();
+
+ @BeforeClass
+ public static void setup() throws Exception {
+ manager = new StructureRDFManager();
+ Assert.assertNotNull(manager);
+ manager.createDatabase(database1);
+ manager.createDatabase(database2);
+ }
+
public IBioclipseManager getManager() {
return new StructureRDFManager();
}
@@ -42,6 +66,49 @@ public IBioclipseManager getManager() {
@Test public void testAllLabels() {
Assert.fail("Not implemented yet.");
}
+
+ public void testCreatingAndRetrievingStructures() throws Exception {
+ ICDKManager cdk = new CDKManager();
+
+ ICDKMolecule mol1 = cdk.loadMolecule(
+ new MockIFile( StructureRDFManagerTest.class
+ .getClassLoader()
+ .getResourceAsStream(
+ "testData/0037.cml") ) );
+ Assert.assertNotNull(mol1);
+
+ DBMolecule structure1 = manager
+ .createMolecule( database1,
+ "0037",
+ mol1 );
+ Assert.assertNotNull(structure1);
+
+ DBMolecule structure2
+ = manager.createMolecule(
+ database1,
+ "0106",
+ cdk.loadMolecule(
+ new MockIFile( StructureRDFManagerTest.class
+ .getClassLoader()
+ .getResourceAsStream(
+ "testData/0106.cml") ) ) );
+
+ Assert.assertNotNull(structure2);
+
+ Assert.assertTrue( manager
+ .allMoleculesByName( database1,
+ structure1.getName() )
+ .contains(structure1) );
+ Assert.assertTrue( manager
+ .allMoleculesByName( database1,
+ structure2.getName() )
+ .contains(structure2) );
+
+ List<DBMolecule> dBMolecules = manager.allMolecules(database1);
+
+ Assert.assertTrue( dBMolecules.contains(structure1) );
+ Assert.assertTrue( dBMolecules.contains(structure2) );
+ }
@Test public void testCreatingChoiceAnnotation() {
Assert.fail("Not implemented yet.");
@@ -0,0 +1 @@
+<cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110444"><atomArray><atom id="a1" elementType="C" x2="2.89" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="2.89" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="2.17" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="1.44" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="1.44" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="0.72" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.61" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="2.17" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="2.89" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="1.44" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-4.58" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="C" x2="0.72" y2="-5.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="C" x2="0.0" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="C" x2="2.89" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="C" x2="3.61" y2="-4.17" formalCharge="0" hydrogenCount="0" /><atom id="a16" elementType="C" x2="4.33" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a17" elementType="C" x2="4.33" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a18" elementType="C" x2="3.61" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a19" elementType="O" x2="1.44" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a20" elementType="N" x2="2.17" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a21" elementType="N" x2="0.0" y2="-2.08" formalCharge="0" hydrogenCount="0" /><atom id="a22" elementType="Si" x2="0.72" y2="-4.17" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a20" order="S" /><bond id="b2" atomRefs2="a1 a2" order="S" /><bond id="b3" atomRefs2="a1 a7" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a3 a4" order="S" /><bond id="b6" atomRefs2="a4 a5" order="S" /><bond id="b7" atomRefs2="a5 a20" order="S" /><bond id="b8" atomRefs2="a5 a6" order="S" /><bond id="b9" atomRefs2="a6 a21" order="T" /><bond id="b10" atomRefs2="a8 a20" order="S" /><bond id="b11" atomRefs2="a8 a9" order="S" /><bond id="b12" atomRefs2="a8 a10" order="S" /><bond id="b13" atomRefs2="a9 a14" order="D" /><bond id="b14" atomRefs2="a9 a18" order="S" /><bond id="b15" atomRefs2="a10 a19" order="S" /><bond id="b16" atomRefs2="a11 a22" order="S" /><bond id="b17" atomRefs2="a12 a22" order="S" /><bond id="b18" atomRefs2="a13 a22" order="S" /><bond id="b19" atomRefs2="a14 a15" order="S" /><bond id="b20" atomRefs2="a15 a16" order="D" /><bond id="b21" atomRefs2="a16 a17" order="S" /><bond id="b22" atomRefs2="a17 a18" order="D" /><bond id="b23" atomRefs2="a19 a22" order="S" /></bondArray></molecule></cml>
@@ -0,0 +1 @@
+<cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110098"><atomArray><atom id="a1" elementType="C" x2="1.73" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="1.73" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="0.87" y2="-1.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="2.6" y2="-1.0" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="2.6" y2="-3.0" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="3.46" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.46" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="5.0" y2="-2.0" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="4.41" y2="-1.19" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="0.87" y2="-3.0" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="O" x2="2.6" y2="-4.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="O" x2="2.6" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="N" x2="0.0" y2="-1.5" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="N" x2="4.41" y2="-2.81" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="D" /><bond id="b2" atomRefs2="a1 a5" order="S" /><bond id="b3" atomRefs2="a1 a10" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a2 a4" order="S" /><bond id="b6" atomRefs2="a3 a14" order="D" /><bond id="b7" atomRefs2="a4 a7" order="S" /><bond id="b8" atomRefs2="a4 a13" order="D" /><bond id="b9" atomRefs2="a5 a6" order="S" /><bond id="b10" atomRefs2="a5 a12" order="D" /><bond id="b11" atomRefs2="a6 a7" order="D" /><bond id="b12" atomRefs2="a6 a15" order="S" /><bond id="b13" atomRefs2="a7 a9" order="S" /><bond id="b14" atomRefs2="a8 a9" order="D" /><bond id="b15" atomRefs2="a8 a15" order="S" /><bond id="b16" atomRefs2="a10 a11" order="D" /><bond id="b17" atomRefs2="a11 a14" order="S" /></bondArray></molecule></cml>
@@ -0,0 +1,54 @@
+/*******************************************************************************
+ * Copyright (c) 2007-2008 Bioclipse Project
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *
+ *******************************************************************************/
+package testData;
+
+import java.io.File;
+import java.io.InputStream;
+
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.ChemObject;
+import org.openscience.cdk.Molecule;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.io.MDLReader;
+
+/**
+ * Instatiates some testdata from files in the testdata package
+ *
+ * @author jonalv
+ *
+ */
+public abstract class TestData {
+
+ private TestData() {
+ }
+
+ public static AtomContainer getCycloPropane() throws CDKException {
+ return readFromFile( "testData/cyclopropane.mol" );
+
+ }
+
+ public static AtomContainer getCycloOctan() throws CDKException {
+ return readFromFile( "testData/cyclooctan.mol" );
+ }
+
+ public static AtomContainer readFromFile(String path) throws CDKException {
+ InputStream ins = TestData.class.getClassLoader().getResourceAsStream(path);
+ MDLReader reader = new MDLReader(ins);
+ return (AtomContainer) reader.read( (ChemObject)new Molecule() );
+ }
+
+ public static String getTestSDFFilePath() {
+ return TestData.class
+ .getClassLoader()
+ .getResource("testData/sdfTestFile.sdf")
+ .getPath();
+ }
+}
@@ -0,0 +1,69 @@
+
+ Marvin 07140515482D
+
+ 31 33 0 0 0 0 999 V2000
+ 0.4239 -4.2648 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.4239 -3.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1384 -3.0273 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.1384 -2.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.4239 -1.7898 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ -0.2906 -2.2023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.0752 -1.9474 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.5601 -2.6148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.0752 -3.2823 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ -0.2906 -3.0273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.3301 -1.1628 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
+ -0.8452 -0.4953 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.3301 0.1721 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
+ -1.0752 0.9567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -0.2682 1.1283 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ -0.0133 1.9129 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0
+ -0.7979 2.1678 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.7713 1.6579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.2417 2.6975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.0486 2.8690 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0
+ 0.8771 3.6760 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.2202 2.0621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.8556 3.0406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.4076 2.4275 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.0207 2.9795 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.7945 1.8754 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.9597 1.8144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.1147 -0.0828 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
+ -2.7822 0.4021 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.1147 -0.9078 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
+ -2.7822 -1.3927 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 4 0 0 0 0
+ 3 4 4 0 0 0 0
+ 4 5 4 0 0 0 0
+ 5 6 4 0 0 0 0
+ 6 7 4 0 0 0 0
+ 7 8 4 0 0 0 0
+ 8 9 4 0 0 0 0
+ 9 10 4 0 0 0 0
+ 2 10 4 0 0 0 0
+ 6 10 4 0 0 0 0
+ 7 11 1 0 0 0 0
+ 11 12 1 0 0 0 0
+ 12 13 1 0 0 0 0
+ 13 14 1 0 0 0 0
+ 14 15 1 0 0 0 0
+ 15 16 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 16 18 2 0 0 0 0
+ 16 19 1 0 0 0 0
+ 19 20 1 0 0 0 0
+ 20 21 1 0 0 0 0
+ 20 22 2 0 0 0 0
+ 20 23 1 0 0 0 0
+ 23 24 1 0 0 0 0
+ 24 25 1 0 0 0 0
+ 24 26 1 0 0 0 0
+ 24 27 2 0 0 0 0
+ 13 28 1 0 0 0 0
+ 28 29 1 0 0 0 0
+ 28 30 1 0 0 0 0
+ 11 30 1 0 0 0 0
+ 30 31 1 0 0 0 0
+M END
@@ -0,0 +1,22 @@
+
+ CDK
+
+ 8 8 0 0 0 0 0 0 0 0999 V2000
+ 258.0000 1001.9637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 224.7403 1015.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 291.2597 1015.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 210.9637 1049.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 305.0363 1049.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 224.7403 1082.2596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 291.2597 1082.2596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 258.0000 1096.0363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 3 1 1 0 0 0 0
+ 2 4 1 0 0 0 0
+ 5 3 1 0 0 0 0
+ 4 6 1 0 0 0 0
+ 7 5 1 0 0 0 0
+ 6 8 1 0 0 0 0
+ 8 7 1 0 0 0 0
+M END
+$$$$
@@ -0,0 +1,23 @@
+cyclopropane.mol
+
+
+ 9 9 0 0 0 1 V2000
+ -0.0073 -0.5272 0.9655 C 0 0 0 0 0
+ -0.6776 -0.7930 -0.3498 C 0 0 0 0 0
+ 0.2103 0.4053 -0.1891 C 0 0 0 0 0
+ 0.8019 -1.1711 1.2970 H 0 0 0 0 0
+ -0.6000 -0.2021 1.8155 H 0 0 0 0 0
+ -1.7511 -0.6586 -0.4435 H 0 0 0 0 0
+ -0.3492 -1.6277 -0.9620 H 0 0 0 0 0
+ 1.1755 0.4303 -0.6860 H 0 0 0 0 0
+ -0.2264 1.3994 -0.1675 H 0 0 0 0 0
+ 1 2 1 6 0 0
+ 1 3 1 6 0 0
+ 1 4 1 0 0 0
+ 1 5 1 1 0 0
+ 2 3 1 0 0 0
+ 2 6 1 0 0 0
+ 2 7 1 6 0 0
+ 3 8 1 6 0 0
+ 3 9 1 0 0 0
+M END
@@ -0,0 +1,29 @@
+
+ MassFron052fd10709212D
+
+ 4 4 0 0 0 0 0 0 0 0 2 V2000
+ 1.8966 -3.2759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.8966 -4.0345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.2759 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.5172 -4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 2 4 1 0 0 0 0
+ 3 4 1 0 0 0 0
+M CHG 1 3 1
+M END
+$$$$
+
+ MassFron052poiiiiiiii10709212D
+
+ 4 3 0 0 0 0 0 0 0 0 2 V2000
+ 4.5172 2.7931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 4.5172 3.5517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.1724 3.9310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.1724 4.6897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 3 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+M CHG 1 2 1
+M END
+$$$$

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