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johnmayegonw
johnmay
authored and
egonw
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Seperate cdk-qsarmolecular from testdata, 4 files need duplicating to other modules as well.
1 parent 2ed0d09 commit f0e982b

39 files changed

+664
-64
lines changed

‎base/test-standard/src/test/java/org/openscience/cdk/graph/ConnectivityCheckerTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -198,7 +198,7 @@ public void testIsConnectedFromHINFile() throws Exception {
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*/
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@Test
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public void testIsConnectedFromSDFile() throws Exception {
201-
String filename = "data/mdl/mdeotest.sdf";
201+
String filename = "mdeotest.sdf";
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InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
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ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
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ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());

‎base/testdata/src/test/resources/data/mdl/mdeotest.sdf renamed to ‎base/test-standard/src/test/resources/org/openscience/cdk/graph/mdeotest.sdf

File renamed without changes.

‎descriptor/qsarmolecular/pom.xml

Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -153,13 +153,6 @@
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<version>${project.parent.version}</version>
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<scope>test</scope>
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</dependency>
156-
<dependency>
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<groupId>${project.groupId}</groupId>
158-
<artifactId>cdk-testdata</artifactId>
159-
<version>${project.parent.version}</version>
160-
<type>test-jar</type>
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<scope>test</scope>
162-
</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>cdk-diff</artifactId>

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/geometry/surface/NumericalSurfaceTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ public class NumericalSurfaceTest {
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public void testCranbinSurface() throws Exception {
4747
IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
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IChemFile chemFile;
49-
String path = "/data/pdb/1CRN.pdb";
49+
String path = "1CRN.pdb";
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try (InputStream in = getClass().getResourceAsStream(path);
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PDBReader pdbr = new PDBReader(in)) {
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chemFile = pdbr.read(bldr.newInstance(IChemFile.class));

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/graph/matrix/TopologicalMatrixTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ public class TopologicalMatrixTest extends CDKTestCase {
1818

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@Ignore // not actually asserting anything
2020
public void testTopologicalMatrix_IAtomContainer() throws Exception {
21-
String filename = "data/mdl/clorobenzene.mol";
21+
String filename = "data/mdl/chlorobenzene.mol";
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InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
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MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
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IAtomContainer container = (IAtomContainer) reader.read(new AtomContainer());

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/DescriptorNamesTest.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -55,8 +55,8 @@ public void checkUniqueMolecularDescriptorNames() throws Exception {
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List<IImplementationSpecification> specs = engine.getDescriptorSpecifications();
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// we work with a simple molecule with 3D coordinates
58-
String filename = "data/mdl/lobtest2.sdf";
59-
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
58+
String filename = "descriptors/molecular/lobtest2.sdf";
59+
InputStream ins = this.getClass().getResourceAsStream(filename);
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ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
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ChemFile content = (ChemFile) reader.read(new ChemFile());
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List cList = ChemFileManipulator.getAllAtomContainers(content);

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorChargeTest.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,8 +27,8 @@ public void setUp() throws Exception {
2727

2828
@Test
2929
public void test1() throws Exception {
30-
String filename = "data/mdl/clorobenzene.mol";
31-
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
30+
String filename = "chlorobenzene.mol";
31+
InputStream ins = this.getClass().getResourceAsStream(filename);
3232
MDLV2000Reader reader = new MDLV2000Reader(ins);
3333
IAtomContainer container = reader.read(new AtomContainer());
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DescriptorValue count = descriptor.calculate(container);

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,8 +45,8 @@ public void setUp() throws Exception {
4545

4646
@Test
4747
public void test1() throws Exception {
48-
String filename = "data/mdl/clorobenzene.mol";
49-
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
48+
String filename = "chlorobenzene.mol";
49+
InputStream ins = this.getClass().getResourceAsStream(filename);
5050
MDLV2000Reader reader = new MDLV2000Reader(ins);
5151
IAtomContainer container = reader.read(new AtomContainer());
5252
DescriptorValue count = new AutocorrelationDescriptorMass().calculate(container);

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizabilityTest.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@ public void setUp() throws Exception {
2525
}
2626

2727
public void ignoreCalculate_IAtomContainer() throws Exception {
28-
String filename = "data/mdl/clorobenzene.mol";
28+
String filename = "data/mdl/chlorobenzene.mol";
2929
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
3030
MDLV2000Reader reader = new MDLV2000Reader(ins);
3131
IAtomContainer container = reader.read(new AtomContainer());

‎descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptorTest.java

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -56,8 +56,8 @@ public void setUp() throws Exception {
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5757
@Test
5858
public void testBCUT() throws Exception {
59-
String filename = "data/hin/gravindex.hin";
60-
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
59+
String filename = "gravindex.hin";
60+
InputStream ins = this.getClass().getResourceAsStream(filename);
6161
ISimpleChemObjectReader reader = new HINReader(ins);
6262
ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
6363
List cList = ChemFileManipulator.getAllAtomContainers(content);
@@ -105,8 +105,8 @@ public void testBCUT() throws Exception {
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106106
@Test
107107
public void testExtraEigenvalues() throws Exception {
108-
String filename = "data/hin/gravindex.hin";
109-
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
108+
String filename = "gravindex.hin";
109+
InputStream ins = this.getClass().getResourceAsStream(filename);
110110
ISimpleChemObjectReader reader = new HINReader(ins);
111111
ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
112112
List cList = ChemFileManipulator.getAllAtomContainers(content);

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