Eliminate testdata from cdk-builder3d moving all resources to the mod…

…ule (and package) where they are used. We need to duplicate one resource also used in cdk-io test.
cdk · Dec 29, 2021 · c2066cc · c2066cc
1 parent 96566b9
commit c2066cc
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Showing 11 changed files with 114 additions and 23 deletions.
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -337,9 +337,9 @@ public void testPolycarpol() throws Exception {
 
     @Test
     public void testReserpine() throws Exception {
-        String filename = "data/mdl/reserpine.mol";
+        String filename = "reserpine.mol";
         logger.info("Testing: " + filename);
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = reader.read(new ChemFile());
         reader.close();

diff --git a/...src/test/resources/data/mdl/reserpine.mol → ...rces/org/openscience/cdk/io/reserpine.mol b/...src/test/resources/data/mdl/reserpine.mol → ...rces/org/openscience/cdk/io/reserpine.mol
diff --git a/tool/builder3d/pom.xml b/tool/builder3d/pom.xml
@@ -81,13 +81,6 @@
             <type>test-jar</type>
             <scope>test</scope>            
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-testdata</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-builder3dtools</artifactId>

diff --git a/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java b/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java
@@ -146,8 +146,8 @@ public void testAllHeavyAtomsPlaced_IAtomContainer() {
 
     @Test
     public void testFindHeavyAtomsInChain_IAtomContainer_IAtomContainer() throws Exception {
-        String filename = "data/mdl/allmol232.mol";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "allmol232.mol";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         // TODO: shk3-cleanuptests: best to use the STRICT IO mode here
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());

diff --git a/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java b/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java
@@ -212,8 +212,8 @@ public void testModelBuilder3D_232() throws Exception {
         Assume.assumeTrue(runSlowTests());
 
         ModelBuilder3D mb3d = ModelBuilder3D.getInstance(DefaultChemObjectBuilder.getInstance());
-        String filename = "data/mdl/allmol232.mol";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "allmol232.mol";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
         reader.close();
@@ -239,8 +239,8 @@ public void testModelBuilder3D_231() throws Exception {
         Assume.assumeTrue(runSlowTests());
 
         ModelBuilder3D mb3d = ModelBuilder3D.getInstance(DefaultChemObjectBuilder.getInstance());
-        String filename = "data/mdl/allmol231.mol";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "allmol231.mol";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
         reader.close();
@@ -367,8 +367,8 @@ public void testModel3D_bug_1610997() throws Exception {
     @Category(SlowTest.class)
     public void testModelBuilder3D_bug_1241421() throws Exception {
         ModelBuilder3D mb3d = ModelBuilder3D.getInstance(DefaultChemObjectBuilder.getInstance());
-        String filename = "data/mdl/bug1241421.mol";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "bug1241421.mol";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
         reader.close();
@@ -382,8 +382,8 @@ public void testModelBuilder3D_bug_1241421() throws Exception {
     @Category(SlowTest.class)
     public void testModelBuilder3D_reserpine() throws Exception {
         ModelBuilder3D mb3d = ModelBuilder3D.getInstance(DefaultChemObjectBuilder.getInstance());
-        String filename = "data/mdl/reserpine.mol";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "reserpine.mol";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
         reader.close();

diff --git a/...builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java b/...builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java
@@ -75,8 +75,8 @@ public void testFingerprints() throws Exception {
             parseBitSet("{3, 18, 26, 32, 33, 43, 140, 155, 188, 189, 226, 238, 262, 267, 287, 315, 319, 326, 375, 450, 577, 629, 644, 690, 719, 732, 745, 746, 751, 775, 847, 850, 881, 959, 971, 995, 1015, 1019}"),
             parseBitSet("{3, 18, 29, 33, 90, 105, 125, 272, 280, 301, 433, 521, 590, 618, 651, 672, 696, 698, 745, 760, 829, 844, 876, 890, 899, 924, 1013}")};
 
-        String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "fingerprints_from_modelbuilder3d.sdf";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         List<IBitFingerprint> data = new TemplateExtractor().makeFingerprintsFromSdf(true, false,
                 new HashMap<String, Integer>(), new BufferedReader(new InputStreamReader(ins)), 10);
         QueryChemObject obj = new QueryChemObject(DefaultChemObjectBuilder.getInstance());
@@ -101,8 +101,8 @@ public void testAnonFingerprints() throws Exception {
             parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}"),
             parseBitSet("{148, 206, 392, 542, 637, 742, 752, 830}")};
 
-        String filename = "data/mdl/fingerprints_from_modelbuilder3d.sdf";
-        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+        String filename = "fingerprints_from_modelbuilder3d.sdf";
+        InputStream ins = this.getClass().getResourceAsStream(filename);
         List<IBitFingerprint> data = new TemplateExtractor().makeFingerprintsFromSdf(true, true,
                                                                                      new HashMap<String, Integer>(), new BufferedReader(new InputStreamReader(ins)), 10);
         QueryChemObject obj = new QueryChemObject(DefaultChemObjectBuilder.getInstance());

diff --git a/...src/test/resources/data/mdl/allmol231.mol → ...ence/cdk/modeling/builder3d/allmol231.mol b/...src/test/resources/data/mdl/allmol231.mol → ...ence/cdk/modeling/builder3d/allmol231.mol
diff --git a/...src/test/resources/data/mdl/allmol232.mol → ...ence/cdk/modeling/builder3d/allmol232.mol b/...src/test/resources/data/mdl/allmol232.mol → ...ence/cdk/modeling/builder3d/allmol232.mol
diff --git a/...rc/test/resources/data/mdl/bug1241421.mol → ...nce/cdk/modeling/builder3d/bug1241421.mol b/...rc/test/resources/data/mdl/bug1241421.mol → ...nce/cdk/modeling/builder3d/bug1241421.mol
diff --git a/.../mdl/fingerprints_from_modelbuilder3d.sdf → ...er3d/fingerprints_from_modelbuilder3d.sdf b/.../mdl/fingerprints_from_modelbuilder3d.sdf → ...er3d/fingerprints_from_modelbuilder3d.sdf
diff --git a/tool/builder3d/src/test/resources/org/openscience/cdk/modeling/builder3d/reserpine.mol b/tool/builder3d/src/test/resources/org/openscience/cdk/modeling/builder3d/reserpine.mol
@@ -0,0 +1,98 @@
+0-reserpin.mol
+  ChemDraw09189816272D
+
+ 44 49  0  0  0  0  0  0  0  0  1 V2000
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+M  END