Remove test-jar dependencies on cdk-qsar. We can relocate the required interfaces to cdk-interfaces and add an optional setDescriptor method that takes a builder. We can then move it to cdk-test.

johnmay · egonw · commit be2f78db7d84 · 2021-12-24T09:03:56.000+01:00
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/IImplementationSpecification.java b/base/interfaces/src/main/java/org/openscience/cdk/IImplementationSpecification.java
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/qsar/IDescriptor.java b/base/interfaces/src/main/java/org/openscience/cdk/qsar/IDescriptor.java
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/qsar/result/IDescriptorResult.java b/base/interfaces/src/main/java/org/openscience/cdk/qsar/result/IDescriptorResult.java
diff --git a/base/test/src/test/java/org/openscience/cdk/qsar/descriptors/DescriptorTest.java b/base/test/src/test/java/org/openscience/cdk/qsar/descriptors/DescriptorTest.java
@@ -23,8 +23,8 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
-import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.IImplementationSpecification;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.qsar.IDescriptor;
 
 /**
@@ -42,7 +42,15 @@ public void setDescriptor(Class<? extends T> descriptorClass) throws Exception {
         if (descriptor == null) {
             Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor();
             this.descriptor = defaultConstructor.newInstance();
-            this.descriptor.initialise(DefaultChemObjectBuilder.getInstance());
+        }
+    }
+
+    public void setDescriptor(Class<? extends T> descriptorClass,
+                              IChemObjectBuilder builder) throws Exception {
+        if (descriptor == null) {
+            Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor();
+            this.descriptor = defaultConstructor.newInstance();
+            this.descriptor.initialise(builder);
         }
     }
 
diff --git a/descriptor/qsaratomic/pom.xml b/descriptor/qsaratomic/pom.xml
@@ -93,13 +93,6 @@
             <type>test-jar</type>
             <scope>test</scope>            
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-qsar</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-diff</artifactId>
diff --git a/descriptor/qsarbond/pom.xml b/descriptor/qsarbond/pom.xml
@@ -73,13 +73,6 @@
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-qsar</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/descriptor/qsarmolecular/pom.xml b/descriptor/qsarmolecular/pom.xml
@@ -141,13 +141,6 @@
             <type>test-jar</type>
             <scope>test</scope>            
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-qsar</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>            
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-qsaratomic</artifactId>
diff --git a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java
@@ -24,6 +24,7 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -39,7 +40,8 @@ public class AcidicGroupCountDescriptorTest extends MolecularDescriptorTest {
 
     @Before
     public void setUp() throws Exception {
-        setDescriptor(AcidicGroupCountDescriptor.class);
+        setDescriptor(AcidicGroupCountDescriptor.class,
+                      DefaultChemObjectBuilder.getInstance());
     }
 
     @Test
diff --git a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java
@@ -22,6 +22,7 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -38,7 +39,8 @@ public class BasicGroupCountDescriptorTest extends MolecularDescriptorTest {
 
     @Before
     public void setUp() throws Exception {
-        setDescriptor(BasicGroupCountDescriptor.class);
+        setDescriptor(BasicGroupCountDescriptor.class,
+                      DefaultChemObjectBuilder.getInstance());
     }
 
     @Test
diff --git a/descriptor/qsarprotein/pom.xml b/descriptor/qsarprotein/pom.xml
@@ -69,13 +69,6 @@
             <type>test-jar</type>
             <scope>test</scope>            
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-qsar</artifactId>
-            <version>${project.parent.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-testdata</artifactId>
@@ -88,7 +81,7 @@
             <artifactId>cdk-qsarmolecular</artifactId>
             <version>${project.parent.version}</version>
             <type>test-jar</type>
-            <scope>test</scope>            
+            <scope>test</scope>
         </dependency>
     </dependencies>
 
