Release 2.6.1

Merge branch '2.6.1'
bioclipse · Sep 30, 2013 · 2202e0e · 2202e0e
2 parents 4a32519 + 296bfe3
commit 2202e0e
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diff --git a/features/net.bioclipse.cdk_feature/feature.xml b/features/net.bioclipse.cdk_feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="net.bioclipse.cdk_feature"
       label="Bioclipse CDK Feature"
-      version="2.6.0.vqualifier"
+      version="2.6.1.qualifier"
       provider-name="The Bioclipse Team"
       plugin="net.bioclipse.cdk.debug">
 
@@ -22,11 +22,6 @@ This feature and the accompanying materials are made available under the terms o
 The Eclipse Public License accompanies this distribution, and is available at http://www.eclipse.org/legal/epl-v10.html
    </license>
 
-   <url>
-      <update label="Bioclipse Update Site" url="http://update2.bioclipse.net"/>
-      <discovery label="The CDK Homepage" url="http://cdk.sf.net"/>
-   </url>
-
    <requires>
       <import feature="net.bioclipse.chemoinformatics_feature"/>
    </requires>

diff --git a/features/net.bioclipse.cheminformatics.test_feature/feature.xml b/features/net.bioclipse.cheminformatics.test_feature/feature.xml
@@ -22,11 +22,6 @@ This feature and the accompanying materials are made available under the terms o
 The Eclipse Public License accompanies this distribution, and is available at http://www.eclipse.org/legal/epl-v10.html
    </license>
 
-   <url>
-      <update label="Bioclipse Update Site" url="http://update2.bioclipse.net"/>
-      <discovery label="The CDK Homepage" url="http://cdk.sf.net"/>
-   </url>
-
    <includes
          id="net.bioclipse.platform_feature"
          version="0.0.0"/>
@@ -123,4 +118,11 @@ The Eclipse Public License accompanies this distribution, and is available at ht
          version="0.0.0"
          unpack="false"/>
 
+   <plugin
+         id="net.bioclipse.opsin.test"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
 </feature>
diff --git a/features/net.bioclipse.chemoinformatics_feature/feature.xml b/features/net.bioclipse.chemoinformatics_feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="net.bioclipse.chemoinformatics_feature"
       label="Bioclipse Chemoinformatics"
-      version="2.6.0.vqualifier"
+      version="2.6.1.qualifier"
       provider-name="The Bioclipse Team"
       plugin="net.bioclipse.chemoinformatics">
 
@@ -22,10 +22,6 @@ This feature and the accompanying materials are made available under the terms o
 The Eclipse Public License accompanies this distribution, and is available at http://www.eclipse.org/legal/epl-v10.html
    </license>
 
-   <url>
-      <update label="Bioclipse2 update site" url="http://update2.bioclipse.net"/>
-   </url>
-
    <requires>
       <import plugin="org.openscience.cdk.io"/>
       <import plugin="org.openscience.cdk.core"/>

diff --git a/net.bioclipse.cheminformatics_releng/buckminster.cspec b/net.bioclipse.cheminformatics_releng/buckminster.cspec
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cspec xmlns="http://www.eclipse.org/buckminster/CSpec-1.0" name="net.bioclipse.cheminformatics_releng" componentType="buckminster" version="2.6.1">
+    <dependencies>
+        <dependency name="net.bioclipse.chemoinformatics_site" componentType="eclipse.feature" versionDesignator="0.0.1"/>
+        <dependency name="com.springsource.javax.mail" componentType="osgi.bundle"/>
+        <dependency name="org.slf4j.api" componentType="osgi.bundle"/>
+        <dependency name="javax.wsdl" componentType="osgi.bundle"/>
+        <dependency name="jcl.over.slf4j" componentType="osgi.bundle"/>
+        <dependency name="net.bioclipse.core_feature" componentType="eclipse.feature"/>
+        <!--
+        <dependency name="log4j.over.slf4j" componentType="osgi.bundle"/>
+        -->
+    </dependencies>
+    <actions>
+      <public name="site.mirror.p2" actor="p2SiteMirror">
+        <prerequisites>
+          <attribute name="site.p2" alias="site"/>
+        </prerequisites>
+        <products base="${bioclipse.mirror}/${bioclipse.mirror.name}" upToDatePolicy="ACTOR" />
+      </public>
+    </actions>
+    <groups>
+        <public name="site.p2">
+            <attribute name="site.p2" component="net.bioclipse.chemoinformatics_site"/>
+        </public>
+    </groups>
+</cspec>
diff --git a/net.bioclipse.chemspider.test/META-INF/MANIFEST.MF b/net.bioclipse.chemspider.test/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Chemspider Test
 Bundle-SymbolicName: net.bioclipse.chemspider.test
-Bundle-Version: 0.1.1
+Bundle-Version: 2.6.1.qualifier
 Bundle-Vendor: bioclipse.net
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,

diff --git a/plugins/net.bioclipse.cdk.business.test/META-INF/MANIFEST.MF b/plugins/net.bioclipse.cdk.business.test/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: CDK Business Test Plug-in
 Bundle-SymbolicName: net.bioclipse.cdk.business.test
-Bundle-Version: 2.6.0.vqualifier
+Bundle-Version: 2.6.1.qualifier
 Bundle-Activator: net.bioclipse.cdk.business.test.Activator
 Bundle-Vendor: The Bioclipse Team
 Require-Bundle: org.eclipse.ui,

diff --git a/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java b/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java
@@ -24,6 +24,8 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
 import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URI;
@@ -550,13 +552,16 @@ public void testCreateSMILES() throws BioclipseException,
         assertTrue(smiles.contains("[Si]"));
     }
 
-    @Test 
-    public void testBug3394() throws BioclipseException {
-    	try {
-    	cdk.fromSMILES("OCC1OC(O)C(O)C(Op2(OC3C(O)C(O)OC(CO)C3O)np(OC4C(O)C(O)OC(CO)C4O)(OC5C(O)C(O)OC(CO)C5O)np(OC6C(O)C(O)OC(CO)C6O)(OC7C(O)C(O)OC(CO)C7O)n2)C1O");
-    	} catch (RuntimeException e) {
-    		Assert.fail("Failed with exception");
-    	}
+    @Test
+    public void testBug3394() throws BioclipseException, RuntimeException {
+
+        try {
+            cdk.fromSMILES("OCC1OC(O)C(O)C(Op2(OC3C(O)C(O)OC(CO)C3O)np(OC4C(O)C(O)OC(CO)C4O)(OC5C(O)C(O)OC(CO)C5O)np(OC6C(O)C(O)OC(CO)C6O)(OC7C(O)C(O)OC(CO)C7O)n2)C1O");
+        } catch ( RuntimeException e ) {
+            StringWriter sw = new StringWriter();
+            e.printStackTrace( new PrintWriter( sw ) );
+            fail( sw.toString() );
+        }
     }
     @Test
     public void testCreateMoleculeFromSMILES() throws BioclipseException {
@@ -1421,8 +1426,12 @@ public void testAppendToSDF() throws Exception {
 
             ICDKMolecule ethane  = cdk.fromSMILES("CC");
             String path = "/testAppendToSDF/testSaveSDF" + propane.hashCode() + ".mol";
+            IFile file = project.getFile( path );
             cdk.saveSDFile( path, new ArrayList() {{add(propane);}} );
-
+            int i = 100;
+            while ( i-- > 0 && !file.exists() ) {
+                Thread.sleep( 50 );
+            }
             assertEquals(1, cdk.loadMolecules(path).size());
 
             cdk.appendToSDF( path, ethane );

diff --git a/plugins/net.bioclipse.cdk.business/META-INF/MANIFEST.MF b/plugins/net.bioclipse.cdk.business/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: CDK Business
 Bundle-SymbolicName: net.bioclipse.cdk.business;singleton:=true
-Bundle-Version: 2.6.0.vqualifier
+Bundle-Version: 2.6.1.qualifier
 Bundle-Activator: net.bioclipse.cdk.business.Activator
 Bundle-Vendor: The Bioclipse Team
 Require-Bundle: org.openscience.cdk.io,
@@ -41,8 +41,10 @@ Require-Bundle: org.openscience.cdk.io,
  net.bioclipse.inchi,
  net.bioclipse.ui.business,
  net.sf.cglib,
- org.openscience.cdk.silent;bundle-version="1.4.10",
- org.openscience.cdk.tautomer
+ org.openscience.cdk.silent,
+ org.openscience.cdk.tautomer,
+ org.openscience.cdk.renderbasic,
+ org.openscience.cdk.renderawt
 Bundle-ActivationPolicy: lazy
 Export-Package: net.bioclipse.cdk.business,
  net.bioclipse.cdk.domain,

diff --git a/plugins/net.bioclipse.cdk.business/plugin.xml b/plugins/net.bioclipse.cdk.business/plugin.xml
@@ -34,6 +34,20 @@
                type="org.eclipse.jface.resource.ImageDescriptor">
          </adapter>
       </factory>
+      <factory
+            adaptableType="net.bioclipse.core.domain.SMILESMolecule"
+            class="net.bioclipse.cdk.domain.SMILESAdapterFactory">
+         <adapter
+               type="net.bioclipse.cdk.domain.ICDKMolecule">
+         </adapter>
+      </factory>
+      <factory
+            adaptableType="net.bioclipse.core.domain.CMLMolecule"
+            class="net.bioclipse.cdk.domain.CMLAdapterFactory">
+         <adapter
+               type="net.bioclipse.cdk.domain.ICDKMolecule">
+         </adapter>
+      </factory>
    </extension>
    <extension
          point="org.eclipse.ui.preferencePages">

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKInitializer.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKInitializer.java
@@ -15,7 +15,7 @@
 import org.openscience.cdk.config.AtomTypeFactory;
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 /**
@@ -30,7 +30,7 @@ public void run() {
 		// set up IsotopeFactories
 		try {
 			IsotopeFactory.getInstance(
-				NoNotificationChemObjectBuilder.getInstance()
+				SilentChemObjectBuilder.getInstance()
 			);
 		} catch (IOException e) {
 			// do not care about the exception right now
@@ -49,7 +49,7 @@ public void run() {
 		// Load the CDK atom type lists
 		AtomTypeFactory.getInstance(
 			"org/openscience/cdk/dict/data/cdk-atom-types.owl",
-			NoNotificationChemObjectBuilder.getInstance()
+			SilentChemObjectBuilder.getInstance()
 		);
 		AtomTypeFactory.getInstance(
 			"org/openscience/cdk/dict/data/cdk-atom-types.owl",