From: Patric Plitzner <p.plitzner@bgbm.org>
Date: Wed, 15 Jul 2015 08:47:19 +0000 (+0000)
Subject:  - fixed dependencies
X-Git-Tag: 3.8.0^2~59^2~20
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/98432a1a606a8ca17137259cf79e9827f47cd20f?hp=bcdf4797cd69fdf7c94745155886b3d79a994f90

 - fixed dependencies
---

diff --git a/eu.etaxonomy.taxeditor.molecular/.classpath b/eu.etaxonomy.taxeditor.molecular/.classpath
index c5dd8f359..fa2d0d0b9 100644
--- a/eu.etaxonomy.taxeditor.molecular/.classpath
+++ b/eu.etaxonomy.taxeditor.molecular/.classpath
@@ -1,20 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+	<classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/core-1.9.2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry including="**/*.java" kind="src" path="src"/>
-	<classpathentry kind="lib" path="commons-logging-1.1.1.jar" sourcepath="/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-sources.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="jar:file:/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-javadoc.jar!/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry exported="true" kind="lib" path="bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="bioinfweb-commons-core-2-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="libralign-core-0-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="libralign-swt-0-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="tic-core-2-SNAPSHOT.jar"/>
-	<classpathentry exported="true" kind="lib" path="tic-swt-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/libralign-core-0-SNAPSHOT.jar"/>
+	<classpathentry exported="true" kind="lib" path="lib/libralign-swt-0-SNAPSHOT.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/eu.etaxonomy.taxeditor.molecular/.project b/eu.etaxonomy.taxeditor.molecular/.project
index c19e3549e..3826881f3 100644
--- a/eu.etaxonomy.taxeditor.molecular/.project
+++ b/eu.etaxonomy.taxeditor.molecular/.project
@@ -25,51 +25,4 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.pde.PluginNature</nature>
 	</natures>
-	<linkedResources>
-		<link>
-			<name>bioinfweb-commons-bio-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-bio/2-SNAPSHOT/bioinfweb-commons-bio-2-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>bioinfweb-commons-core-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-core/2-SNAPSHOT/bioinfweb-commons-core-2-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>bioinfweb-commons-swing-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-swing/2-SNAPSHOT/bioinfweb-commons-swing-2-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>bioinfweb-commons-swt-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-swt/2-SNAPSHOT/bioinfweb-commons-swt-2-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>commons-logging-1.1.1.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar</location>
-		</link>
-		<link>
-			<name>libralign-core-0-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/libralign/libralign-core/0-SNAPSHOT/libralign-core-0-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>libralign-swt-0-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/libralign/libralign-swt/0-SNAPSHOT/libralign-swt-0-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>tic-core-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/tic/tic-core/2-SNAPSHOT/tic-core-2-SNAPSHOT.jar</location>
-		</link>
-		<link>
-			<name>tic-swt-2-SNAPSHOT.jar</name>
-			<type>1</type>
-			<location>/home/pplitzner/.m2/repository/info/bioinfweb/tic/tic-swt/2-SNAPSHOT/tic-swt-2-SNAPSHOT.jar</location>
-		</link>
-	</linkedResources>
 </projectDescription>
diff --git a/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
index 5814c8540..c7331abc7 100644
--- a/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
@@ -7,20 +7,21 @@ Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  org.eclipse.core.expressions,
- eu.etaxonomy.taxeditor.store,
  eu.etaxonomy.taxeditor.cdmlib,
- eu.etaxonomy.taxeditor.editor
+ eu.etaxonomy.taxeditor.store,
+ eu.etaxonomy.taxeditor.editor,
+ eu.etaxonomy.taxeditor.bulkeditor
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Bundle-ActivationPolicy: lazy
 Bundle-Vendor: EDIT
-Bundle-ClassPath: .,
- commons-logging-1.1.1.jar,
- bioinfweb-commons-bio-2-SNAPSHOT.jar,
- bioinfweb-commons-core-2-SNAPSHOT.jar,
- bioinfweb-commons-swing-2-SNAPSHOT.jar,
- bioinfweb-commons-swt-2-SNAPSHOT.jar,
- libralign-core-0-SNAPSHOT.jar,
- libralign-swt-0-SNAPSHOT.jar,
- tic-core-2-SNAPSHOT.jar,
- tic-swt-2-SNAPSHOT.jar
-Import-Package: eu.etaxonomy.cdm.model.molecular
+Bundle-ClassPath: lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
+ lib/libralign-core-0-SNAPSHOT.jar,
+ lib/libralign-swt-0-SNAPSHOT.jar,
+ lib/libralign-biojava1-0-SNAPSHOT.jar,
+ lib/core-1.9.2-SNAPSHOT.jar,
+ lib/sequencing-1.9.2-SNAPSHOT.jar,
+ lib/tic-core-2-SNAPSHOT.jar,
+ lib/tic-swt-2-SNAPSHOT.jar
diff --git a/eu.etaxonomy.taxeditor.molecular/build.properties b/eu.etaxonomy.taxeditor.molecular/build.properties
index 18f963739..2884574bb 100644
--- a/eu.etaxonomy.taxeditor.molecular/build.properties
+++ b/eu.etaxonomy.taxeditor.molecular/build.properties
@@ -1,12 +1,19 @@
-source.. = src/
 output.. = bin/
 bin.includes = META-INF/,\
                plugin.xml,\
-               lib/libralign-core-0-20150713.112743-1.jar,\
-               lib/libralign-swt-0-20150713.113034-1.jar,\
                icons/,\
-               OSGI-INF/
-source.. = src/
+               OSGI-INF/,\
+               lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,\
+               lib/bioinfweb-commons-core-2-SNAPSHOT.jar,\
+               lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,\
+               lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,\
+               lib/libralign-core-0-SNAPSHOT.jar,\
+               lib/libralign-swt-0-SNAPSHOT.jar,\
+               lib/libralign-biojava1-0-SNAPSHOT.jar,\
+               lib/core-1.9.2-SNAPSHOT.jar,\
+               lib/sequencing-1.9.2-SNAPSHOT.jar,\
+               lib/tic-core-2-SNAPSHOT.jar,\
+               lib/tic-swt-2-SNAPSHOT.jar
 src.includes = src/,\
                plugin.xml,\
                icons/,\
diff --git a/eu.etaxonomy.taxeditor.molecular/pom.xml b/eu.etaxonomy.taxeditor.molecular/pom.xml
index a30133305..762eed310 100644
--- a/eu.etaxonomy.taxeditor.molecular/pom.xml
+++ b/eu.etaxonomy.taxeditor.molecular/pom.xml
@@ -14,50 +14,113 @@
   <name>Molecular Bundle</name>
   <description>Provides editors, views and operations for handling molecular data and alignments</description>
 
-  <!-- <build> -->
-  <!-- <plugins> -->
-  <!-- <plugin> -->
-  <!-- <groupId>org.apache.maven.plugins</groupId> -->
-  <!-- <artifactId>maven-dependency-plugin</artifactId> -->
-  <!-- <version>2.4</version> -->
-  <!-- <executions> -->
-  <!-- <execution> -->
-  <!-- <id>copy-dependencies</id> -->
-  <!-- <phase>validate</phase> -->
-  <!-- <goals> -->
-  <!-- <goal>copy-dependencies</goal> -->
-  <!-- </goals> -->
-  <!-- <configuration> -->
-  <!-- <includeGroupIds>info.bioinfweb.libralign, info.bioinfweb.commons.java</includeGroupIds> -->
-  <!-- <includeArtifactIds>libralign-swt, libralign-core</includeArtifactIds> -->
-  <!-- <outputDirectory>lib</outputDirectory> -->
-  <!-- <overWriteReleases>true</overWriteReleases> -->
-  <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
-  <!-- <excludeTransitive>true</excludeTransitive> -->
-  <!-- </configuration> -->
-  <!-- </execution> -->
-  <!-- <execution> -->
-  <!-- <id>copy-dependencies-sources</id> -->
-  <!-- <phase>validate</phase> -->
-  <!-- <goals> -->
-  <!-- <goal>copy-dependencies</goal> -->
-  <!-- </goals> -->
-  <!-- <configuration> -->
-  <!-- <classifier>sources</classifier> -->
-  <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
-  <!-- <outputDirectory>lib</outputDirectory> -->
-  <!-- <overWriteReleases>true</overWriteReleases> -->
-  <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
-  <!-- <excludeTransitive>true</excludeTransitive> -->
-  <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
-  <!-- </configuration> -->
-  <!-- </execution> -->
-  <!-- </executions> -->
-  <!-- </plugin> -->
-  <!-- </plugins> -->
-  <!-- </build> -->
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>2.4</version>
+        <executions>
+          <execution>
+            <id>copy-dependencies</id>
+            <phase>validate</phase>
+            <goals>
+              <goal>copy-dependencies</goal>
+            </goals>
+            <configuration>
+              <includeArtifactIds>libralign-swt, libralign-core,
+                bioinfweb-commons-swt, bioinfweb-commons-core,
+                bioinfweb-commons-bio, bioinfweb-commons-swing,
+                tic-core, libralign-biojava1, core, sequencing, tic-swt</includeArtifactIds>
+              <outputDirectory>lib</outputDirectory>
+              <overWriteReleases>true</overWriteReleases>
+              <overWriteSnapshots>true</overWriteSnapshots>
+              <excludeTransitive>true</excludeTransitive>
+            </configuration>
+          </execution>
+          <!-- <execution> -->
+          <!-- <id>copy-dependencies-sources</id> -->
+          <!-- <phase>validate</phase> -->
+          <!-- <goals> -->
+          <!-- <goal>copy-dependencies</goal> -->
+          <!-- </goals> -->
+          <!-- <configuration> -->
+          <!-- <classifier>sources</classifier> -->
+          <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
+          <!-- <outputDirectory>lib</outputDirectory> -->
+          <!-- <overWriteReleases>true</overWriteReleases> -->
+          <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
+          <!-- <excludeTransitive>true</excludeTransitive> -->
+          <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
+          <!-- </configuration> -->
+          <!-- </execution> -->
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-antrun-plugin</artifactId>
+        <version>1.7</version>
+        <executions>
+          <execution>
+            <id>remove-existing-jars</id>
+            <phase>clean</phase>
+            <goals>
+              <goal>run</goal>
+            </goals>
+            <configuration>
+              <target>
+                <echo>Remove all jars</echo>
+                <delete>
+                  <fileset dir="./lib" includes="*" />
+                </delete>
+              </target>
+            </configuration>
+          </execution>
+          <execution>
+            <id>update-snapshot-jar-names</id>
+            <phase>validate</phase>
+            <goals>
+              <goal>run</goal>
+            </goals>
+            <configuration>
+              <target>
+                <echo>Update jars to SNAPSHOT when build with
+                  timestamp</echo>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^bioinfweb\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^libralign\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^tic\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^core\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
+                </move>
+                <move todir="./lib">
+                  <fileset dir="./lib" />
+                  <mapper type="regexp"
+                    from="(^sequencing\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
+                </move>
+              </target>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
 
   <dependencies>
+    <!-- LibrAling -->
     <dependency>
       <groupId>info.bioinfweb.libralign</groupId>
       <artifactId>libralign-core</artifactId>
@@ -73,7 +136,8 @@
       <artifactId>libralign-biojava1</artifactId>
       <version>0-SNAPSHOT</version>
     </dependency>
-<!--     <dependency>
+    <!-- commons -->
+    <dependency>
       <groupId>info.bioinfweb.commons.java</groupId>
       <artifactId>bioinfweb-commons-swt</artifactId>
       <version>2-SNAPSHOT</version>
@@ -93,11 +157,18 @@
       <artifactId>bioinfweb-commons-swing</artifactId>
       <version>2-SNAPSHOT</version>
     </dependency>
+    <!-- tic -->
     <dependency>
       <groupId>info.bioinfweb.tic</groupId>
       <artifactId>tic-core</artifactId>
       <version>2-SNAPSHOT</version>
     </dependency>
+    <dependency>
+      <groupId>info.bioinfweb.tic</groupId>
+      <artifactId>tic-swt</artifactId>
+      <version>2-SNAPSHOT</version>
+    </dependency>
+    <!-- biojava -->
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>core</artifactId>
@@ -107,7 +178,7 @@
       <groupId>org.biojava</groupId>
       <artifactId>sequencing</artifactId>
       <version>1.9.2</version>
-    </dependency> -->
+    </dependency>
   </dependencies>
 
   <repositories>