Changeset 1103 for extensions/net.sf.basedb.genepattern

Timestamp:

May 29, 2009, 8:45:00 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #223: Add target in build.xml for downloading required GenePattern? jar files

Downloads some of required JAR files. There are probably some more, but which ones we need depends on the code we are writing.

Location:

extensions/net.sf.basedb.genepattern/trunk

Files:

• build.xml (modified) (3 diffs)
• lib/genepattern (added)
• lib/genepattern/readme.txt (added)

extensions/net.sf.basedb.genepattern/trunk/build.xml

@@ -24 +24 @@
   <property name="javac.encoding" value="UTF-8" />
   <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.12.0" />
+  <property name="genepattern.jars" value="http://genepattern.broad.mit.edu/gp/downloads" />
 
   <!-- set up classpath for compiling -->
@@ -112 +113 @@
     <available classname="net.sf.basedb.info.BioAssaySetInfo" 
       classpathref="classpath" property="base2webservice" />
+    <available classname="org.genepattern.client.GPClient"
+      classpathref="classpath" property="genepattern.lib" />
     <fail unless="base2core" message="Can't find BASE2Core.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     <fail unless="base2plugins" message="Can't find BASE2CorePlugins.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     <fail unless="base2web" message="Can't find BASE2Webclient.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     <fail unless="base2webservice" message="Can't find BASE2WSClient.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
-    <echo>Found BASE2Core.jar, BASE2CorePlugins.jar, BASE2Webclient.jar and BASE2WSClient.jar.</echo>
+    <fail unless="genepattern.lib" message="Can't find GenePattern.jar in ./lib/genepattern. Try 'ant download-lib' to download the missing file." />
+    <echo>Found all required BASE and GenePattern JAR files.</echo>
   </target>
   
   <target 
     name="download-lib"
-    description="Download BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar"
+    description="Download BASE and GenePattern JAR files"
     >
     <echo>
 -------------------------------------------------------   
 NOTE! You may specifiy a different download location by 
-creating the file './build.properties' and
-setting 'depend.jars' to the URL to download from.
+creating the file './build.properties' and setting
+'depend.jars' and 'genepattern.jars' to the URLs to 
+download from.
 -------------------------------------------------------
     </echo>
@@ -134 +139 @@
     <download-lib file="BASE2Webclient.jar" />
     <download-lib file="BASE2WSClient.jar" />
+    <!-- We only need some files from the GenePattern.zip file -->
+    <download-lib file="GenePattern.zip" todir="${build}" from="${genepattern.jars}" />
+    <unzip dest="lib/genepattern" src="${build}/GenePattern.zip">
+      <patternset>
+        <include name="GenePattern.jar" />
+        <include name="lib/gp-modules.jar" />
+      </patternset>
+      <mapper type="flatten"/>
+    </unzip>
   </target>
   
   <macrodef name="download-lib" description="Download BASE core JAR files">
     <attribute name="file" />
+    <attribute name="todir" default="lib/compile"/>
+    <attribute name="from" default="${depend.jars}" />
     <sequential>
       <get 
-        dest="lib/compile/@{file}" 
-        src="${depend.jars}/@{file}" 
+        dest="@{todir}/@{file}" 
+        src="@{from}/@{file}" 
         usetimestamp="true" 
         verbose="true"