Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.

The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.

To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.

Also did some minor unrelated cleanup in build.xml

build.xml

@@ -28,6 +28,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="lib.dir" value="lib" />
     <property name="external.dir" value="external" />
     <property name="public.dir" value="public" />
     <property name="private.dir" value="private" />
@@ -44,11 +45,11 @@
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
     
     <!-- Contracts for Java -->
-    <!-- uncomment out to enable building contracts -->
+    <!-- To disable, run with -Duse.contracts=false -->
-    <property name="use.contracts" value="true" /> 
+    <property name="use.contracts" value="true" />
     <property name="java.contracts" value="${build.dir}/java/contracts" />
-    <property name="cofojaDir" value="settings/repository/com.google/"/>
+    <property name="contracts.version" value="1.0-20110609" />
-    <property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
+    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -69,7 +70,7 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
+    <property name="drmaa.jar" value="${env.SGE_ROOT}/${lib.dir}/drmaa.jar" />
 
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
@@ -103,7 +104,7 @@
     </patternset>
     
     <path id="external.dependencies">
-      <fileset dir="lib">
+      <fileset dir="${lib.dir}">
         <patternset refid="dependency.mask" />
       </fileset>
     </path>
@@ -128,14 +129,14 @@
         <!-- ivy properties -->
         <property name="ivy.install.version" value="2.2.0"/>
         <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/lib"/>
+        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
   
-      <mkdir dir="lib"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${ivy.jar.dir}"/>
-      <copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
+
       <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
            dest="${ivy.jar.dir}/${ivy.jar.file}"
            usetimestamp="true"/>
@@ -147,7 +148,7 @@
     </target>
 
     <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
+        <copy todir="${lib.dir}" file="${drmaa.jar}"/>
     </target>
 
     <target name="resolve" depends="init.resolve,init,init.gridengine"
@@ -229,6 +230,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.contracts">
+        <equals arg1="${use.contracts}" arg2="true" />
+      </condition>
+
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
       <mkdir dir="${java.classes}"/>
@@ -252,7 +257,7 @@
     <target name="init.scala.compile" depends="resolve"
             description="Initializes the scala ant tasks from scala-compiler.jar">
         <path id="scala.classpath">
-            <fileset dir="lib">
+            <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
             </fileset>
@@ -287,7 +292,7 @@
             depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" 
             description="compile the GATK source" />
 
-   <target name="gatk.contracts.public" depends="gatk.compile.source">
+   <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -299,7 +304,16 @@
         </javac>   
    </target>
 
-   <target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
+    <target name="check.contracts.private" depends="gatk.contracts.public">
+        <condition property="include.contracts.private">
+          <and>
+            <isset property="include.contracts" />
+            <isset property="include.private" />
+          </and>
+        </condition>
+    </target>
+
+   <target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -312,7 +326,7 @@
    </target>
 
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
-            description="create GATK contracts" if="use.contracts" />
+            description="create GATK contracts" if="include.contracts" />
     
     <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
 
@@ -452,7 +466,7 @@
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
         <copy todir="${dist.dir}">
-            <fileset dir="lib" includes="*.jar"/>
+            <fileset dir="${lib.dir}" includes="*.jar"/>
         </copy>
     </target>
 
@@ -663,7 +677,7 @@
                 <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
             <compilerarg value="-proc:none"/>
 <!-- 
@@ -687,7 +701,7 @@
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
         </scalac>
     </target>
@@ -727,9 +741,13 @@
                 <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
             </condition>
 
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
             <mkdir dir="${report}/@{testtype}"/>
             <echo message="Sting: Running @{testtype} test cases!"/>
-            <taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
             <testng outputDir="${report}/@{testtype}"
                     haltOnFailure="false" failureProperty="test.failure"
                     verbose="2"
@@ -740,9 +758,7 @@
                 <jvmarg value="-Djava.awt.headless=true" />
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <!-- needs to be if -->
+                <jvmarg line="${cofoja.jvm.args}"/>
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
@@ -820,7 +836,7 @@
 
     <!-- copy the compiled library -->
     <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
         </copy>
     </target>
@@ -828,7 +844,7 @@
     <!-- copy the precompiled library -->
     <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
         <echo message="Copying the Tribble Library..."/>
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
         </copy>
     </target>
@@ -921,8 +937,8 @@
       <pathconvert property="required.picard.jars" pathsep=":">
         <fileset dir="${basedir}">
 	     <include name="staging" />
-	     <include name="lib/picard-*.*.*.jar" />
+	     <include name="${lib.dir}/picard-*.*.*.jar" />
-	     <include name="lib/sam-*.jar" />
+	     <include name="${lib.dir}/sam-*.jar" />
 	   </fileset>
       </pathconvert>
       <echo message="required.picard.jars=${required.picard.jars}" />
@@ -944,7 +960,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -969,7 +985,7 @@
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
-        <delete dir="lib"/>
+        <delete dir="${lib.dir}"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>

ivy.xml

@@ -60,6 +60,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- Contracts for Java and dependencies -->
+    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
+    <dependency org="asm" name="asm-all" rev="3.3.1" />
+
     <!-- POI, for reading pipeline files -->
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />

settings/ivysettings.xml

@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="com.google.code.cofoja" resolver="projects" />
   </modules>
 </ivysettings>

settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
+</ivy-module>