X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=4931cfb5ea521224b6c048e284f47e607b1d5be8;hb=refs%2Fheads%2Ffeature%2FJAL-2909bamfiles;hp=2b81b212a735ff430f983b53cd5a423623a71e87;hpb=2360f48ca9907aaf2cbd6ab9a868705156610c70;p=jalview.git

diff --git a/build.xml b/build.xml
index 2b81b21..4931cfb 100755
--- a/build.xml
+++ b/build.xml
@@ -27,7 +27,10 @@
     <echo message="build - compiles all necessary files for Application" />
     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
-    <echo message="              this needs a keystore and key. See docs/building.html for more information." />
+    <echo message="              this needs a keystore and key."/>
+    <echo message="              Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
+    <echo message="              See docs/building.html for more information." />
     <echo message="compileApplet - compiles all necessary files for Applet" />
     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
@@ -82,7 +85,16 @@
     <property name="jalview.key" value="jalview" />
     <!-- Key Password -->
     <property name="jalview.key.pass" value="alignmentisfun" />
-
+    <!-- time stamp server URL -->
+    <property name="jalview.tsaurl" value="" />
+    <!-- locally valid proxy for signing with external time server -->
+    <property name="proxyPort" value="80"/>
+    <property name="proxyHost" value="sqid"/>
+    <!-- key sign/digest algorithms -->
+    <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+    <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
+
+    <!-- default TestNG groups to run -->
     <property name="testng-groups" value="Functional" />
 
     <!-- Don't change anything below here unless you know what you are doing! -->
@@ -116,7 +128,7 @@
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
-    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
     <property name="varnaJar" value="VARNAv3-93.jar" />
     <property name="jsoup" value="jsoup-1.8.1.jar" />
     <property name="jsonSimple" value="json_simple-1.1.jar" />
@@ -181,9 +193,9 @@
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
-      <pathelement location="lib/${jsoup}" />
-      <pathelement location="lib/${jsonSimple}" />
-      <pathelement location="lib/${javaJson}" />
+      <pathelement location="appletlib/${jsoup}" />
+      <pathelement location="appletlib/${jsonSimple}" />
+      <pathelement location="appletlib/${javaJson}" />
 
     </path>
     <!-- default location for outputting javadoc -->
@@ -268,7 +280,7 @@
     <delete dir="${testOutputDir}" includes="*,**/*" />
   </target>
 
-  <target name="prepareTests" depends="init,clean">
+  <target name="prepareTests" depends="init,testclean">
     <mkdir dir="${testOutputDir}" />
   </target>
 
@@ -296,7 +308,7 @@
     </java>
   </target>
 
-  <target name="makefulldist" depends="makedist">
+  <target name="preparejnlp" depends="makedist">
     <copy todir="${packageDir}">
       <fileset dir="${resourceDir}/images">
         <include name="${WebStartImage}" />
@@ -364,15 +376,29 @@
         <association mime-type="application-x/ext-file" extensions="amsa"/>
         <association mime-type="application-x/ext-file" extensions="stk"/>
         <association mime-type="application-x/ext-file" extensions="jar"/>-->
-    <!-- and sign the jars -->
-    <!-- the default keystore details might need to be edited here -->
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+  </target>
+
+  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
+      tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+      <fileset dir="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+  </target>
+  <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
       </fileset>
     </signjar>
   </target>
 
+  <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
+    <!-- and sign the jars -->
+    <!-- the default keystore details might need to be edited here -->
+  </target>
+
   <target name="runenv" depends="init">
     <path id="run.classpath">
       <pathelement location="${outputDir}" />
@@ -399,19 +425,17 @@
           <offline_allowed />
         </information>
         <resources>
-          <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
-          <fileset dir="${packageDir}">
-            <include name="jalview.jar" />
-          </fileset>
+          <j2se version="1.7+" />
+          <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
+            <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="jalview.jar" />
             <exclude name="*jnilib.jar" />
           </fileset>
+          <property name="jalview.version" value="${JALVIEW_VERSION}" />
         </resources>
         <resources os="Mac OS X">
-          <property name="jalview.version" value="${JALVIEW_VERSION}" />
           <fileset dir="${packageDir}">
             <include name="*quaqua*.jnilib.jar" />
           </fileset>
@@ -426,7 +450,11 @@
     </presetdef>
 
     <jnlpf toFile="${jnlpFile}" />
-
+    <!-- add the add-modules j2se attribute for java 9 -->
+    <replace file="${jnlpFile}" value="j2se version=&quot;1.7+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
+          <replacetoken>j2se version="1.7+"</replacetoken>
+           
+        </replace>
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
@@ -497,7 +525,7 @@
   </axis-wsdl2java>
 </target>
 
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -549,7 +577,7 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -588,12 +616,17 @@
   <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}" />
     <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="lib/${varnaJar}" />
+    <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
+    <fileset dir="${java.home}/lib">
+      <include name="plugin.jar" />
+    </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
-  <proguard>
+  <proguard verbose="true" >
     <injar file="in.jar" />
     <outjar file="${jalviewLiteJar}" />
     <libraryjar refid="obfuscateDeps.path" />
@@ -608,6 +641,31 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
+
+    <keep name="jalview.json.binding**">
+      <constructor/>
+      <method name="*"/>
+    </keep>
+
+    <keep access="public" type="class" name="MCview.PDBfile">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -643,8 +701,13 @@
 </target>
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
-  <tar destfile="${source.dist.name}" compression="gzip">
-    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
+      <exclude name=".*" />
+      <exclude name="**/.*" />
+      <exclude name="*.class" />
+      <exclude name="**/*.class" />
       <include name="LICENSE" />
       <include name="README" />
       <include name="build.xml" />
@@ -662,21 +725,50 @@
       <include name="${resourceDir}/**/*" />
       <include name="${helpDir}/**/*" />
       <include name="appletlib/${jmolJar}" />
+      <include name="appletlib/${jsonSimple}" />
+      <include name="appletlib/${javaJson}" />
       <exclude name="**/*locales" />
       <exclude name="*locales/**" />
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/.build*.*/**" />
       <exclude name="utils/InstallAnywhere/**locale*" />
       <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
       <include name="${schemaDir}/**/*" />
       <include name="utils/**/*" />
       <include name="${docDir}/**/*" />
       <include name="examples/**/*" />
+    </fileset>
+  </copy>
+
+  <tstamp prefix="build">
+    <format property="year" pattern="yyyy" />
+  </tstamp>
+  <!-- each replacetoken CDATA body must be on one line - 
+       otherwise the pattern doesn't match -->
+  <replace value="${JALVIEW_VERSION}">
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+  <replace dir="_sourcedist" value="${build.year}">
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
     </tarfileset>
   </tar>
+
+  <delete dir="_sourcedist" />
 </target>
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+<target name="prepubapplet_1" depends="makeApplet">
   <copy todir="${packageDir}/examples">
     <fileset dir="examples">
       <include name="**/*" />
@@ -702,11 +794,7 @@
       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
     </manifest>
   </jar>
-  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-    <fileset dir="${packageDir}/examples">
-      <include name="*.jar" />
-    </fileset>
-  </signjar>
+
   <presetdef name="ap_applet.jar">
     <!-- build a signed applet with 'all-permissions' - 
 			  Needs 'param name="permissions' value="all-permissions"' in applet tag
@@ -805,31 +893,50 @@
   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 
-  <!-- todo - write examples/downloads for alternate versions of the applet -->
+  <!-- todo - write examples/downloads for alternate versions of the applet 
+    probably don't need to do this now since we don't have alternate versions anymore !-->
+</target>
+<target name="-signapplet" depends="prepubapplet_1">
+  <fileset id="signappletjarset" dir="${packageDir}/examples">
+    <exclude name="u_*.jar" />
+    <include name="${jalviewLiteJar}" />
+    <include name="${jmolJar}" />
+    <include name="${javaJson}" />
+    <include name="${jsonSimple}" />
+    <include name="to_${jalviewLiteJar}" />
+    <include name="to_${jmolJar}" />
+    <include name="to_${javaJson}" />
+    <include name="to_${jsonSimple}" />
+    <include name="tl_${jalviewLiteJar}" />
+    <include name="tl_${jmolJar}" />
+    <include name="tl_${javaJson}" />
+    <include name="tl_${jsonSimple}" />
+    <include name="ap_${jalviewLiteJar}" />
+    <include name="ap_${jmolJar}" />
+    <include name="ap_${javaJson}" />
+    <include name="ap_${jsonSimple}" />
+  </fileset>
+</target>
+<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+    <fileset refid="signappletjarset" />
+  </signjar>
+</target>
 
-    <fileset dir="${packageDir}/examples">
-      <exclude name="u_*.jar" />
-      <include name="${jalviewLiteJar}" />
-      <include name="${jmolJar}" />
-      <include name="${javaJson}" />
-      <include name="${jsonSimple}" />
-      <include name="to_${jalviewLiteJar}" />
-      <include name="to_${jmolJar}" />
-      <include name="to_${javaJson}" />
-      <include name="to_${jsonSimple}" />
-      <include name="tl_${jalviewLiteJar}" />
-      <include name="tl_${jmolJar}" />
-      <include name="tl_${javaJson}" />
-      <include name="tl_${jsonSimple}" />
-      <include name="ap_${jalviewLiteJar}" />
-      <include name="ap_${jmolJar}" />
-      <include name="ap_${javaJson}" />
-      <include name="ap_${jsonSimple}" />
-    </fileset>
+<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+  <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+    <fileset refid="signappletjarset" />
   </signjar>
+</target>
+
+<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+  <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
   <!-- finally, replace any launchApp servlet tags with a version specification -->
   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
     <replacetoken>
@@ -855,4 +962,11 @@
     </packageset>
   </javadoc>
 </target>
+<target name="linkcheck" depends="init,prepare">
+  <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
+    <arg value="-nointernet"/>
+  </java>
+</target>
 </project>