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JAL-1400 explicit security permissions for Desktop
[jalview.git] / build.xml
diff --git a/build.xml b/build.xml
index 6cfaf4e..3eae6af 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -88,6 +88,8 @@
                <!-- Don't change anything below here unless you know what you are doing! -->
                <!-- Url path for WebStart in JNLP file -->
                <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+               <!-- Webstart Image - looked for in resources/images -->
+               <property name="WebStartImage" value="JalviewLogo_big.png"/>
                <!-- J2SE version needed for webstart launch -->
                <property name="j2sev" value="1.6+"/>
                <!-- build directory configuration -->
@@ -101,7 +103,7 @@
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
                <!-- Jalview Applet JMol Jar Dependency -->
-               <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+               <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
                <property name="jalviewLiteJar" value="jalviewApplet.jar" />
                <!-- switch to indicate if we should obfuscate jalviewLite -->
                <!--<property name="donotobfuscate" value="true"/> -->
@@ -232,49 +234,16 @@
                                <include name="*.jar" />
                        </fileset>
                </signjar>
+               <copy todir="${packageDir}">
+                       <fileset dir="${resourceDir}/images">
+                               <include name="${WebStartImage}"/>
+                       </fileset>
+                                       </copy>
+               
                <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 
                <!--    codebase="http://www.jalview.org/jalview/webstart" -->
                <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
-               <jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${WebStartLocation}">
-                       <information>
-                               <title>Jalview</title>
-                               <vendor>The Barton Group</vendor>
-                               <homepage href="http://www.jalview.org" />
-                               <description>Jalview Multiple Alignment Editor</description>
-                               <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
-                               <offline_allowed />
-                               <!--
-                               <association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-                       </information>
-                       <resources>
-                               <j2se version="${j2sev}" initial_heap_size="10M"  />
-                               <fileset dir="${packageDir}">
-                                       <include name="jalview.jar" />
-                               </fileset>
-                               <fileset dir="${packageDir}">
-                                       <include name="*.jar" />
-                                       <include name="*_*.jar" />
-                                       <exclude name="jalview.jar" />
-                               </fileset>
-                               <property name="jalview.version" value="${JALVIEW_VERSION}" />
-                       </resources>
-                       <application_desc main_class="jalview.bin.Jalview">
-                       </application_desc>
-                       <security>
-                               <all_permissions />
-                       </security>
-               </jnlp>
                <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
                        <information>
                                <title>Jalview</title>
@@ -282,61 +251,11 @@
                                <homepage href="http://www.jalview.org" />
                                <description>Jalview Multiple Alignment Editor</description>
                                <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
-                               <offline_allowed />
-                               <association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
+                               <icon href="${WebStartImage}" />
+                               <offline_allowed/>
                        </information>
                        <resources>
-                               <j2se version="${j2sev}" initial_heap_size="10M"/>
-                               <fileset dir="${packageDir}">
-                                       <include name="jalview.jar" />
-                               </fileset>
-                               <fileset dir="${packageDir}">
-                                       <include name="*.jar" />
-                                       <include name="*_*.jar" />
-                                       <exclude name="jalview.jar" />
-                               </fileset>
-                               <property name="jalview.version" value="${JALVIEW_VERSION}" />
-                       </resources>
-                       <application_desc main_class="jalview.bin.Jalview">
-                       </application_desc>
-                       <security>
-                               <all_permissions />
-                       </security>
-               </jnlp>
-               
-               <jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${WebStartLocation}">
-                       <information>
-                               <title>Jalview</title>
-                               <vendor>The Barton Group</vendor>
-                               <homepage href="http://www.jalview.org" />
-                               <description>Jalview Multiple Alignment Editor</description>
-                               <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
-                               <offline_allowed />
-                               <!--
-                               <association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-                       </information>
-                       <resources>
-                               <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
+                               <j2se version="${j2sev}" initial_heap_size="10M"  />
                                <fileset dir="${packageDir}">
                                        <include name="jalview.jar" />
                                </fileset>
@@ -352,7 +271,7 @@
                        <security>
                                <all_permissions />
                        </security>
-               </jnlp>
+               </jnlp>         
                <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
                        <information>
                                <title>Jalview</title>
@@ -360,18 +279,8 @@
                                <homepage href="http://www.jalview.org" />
                                <description>Jalview Multiple Alignment Editor</description>
                                <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
+                               <icon href="${WebStartImage}" />
                                <offline_allowed />
-                               <association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
                        </information>
                        <resources>
                                <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
@@ -391,27 +300,15 @@
                                <all_permissions />
                        </security>
                </jnlp>
-               <jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
+               <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
                        <information>
                                <title>Jalview</title>
                                <vendor>The Barton Group</vendor>
                                <homepage href="http://www.jalview.org" />
                                <description>Jalview Multiple Alignment Editor</description>
                                <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
+                               <icon href="${WebStartImage}" />
                                <offline_allowed />
-                               <!--
-                               <association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-                       -->
                        </information>
                        <resources>
                                <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
@@ -431,15 +328,15 @@
                                <all_permissions />
                        </security>
                </jnlp>
-               <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
-                       <information>
-                               <title>Jalview</title>
-                               <vendor>The Barton Group</vendor>
-                               <homepage href="http://www.jalview.org" />
-                               <description>Jalview Multiple Alignment Editor</description>
-                               <description kind="short">Jalview</description>
-                               <icon href="logo_big.gif" />
-                               <offline_allowed />
+                       <!-- finally, need to postprocess to add in associations at end of 'information' element 
+                       
+                       <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+               
+               </xslt>
+                       
+                       
+                       -->
+                                       <!--
                                <association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
@@ -450,26 +347,8 @@
         <association mime-type="application-x/ext-file" extensions="pir"/>
         <association mime-type="application-x/ext-file" extensions="amsa"/>
         <association mime-type="application-x/ext-file" extensions="stk"/>
-                       </information>
-                       <resources>
-                               <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
-                               <fileset dir="${packageDir}">
-                                       <include name="jalview.jar" />
-                               </fileset>
-                               <fileset dir="${packageDir}">
-                                       <include name="*.jar" />
-                                       <include name="*_*.jar" />
-                                       <exclude name="jalview.jar" />
-                               </fileset>
-                               <property name="jalview.version" value="${JALVIEW_VERSION}" />
-                       </resources>
-                       <application_desc main_class="jalview.bin.Jalview">
-                       </application_desc>
-                       <security>
-                               <all_permissions />
-                       </security>
-               </jnlp>
-
+        <association mime-type="application-x/ext-file" extensions="jar"/>-->
+       
        </target>
 
        <target name="runenv" depends="init">
@@ -536,6 +415,10 @@
                <jar destfile="${packageDir}/${outputJar}">
                        <manifest>
                                <attribute name="Main-Class" value="jalview.bin.Jalview" />
+        <attribute name="Permissions" value="all-permissions" />
+        <!--<attribute name="Trusted-Lib" value="true" /> -->
+        <attribute name="Application-Name" value="Jalview Desktop"/>
+        <attribute name="Codebase" value="*"/>
                        </manifest>
                        <fileset dir="${outputDir}/">
                                <exclude name="cache*/**" />