From 420cef40947cbf47e0f1e8172e407a6cac3197cf Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 15 Jan 2010 23:31:29 +0000
Subject: [PATCH] Added version numbers to the help doclet extractor.  Since
 the help system is behaving more like a resource bundle at this point,
 changed it over to use the Java ResourceBundle support classes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                     |  8 ++++----
 .../sting/gatk/WalkerManager.java             | 20 ++++++-------------
 ...ava => ResourceBundleExtractorDoclet.java} | 13 +++++++++++-
 packages/CreatePackager.xsl                   |  9 ++++++++-
 packages/FixBAMSortOrder.xml                  |  4 +++-
 packages/GATK-GSA-Pipeline.xml                |  3 +++
 packages/GATK-Picard.xml                      |  3 +++
 packages/GenomeAnalysisTK.xml                 |  4 ++++
 8 files changed, 43 insertions(+), 21 deletions(-)
 rename java/src/org/broadinstitute/sting/utils/help/{HelpExtractorDoclet.java => ResourceBundleExtractorDoclet.java} (91%)

diff --git a/build.xml b/build.xml
index 35ddb091f..80e685ab4 100644
--- a/build.xml
+++ b/build.xml
@@ -6,7 +6,7 @@
     <property name="source.dir" value="java/src" />
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
-    <property name="help.file" value="${build.dir}/help.properties" />
+    <property name="resource.file" value="StingText.properties" />
 
     <property name="single" value="*Test" />
     <property name="singleintegration" value="*IntegrationTest" />
@@ -99,10 +99,10 @@
     <target name="extracthelp" depends="compile" 
 	    description="Extract help key/value pair file from the JavaDoc tags."
 	    unless="disable.help">
-      <javadoc doclet="org.broadinstitute.sting.utils.help.HelpExtractorDoclet"
+      <javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
 	       docletpath="build"
 	       classpathref="runtime.dependencies"
-	       additionalparam="-out ${help.file}">
+	       additionalparam="-out ${build.dir}/${resource.file}">
 	<packageset refid="source.files"/>
       </javadoc>
     </target>
@@ -124,7 +124,7 @@
 
         <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
             <fileset dir="build">
-	      <include name="help.properties" />
+	      <include name="${resource.file}" />
               <include name="**/gatk/**/*.class" />
               <include name="**/alignment/**/*.class"/>
               <include name="**/oneoffprojects/**/*.class" />
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index bd6dc5e9d..fb3d9f2c3 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -58,19 +58,11 @@ public class WalkerManager extends PluginManager<Walker> {
     /**
      * A collection of help text for walkers and their enclosing packages.
      */
-    private Properties helpText = new Properties();
+    private ResourceBundle helpText;
 
     public WalkerManager() {
         super(Walker.class,"walker","Walker");
-        InputStream helpSourceFile = getClass().getClassLoader().getResourceAsStream("help.properties");
-        if(helpSourceFile != null) {
-            try {
-                helpText.load(helpSourceFile);
-            }
-            catch(IOException ex) {
-                throw new StingException("Unable to process help data");
-            }
-        }
+        helpText = ResourceBundle.getBundle("StingText");
     }
 
     /**
@@ -100,7 +92,7 @@ public class WalkerManager extends PluginManager<Walker> {
         String displayNameKey = String.format("%s.%s",packageName,DisplayNameTaglet.NAME);
         String displayName = null;
         if(helpText.containsKey(displayNameKey)) {
-            displayName = helpText.getProperty(displayNameKey);
+            displayName = helpText.getString(displayNameKey);
         }
         else {
             // If no override exists...
@@ -121,7 +113,7 @@ public class WalkerManager extends PluginManager<Walker> {
         String key = String.format("%s.%s",packageName,SummaryTaglet.NAME);
         if(!helpText.containsKey(key))
             return "";
-        return helpText.getProperty(key);    
+        return helpText.getString(key);
     }
 
     /**
@@ -133,7 +125,7 @@ public class WalkerManager extends PluginManager<Walker> {
         String walkerSummary = String.format("%s.%s",walkerType.getName(), SummaryTaglet.NAME);
         if(!helpText.containsKey(walkerSummary))
             return "";
-        return helpText.getProperty(walkerSummary);
+        return helpText.getString(walkerSummary);
     }
 
     /**
@@ -145,7 +137,7 @@ public class WalkerManager extends PluginManager<Walker> {
         String walkerDescription = String.format("%s.%s",walkerType.getName(), DescriptionTaglet.NAME);
         if(!helpText.containsKey(walkerDescription))
             return "";
-        return helpText.getProperty(walkerDescription);
+        return helpText.getString(walkerDescription);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java
rename to java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index a5edb412d..1ea8e2806 100644
--- a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -17,7 +17,12 @@ import org.broadinstitute.sting.utils.StingException;
  * @author mhanna
  * @version 0.1
  */
-public class HelpExtractorDoclet {
+public class ResourceBundleExtractorDoclet {
+    /**
+     * Taglet for the particular version number.
+     */
+    private static final String VERSION_TAGLET_NAME = "version";
+
     /**
      * Extracts the contents of certain types of javadoc and adds them to an XML file.
      * @param rootDoc The documentation root.
@@ -72,6 +77,7 @@ public class HelpExtractorDoclet {
     private static void renderHelpText(String elementName, Doc element, PrintStream out) {
         // Extract overrides from the doc tags.
         String name = null;
+        String version = null;
         StringBuilder summaryBuilder = new StringBuilder();
         for(Tag tag: element.firstSentenceTags())
              summaryBuilder.append(tag.text());
@@ -84,6 +90,8 @@ public class HelpExtractorDoclet {
                     throw new StingException("Only one display name tag can be used per package / walker.");
                 name = tag.text();
             }
+            else if(tag.name().equals("@"+VERSION_TAGLET_NAME))
+                version = tag.text();
             else if(tag.name().equals("@"+SummaryTaglet.NAME))
                 summary = tag.text();
             else if(tag.name().equals("@"+DescriptionTaglet.NAME))
@@ -94,6 +102,9 @@ public class HelpExtractorDoclet {
         if(name != null)
             out.printf("%s.%s=%s%n",elementName,DisplayNameTaglet.NAME,name);
 
+        if(version != null)
+            out.printf("%s.%s=%s%n",elementName,VERSION_TAGLET_NAME,version);
+
         // Write out an alternate element summary, if exists.
         out.printf("%s.%s=%s%n",elementName,SummaryTaglet.NAME,formatText(summary));
 
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 7b1233007..b5e618cef 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -24,6 +24,10 @@
 	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
 	<fail message="Class {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
+      <xsl:for-each select="//properties">
+	<available property="is.{current()}.present" file="{$staging.dir}/{current()}"/>
+	<fail message="Property file {current()} not found" unless="is.{current()}.present" />
+      </xsl:for-each>
 
       <!-- Create an output directory for the package -->
       <mkdir dir="{$package.dir}"/>
@@ -40,8 +44,11 @@
               <root classname="{current()}" />
             </xsl:for-each>
           </classfileset>
+          <xsl:for-each select="dependencies/properties">
+            <fileset file="{$staging.dir}/{current()}" />
+          </xsl:for-each>
           <xsl:for-each select="dependencies/file">
-            <fileset file="{current()}" />
+            <fileset file="{$staging.dir}/{current()}" />
           </xsl:for-each>
           <manifest>
             <attribute name="Main-Class" value="{main-class}"/>
diff --git a/packages/FixBAMSortOrder.xml b/packages/FixBAMSortOrder.xml
index 51f30cab7..1c9491f32 100644
--- a/packages/FixBAMSortOrder.xml
+++ b/packages/FixBAMSortOrder.xml
@@ -4,8 +4,10 @@
   <executable>
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-    
     <dependencies>
+      <!-- Text extracted from the javadocs -->
+      <properties>StingText.properties</properties>
+      <!-- The walker -->
       <class>org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag</class>
     </dependencies>
   </executable>
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 7ca07ad7c..9181d2382 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -7,6 +7,9 @@
     <name>GATK-GSA-Pipeline</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <dependencies>
+      <!-- Text extracted from the javadocs -->
+      <properties>StingText.properties</properties>
+      <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
       <!-- Quality scores recalibration -->
       <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 26f53d040..096fd54ed 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -8,6 +8,9 @@
     <name>GATK-Picard</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <dependencies>
+      <!-- Text extracted from the javadocs -->
+      <properties>StingText.properties</properties>
+      <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
       <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 9a32eb94d..4127c9e0e 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -5,7 +5,11 @@
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <dependencies>
+      <!-- Text extracted from the javadocs -->
+      <properties>StingText.properties</properties>
+      <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
+      <!-- Basic qc walkers -->
       <class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
       <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>