Split GATKDoclet from ResourceBundleDoclet. Refactored GaTKDocWorkUnit

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java

@@ -28,7 +28,6 @@ import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.RootDoc;
 
 import java.io.*;
-import java.util.Map;
 import java.util.Set;
 
 /**
@@ -52,5 +51,5 @@ public abstract class DocumentedGATKFeatureHandler {
     }
 
     public abstract String getTemplateName(ClassDoc doc) throws IOException;
-    public abstract void processOne(RootDoc rootDoc, GATKDoclet.DocWorkUnit toProcess, Set<GATKDoclet.DocWorkUnit> all);
+    public abstract void processOne(RootDoc rootDoc, GATKDocWorkUnit toProcess, Set<GATKDocWorkUnit> all);
 }

public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java

@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.help;
+
+import com.sun.javadoc.ClassDoc;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+* Created by IntelliJ IDEA.
+* User: depristo
+* Date: 7/24/11
+* Time: 7:59 PM
+* To change this template use File | Settings | File Templates.
+*/
+public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
+    // known at the start
+    final String name, filename, group;
+    final DocumentedGATKFeatureHandler handler;
+    final ClassDoc classDoc;
+    final Class clazz;
+    final DocumentedGATKFeature annotation;
+    final String buildTimestamp, absoluteVersion;
+
+    // set by the handler
+    String summary;
+    Map<String, Object> forTemplate;
+
+    public GATKDocWorkUnit(String name, String filename, String group,
+                           DocumentedGATKFeature annotation, DocumentedGATKFeatureHandler handler,
+                           ClassDoc classDoc, Class clazz,
+                           String buildTimestamp, String absoluteVersion) {
+        this.annotation = annotation;
+        this.name = name;
+        this.filename = filename;
+        this.group = group;
+        this.handler = handler;
+        this.classDoc = classDoc;
+        this.clazz = clazz;
+        this.buildTimestamp = buildTimestamp;
+        this.absoluteVersion = absoluteVersion;
+    }
+
+    public void setHandlerContent(String summary, Map<String, Object> forTemplate) {
+        this.summary = summary;
+        this.forTemplate = forTemplate;
+    }
+
+    public Map<String, String> toMap() {
+        Map<String, String> data = new HashMap<String, String>();
+        data.put("name", name);
+        data.put("summary", summary);
+        data.put("filename", filename);
+        data.put("group", group);
+        return data;
+    }
+
+    public int compareTo(GATKDocWorkUnit other) {
+        return this.name.compareTo(other.name);
+    }
+}

public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java

@@ -33,7 +33,6 @@ import freemarker.template.TemplateException;
 import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import sun.misc.IOUtils;
 
 import java.io.*;
 import java.util.*;
@@ -41,57 +40,11 @@ import java.util.*;
 /**
  *
  */
-public class GATKDoclet extends ResourceBundleExtractorDoclet {
+public class GATKDoclet {
     final protected static File SETTINGS_DIR = new File("settings/helpTemplates");
     final protected static File DESTINATION_DIR = new File("gatkdocs");
     final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
-
+    protected static String buildTimestamp = null, absoluteVersion = null;
-    public static class DocWorkUnit implements Comparable<DocWorkUnit> {
-        // known at the start
-        final String name, filename, group;
-        final DocumentedGATKFeatureHandler handler;
-        final ClassDoc classDoc;
-        final Class clazz;
-        final DocumentedGATKFeature annotation;
-        final String buildTimestamp, absoluteVersion;
-
-        // set by the handler
-        String summary;
-        Map<String, Object> forTemplate;
-
-        public DocWorkUnit(String name, String filename, String group,
-                           DocumentedGATKFeature annotation, DocumentedGATKFeatureHandler handler,
-                           ClassDoc classDoc, Class clazz,
-                           String buildTimestamp, String absoluteVersion) {
-            this.annotation = annotation;
-            this.name = name;
-            this.filename = filename;
-            this.group = group;
-            this.handler = handler;
-            this.classDoc = classDoc;
-            this.clazz = clazz;
-            this.buildTimestamp = buildTimestamp;
-            this.absoluteVersion = absoluteVersion;
-        }
-
-        public void setHandlerContent(String summary, Map<String, Object> forTemplate) {
-            this.summary = summary;
-            this.forTemplate = forTemplate;
-        }
-
-        public Map<String, String> toMap() {
-            Map<String, String> data = new HashMap<String, String>();
-            data.put("name", name);
-            data.put("summary", summary);
-            data.put("filename", filename);
-            data.put("group", group);
-            return data;
-        }
-
-        public int compareTo(DocWorkUnit other) {
-            return this.name.compareTo(other.name);
-        }
-    }
 
     RootDoc rootDoc;
 
@@ -102,17 +55,33 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
      * @throws java.io.IOException if output can't be written.
      */
     public static boolean start(RootDoc rootDoc) throws IOException {
+        // load arguments
+        for(String[] options: rootDoc.options()) {
+            if(options[0].equals("-build-timestamp"))
+                buildTimestamp = options[1];
+            if (options[0].equals("-absolute-version"))
+                absoluteVersion = options[1];
+        }
+
         GATKDoclet doclet = new GATKDoclet();
-        doclet.processDocs(rootDoc, null);
+        doclet.processDocs(rootDoc);
         return true;
     }
 
+    /**
+     * Validate the given options against options supported by this doclet.
+     * @param option Option to validate.
+     * @return Number of potential parameters; 0 if not supported.
+     */
     public static int optionLength(String option) {
-        return ResourceBundleExtractorDoclet.optionLength(option);
+        if(option.equals("-build-timestamp") || option.equals("-absolute-version") ) {
+            return 2;
+        }
+        return 0;
     }
 
-    public Set<DocWorkUnit> workUnits() {
+    public Set<GATKDocWorkUnit> workUnits() {
-        TreeSet<DocWorkUnit> m = new TreeSet<DocWorkUnit>();
+        TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();
 
         for ( ClassDoc doc : rootDoc.classes() ) {
             System.out.printf("Considering %s%n", doc);
@@ -121,7 +90,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
             if ( handler != null && handler.shouldBeProcessed(doc) ) {
                 String filename = handler.getDestinationFilename(doc);
-                DocWorkUnit unit = new DocWorkUnit(doc.name(),
+                GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
                         filename, feature.groupName(),
                         feature, handler, doc, clazz,
                         buildTimestamp, absoluteVersion);
@@ -133,7 +102,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
     }
 
     @Override
-    protected void processDocs(RootDoc rootDoc, PrintStream ignore) {
+    protected void processDocs(RootDoc rootDoc) {
         // setup the global access to the root
         this.rootDoc = rootDoc;
         super.loadData(rootDoc, false);
@@ -152,12 +121,12 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             // Specify how templates will see the data-model. This is an advanced topic...
             cfg.setObjectWrapper(new DefaultObjectWrapper());
 
-            Set<DocWorkUnit> myWorkUnits = workUnits();
+            Set<GATKDocWorkUnit> myWorkUnits = workUnits();
-            for ( DocWorkUnit workUnit : myWorkUnits ) {
+            for ( GATKDocWorkUnit workUnit : myWorkUnits ) {
                 processDocWorkUnit(cfg, workUnit, myWorkUnits);
             }
 
-            processIndex(cfg, new ArrayList<DocWorkUnit>(myWorkUnits));
+            processIndex(cfg, new ArrayList<GATKDocWorkUnit>(myWorkUnits));
         } catch ( FileNotFoundException e ) {
             throw new RuntimeException(e);
         } catch ( IOException e ) {
@@ -214,7 +183,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
         return rootDoc.classNamed(clazz.getName());
     }
 
-    private void processIndex(Configuration cfg, List<DocWorkUnit> indexData) throws IOException {
+    private void processIndex(Configuration cfg, List<GATKDocWorkUnit> indexData) throws IOException {
         /* Get or create a template */
         Template temp = cfg.getTemplate("generic.index.template.html");
 
@@ -228,7 +197,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
         }
     }
 
-    private Map<String, Object> groupIndexData(List<DocWorkUnit> indexData) {
+    private Map<String, Object> groupIndexData(List<GATKDocWorkUnit> indexData) {
         //
         // root -> data -> { summary -> y, filename -> z }, etc
         //      -> groups -> group1, group2, etc.
@@ -238,7 +207,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
 
         Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
-        for ( DocWorkUnit workUnit : indexData ) {
+        for ( GATKDocWorkUnit workUnit : indexData ) {
             data.add(workUnit.toMap());
             docFeatures.add(workUnit.annotation);
         }
@@ -263,14 +232,14 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
         return root;
     }
 
-    public final static DocWorkUnit findWorkUnitForClass(Class c, Set<DocWorkUnit> all) {
+    public final static GATKDocWorkUnit findWorkUnitForClass(Class c, Set<GATKDocWorkUnit> all) {
-        for ( final DocWorkUnit unit : all )
+        for ( final GATKDocWorkUnit unit : all )
             if ( unit.clazz.equals(c) )
                 return unit;
         return null;
     }
 
-    private void processDocWorkUnit(Configuration cfg, DocWorkUnit unit, Set<DocWorkUnit> all)
+    private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit, Set<GATKDocWorkUnit> all)
             throws IOException {
         System.out.printf("Processing documentation for class %s%n", unit.classDoc);
 

public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java

@@ -32,7 +32,6 @@ import com.sun.javadoc.Tag;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
@@ -43,9 +42,9 @@ import java.util.*;
  *
  */
 public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
-    GATKDoclet.DocWorkUnit toProcess;
+    GATKDocWorkUnit toProcess;
     ClassDoc classdoc;
-    Set<GATKDoclet.DocWorkUnit> all;
+    Set<GATKDocWorkUnit> all;
     RootDoc rootDoc;
 
     @Override
@@ -66,7 +65,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     }
 
     @Override
-    public void processOne(RootDoc rootDoc, GATKDoclet.DocWorkUnit toProcessArg, Set<GATKDoclet.DocWorkUnit> allArg) {
+    public void processOne(RootDoc rootDoc, GATKDocWorkUnit toProcessArg, Set<GATKDocWorkUnit> allArg) {
         this.rootDoc = rootDoc;
         this.toProcess = toProcessArg;
         this.all = allArg;
@@ -132,7 +131,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
         // add in all of the explicitly related items
         for ( final Class extraDocClass : toProcess.annotation.extraDocs() ) {
-            final GATKDoclet.DocWorkUnit otherUnit = GATKDoclet.findWorkUnitForClass(extraDocClass, all);
+            final GATKDocWorkUnit otherUnit = GATKDoclet.findWorkUnitForClass(extraDocClass, all);
             if ( otherUnit == null )
                 throw new ReviewedStingException("Requested extraDocs for class without any documentation: " + extraDocClass);
             extraDocsData.add(
@@ -143,7 +142,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         }
 
         List<Map<String, Object>> hierarchyDocs = new ArrayList<Map<String, Object>>();
-        for (final GATKDoclet.DocWorkUnit other : all ) {
+        for (final GATKDocWorkUnit other : all ) {
             final String relation = classRelationship(toProcess.clazz, other.clazz);
             if ( relation != null )
                 hierarchyDocs.add(