Merge pull request #277 from broadinstitute/dr_fix_com_sun_dependency

Remove com.sun.javadoc.* dependencies from the GATK proper, and isolate them for doclet use only

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

@@ -0,0 +1,76 @@
+/*
+* Copyright (c) 2012 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.FieldDoc;
+import com.sun.javadoc.PackageDoc;
+import com.sun.javadoc.ProgramElementDoc;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+
+import java.lang.reflect.Field;
+
+/**
+ * Methods in the class must ONLY be used by doclets, since the com.sun.javadoc.* classes are not
+ * available on all systems, and we don't want the GATK proper to depend on them.
+ */
+public class DocletUtils {
+
+    protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
+        try {
+            Class type = getClassForDoc(classDoc);
+            return lhsClass.isAssignableFrom(type) && (!requireConcrete || JVMUtils.isConcrete(type));
+        } catch (Throwable t) {
+            // Ignore errors.
+            return false;
+        }
+    }
+
+    protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
+        return Class.forName(getClassName(doc));
+    }
+
+    protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
+        try {
+            Class clazz = getClassForDoc(fieldDoc.containingClass());
+            return JVMUtils.findField(clazz, fieldDoc.name());
+        } catch (ClassNotFoundException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    /**
+     * Reconstitute the class name from the given class JavaDoc object.
+     *
+     * @param doc the Javadoc model for the given class.
+     * @return The (string) class name of the given class.
+     */
+    protected static String getClassName(ProgramElementDoc doc) {
+        PackageDoc containingPackage = doc.containingPackage();
+        return containingPackage.name().length() > 0 ?
+                String.format("%s.%s", containingPackage.name(), doc.name()) :
+                String.format("%s", doc.name());
+    }
+}

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

@@ -352,7 +352,7 @@ public class GATKDoclet {
     private Class<? extends Object> getClassForClassDoc(ClassDoc doc) {
         try {
             // todo -- what do I need the ? extends Object to pass the compiler?
-            return (Class<? extends Object>) HelpUtils.getClassForDoc(doc);
+            return (Class<? extends Object>) DocletUtils.getClassForDoc(doc);
         } catch (ClassNotFoundException e) {
             //logger.warn("Couldn't find class for ClassDoc " + doc);
             // we got a classdoc for a class we can't find.  Maybe in a library or something

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

@@ -68,7 +68,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     @Override
     public boolean includeInDocs(ClassDoc doc) {
         try {
-            Class type = HelpUtils.getClassForDoc(doc);
+            Class type = DocletUtils.getClassForDoc(doc);
             boolean hidden = !getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
             return !hidden && JVMUtils.isConcrete(type);
         } catch (ClassNotFoundException e) {
@@ -157,7 +157,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         root.put("arguments", args);
         try {
             // loop over all of the arguments according to the parsing engine
-            for (final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc))) {
+            for (final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(DocletUtils.getClassForDoc(toProcess.classDoc))) {
                 // todo -- why can you have multiple ones?
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(toProcess.classDoc, argumentSource.field.getName());
@@ -663,7 +663,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             if (fieldDoc.name().equals(name))
                 return fieldDoc;
 
-            Field field = HelpUtils.getFieldForFieldDoc(fieldDoc);
+            Field field = DocletUtils.getFieldForFieldDoc(fieldDoc);
             if (field == null)
                 throw new RuntimeException("Could not find the field corresponding to " + fieldDoc + ", presumably because the field is inaccessible");
             if (field.isAnnotationPresent(ArgumentCollection.class)) {

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

@@ -25,57 +25,20 @@
 
 package org.broadinstitute.sting.utils.help;
 
-import com.sun.javadoc.FieldDoc;
-import com.sun.javadoc.PackageDoc;
-import com.sun.javadoc.ProgramElementDoc;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 
-import java.lang.reflect.Field;
 import java.util.List;
 
+/**
+ * NON-javadoc/doclet help-related utility methods should go here. Anything with a com.sun.javadoc.* dependency
+ * should go into DocletUtils for use only by doclets.
+ */
 public class HelpUtils {
 
-    protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
-        try {
-            Class type = getClassForDoc(classDoc);
-            return lhsClass.isAssignableFrom(type) && (!requireConcrete || JVMUtils.isConcrete(type));
-        } catch (Throwable t) {
-            // Ignore errors.
-            return false;
-        }
-    }
-
-    protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
-        return Class.forName(getClassName(doc));
-    }
-
-    protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
-        try {
-            Class clazz = getClassForDoc(fieldDoc.containingClass());
-            return JVMUtils.findField(clazz, fieldDoc.name());
-        } catch (ClassNotFoundException e) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    /**
-     * Reconstitute the class name from the given class JavaDoc object.
-     *
-     * @param doc the Javadoc model for the given class.
-     * @return The (string) class name of the given class.
-     */
-    protected static String getClassName(ProgramElementDoc doc) {
-        PackageDoc containingPackage = doc.containingPackage();
-        return containingPackage.name().length() > 0 ?
-                String.format("%s.%s", containingPackage.name(), doc.name()) :
-                String.format("%s", doc.name());
-    }
-
     /**
      * Simple method to print a list of available annotations.
      */
@@ -98,5 +61,4 @@ public class HelpUtils {
             System.out.println("\t" + c.getSimpleName());
         System.out.println();
     }
-
+}
-}

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

@@ -108,7 +108,7 @@ public class ResourceBundleExtractorDoclet {
             if(isRequiredJavadocMissing(currentClass) && isWalker(currentClass))
                 undocumentedWalkers.add(currentClass.name());
 
-            renderHelpText(HelpUtils.getClassName(currentClass),currentClass);
+            renderHelpText(DocletUtils.getClassName(currentClass),currentClass);
         }
 
         for(PackageDoc currentPackage: packages)
@@ -173,7 +173,7 @@ public class ResourceBundleExtractorDoclet {
      * @return True if the class of the given name is a walker.  False otherwise.
      */
     protected static boolean isWalker(ClassDoc classDoc) {
-        return HelpUtils.assignableToClass(classDoc, Walker.class, true);
+        return DocletUtils.assignableToClass(classDoc, Walker.class, true);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/runtime/ProcessSettings.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.utils.runtime;
 
-import com.sun.corba.se.spi.orbutil.fsm.Input;
 
 import java.io.File;
 import java.util.Map;