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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
This commit is contained in:
Mark DePristo 2013-06-13 13:12:45 -07:00
parent d93bed5d61 f9c986be74
commit 908183aba7
6 changed files with 87 additions and 50 deletions
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76
public/java/src/org/broadinstitute/sting/utils/help/DocletUtils.java 100644
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@ -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());
}
}

2
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -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

6
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -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)) {

48
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
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@ -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();
}
}
}

4
public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
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@ -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);
}
/**

1
public/java/src/org/broadinstitute/sting/utils/runtime/ProcessSettings.java
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@ -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;