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Split GATKDoclet from ResourceBundleDoclet. Refactored GaTKDocWorkUnit

This commit is contained in:
Mark DePristo 2011-07-24 20:00:04 -04:00
parent 7b84347047
commit 9f06f6c493
4 changed files with 123 additions and 72 deletions
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3
public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
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@ -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);
}

84
public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java 100644
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@ -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);
}
}

97
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -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);
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);
}
}
protected static String buildTimestamp = null, absoluteVersion = null;
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() {
TreeSet<DocWorkUnit> m = new TreeSet<DocWorkUnit>();
public Set<GATKDocWorkUnit> workUnits() {
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();
for ( DocWorkUnit workUnit : myWorkUnits ) {
Set<GATKDocWorkUnit> myWorkUnits = workUnits();
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) {
for ( final DocWorkUnit unit : all )
public final static GATKDocWorkUnit findWorkUnitForClass(Class c, Set<GATKDocWorkUnit> 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);

11
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -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(