Default values now displayed in arguments
DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log. Logger now used instead of standard out, with INFO the default level.
This commit is contained in:
Mark DePristo
parent
c43b5981f2
commit
2039ce6102
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import java.io.File;
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import java.io.PrintStream;
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import java.util.Arrays;
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import java.util.List;
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/**
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@ -182,11 +183,11 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName="showItemizedDifferences", shortName="SID", doc="Should we enumerate all differences between the files?", required=false)
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boolean showItemizedDifferences = false;
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final DiffEngine diffEngine = new DiffEngine();
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DiffEngine diffEngine;
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@Override
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public void initialize() {
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this.diffEngine = new DiffEngine();
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}
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@Override
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@ -31,6 +31,7 @@ import freemarker.template.DefaultObjectWrapper;
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import freemarker.template.Template;
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import freemarker.template.TemplateException;
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import org.apache.commons.io.FileUtils;
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import org.apache.log4j.Level;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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@ -56,6 +57,7 @@ public class GATKDoclet {
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* @throws java.io.IOException if output can't be written.
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*/
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public static boolean start(RootDoc rootDoc) throws IOException {
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logger.setLevel(Level.INFO);
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// load arguments
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for(String[] options: rootDoc.options()) {
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if(options[0].equals("-build-timestamp"))
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@ -91,11 +93,12 @@ public class GATKDoclet {
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TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();
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for ( ClassDoc doc : rootDoc.classes() ) {
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System.out.printf("Considering %s%n", doc);
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logger.debug("Considering " + doc);
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Class clazz = getClassForClassDoc(doc);
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DocumentedGATKFeature feature = getFeatureForClassDoc(doc);
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DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
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if ( handler != null && handler.shouldBeProcessed(doc) ) {
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logger.info("Going to generate documentation for class " + doc);
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String filename = handler.getDestinationFilename(doc);
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GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
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filename, feature.groupName(),
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@ -246,7 +249,7 @@ public class GATKDoclet {
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private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit, Set<GATKDocWorkUnit> all)
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throws IOException {
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System.out.printf("Processing documentation for class %s%n", unit.classDoc);
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//System.out.printf("Processing documentation for class %s%n", unit.classDoc);
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unit.handler.processOne(rootDoc, unit, all);
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@ -29,9 +29,11 @@ import com.sun.javadoc.ClassDoc;
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import com.sun.javadoc.FieldDoc;
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import com.sun.javadoc.RootDoc;
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import com.sun.javadoc.Tag;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.classloader.JVMUtils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import java.io.*;
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@ -42,6 +44,7 @@ import java.util.*;
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*
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*/
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public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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private static Logger logger = Logger.getLogger(GenericDocumentationHandler.class);
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GATKDocWorkUnit toProcess;
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ClassDoc classdoc;
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Set<GATKDocWorkUnit> all;
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@ -71,7 +74,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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this.all = allArg;
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this.classdoc = toProcess.classDoc;
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System.out.printf("%s class %s%n", toProcess.group, toProcess.classDoc);
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//System.out.printf("%s class %s%n", toProcess.group, toProcess.classDoc);
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Map<String, Object> root = new HashMap<String, Object>();
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addHighLevelBindings(root);
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@ -87,7 +90,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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// Extract overrides from the doc tags.
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StringBuilder summaryBuilder = new StringBuilder();
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for(Tag tag: classdoc.firstSentenceTags())
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summaryBuilder.append(tag.text());
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summaryBuilder.append(tag.text());
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root.put("summary", summaryBuilder.toString());
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root.put("description", classdoc.commentText());
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root.put("timestamp", toProcess.buildTimestamp);
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@ -101,6 +104,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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protected void addArgumentBindings(Map<String, Object> root) {
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ParsingEngine parsingEngine = createStandardGATKParsingEngine();
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// attempt to instantiate the class
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Object instance = makeInstanceIfPossible(toProcess.clazz);
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Map<String, List<Object>> args = new HashMap<String, List<Object>>();
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root.put("arguments", args);
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args.put("all", new ArrayList<Object>());
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@ -114,15 +120,23 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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FieldDoc fieldDoc = getFieldDoc(classdoc, argumentSource.field.getName());
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Map<String, Object> argBindings = docForArgument(fieldDoc, argumentSource, argDef); // todo -- why can you have multiple ones?
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if ( ! argumentSource.isHidden() || getDoclet().showHiddenFeatures() ) {
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System.out.printf("Processing %s%n", argumentSource);
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logger.debug(String.format("Processing %s", argumentSource));
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String kind = "optional";
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if ( argumentSource.isRequired() ) kind = "required";
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else if ( argumentSource.isHidden() ) kind = "hidden";
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else if ( argumentSource.isDeprecated() ) kind = "depreciated";
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// get the value of the field
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if ( instance != null ) {
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Object value = getFieldValue(toProcess.clazz, instance, fieldDoc.name());
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if ( value != null )
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argBindings.put("defaultValue", prettyPrintValueString(value));
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}
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args.get(kind).add(argBindings);
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args.get("all").add(argBindings);
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} else {
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System.out.printf("Skipping hidden feature %s%n", argumentSource);
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logger.debug(String.format("Skipping hidden feature %s", argumentSource));
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}
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}
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} catch ( ClassNotFoundException e ) {
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@ -130,6 +144,90 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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}
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}
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private Object getFieldValue(Class c, Object instance, String fieldName) {
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Field field = JVMUtils.findField(c, fieldName);
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if ( field != null ) {
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Object value = JVMUtils.getFieldValue(field, instance);
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//System.out.printf("Fetched value of field %s in class %s: %s%n", fieldName, c, value);
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return value;
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} else {
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return findFieldValueInArgumentCollections(c, instance, fieldName);
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}
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}
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private Object findFieldValueInArgumentCollections(Class c, Object instance, String fieldName) {
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for ( Field field : JVMUtils.getAllFields(c) ) {
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if ( field.isAnnotationPresent(ArgumentCollection.class) ) {
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//System.out.printf("Searching for %s in argument collection field %s%n", fieldName, field);
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Object fieldValue = JVMUtils.getFieldValue(field, instance);
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Object value = getFieldValue(fieldValue.getClass(), fieldValue, fieldName);
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if ( value != null )
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return value;
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}
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}
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return null;
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}
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/**
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* Assumes value != null
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* @param value
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* @return
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*/
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private Object prettyPrintValueString(Object value) {
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if ( value.getClass().isArray() ) {
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Class type = value.getClass().getComponentType();
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if ( boolean.class.isAssignableFrom(type) )
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return Arrays.toString((boolean[])value);
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if ( byte.class.isAssignableFrom(type) )
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return Arrays.toString((byte[])value);
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if ( char.class.isAssignableFrom(type) )
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return Arrays.toString((char[])value);
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if ( double.class.isAssignableFrom(type) )
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return Arrays.toString((double[])value);
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if ( float.class.isAssignableFrom(type) )
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return Arrays.toString((float[])value);
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if ( int.class.isAssignableFrom(type) )
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return Arrays.toString((int[])value);
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if ( long.class.isAssignableFrom(type) )
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return Arrays.toString((long[])value);
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if ( short.class.isAssignableFrom(type) )
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return Arrays.toString((short[])value);
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if ( Object.class.isAssignableFrom(type) )
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return Arrays.toString((Object[])value);
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else
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throw new RuntimeException("Unexpected array type in prettyPrintValue. Value was " + value + " type is " + type);
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} else
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return value.toString();
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}
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private Object makeInstanceIfPossible(Class c) {
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Object instance = null;
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try {
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// don't try to make something where we will obviously fail
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if (! c.isEnum() && ! c.isAnnotation() && ! c.isAnonymousClass() &&
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! c.isArray() && ! c.isPrimitive() & JVMUtils.isConcrete(c) ) {
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instance = c.newInstance();
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//System.out.printf("Created object of class %s => %s%n", c, instance);
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return instance;
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} else
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return null;
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}
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catch (IllegalAccessException e ) { }
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catch (InstantiationException e ) { }
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catch (ExceptionInInitializerError e ) { }
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catch (SecurityException e ) { }
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// this last one is super dangerous, but some of these methods catch ClassNotFoundExceptions
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// and rethrow then as RuntimeExceptions
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catch (RuntimeException e) {}
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finally {
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if ( instance == null )
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logger.warn(String.format("Unable to create instance of class %s => %s", c, instance));
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}
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return instance;
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}
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protected void addRelatedBindings(Map<String, Object> root) {
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List<Map<String, Object>> extraDocsData = new ArrayList<Map<String, Object>>();
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@ -2,11 +2,12 @@
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<#macro argumentlist name myargs>
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<#if myargs?size != 0>
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<tr><th colspan="3" id="row-divider">${name}</th></tr>
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<tr><th colspan="4" id="row-divider">${name}</th></tr>
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<#list myargs as arg>
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<tr>
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<td><a href="#${arg.name}">${arg.name}</a></td>
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<td>${arg.type}</td>
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<td>${arg.defaultValue!"No default"}</td>
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<td>${arg.summary}</td>
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</tr>
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<#--
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@ -18,7 +19,7 @@
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<#macro argumentDetails arg>
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<h3><a name="${arg.name}">${arg.name}<#if arg.synonyms??> / ${arg.synonyms}</#if></a>
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(<#if arg.attributes??>${arg.attributes} </#if>${arg.type})</h3>
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(<#if arg.attributes??>${arg.attributes} </#if>${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>)</h3>
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${arg.summary}. ${arg.fulltext}<br>
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<#if arg.options??>
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<p>The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:</p>
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@ -70,6 +71,7 @@
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<tr>
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<th>Name</th>
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<th>Type</th>
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<th>Default value</th>
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<th>Summary</th>
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</tr>
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</thead>
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