Merge pull request #40 from broadinstitute/gg_retrieve_readfilters_GSATDG-63
This commit is contained in:
MauricioCarneiro
commit
76810465aa
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@ -224,7 +224,7 @@ public class GATKDoclet {
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File forumKeyFile = new File(FORUM_KEY_FILE);
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if (forumKeyFile.exists()) {
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String forumKey = null;
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// Read ing a one-line file so we can do a for loop
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// Read in a one-line file so we can do a for loop
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for (String line : new XReadLines(forumKeyFile))
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forumKey = line;
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updateForum(myWorkUnits, forumKey);
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@ -283,7 +283,7 @@ public class GATKDoclet {
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DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
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DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
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if (handler != null && handler.includeInDocs(doc)) {
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logger.info("Generating documentation for class " + doc);
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//logger.info("Generating documentation for class " + doc);
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String filename = handler.getDestinationFilename(doc, clazz);
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GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
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filename, feature.groupName(), feature, handler, doc, clazz,
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@ -35,6 +35,7 @@ import org.broad.tribble.Feature;
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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.gatk.refdata.tracks.FeatureManager;
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import org.broadinstitute.sting.gatk.walkers.ReadFilters;
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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.collections.Pair;
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@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import java.io.IOException;
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import java.lang.annotation.Annotation;
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import java.lang.reflect.*;
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import java.util.*;
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@ -91,6 +93,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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addRelatedBindings(root);
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root.put("group", toProcess.group);
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// Adding in retrieval of peripheral info (rf annotations etc)
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getClazzAnnotations(toProcess.clazz, root);
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toProcess.setHandlerContent((String) root.get("summary"), root);
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}
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@ -135,7 +140,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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put("filename", otherUnit.filename);
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put("name", otherUnit.name);
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}});
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}
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root.put("extradocs", extraDocsData);
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}
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@ -270,6 +274,66 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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}
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}
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/**
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* Umbrella function that groups the collection of values for specific annotations applied to an
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* instance of class c. Lists of collected values are added directly to the "toProcess" object.
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* Requires being able to instantiate the class.
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*
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* @param classToProcess the object to instantiate and query for the annotation
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* @param root the root of the document handler, to which we'll store collected annotations
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*/
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private void getClazzAnnotations(Class classToProcess, Map<String, Object> root) {
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//
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// attempt to instantiate the class
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final Object instance = makeInstanceIfPossible(classToProcess);
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if (instance != null) {
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final Class myClass = instance.getClass();
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// TODO: get top relevant superclass (last before object? abstract?)
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// TODO: get parallelism options (TreeReducible or Nanoschedulable)
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// Get read filter annotations (ReadFilters)
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final HashSet<HashMap<String, Object>> bucket= new HashSet<HashMap<String, Object>>();
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bucket.addAll(getReadFilters(myClass, bucket));
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root.put("readfilters", bucket);
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// TODO: get annotators (AnnotatorCompatible)
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// anything else?
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} else {
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root.put("readfilters", new ArrayList<HashMap<String, Object>>()); // put empty list to avoid blowups
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}
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}
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/**
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* Utility function that finds the values of ReadFilters annotation applied to an instance of class c.
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*
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* @param myClass the class to query for the annotation
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* @param bucket a container in which we store the annotations collected
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* @return a list of values, otherwise null
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*/
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private HashSet<HashMap<String, Object>> getReadFilters(Class myClass, HashSet<HashMap<String, Object>> bucket) {
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//
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// Retrieve annotation
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if (myClass.isAnnotationPresent(ReadFilters.class)) {
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final Annotation thisAnnotation = myClass.getAnnotation(ReadFilters.class);
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if(thisAnnotation instanceof ReadFilters) {
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final ReadFilters rfAnnotation = (ReadFilters) thisAnnotation;
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for (Class<?> filter : rfAnnotation.value()) {
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// make hashmap of simplename and url
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final HashMap<String, Object> nugget = new HashMap<String, Object>();
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nugget.put("name", filter.getSimpleName());
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nugget.put("filename", GATKDocUtils.htmlFilenameForClass(filter));
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bucket.add(nugget);
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}
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}
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}
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// Look up superclasses recursively
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final Class mySuperClass = myClass.getSuperclass();
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if (mySuperClass.getSimpleName().equals("Object")) {
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return bucket;
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}
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return getReadFilters(mySuperClass, bucket);
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}
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/**
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* Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in
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* instance of class c.
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@ -287,6 +351,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
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// @ArgumentCollection
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// protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
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//
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for (Field field : JVMUtils.getAllFields(instance.getClass())) {
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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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@ -71,7 +71,6 @@
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</#if>
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</p>
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</#macro>
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<#macro relatedByType name type>
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<#list relatedDocs as relatedDoc>
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<#if relatedDoc.relation == type>
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@ -143,12 +142,27 @@
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</#if>
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<#-- Create references to additional capabilities if appropriate -->
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<#if readfilters?size != 0>
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<hr>
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<h3>Read Filters</h3>
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<#if readfilters?size = 1>
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<p>This Read Filter is automatically applied to the data by the Engine before processing by ${name}.</p>
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</#if>
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<#if (readfilters?size > 1) >
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<p>These Read Filters are automatically applied to the data by the Engine before processing by ${name}.</p>
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</#if>
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<ul>
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<#list readfilters as filter>
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<li><a href="${filter.filename}">${filter.name}</a></li>
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</#list>
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</ul>
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</#if>
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<#if extradocs?size != 0>
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<hr>
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<h2>Additional capabilities</h2>
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The arguments described in the entries below can be supplied to this tool to modify
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<p>The arguments described in the entries below can be supplied to this tool to modify
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its behavior. For example, the -L argument directs the GATK engine restricts processing
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to specific genomic intervals. This capability is available to all GATK walkers.
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to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).</p>
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<ul>
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<#list extradocs as extradoc>
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<li><a href="${extradoc.filename}">${extradoc.name}</a></li>
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