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Added GATKDocs fct to indicate default Read Filters for each tool 

-- Added getClazzAnnotations() as hub to retrieve various annotations values and class properties through reflection
-- Added getReadFilters() method to retrieve Read Filter annotations
-- getReadFilters() uses recursion to walk up the inheritance to also capture superclass annotations
-- getClazzAnnotations() stores collected info in doc handler root, which is unit.forTemplate in Doclet
-- Modified FreeMarker template to use the Readfilters info (displayed after arg table, before additional capabilities)
-- Tadaaa :-) #GSATDG-63 resolve
This commit is contained in:
Geraldine Van der Auwera 2013-02-13 01:14:57 -05:00
parent 8eda0c50df
commit faef85841b
3 changed files with 85 additions and 6 deletions
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4
public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -224,7 +224,7 @@ public class GATKDoclet {
File forumKeyFile = new File(FORUM_KEY_FILE);
if (forumKeyFile.exists()) {
String forumKey = null;
// Read ing a one-line file so we can do a for loop
// Read in a one-line file so we can do a for loop
for (String line : new XReadLines(forumKeyFile))
forumKey = line;
updateForum(myWorkUnits, forumKey);
@ -283,7 +283,7 @@ public class GATKDoclet {
DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
if (handler != null && handler.includeInDocs(doc)) {
logger.info("Generating documentation for class " + doc);
//logger.info("Generating documentation for class " + doc);
String filename = handler.getDestinationFilename(doc, clazz);
GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
filename, feature.groupName(), feature, handler, doc, clazz,

67
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -35,6 +35,7 @@ import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.IOException;
import java.lang.annotation.Annotation;
import java.lang.reflect.*;
import java.util.*;
@ -91,6 +93,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
addRelatedBindings(root);
root.put("group", toProcess.group);
// Adding in retrieval of peripheral info (rf annotations etc)
getClazzAnnotations(toProcess.clazz, root);
toProcess.setHandlerContent((String) root.get("summary"), root);
}
@ -135,7 +140,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
put("filename", otherUnit.filename);
put("name", otherUnit.name);
}});
}
root.put("extradocs", extraDocsData);
}
@ -270,6 +274,66 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
}
}
/**
* Umbrella function that groups the collection of values for specific annotations applied to an
* instance of class c. Lists of collected values are added directly to the "toProcess" object.
* Requires being able to instantiate the class.
*
* @param classToProcess the object to instantiate and query for the annotation
* @param root the root of the document handler, to which we'll store collected annotations
*/
private void getClazzAnnotations(Class classToProcess, Map<String, Object> root) {
//
// attempt to instantiate the class
final Object instance = makeInstanceIfPossible(classToProcess);
if (instance != null) {
final Class myClass = instance.getClass();
// TODO: get top relevant superclass (last before object? abstract?)
// TODO: get parallelism options (TreeReducible or Nanoschedulable)
// Get read filter annotations (ReadFilters)
final HashSet<HashMap<String, Object>> bucket= new HashSet<HashMap<String, Object>>();
bucket.addAll(getReadFilters(myClass, bucket));
root.put("readfilters", bucket);
// TODO: get annotators (AnnotatorCompatible)
// anything else?
} else {
root.put("readfilters", new ArrayList<HashMap<String, Object>>()); // put empty list to avoid blowups
}
}
/**
* Utility function that finds the values of ReadFilters annotation applied to an instance of class c.
*
* @param myClass the class to query for the annotation
* @param bucket a container in which we store the annotations collected
* @return a list of values, otherwise null
*/
private HashSet<HashMap<String, Object>> getReadFilters(Class myClass, HashSet<HashMap<String, Object>> bucket) {
//
// Retrieve annotation
if (myClass.isAnnotationPresent(ReadFilters.class)) {
final Annotation thisAnnotation = myClass.getAnnotation(ReadFilters.class);
if(thisAnnotation instanceof ReadFilters) {
final ReadFilters rfAnnotation = (ReadFilters) thisAnnotation;
for (Class<?> filter : rfAnnotation.value()) {
// make hashmap of simplename and url
final HashMap<String, Object> nugget = new HashMap<String, Object>();
nugget.put("name", filter.getSimpleName());
nugget.put("filename", GATKDocUtils.htmlFilenameForClass(filter));
bucket.add(nugget);
}
}
}
// Look up superclasses recursively
final Class mySuperClass = myClass.getSuperclass();
if (mySuperClass.getSimpleName().equals("Object")) {
return bucket;
}
return getReadFilters(mySuperClass, bucket);
}
/**
* Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in
* instance of class c.
@ -287,6 +351,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
// @ArgumentCollection
// protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
//
for (Field field : JVMUtils.getAllFields(instance.getClass())) {
if (field.isAnnotationPresent(ArgumentCollection.class)) {
//System.out.printf("Searching for %s in argument collection field %s%n", fieldName, field);

20
settings/helpTemplates/generic.template.html
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@ -71,7 +71,6 @@
</#if>
</p>
</#macro>
<#macro relatedByType name type>
<#list relatedDocs as relatedDoc>
<#if relatedDoc.relation == type>
@ -143,12 +142,27 @@
</#if>
<#-- Create references to additional capabilities if appropriate -->
<#if readfilters?size != 0>
<hr>
<h3>Read Filters</h3>
<#if readfilters?size = 1>
<p>This Read Filter is automatically applied to the data by the Engine before processing by ${name}.</p>
</#if>
<#if (readfilters?size > 1) >
<p>These Read Filters are automatically applied to the data by the Engine before processing by ${name}.</p>
</#if>
<ul>
<#list readfilters as filter>
<li><a href="${filter.filename}">${filter.name}</a></li>
</#list>
</ul>
</#if>
<#if extradocs?size != 0>
<hr>
<h2>Additional capabilities</h2>
The arguments described in the entries below can be supplied to this tool to modify
<p>The arguments described in the entries below can be supplied to this tool to modify
its behavior. For example, the -L argument directs the GATK engine restricts processing
to specific genomic intervals. This capability is available to all GATK walkers.
to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).</p>
<ul>
<#list extradocs as extradoc>
<li><a href="${extradoc.filename}">${extradoc.name}</a></li>