[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Fri Apr  9 20:40:17 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv14854/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	RegexFilterBeanShell 
Log Message:
Added support for filter inversion (boolean negation)
moby-live/Java/src/main/ca/ucalgary/seahawk/resources RegexFilterBeanShell,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/09 15:49:18	1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/RegexFilterBeanShell	2010/04/10 00:40:17	1.3
@@ -11,9 +11,12 @@
 List nodelist = document.selectNodes(xpath);
 
 ArrayList outputXmlList = new ArrayList();
+ArrayList outputXmlList_false = new ArrayList();
 int i = 1;
 Map collections = new LinkedHashMap();
 Map collectionsEnd = new HashMap();
+Map collections_false = new LinkedHashMap();
+Map collectionsEnd_false = new HashMap();
 Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL | (Boolean.parseBoolean(case_sensitive) ? 0 : Pattern.CASE_INSENSITIVE));
 for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
         Node node = (Node) iter.next();
@@ -31,10 +34,17 @@
                         break;
                 default: break;
         }
-        if(!match){
-                continue;
-        }
 
+	Map cs = null;
+	Map csEnd = null;
+        if(match){
+		cs = collections;
+		csEnd = collectionsEnd;
+	}
+	else{
+		cs = collections_false;
+		csEnd = collectionsEnd_false;
+        }
         //go up the tree until we hit a mobyData...this is the unit we can forward
         StringBuilder collection = null;
         StringBuilder collectionEnd = null;
@@ -43,11 +53,11 @@
                    node.getParent().getName().equals("Collection")){
                         collection = new StringBuilder();  //start tracking parents
                         collectionEnd = new StringBuilder();
-                        if(!collections.containsKey(collection)){
-                                collections.put(collection, new Vector());
-                                collectionsEnd.put(collection, collectionEnd);
+                        if(!cs.containsKey(collection)){
+                                cs.put(collection, new Vector());
+                                csEnd.put(collection, collectionEnd);
                         }
-                        ((Vector)collections.get(collection)).add(node.asXML());
+                        ((Vector)cs.get(collection)).add(node.asXML());
                 }
                 node = node.getParent();
                 if(node != null && collection != null){
@@ -61,14 +71,17 @@
                         collectionEnd.append("</"+((Element) node).getQualifiedName()+">");
                 }
         }
-        if(node == null){
+        if(node == null){ // wasn't part of a mobyData block
                 continue;
         }
-        // At mobyData level if we got here
+        // At mobyData level if we got here, add if job not already present
         if(collection == null){
-                outputXmlList.add(
-                "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
-                "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>");
+		String jobData = "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>"+
+                		 "<moby:mobyContent>"+node.asXML()+"</moby:mobyContent></moby:MOBY>";
+                List list = (match ? outputXmlList : outputXmlList_false);
+		if(!list.contains(jobData)){
+			list.add(jobData);
+		}
         }
 }
 
@@ -83,6 +96,16 @@
         }
         ((List) uniqueCollections.get(keyString)).addAll((List) collection.getValue());
 }
+Map uniqueCollections_false = new LinkedHashMap();
+Map uniqueCollectionsEnd_false = new LinkedHashMap();
+for(Map.Entry collection: collections_false.entrySet()){
+        String keyString = collection.getKey().toString();
+        if(!uniqueCollections_false.containsKey(keyString)){
+                uniqueCollections_false.put(keyString, new Vector());
+                uniqueCollectionsEnd_false.put(keyString, collectionsEnd_false.get(collection.getKey()));
+        }
+        ((List) uniqueCollections_false.get(keyString)).addAll((List) collection.getValue());
+}
 
 //Now concat the collection members that pass the filter
 for(Map.Entry collection: uniqueCollections.entrySet()){
@@ -99,6 +122,21 @@
 
         outputXmlList.add(block.toString());
 }
+for(Map.Entry collection: uniqueCollections_false.entrySet()){
+        StringBuilder block = new StringBuilder();
+        block.append("<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' xmlns='http://www.biomoby.org/moby'>\n");
+        block.append("<moby:mobyContent>\n");
+        block.append(collection.getKey().toString());
+        for(String val: (List) collection.getValue()){
+                block.append(val);
+        }
+        block.append(uniqueCollectionsEnd_false.get(collection.getKey().toString()));  // closing tags
+        block.append("</moby:mobyContent>\n");
+        block.append("</moby:MOBY>\n");
+
+        outputXmlList_false.add(block.toString());
+}
 
-List nodelistAsXML=outputXmlList;
+List TRUE_nodelistAsXML=outputXmlList;
+List FALSE_nodelistAsXML=outputXmlList_false;