Changeset 20774

Timestamp:

03/03/10 11:05:59 (2 years ago)

Author:

contrino

Message:

modmine web: cleaned and improved feature location checking

Location:

trunk/modmine/webapp/src/org/modmine/web

Files:

• FeaturesAction.java (modified) (12 diffs)
• MetadataCache.java (modified) (7 diffs)

trunk/modmine/webapp/src/org/modmine/web/FeaturesAction.java

@@ -11 +11 @@
  */
 
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 
@@ -21 +19 @@
 import javax.servlet.http.HttpSession;
 
-import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionForm;
 import org.apache.struts.action.ActionForward;
@@ -64 +61 @@
      *  an exception
      */
-    
-    
-    
-    private static final Logger LOG = Logger.getLogger(MetadataCache.class);
-
-    
+
+//    private static final Logger LOG = Logger.getLogger(MetadataCache.class);
+
     public ActionForward execute(ActionMapping mapping,
-                                 ActionForm form,
-                                 HttpServletRequest request,
-                                 @SuppressWarnings("unused") HttpServletResponse response)
+            ActionForm form,
+            HttpServletRequest request,
+            @SuppressWarnings("unused") HttpServletResponse response)
     throws Exception {
         HttpSession session = request.getSession();
@@ -79 +73 @@
         ObjectStore os = im.getObjectStore();
         Model model = im.getModel();
-        
+
         String type = (String) request.getParameter("type");
         String featureType = (String) request.getParameter("feature");
@@ -85 +79 @@
         String dccId = null;
         String experimentName = null;
-        
+
         PathQuery q = new PathQuery(model);
-        
+
         if (type.equals("experiment")) {
             experimentName = (String) request.getParameter("experiment");
             DisplayExperiment exp = MetadataCache.getExperimentByName(os, experimentName);
-            
+
             List<String> expSubsIds = exp.getSubmissionsDccId();
-            List<String> notLocated = new ArrayList<String>();
-
-            LOG.info("HERE THEY ARE: EXP " + expSubsIds + "<-");
+            Set<String> allUnlocated = new HashSet<String>();
 
             for (String subId : expSubsIds){
-                
-                Integer id = Integer.valueOf(subId); 
-                LOG.info("HERE THEY ARE: FOR " + subId + "<->" + id +"|");
-                
                 if (MetadataCache.getUnlocatedFeatureTypes(os).containsKey(new Integer(subId))){
-//                if (MetadataCache.getUnlocatedFeatureTypes(os).get(subId) != null)
-                    LOG.info("HERE THEY ARE: LIST " + subId + "<-" );
-                
-                    notLocated.addAll(MetadataCache.getUnlocatedFeatureTypes(os).get(new Integer(subId)));
+                    allUnlocated.addAll(MetadataCache.getUnlocatedFeatureTypes(os).get(new Integer(subId)));
                 }
             }
-            
-            Set allUnlocated = 
-                new HashSet(notLocated);
-            
-            LOG.info("HERE THEY ARE: UNL " + allUnlocated.toString()+ "<-");
-            
-            
-//            Set<String> subWithNotLocatedFeats = MetadataCache.getUnlocatedFeatureTypes(os).keySet();
-//            
-//            Set allExpSubs = 
-//                new HashSet(expSubsIds);
-//            
-//            Set<String> intersection = new HashSet<String>(allExpSubs);
-//            intersection.retainAll(subWithNotLocatedFeats);
-//
-//            if (!intersection.isEmpty()){
-//             Set unLocatedFTypes =   MetadataCache.getUnlocatedFeatureTypes(os).entrySet() 
-//            }
-            
 
             if (allUnlocated.contains(featureType)){
@@ -136 +102 @@
                 q.addConstraint(featureType + ".submissions.experiment.name", 
                         Constraints.eq(experimentName));
-           
-                String ef = getFactors(exp);            
-                String description = "All " + featureType + " features generated by experiment '"
-                + exp.getName() + "' in " + StringUtil.prettyList(exp.getOrganisms()) 
-                + " (" + exp.getPi() + ")." + ef;
-                q.setDescription(description);
-                
+
             } else {
                 q.addView(featureType + ".primaryIdentifier");
@@ -156 +116 @@
                 q.addOrderBy(featureType + ".chromosome.primaryIdentifier"); 
                 q.addOrderBy(featureType + ".chromosomeLocation.start"); 
-           
-                String ef = getFactors(exp);            
-                String description = "All " + featureType + " features generated by experiment '"
-                + exp.getName() + "' in " + StringUtil.prettyList(exp.getOrganisms()) 
-                + " (" + exp.getPi() + ")." + ef;
-                q.setDescription(description);
-                
-            }
-            
-            
-                        
-//            q.addView(featureType + ".primaryIdentifier");
-//            q.addView(featureType + ".score");
-//            q.addView(featureType + ".chromosome.primaryIdentifier");
-//            q.addView(featureType + ".chromosomeLocation.start");
-//            q.addView(featureType + ".chromosomeLocation.end");
-//            q.addView(featureType + ".chromosomeLocation.strand");
-//            q.addView(featureType + ".submissions:experimentalFactors.type");
-//            q.addView(featureType + ".submissions:experimentalFactors.name");
-//            q.addConstraint(featureType + ".submissions.experiment.name", 
-//                    Constraints.eq(experimentName));
-//            q.addOrderBy(featureType + ".chromosome.primaryIdentifier"); 
-//            q.addOrderBy(featureType + ".chromosomeLocation.start"); 
-//       
-//            String ef = getFactors(exp);            
-//            String description = "All " + featureType + " features generated by experiment '"
-//            + exp.getName() + "' in " + StringUtil.prettyList(exp.getOrganisms()) 
-//            + " (" + exp.getPi() + ")." + ef;
-//            q.setDescription(description);
-            
+
+            }
+
+            String ef = getFactors(exp);            
+            String description = "All " + featureType + " features generated by experiment '"
+            + exp.getName() + "' in " + StringUtil.prettyList(exp.getOrganisms()) 
+            + " (" + exp.getPi() + ")." + ef;
+            q.setDescription(description);
+
         } else if (type.equals("submission")) {
             dccId = (String) request.getParameter("submission");
             Submission sub = MetadataCache.getSubmissionByDccId(os, new Integer(dccId));
 
-//            Map <Integer, String> QQ = MetadataCache.getLocatedFeatureTypes(os);
-//            String  locFeature = MetadataCache.getLocatedFeatureTypes(os).get(dccId);
-//            int dccNr = new Integer(dccId).intValue();
-//            String qq = QQ.get(dccNr);
-
-            List<String>  locFeatures = MetadataCache.getLocatedFeatureTypes(os).get(new Integer(dccId));
-
-//          Map <Integer, String> QQ = MetadataCache.getLocatedFeatureTypes(os);
-//          String  locFeature = MetadataCache.getLocatedFeatureTypes(os).get(ddccId);
-
-            //            LOG.info("HERE THEY ARE: " +QQ + "|" +qq + "<-");
-            
-            LOG.info("HERE THEY ARE: " + dccId + "|" +locFeatures + "<-");
-            
-            if (locFeatures.contains(featureType)){
+            List<String>  unlocFeatures = MetadataCache.getUnlocatedFeatureTypes(os).get(new Integer(dccId));
+
+            if (!unlocFeatures.contains(featureType)){
                 q.addView(featureType + ".primaryIdentifier");
                 q.addView(featureType + ".score");
@@ -216 +143 @@
                 q.addOrderBy(featureType + ".chromosome.primaryIdentifier"); 
                 q.addOrderBy(featureType + ".chromosomeLocation.start"); 
-                
-                String experimentType = "";
-                if (sub.getExperimentType() != null) {
-                    experimentType = StringUtil.indefiniteArticle(sub.getExperimentType()) 
-                    + " " + sub.getExperimentType() + " experiment in";
-                }
-                
-                String efSub = "";
-                if (SubmissionHelper.getExperimentalFactorString(sub).length() > 1){
-                    efSub = " using " + SubmissionHelper.getExperimentalFactorString(sub);
-                }
-                
-                String description = "All " + featureType + " features generated by submission " + dccId
-                    + ", " + experimentType + " "
-                    + sub.getOrganism().getShortName() + efSub 
-                    + " (" + sub.getProject().getSurnamePI() + ").";
-                q.setDescription(description);
 
             } else {
@@ -241 +151 @@
                 q.addView(featureType + ".submissions:experimentalFactors.name");
                 q.addConstraint(featureType + ".submissions.DCCid", Constraints.eq(new Integer(dccId)));
-                
-                String experimentType = "";
-                if (sub.getExperimentType() != null) {
-                    experimentType = StringUtil.indefiniteArticle(sub.getExperimentType()) 
-                    + " " + sub.getExperimentType() + " experiment in";
-                }
-                
-                String efSub = "";
-                if (SubmissionHelper.getExperimentalFactorString(sub).length() > 1){
-                    efSub = " using " + SubmissionHelper.getExperimentalFactorString(sub);
-                }
-                
-                String description = "All " + featureType + " features generated by submission " + dccId
-                    + ", " + experimentType + " "
-                    + sub.getOrganism().getShortName() + efSub 
-                    + " (" + sub.getProject().getSurnamePI() + ").";
-                q.setDescription(description);
-            }
-            
-            
-        }
-        
+            }
+
+            String experimentType = "";
+            if (sub.getExperimentType() != null) {
+                experimentType = StringUtil.indefiniteArticle(sub.getExperimentType()) 
+                + " " + sub.getExperimentType() + " experiment in";
+            }
+
+            String efSub = "";
+            if (SubmissionHelper.getExperimentalFactorString(sub).length() > 1){
+                efSub = " using " + SubmissionHelper.getExperimentalFactorString(sub);
+            }
+
+            String description = "All " + featureType + " features generated by submission " + dccId
+            + ", " + experimentType + " "
+            + sub.getOrganism().getShortName() + efSub 
+            + " (" + sub.getProject().getSurnamePI() + ").";
+            q.setDescription(description);
+        }
+
         if (action.equals("results")) {
             String qid = SessionMethods.startQueryWithTimeout(request, false, q);
@@ -272 +180 @@
         } else if (action.equals("export")) {
             String format = request.getParameter("format");
-            
+
             Profile profile = SessionMethods.getProfile(session);
             WebResultsExecutor executor = im.getWebResultsExecutor(profile);
@@ -296 +204 @@
             // will get only required export data
             return null;
-            
+
         } else if (action.equals("list")) {
             // need to select just id of featureType to create list
@@ -306 +214 @@
 
             String bagName = (dccId != null ? "submission_" + dccId : experimentName)
-                + "_" + featureType + "_features";            
+            + "_" + featureType + "_features";            
             bagName = NameUtil.generateNewName(profile.getSavedBags().keySet(), bagName);
             BagHelper.createBagFromPathQuery(q, bagName, q.getDescription(), featureType, profile,

trunk/modmine/webapp/src/org/modmine/web/MetadataCache.java

@@ -107 +107 @@
     /**
      * Fetch experiment details for display.
-     * @param os the production objectstore
+     * @param os the production objectStore
      * @return a list of experiments
      */
@@ -131 +131 @@
 
     /**
-     * Fetch input/output file names per submission.
-     * @param os the production objectstore
-     * @return map
+     * Fetch unlocated feature types per submission.
+     * @param os the production objectStore
+     * @return map of unlocated feature types
      */
     public static synchronized Map<Integer, List<String>> getUnlocatedFeatureTypes(ObjectStore os) {
         if (submissionUnlocatedFeatureTypes == null) {
-            LOG.info("BEFORE readUNL ");
-            
             readUnlocatedFeatureTypes(os);
-            LOG.info("AFTER readUNL ");
         }
         return submissionUnlocatedFeatureTypes;
@@ -147 +144 @@
     /**
      * Fetch input/output file names per submission.
-     * @param os the production objectstore
+     * @param os the production objectStore
      * @return map
      */
@@ -159 +156 @@
     /**
      * Fetch number of input/output file per submission.
-     * @param os the production objectstore
+     * @param os the production objectStore
      * @return map
      */
@@ -178 +175 @@
 
     /**
-     * Fetch which featureType are located for each sub
-     * TODO: the opposite (not located feature types)
-     * @param os the production objectstore
-     * @return map
-     */
-    public static synchronized Map<Integer, List<String>> getLocatedFeatureTypes(ObjectStore os) {
-        if (submissionLocatedFeatureTypes == null) {
-            LOG.info("BEFORE readSubmissionLocatedFeature ");
-            readSubmissionLocatedFeature(os);
-            LOG.info("AFTER readSubmissionLocatedFeature ");
+     * Fetch a list of file names for a given submission.
+     * @param os the objectStore
+     * @param dccId the modENCODE submission id
+     * @return a list of file names
+     */
+    public static synchronized List<String> getFilesByDccId(ObjectStore os,
+            Integer dccId) {
+        if (submissionFilesCache == null) {
+            readSubmissionFiles(os);
+        }
+        return new ArrayList<String>(submissionFilesCache.get(dccId));
+    }
+
+    /**
+     * Fetch a list of file names for a given submission.
+     * @param dccId the modENCODE submission id
+     * @return a list of file names
+     */
+    public static synchronized List<GBrowseTrack> getTracksByDccId(Integer dccId) {
+        if (submissionTracksCache == null) {
+            readGBrowseTracks();
+        }
+        return new ArrayList<GBrowseTrack>(submissionTracksCache.get(dccId));
+    }
+
+    /**
+     * Fetch a map from feature type to count for a given submission.
+     * @param os the objectStore
+     * @param dccId the modENCODE submission id
+     * @return a map from feature type to count
+     */
+    public static synchronized Map<String, Long> getSubmissionFeatureCounts(ObjectStore os,
+            Integer dccId) {
+        if (submissionFeatureCounts == null) {
+            readSubmissionFeatureCounts(os);
+        }
+        return submissionFeatureCounts.get(dccId);
+    }
+
+    /**
+     * Fetch a submission by the modENCODE submission ids
+     * @param os the objectStore
+     * @param dccId the modENCODE submission id
+     * @return the requested submission
+     * @throws ObjectStoreException if error reading database
+     */
+    public static synchronized Submission getSubmissionByDccId(ObjectStore os, Integer dccId)
+    throws ObjectStoreException {
+        if (submissionIdCache == null) {
+            readSubmissionFeatureCounts(os);
+        }
+        return (Submission) os.getObjectById(submissionIdCache.get(dccId));
+    }
+
+    /**
+     * Get experiment information by name
+     * @param os the objectStore
+     * @param name of the experiment to fetch
+     * @return details of the experiment
+     * @throws ObjectStoreException if error reading database
+     */
+    public static synchronized DisplayExperiment getExperimentByName(ObjectStore os, String name)
+    throws ObjectStoreException {
+        if (experimentCache == null) {
+            readExperiments(os);
+        }
+        return experimentCache.get(name);
+    }
+
+   
+    /**
+     * Method to obtain the map of unlocated feature types by submission id
+     *
+     * @param os the objectStore
+     * @return submissionUnlocatedFeatureTypes
+     */
+    private static Map<Integer, List<String>> readUnlocatedFeatureTypes(ObjectStore os) {
+        try {
+
+            if (submissionUnlocatedFeatureTypes != null) {
+                return submissionUnlocatedFeatureTypes;
+            }
+
+            submissionUnlocatedFeatureTypes = new HashMap<Integer, List<String>>();
+
             
-        }
-        return submissionLocatedFeatureTypes;
+            if (submissionLocatedFeatureTypes == null) {
+                readSubmissionLocatedFeature(os);
+            }
+
+            if (submissionFeatureCounts == null) {
+                readSubmissionFeatureCounts(os);
+            }
+
+            for (Integer subId : submissionFeatureCounts.keySet()) {
+
+                Set<String> allFeatures = submissionFeatureCounts.get(subId).keySet();
+                Set<String> difference = new HashSet<String>(allFeatures);
+                difference.removeAll(submissionLocatedFeatureTypes.get(subId));
+                
+                if (!difference.isEmpty()){
+                    List <String> thisUnlocated = new ArrayList<String>();
+
+                    for (String fType : difference){
+                        thisUnlocated.add(fType);
+                    }
+                    submissionUnlocatedFeatureTypes.put(subId, thisUnlocated);
+                }
+            }
+        } catch (Exception err) {
+            err.printStackTrace();
+        }
+        return submissionUnlocatedFeatureTypes;
+    }
+
+    
+    public static Map<String, List<GBrowseTrack>> getExperimentGBrowseTracks(ObjectStore os) {
+        Map<String, List<GBrowseTrack>> tracks = new HashMap<String, List<GBrowseTrack>>();
+
+        Map<Integer, List<GBrowseTrack>> subTracksMap = getGBrowseTracks();
+
+        for (DisplayExperiment exp : getExperiments(os)) {
+            List<GBrowseTrack> expTracks = new ArrayList<GBrowseTrack>();
+            tracks.put(exp.getName(), expTracks);
+            for (Submission sub : exp.getSubmissions()) {
+                List<GBrowseTrack> subTracks = subTracksMap.get(sub.getdCCid());
+                if (subTracks != null) {
+                    // check so it is unique
+                    // expTracks.addAll(subTracks);
+                    addToList(expTracks, subTracks);
+                }
+            }
+        }
+        return tracks;
+    }
+
+    /**
+     * adds the elements of a list i to a list l only if they are not yet
+     * there
+     * @param l the receiving list
+     * @param i the donating list
+     */
+    private static void addToList(List<GBrowseTrack> l, List<GBrowseTrack> i) {
+        Iterator <GBrowseTrack> it  = i.iterator();
+        while (it.hasNext()) {
+            GBrowseTrack thisId = it.next();
+            if (!l.contains(thisId)) {
+                l.add(thisId);
+            }
+        }
+    }
+
+
+
+
+
+    /**
+     * Fetch a map from project name to experiment.
+     * @param os the production ObjectStore
+     * @return a map from project name to experiment
+     */
+    public static Map<String, List<DisplayExperiment>>
+    getProjectExperiments(ObjectStore os) {
+        long startTime = System.currentTimeMillis();
+        Map<String, List<DisplayExperiment>> projectExperiments
+        = new TreeMap<String, List<DisplayExperiment>>();
+        for (DisplayExperiment exp : getExperiments(os)) {
+            List<DisplayExperiment> exps = projectExperiments.get(exp.getProjectName());
+            if (exps == null) {
+                exps = new ArrayList<DisplayExperiment>();
+                projectExperiments.put(exp.getProjectName(), exps);
+            }
+            exps.add(exp);
+        }
+        long totalTime = System.currentTimeMillis() - startTime;
+        LOG.info("Made project map: " + projectExperiments.size()
+                + " took: " + totalTime + " ms.");
+        return projectExperiments;
+    }
+
+    private static void readExperiments(ObjectStore os) {
+        long startTime = System.currentTimeMillis();
+        Map <String, Map<String, Long>> featureCounts = getExperimentFeatureCounts(os);
+
+        try {
+            Query q = new Query();
+            QueryClass qcProject = new QueryClass(Project.class);
+            QueryField qcName = new QueryField(qcProject, "name");
+
+            q.addFrom(qcProject);
+            q.addToSelect(qcProject);
+
+            QueryClass qcExperiment = new QueryClass(Experiment.class);
+            q.addFrom(qcExperiment);
+            q.addToSelect(qcExperiment);
+
+            QueryCollectionReference projExperiments = new QueryCollectionReference(qcProject,
+            "experiments");
+            ContainsConstraint cc = new ContainsConstraint(projExperiments, ConstraintOp.CONTAINS,
+                    qcExperiment);
+
+            q.setConstraint(cc);
+            q.addToOrderBy(qcName);
+
+            Results results = os.execute(q);
+
+            experimentCache = new HashMap<String, DisplayExperiment>();
+
+            Iterator i = results.iterator();
+            while (i.hasNext()) {
+                ResultsRow row = (ResultsRow) i.next();
+
+                Project project = (Project) row.get(0);
+                Experiment experiment = (Experiment) row.get(1);
+
+                Map<String, Long> expFeatureCounts = featureCounts.get(experiment.getName());
+                DisplayExperiment displayExp = new DisplayExperiment(experiment, project,
+                        expFeatureCounts, os);
+                experimentCache.put(displayExp.getName(), displayExp);
+            }
+        } catch (Exception err) {
+            err.printStackTrace();
+        }
+        long timeTaken = System.currentTimeMillis() - startTime;
+        LOG.info("Primed experiment cache, took: " + timeTaken + "ms");
+    }
+
+
+    private static Map<String, Map<String, Long>> getExperimentFeatureCounts(ObjectStore os) {
+        long startTime = System.currentTimeMillis();
+        Query q = new Query();
+        q.setDistinct(false);
+
+        QueryClass qcExp = new QueryClass(Experiment.class);
+        QueryClass qcSub = new QueryClass(Submission.class);
+        QueryClass qcLsf = new QueryClass(LocatedSequenceFeature.class);
+
+        QueryField qfName = new QueryField(qcExp, "name");
+        QueryField qfClass = new QueryField(qcLsf, "class");
+
+        q.addFrom(qcSub);
+        q.addFrom(qcLsf);
+        q.addFrom(qcExp);
+
+        q.addToSelect(qfName);
+        q.addToSelect(qfClass);
+        q.addToSelect(new QueryFunction());
+
+        q.addToGroupBy(qfName);
+        q.addToGroupBy(qfClass);
+
+        q.addToOrderBy(qfName);
+        q.addToOrderBy(qfClass);
+
+        ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
+
+        QueryCollectionReference submissions = new QueryCollectionReference(qcExp, "submissions");
+        ContainsConstraint ccSubs = new ContainsConstraint(submissions, ConstraintOp.CONTAINS,
+                qcSub);
+        cs.addConstraint(ccSubs);
+
+        QueryCollectionReference features = new QueryCollectionReference(qcSub, "features");
+        ContainsConstraint ccFeats = new ContainsConstraint(features, ConstraintOp.CONTAINS, qcLsf);
+        cs.addConstraint(ccFeats);
+
+        q.setConstraint(cs);
+
+        Results results = os.execute(q);
+
+        Map<String, Map<String, Long>> featureCounts =
+            new LinkedHashMap<String, Map<String, Long>>();
+
+        // for each classes set the values for jsp
+        for (Iterator<ResultsRow> iter = results.iterator(); iter.hasNext(); ) {
+            ResultsRow row = iter.next();
+            String expName = (String) row.get(0);
+            Class feat = (Class) row.get(1);
+            Long count = (Long) row.get(2);
+
+            Map<String, Long> expFeatureCounts = featureCounts.get(expName);
+            if (expFeatureCounts == null) {
+                expFeatureCounts = new HashMap<String, Long>();
+                featureCounts.put(expName, expFeatureCounts);
+            }
+            expFeatureCounts.put(TypeUtil.unqualifiedName(feat.getName()), count);
+        }
+        long timeTaken = System.currentTimeMillis() - startTime;
+        LOG.info("Read experiment feature counts, took: " + timeTaken + "ms");
+
+        return featureCounts;
+    }
+
+    private static void readSubmissionFeatureCounts(ObjectStore os) {
+        long startTime = System.currentTimeMillis();
+
+        submissionFeatureCounts = new LinkedHashMap<Integer, Map<String, Long>>();
+        submissionIdCache = new HashMap<Integer, Integer>();
+
+        Query q = new Query();
+        q.setDistinct(false);
+
+        QueryClass qcSub = new QueryClass(Submission.class);
+        QueryClass qcLsf = new QueryClass(LocatedSequenceFeature.class);
+
+        QueryField qfClass = new QueryField(qcLsf, "class");
+
+        q.addFrom(qcSub);
+        q.addFrom(qcLsf);
+
+        q.addToSelect(qcSub);
+        q.addToSelect(qfClass);
+        q.addToSelect(new QueryFunction());
+
+        q.addToGroupBy(qcSub);
+        q.addToGroupBy(qfClass);
+
+        q.addToOrderBy(qcSub);
+        q.addToOrderBy(qfClass);
+
+        ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
+
+        QueryCollectionReference features = new QueryCollectionReference(qcSub, "features");
+        ContainsConstraint ccFeats = new ContainsConstraint(features, ConstraintOp.CONTAINS, qcLsf);
+        cs.addConstraint(ccFeats);
+
+        q.setConstraint(cs);
+
+        Results results = os.execute(q);
+
+        // for each classes set the values for jsp
+        for (Iterator<ResultsRow> iter = results.iterator(); iter.hasNext(); ) {
+            ResultsRow row = iter.next();
+            Submission sub = (Submission) row.get(0);
+            Class feat = (Class) row.get(1);
+            Long count = (Long) row.get(2);
+
+            submissionIdCache.put(sub.getdCCid(), sub.getId());
+
+            Map<String, Long> featureCounts = submissionFeatureCounts.get(sub.getdCCid());
+            if (featureCounts == null) {
+                featureCounts = new HashMap<String, Long>();
+                submissionFeatureCounts.put(sub.getdCCid(), featureCounts);
+            }
+            featureCounts.put(TypeUtil.unqualifiedName(feat.getName()), count);
+        }
+        long timeTaken = System.currentTimeMillis() - startTime;
+        LOG.info("Primed submission cache, took: " + timeTaken + "ms");
     }
 
@@ -262 +593 @@
     }
 
-    public static Map<String, List<GBrowseTrack>> getExperimentGBrowseTracks(ObjectStore os) {
-        Map<String, List<GBrowseTrack>> tracks = new HashMap<String, List<GBrowseTrack>>();
-
-        Map<Integer, List<GBrowseTrack>> subTracksMap = getGBrowseTracks();
-
-        for (DisplayExperiment exp : getExperiments(os)) {
-            List<GBrowseTrack> expTracks = new ArrayList<GBrowseTrack>();
-            tracks.put(exp.getName(), expTracks);
-            for (Submission sub : exp.getSubmissions()) {
-                List<GBrowseTrack> subTracks = subTracksMap.get(sub.getdCCid());
-                if (subTracks != null) {
-                    // check so it is unique
-                    // expTracks.addAll(subTracks);
-                    addToList(expTracks, subTracks);
-                }
-            }
-        }
-        return tracks;
-    }
-
-    /**
-     * adds the elements of a list i to a list l only if they are not yet
-     * there
-     * @param l the receiving list
-     * @param i the donating list
-     */
-    private static void addToList(List<GBrowseTrack> l, List<GBrowseTrack> i) {
-        Iterator <GBrowseTrack> it  = i.iterator();
-        while (it.hasNext()) {
-            GBrowseTrack thisId = it.next();
-            if (!l.contains(thisId)) {
-                l.add(thisId);
-            }
-        }
-    }
-
-
-    /**
-     * Fetch a list of file names for a given submission.
-     * @param os the objectstore
-     * @param dccId the modENCODE submission id
-     * @return a list of file names
-     */
-    public static synchronized List<String> getFilesByDccId(ObjectStore os,
-            Integer dccId) {
-        if (submissionFilesCache == null) {
-            readSubmissionFiles(os);
-        }
-        return new ArrayList<String>(submissionFilesCache.get(dccId));
-    }
-
-    /**
-     * Fetch a list of file names for a given submission.
-     * @param dccId the modENCODE submission id
-     * @return a list of file names
-     */
-    public static synchronized List<GBrowseTrack> getTracksByDccId(Integer dccId) {
-        if (submissionTracksCache == null) {
-            readGBrowseTracks();
-        }
-        return new ArrayList<GBrowseTrack>(submissionTracksCache.get(dccId));
-    }
-
-
-    /**
-     * Fetch a map from feature type to count for a given submission.
-     * @param os the objectstore
-     * @param dccId the modENCODE submission id
-     * @return a map from feature type to count
-     */
-    public static synchronized Map<String, Long> getSubmissionFeatureCounts(ObjectStore os,
-            Integer dccId) {
-        if (submissionFeatureCounts == null) {
-            readSubmissionFeatureCounts(os);
-        }
-        return submissionFeatureCounts.get(dccId);
-    }
-
-    /**
-     * Fetch a submission by the modENCODE submission ids
-     * @param os the objectstore
-     * @param dccId the modENCODE submission id
-     * @return the requested submission
-     * @throws ObjectStoreException if error reading database
-     */
-    public static synchronized Submission getSubmissionByDccId(ObjectStore os, Integer dccId)
-    throws ObjectStoreException {
-        if (submissionIdCache == null) {
-            readSubmissionFeatureCounts(os);
-        }
-        return (Submission) os.getObjectById(submissionIdCache.get(dccId));
-    }
-
-    /**
-     * Get experiment information by name
-     * @param os the objectstore
-     * @param name of the experiment to fetch
-     * @return details of the experiment
-     * @throws ObjectStoreException if error reading database
-     */
-    public static synchronized DisplayExperiment getExperimentByName(ObjectStore os, String name)
-    throws ObjectStoreException {
-        if (experimentCache == null) {
-            readExperiments(os);
-        }
-        return experimentCache.get(name);
-    }
-
-    /**
-     * Fetch a map from project name to experiment.
-     * @param os the production ObjectStore
-     * @return a map from project name to experiment
-     */
-    public static Map<String, List<DisplayExperiment>>
-    getProjectExperiments(ObjectStore os) {
-        long startTime = System.currentTimeMillis();
-        Map<String, List<DisplayExperiment>> projectExperiments
-        = new TreeMap<String, List<DisplayExperiment>>();
-        for (DisplayExperiment exp : getExperiments(os)) {
-            List<DisplayExperiment> exps = projectExperiments.get(exp.getProjectName());
-            if (exps == null) {
-                exps = new ArrayList<DisplayExperiment>();
-                projectExperiments.put(exp.getProjectName(), exps);
-            }
-            exps.add(exp);
-        }
-        long totalTime = System.currentTimeMillis() - startTime;
-        LOG.info("Made project map: " + projectExperiments.size()
-                + " took: " + totalTime + " ms.");
-        return projectExperiments;
-    }
-
-    private static void readExperiments(ObjectStore os) {
-        long startTime = System.currentTimeMillis();
-        Map <String, Map<String, Long>> featureCounts = getExperimentFeatureCounts(os);
-
-        try {
-            Query q = new Query();
-            QueryClass qcProject = new QueryClass(Project.class);
-            QueryField qcName = new QueryField(qcProject, "name");
-
-            q.addFrom(qcProject);
-            q.addToSelect(qcProject);
-
-            QueryClass qcExperiment = new QueryClass(Experiment.class);
-            q.addFrom(qcExperiment);
-            q.addToSelect(qcExperiment);
-
-            QueryCollectionReference projExperiments = new QueryCollectionReference(qcProject,
-            "experiments");
-            ContainsConstraint cc = new ContainsConstraint(projExperiments, ConstraintOp.CONTAINS,
-                    qcExperiment);
-
-            q.setConstraint(cc);
-            q.addToOrderBy(qcName);
-
-            Results results = os.execute(q);
-
-            experimentCache = new HashMap<String, DisplayExperiment>();
-
-            Iterator i = results.iterator();
-            while (i.hasNext()) {
-                ResultsRow row = (ResultsRow) i.next();
-
-                Project project = (Project) row.get(0);
-                Experiment experiment = (Experiment) row.get(1);
-
-                Map<String, Long> expFeatureCounts = featureCounts.get(experiment.getName());
-                DisplayExperiment displayExp = new DisplayExperiment(experiment, project,
-                        expFeatureCounts, os);
-                experimentCache.put(displayExp.getName(), displayExp);
-            }
-        } catch (Exception err) {
-            err.printStackTrace();
-        }
-        long timeTaken = System.currentTimeMillis() - startTime;
-        LOG.info("Primed experiment cache, took: " + timeTaken + "ms");
-    }
-
-
-    private static Map<String, Map<String, Long>> getExperimentFeatureCounts(ObjectStore os) {
-        long startTime = System.currentTimeMillis();
-        Query q = new Query();
-        q.setDistinct(false);
-
-        QueryClass qcExp = new QueryClass(Experiment.class);
-        QueryClass qcSub = new QueryClass(Submission.class);
-        QueryClass qcLsf = new QueryClass(LocatedSequenceFeature.class);
-
-        QueryField qfName = new QueryField(qcExp, "name");
-        QueryField qfClass = new QueryField(qcLsf, "class");
-
-        q.addFrom(qcSub);
-        q.addFrom(qcLsf);
-        q.addFrom(qcExp);
-
-        q.addToSelect(qfName);
-        q.addToSelect(qfClass);
-        q.addToSelect(new QueryFunction());
-
-        q.addToGroupBy(qfName);
-        q.addToGroupBy(qfClass);
-
-        q.addToOrderBy(qfName);
-        q.addToOrderBy(qfClass);
-
-        ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
-
-        QueryCollectionReference submissions = new QueryCollectionReference(qcExp, "submissions");
-        ContainsConstraint ccSubs = new ContainsConstraint(submissions, ConstraintOp.CONTAINS,
-                qcSub);
-        cs.addConstraint(ccSubs);
-
-        QueryCollectionReference features = new QueryCollectionReference(qcSub, "features");
-        ContainsConstraint ccFeats = new ContainsConstraint(features, ConstraintOp.CONTAINS, qcLsf);
-        cs.addConstraint(ccFeats);
-
-        q.setConstraint(cs);
-
-        Results results = os.execute(q);
-
-        Map<String, Map<String, Long>> featureCounts =
-            new LinkedHashMap<String, Map<String, Long>>();
-
-        // for each classes set the values for jsp
-        for (Iterator<ResultsRow> iter = results.iterator(); iter.hasNext(); ) {
-            ResultsRow row = iter.next();
-            String expName = (String) row.get(0);
-            Class feat = (Class) row.get(1);
-            Long count = (Long) row.get(2);
-
-            Map<String, Long> expFeatureCounts = featureCounts.get(expName);
-            if (expFeatureCounts == null) {
-                expFeatureCounts = new HashMap<String, Long>();
-                featureCounts.put(expName, expFeatureCounts);
-            }
-            expFeatureCounts.put(TypeUtil.unqualifiedName(feat.getName()), count);
-        }
-        long timeTaken = System.currentTimeMillis() - startTime;
-        LOG.info("Read experiment feature counts, took: " + timeTaken + "ms");
-
-        return featureCounts;
-    }
-
-    private static void readSubmissionFeatureCounts(ObjectStore os) {
-        long startTime = System.currentTimeMillis();
-
-        submissionFeatureCounts = new LinkedHashMap<Integer, Map<String, Long>>();
-        submissionIdCache = new HashMap<Integer, Integer>();
-
-        Query q = new Query();
-        q.setDistinct(false);
-
-        QueryClass qcSub = new QueryClass(Submission.class);
-        QueryClass qcLsf = new QueryClass(LocatedSequenceFeature.class);
-
-        QueryField qfClass = new QueryField(qcLsf, "class");
-
-        q.addFrom(qcSub);
-        q.addFrom(qcLsf);
-
-        q.addToSelect(qcSub);
-        q.addToSelect(qfClass);
-        q.addToSelect(new QueryFunction());
-
-        q.addToGroupBy(qcSub);
-        q.addToGroupBy(qfClass);
-
-        q.addToOrderBy(qcSub);
-        q.addToOrderBy(qfClass);
-
-        ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
-
-        QueryCollectionReference features = new QueryCollectionReference(qcSub, "features");
-        ContainsConstraint ccFeats = new ContainsConstraint(features, ConstraintOp.CONTAINS, qcLsf);
-        cs.addConstraint(ccFeats);
-
-        q.setConstraint(cs);
-
-        Results results = os.execute(q);
-
-
-        // for each classes set the values for jsp
-        for (Iterator<ResultsRow> iter = results.iterator(); iter.hasNext(); ) {
-            ResultsRow row = iter.next();
-            Submission sub = (Submission) row.get(0);
-            Class feat = (Class) row.get(1);
-            Long count = (Long) row.get(2);
-
-            submissionIdCache.put(sub.getdCCid(), sub.getId());
-
-            Map<String, Long> featureCounts = submissionFeatureCounts.get(sub.getdCCid());
-            if (featureCounts == null) {
-                featureCounts = new HashMap<String, Long>();
-                submissionFeatureCounts.put(sub.getdCCid(), featureCounts);
-            }
-            featureCounts.put(TypeUtil.unqualifiedName(feat.getName()), count);
-        }
-        long timeTaken = System.currentTimeMillis() - startTime;
-        LOG.info("Primed submission cache, took: " + timeTaken + "ms");
-    }
-
-
-    
     private static void readSubmissionLocatedFeature(ObjectStore os) {
         long startTime = System.currentTimeMillis();
@@ -606 +633 @@
             Class feat = (Class) row.get(1);
  
-//            addToMap(submissionLocatedFeatureTypes,sub.getdCCid(),
-//            feat.getName().replace("org.intermine.model.bio.", ""));
-  
             addToMap(submissionLocatedFeatureTypes,sub.getdCCid(),
                     TypeUtil.unqualifiedName(feat.getName()));
-            
-            
-//            submissionLocatedFeatureTypes.put(sub.getdCCid().toString(), 
-//                    feat.getName().replace("org.intermine.model.bio.", ""));            
         }     
         long timeTaken = System.currentTimeMillis() - startTime;
         LOG.info("Primed located features cache, took: " + timeTaken + "ms");
-        
-        LOG.info("HERE THEY ARE: " + submissionLocatedFeatureTypes);
-        
-    }
-    
-   
-    
-    /**
-     * Method to obtain the map of unlocated feature types by submission id
-     *
-     * @param os the objectStore
-     * @return submissionUnlocatedFeatureTypes
-     */
-    private static Map<Integer, List<String>> readUnlocatedFeatureTypes(ObjectStore os) {
-        try {
-
-            if (submissionUnlocatedFeatureTypes != null) {
-                return submissionUnlocatedFeatureTypes;
-            }
-
-            submissionUnlocatedFeatureTypes = new HashMap<Integer, List<String>>();
-
-            
-            if (submissionLocatedFeatureTypes == null) {
-                readSubmissionLocatedFeature(os);
-            }
-
-            if (submissionFeatureCounts == null) {
-                readSubmissionFeatureCounts(os);
-            }
-
-            LOG.info("INTO readUNL " + submissionFeatureCounts.keySet());
-
-            
-            for (Integer subId : submissionFeatureCounts.keySet()) {
-
-                Set<String> allFeatures = submissionFeatureCounts.get(subId).keySet();
-                LOG.info("INTO readUNL SFC keys:" + submissionFeatureCounts.keySet());
-                
-                
-                LOG.info("INTO readUNL difference 1 " + subId);
-                Set<String> difference = new HashSet<String>(allFeatures);
-                LOG.info("INTO readUNL difference 2 " + difference);
-
-                LOG.info("INTO readUNL difference ARG " + submissionLocatedFeatureTypes.get(subId));
-               
-                difference.removeAll(submissionLocatedFeatureTypes.get(subId));
-                
-                LOG.info("INTO readUNL difference 3 " + subId);
-                LOG.info("INTO readUNL difference-> " + difference);
-
-                if (!difference.isEmpty()){
-                    List <String> thisUnlocated = new ArrayList<String>();
-
-                    for (String fType : difference){
-                        LOG.info("INTO readUNL ftype: " + subId + "|" + fType);
-                        
-                        thisUnlocated.add(fType);
-                    }
-                    submissionUnlocatedFeatureTypes.put(subId, thisUnlocated);
-                }
-            }
-        } catch (Exception err) {
-            err.printStackTrace();
-        }
-        return submissionUnlocatedFeatureTypes;
-    }
-
+    }
     
     /**