private LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>> getSubGbrowseTrack(
List<SpanQueryResultRow> spanResults) {
LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>> subGTrack =
new LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>();
for (SpanQueryResultRow aRow : spanResults) {
if (MetadataCache.getTracksByDccId(aRow.getSubDCCid()).size() > 0) {
List<GBrowseTrack> trackList = MetadataCache.getTracksByDccId(aRow.getSubDCCid());
LinkedHashSet<GBrowseTrackInfo> trackInfoList = new LinkedHashSet<GBrowseTrackInfo>();
for (GBrowseTrack aTrack : trackList) {
GBrowseTrackInfo aTrackInfo =
new GBrowseTrackInfo(
aTrack.getOrganism(), aTrack.getTrack(),
aTrack.getSubTrack(), aTrack.getDCCid());
trackInfoList.add(aTrackInfo);
}
subGTrack.put(aRow.getSubDCCid(), trackInfoList);
}
}
return subGTrack;
}
/** The method to run all the queries. */
@SuppressWarnings("rawtypes")
private void queryExecutor() {
// Use spanOverlapFullResultMap to store the data in the session
@SuppressWarnings("unchecked")
Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>> spanOverlapFullResultMap =
(Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>>)
request.getSession().getAttribute("spanOverlapFullResultMap");
if (spanOverlapFullResultMap == null) {
spanOverlapFullResultMap =
new HashMap<String, Map<GenomicRegion, List<SpanQueryResultRow>>>();
}
Map<GenomicRegion, List<SpanQueryResultRow>> spanOverlapResultDisplayMap =
Collections.synchronizedMap(new LinkedHashMap<GenomicRegion, List<SpanQueryResultRow>>());
// GBrowse track
@SuppressWarnings("unchecked")
Map<String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>
gbrowseFullTrackMap =
(HashMap<
String,
Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>)
request.getSession().getAttribute("gbrowseFullTrackMap");
if (gbrowseFullTrackMap == null) {
gbrowseFullTrackMap =
new HashMap<
String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>();
}
Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>> gbrowseTrackMap =
Collections.synchronizedMap(
new LinkedHashMap<
GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>());
if (!spanOverlapFullResultMap.containsKey(spanUUIDString)) {
spanOverlapFullResultMap.put(spanUUIDString, spanOverlapResultDisplayMap);
request.getSession().setAttribute("spanOverlapFullResultMap", spanOverlapFullResultMap);
gbrowseFullTrackMap.put(spanUUIDString, gbrowseTrackMap);
request.getSession().setAttribute("gbrowseFullTrackMap", gbrowseFullTrackMap);
try {
Query q;
for (GenomicRegion aSpan : spanList) {
q = new Query();
q.setDistinct(true);
String chrPID = aSpan.getChr();
Integer start = aSpan.getStart();
Integer end = aSpan.getEnd();
/*
>>>>> TEST CODE <<<<<
LOG.info("OrgName: " + orgName);
LOG.info("chrPID: " + chrPID);
LOG.info("start: " + start);
LOG.info("end: " + end);
LOG.info("FeatureTypes: " + ftKeys);
LOG.info("Submissions: " + subKeys);
>>>>> TEST CODE <<<<<
*/
// DB tables
QueryClass qcOrg = new QueryClass(Organism.class);
QueryClass qcChr = new QueryClass(Chromosome.class);
QueryClass qcFeature = new QueryClass(SequenceFeature.class);
QueryClass qcLoc = new QueryClass(Location.class);
QueryClass qcSubmission = new QueryClass(Submission.class);
QueryField qfOrgName = new QueryField(qcOrg, "shortName");
QueryField qfChrPID = new QueryField(qcChr, "primaryIdentifier");
QueryField qfFeaturePID = new QueryField(qcFeature, "primaryIdentifier");
QueryField qfFeatureId = new QueryField(qcFeature, "id");
QueryField qfFeatureClass = new QueryField(qcFeature, "class");
QueryField qfSubmissionTitle = new QueryField(qcSubmission, "title");
QueryField qfSubmissionDCCid = new QueryField(qcSubmission, "DCCid");
QueryField qfChr = new QueryField(qcChr, "primaryIdentifier");
QueryField qfLocStart = new QueryField(qcLoc, "start");
QueryField qfLocEnd = new QueryField(qcLoc, "end");
q.addToSelect(qfFeatureId);
q.addToSelect(qfFeaturePID);
q.addToSelect(qfFeatureClass);
q.addToSelect(qfChr);
q.addToSelect(qfLocStart);
q.addToSelect(qfLocEnd);
q.addToSelect(qfSubmissionDCCid);
q.addToSelect(qfSubmissionTitle);
q.addFrom(qcChr);
q.addFrom(qcOrg);
q.addFrom(qcFeature);
q.addFrom(qcLoc);
q.addFrom(qcSubmission);
q.addToOrderBy(qfLocStart, "ascending");
ConstraintSet constraints = new ConstraintSet(ConstraintOp.AND);
q.setConstraint(constraints);
// SequenceFeature.organism = Organism
QueryObjectReference organism = new QueryObjectReference(qcFeature, "organism");
ContainsConstraint ccOrg = new ContainsConstraint(organism, ConstraintOp.CONTAINS, qcOrg);
constraints.addConstraint(ccOrg);
// Organism.name = orgName
SimpleConstraint scOrg =
new SimpleConstraint(qfOrgName, ConstraintOp.EQUALS, new QueryValue(orgName));
constraints.addConstraint(scOrg);
// Location.feature = SequenceFeature
QueryObjectReference locSubject = new QueryObjectReference(qcLoc, "feature");
ContainsConstraint ccLocSubject =
new ContainsConstraint(locSubject, ConstraintOp.CONTAINS, qcFeature);
constraints.addConstraint(ccLocSubject);
// Location.locatedOn = Chromosome
QueryObjectReference locObject = new QueryObjectReference(qcLoc, "locatedOn");
ContainsConstraint ccLocObject =
new ContainsConstraint(locObject, ConstraintOp.CONTAINS, qcChr);
constraints.addConstraint(ccLocObject);
// Chromosome.primaryIdentifier = chrPID
SimpleConstraint scChr =
new SimpleConstraint(qfChrPID, ConstraintOp.EQUALS, new QueryValue(chrPID));
constraints.addConstraint(scChr);
// SequenceFeature.submissions = Submission
QueryCollectionReference submission =
new QueryCollectionReference(qcFeature, "submissions");
ContainsConstraint ccSubmission =
new ContainsConstraint(submission, ConstraintOp.CONTAINS, qcSubmission);
constraints.addConstraint(ccSubmission);
// SequenceFeature.class in a list
constraints.addConstraint(new BagConstraint(qfFeatureClass, ConstraintOp.IN, ftKeys));
// Submission.CCDid in a list
constraints.addConstraint(new BagConstraint(qfSubmissionDCCid, ConstraintOp.IN, subKeys));
OverlapRange overlapInput =
new OverlapRange(new QueryValue(start), new QueryValue(end), locObject);
OverlapRange overlapFeature =
new OverlapRange(
new QueryField(qcLoc, "start"), new QueryField(qcLoc, "end"), locObject);
OverlapConstraint oc =
new OverlapConstraint(overlapInput, ConstraintOp.OVERLAPS, overlapFeature);
constraints.addConstraint(oc);
Results results = im.getObjectStore().execute(q);
/*
>>>>> TEST CODE <<<<<
LOG.info("Query: " + q.toString());
LOG.info("Result Size: " + results.size());
LOG.info("Result >>>>> " + results);
>>>>> TEST CODE <<<<<
*/
List<SpanQueryResultRow> spanResults = new ArrayList<SpanQueryResultRow>();
if (results == null || results.isEmpty()) {
spanOverlapResultDisplayMap.put(aSpan, null);
gbrowseTrackMap.put(aSpan, null);
} else {
for (Iterator<?> iter = results.iterator(); iter.hasNext(); ) {
ResultsRow<?> row = (ResultsRow<?>) iter.next();
SpanQueryResultRow aRow = new SpanQueryResultRow();
aRow.setFeatureId((Integer) row.get(0));
aRow.setFeaturePID((String) row.get(1));
aRow.setFeatureClass(((Class) row.get(2)).getSimpleName());
aRow.setChr((String) row.get(3));
aRow.setStart((Integer) row.get(4));
aRow.setEnd((Integer) row.get(5));
aRow.setSubDCCid((String) row.get(6));
aRow.setSubTitle((String) row.get(7));
spanResults.add(aRow);
}
spanOverlapResultDisplayMap.put(aSpan, spanResults);
gbrowseTrackMap.put(aSpan, getSubGbrowseTrack(spanResults)); // Gbrowse
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}