/** Displays the labels and the values for the panel. */
protected void displayPnlFields(HashMap hmPnl) {
if (hmPnl == null || hmPnl.isEmpty()) return;
Iterator keySetItr = hmPnl.keySet().iterator();
String strLabel = "";
String strValue = "";
// if the file is empty, then create an empty set of textfields.
if (hmPnl == null || hmPnl.isEmpty()) {
displayNewTxf("", "");
return;
}
Container container = getParent();
if (container != null) container.setVisible(false);
try {
// Get each set of label and value, and display them.
while (keySetItr.hasNext()) {
strLabel = (String) keySetItr.next();
strValue = (String) hmPnl.get(strLabel);
displayNewTxf(strLabel, strValue);
}
if (container != null) container.setVisible(true);
revalidate();
repaint();
} catch (Exception e) {
Messages.writeStackTrace(e);
// e.printStackTrace();
Messages.postDebug(e.toString());
}
}
/** Extracts document and cluster lists before serialization. */
@Persist
private void beforeSerialization() {
/*
* See http://issues.carrot2.org/browse/CARROT-693; this monitor does not save us
* in multi-threaded environment anyway. A better solution would be to prepare
* this eagerly in the constructor, but we try to balance overhead and full
* correctness here.
*/
synchronized (this) {
query = (String) attributes.get(AttributeNames.QUERY);
if (getDocuments() != null) {
documents = Lists.newArrayList(getDocuments());
} else {
documents = null;
}
if (getClusters() != null) {
clusters = Lists.newArrayList(getClusters());
} else {
clusters = null;
}
otherAttributesForSerialization = MapUtils.asHashMap(SimpleXmlWrappers.wrap(attributes));
otherAttributesForSerialization.remove(AttributeNames.QUERY);
otherAttributesForSerialization.remove(AttributeNames.CLUSTERS);
otherAttributesForSerialization.remove(AttributeNames.DOCUMENTS);
if (otherAttributesForSerialization.isEmpty()) {
otherAttributesForSerialization = null;
}
}
}
protected void pruneUploads() {
if (uploads == null || uploads.isEmpty()) return;
for (Iterator it = uploads.values().iterator(); it.hasNext(); ) {
UploadStatus status = (UploadStatus) it.next();
if (status.isDisposable()) {
it.remove();
}
}
}
private static void writeDuplicates() {
Main.status("Writing duplicates.");
if (!dup_post_list.isEmpty()) {
Main.status(String.format("%s\t%s", "older_post", "newer_post"));
for (Post post : dup_post_list.keySet()) {
Main.status(String.format("%s\t%s", post.post_id, dup_post_list.get(post).post_id));
}
} else {
Main.status("There are no duplicates.");
}
Main.status("Writing duplicates done.");
}
/*5/5/14, JTC, added persistent species data for players; system parameter masterSpeciesList,
replaces mSpecies.
Get previous timestep biomass for all species from web service*/
public HashMap<Integer, SpeciesZoneType> getPrediction(
String networkOrManipulationId,
int startTimestep,
int runTimestep,
Map<Integer, Integer> addSpeciesNodeList,
ZoneNodes zoneNodes)
throws SimulationException {
long milliseconds = System.currentTimeMillis();
Log.printf("\nPrediction at %d\n", startTimestep);
// Get previous timestep biomass for all species from web service
// JTC, use new HashMap containing all current settings from zoneNodes, masterSpeciesList
// HJR changing to make a deep copy here , I am getting a null while iterating
HashMap<Integer, SpeciesZoneType> masterSpeciesList =
new HashMap<Integer, SpeciesZoneType>(zoneNodes.getNodes());
HashMap<Integer, SpeciesZoneType> mNewSpecies = new HashMap<Integer, SpeciesZoneType>();
// JTC, mUpdateBiomass renamed from mUpdateSpecies
HashMap<Integer, SpeciesZoneType> mUpdateBiomass = new HashMap<Integer, SpeciesZoneType>();
// JTC, added new update type, mUpdateParams
HashMap<Integer, SpeciesZoneType> mUpdateParams = new HashMap<Integer, SpeciesZoneType>();
SpeciesZoneType szt;
String nodeConfig = null;
SimJob job = new SimJob();
// {70=2494, 5=2000, 42=240, 14=1752, 31=1415}
for (int node_id : addSpeciesNodeList.keySet()) {
int addedBiomass = addSpeciesNodeList.get(node_id);
if (!masterSpeciesList.containsKey(node_id)) {
szt = createSpeciesZoneType(node_id, addedBiomass);
mNewSpecies.put(node_id, szt);
// jtc - 04/19/15
masterSpeciesList.put(node_id, szt);
} else {
szt = masterSpeciesList.get(node_id);
szt.setCurrentBiomass(Math.max(0, szt.getCurrentBiomass() + addedBiomass));
szt.setBiomassUpdated(true);
}
}
// //JTC, separated this to capture biomass updates made to ZoneNodes that
// //are not received through addSpeciesNodeList (biomass and param updates)
// for (SpeciesZoneType species : masterSpeciesList.values()) {
// //param update also updates biomass, so insert into that list
// //preferentially; o/w use biomass update list
// if (species.paramUpdated) {
// mUpdateParams.put(species.getNodeIndex(), species);
// species.setParamUpdated(false);
// } else if (species.biomassUpdated) {
// mUpdateBiomass.put(species.getNodeIndex(), species);
// species.setBiomassUpdated(false);
// }
// }
// Insert new species using web services
if (!mNewSpecies.isEmpty()) {
zoneNodes.addNodes(mNewSpecies);
}
try {
nodeConfig =
addMultipleSpeciesType(
mNewSpecies, masterSpeciesList, startTimestep, false, networkOrManipulationId);
} catch (Exception ex) {
Log.println_e(ex.getMessage());
}
// // Update biomass changes to existing species using web services
// if (!mUpdateBiomass.isEmpty()) {
// List<NodeBiomass> lNodeBiomass = new ArrayList<NodeBiomass>();
// for (SpeciesZoneType s : mUpdateBiomass.values()) {
// Log.printf("Updating Biomass: [%d] %s %f\n", s.getNodeIndex(), s.getName(),
// s.getCurrentBiomass() / Constants.BIOMASS_SCALE);
// lNodeBiomass.add(new NodeBiomass(
// s.getCurrentBiomass() / Constants.BIOMASS_SCALE, s.getNodeIndex()));
// }
// try {
//// updateBiomass(networkOrManipulationId, lNodeBiomass, startTimestep);
// } catch (Exception ex) {
// Log.println_e(ex.getMessage());
// }
// }
// // JTC Update changes to existing species parameters using web services (also
// // resubmits biomass, but couldn't find a way to do params w/o biomass
// if (!mUpdateParams.isEmpty()) {
// try {
//// increaseMultipleSpeciesType(
//// mUpdateBiomass,
//// masterSpeciesList,
//// startTimestep,
//// false,
//// networkOrManipulationId
//// );
// } catch (Exception ex) {
// Log.println_e(ex.getMessage());
// }
// }
// run(startTimestep, runTimestep, networkOrManipulationId);
// get new predicted biomass
try {
// JTC - changed variable from "mSpecies = " to "mUpdateBiomass = "
// mUpdateBiomass = getBiomass(networkOrManipulationId, 0, startTimestep + runTimestep);
if (!masterSpeciesList.isEmpty() || !mNewSpecies.isEmpty()) {
mUpdateBiomass =
submitManipRequest("ATN", nodeConfig, startTimestep + runTimestep, false, null);
}
} catch (Exception ex) {
Log.println_e(ex.getMessage());
return null;
}
// getBiomassInfo(networkOrManipulationId);
// JTC - add loop to update persistent player species biomass information
SpeciesZoneType updS;
for (SpeciesZoneType priorS : masterSpeciesList.values()) {
System.out.println("priorS.nodeIndex " + priorS.nodeIndex);
updS = mUpdateBiomass.get(priorS.nodeIndex);
if (updS != null && updS.currentBiomass != 0) {
masterSpeciesList
.get(priorS.nodeIndex)
.setCurrentBiomass(Math.ceil(updS.getCurrentBiomass()));
}
// else {
// zoneNodes.removeNode(priorS.nodeIndex);
// }
}
Log.printf(
"Total Time (Get Prediction): %.2f seconds",
Math.round((System.currentTimeMillis() - milliseconds) / 10.0) / 100.0);
return (HashMap) zoneNodes.getNodes();
}
/**
* Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods.
*
* @param request servlet request
* @param response servlet response
* @throws javax.servlet.ServletException if a servlet-specific error occurs
* @throws java.io.IOException if an I/O error occurs
*/
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
XDebug xdebug = new XDebug();
xdebug.startTimer();
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
try {
List resultsList = new LinkedList();
// Get the gene list
String geneList = request.getParameter(QueryBuilder.GENE_LIST);
if (request instanceof XssRequestWrapper) {
geneList = ((XssRequestWrapper) request).getRawParameter(QueryBuilder.GENE_LIST);
}
String cancerStudyIdListString = request.getParameter(QueryBuilder.CANCER_STUDY_LIST);
String[] cancerStudyIdList = cancerStudyIdListString.split(",");
// Get the priority
Integer dataTypePriority;
try {
dataTypePriority =
Integer.parseInt(request.getParameter(QueryBuilder.DATA_PRIORITY).trim());
} catch (NumberFormatException e) {
dataTypePriority = 0;
}
// Cancer All Cancer Studies
List<CancerStudy> cancerStudiesList = accessControl.getCancerStudies();
HashMap<String, Boolean> studyMap = new HashMap<>();
for (String studyId : cancerStudyIdList) {
studyMap.put(studyId, Boolean.TRUE);
}
for (CancerStudy cancerStudy : cancerStudiesList) {
String cancerStudyId = cancerStudy.getCancerStudyStableId();
if (!studyMap.containsKey(cancerStudyId)) {
continue;
}
if (cancerStudyId.equalsIgnoreCase("all")) continue;
Map cancerMap = new LinkedHashMap();
cancerMap.put("studyId", cancerStudyId);
cancerMap.put("typeOfCancer", cancerStudy.getTypeOfCancerId());
// Get all Genetic Profiles Associated with this Cancer Study ID.
ArrayList<GeneticProfile> geneticProfileList =
GetGeneticProfiles.getGeneticProfiles(cancerStudyId);
// Get all Patient Lists Associated with this Cancer Study ID.
ArrayList<SampleList> sampleSetList = GetSampleLists.getSampleLists(cancerStudyId);
// Get the default patient set
AnnotatedSampleSets annotatedSampleSets =
new AnnotatedSampleSets(sampleSetList, dataTypePriority);
SampleList defaultSampleSet = annotatedSampleSets.getDefaultSampleList();
if (defaultSampleSet == null) {
continue;
}
List<String> sampleIds = defaultSampleSet.getSampleList();
// Get the default genomic profiles
CategorizedGeneticProfileSet categorizedGeneticProfileSet =
new CategorizedGeneticProfileSet(geneticProfileList);
HashMap<String, GeneticProfile> defaultGeneticProfileSet = null;
switch (dataTypePriority) {
case 2:
defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultCopyNumberMap();
break;
case 1:
defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultMutationMap();
break;
case 0:
default:
defaultGeneticProfileSet =
categorizedGeneticProfileSet.getDefaultMutationAndCopyNumberMap();
}
String mutationProfile = "", cnaProfile = "";
for (GeneticProfile geneticProfile : defaultGeneticProfileSet.values()) {
GeneticAlterationType geneticAlterationType = geneticProfile.getGeneticAlterationType();
if (geneticAlterationType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION)) {
cnaProfile = geneticProfile.getStableId();
} else if (geneticAlterationType.equals(GeneticAlterationType.MUTATION_EXTENDED)) {
mutationProfile = geneticProfile.getStableId();
}
}
cancerMap.put("mutationProfile", mutationProfile);
cancerMap.put("cnaProfile", cnaProfile);
cancerMap.put("caseSetId", defaultSampleSet.getStableId());
cancerMap.put("caseSetLength", sampleIds.size());
ProfileDataSummary genomicData =
getGenomicData(
cancerStudyId,
defaultGeneticProfileSet,
defaultSampleSet,
geneList,
sampleSetList,
request,
response);
ArrayList<GeneWithScore> geneFrequencyList = genomicData.getGeneFrequencyList();
ArrayList<String> genes = new ArrayList<String>();
for (GeneWithScore geneWithScore : geneFrequencyList) genes.add(geneWithScore.getGene());
int noOfMutated = 0,
noOfCnaUp = 0,
noOfCnaDown = 0,
noOfCnaLoss = 0,
noOfCnaGain = 0,
noOfOther = 0,
noOfAll = 0;
boolean skipStudy = defaultGeneticProfileSet.isEmpty();
if (!skipStudy) {
for (String sampleId : sampleIds) {
if (sampleId == null) {
continue;
}
if (!genomicData.isCaseAltered(sampleId)) continue;
boolean isAnyMutated = false,
isAnyCnaUp = false,
isAnyCnaDown = false,
isAnyCnaLoss = false,
isAnyCnaGain = false;
for (String gene : genes) {
isAnyMutated |= genomicData.isGeneMutated(gene, sampleId);
GeneticTypeLevel cnaLevel = genomicData.getCNALevel(gene, sampleId);
boolean isCnaUp = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Amplified);
isAnyCnaUp |= isCnaUp;
boolean isCnaDown =
cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HomozygouslyDeleted);
isAnyCnaDown |= isCnaDown;
boolean isCnaLoss =
cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HemizygouslyDeleted);
isAnyCnaLoss |= isCnaLoss;
boolean isCnaGain = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Gained);
isAnyCnaGain |= isCnaGain;
}
boolean isAnyCnaChanged = isAnyCnaUp || isAnyCnaDown;
if (isAnyMutated && !isAnyCnaChanged) noOfMutated++;
else if (isAnyMutated && isAnyCnaChanged) noOfOther++;
else if (isAnyCnaUp) noOfCnaUp++;
else if (isAnyCnaDown) noOfCnaDown++;
else if (isAnyCnaGain) noOfCnaGain++;
else if (isAnyCnaLoss) noOfCnaLoss++;
noOfAll++;
}
}
Map alterations = new LinkedHashMap();
cancerMap.put("alterations", alterations);
alterations.put("all", noOfAll);
alterations.put("mutation", noOfMutated);
alterations.put("cnaUp", noOfCnaUp);
alterations.put("cnaDown", noOfCnaDown);
alterations.put("cnaLoss", noOfCnaLoss);
alterations.put("cnaGain", noOfCnaGain);
alterations.put("other", noOfOther);
cancerMap.put("genes", genes);
cancerMap.put("skipped", skipStudy);
resultsList.add(cancerMap);
}
JSONValue.writeJSONString(resultsList, writer);
} catch (DaoException e) {
throw new ServletException(e);
} catch (ProtocolException e) {
throw new ServletException(e);
} finally {
writer.close();
}
}