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Merge branch 'master' into rc
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@jjgao
jjgao committed Jan 26, 2016
2 parents 87b5856 + e4623f3 commit 0d3cd15
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Showing 10 changed files with 48 additions and 81 deletions.
1 change: 1 addition & 0 deletions business/src/main/resources/applicationContext-business.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
<property name="ignoreResourceNotFound" value="true" />
<property name="locations">
<list>
<value>classpath:/portal.properties</value>
<value>file:///${PORTAL_HOME}/src/main/resources/portal.properties</value>
</list>
</property>
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32 changes: 0 additions & 32 deletions core/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java
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Expand Up @@ -351,7 +351,6 @@ public static void addCancerStudy(CancerStudy cancerStudy, boolean overwrite) th
}

setImportDate(cancerStudy.getInternalId());
reCache();
}

/**
Expand All @@ -362,11 +361,6 @@ public static void addCancerStudy(CancerStudy cancerStudy, boolean overwrite) th
*/
public static CancerStudy getCancerStudyByInternalId(int internalId) throws DaoException
{
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& studyNeedsRecaching(null, internalId)) {
System.out.print("Study with internal ID of "+internalId+" updated.");
reCacheAll(System.currentTimeMillis());
}
return byInternalId.get(internalId);
}

Expand All @@ -378,11 +372,6 @@ && studyNeedsRecaching(null, internalId)) {
*/
public static CancerStudy getCancerStudyByStableId(String stableId) throws DaoException
{
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& studyNeedsRecaching(stableId)) {
System.out.print("Study "+stableId+" updated.");
reCacheAll(System.currentTimeMillis());
}
return byStableId.get(stableId);
}

Expand All @@ -393,11 +382,6 @@ && studyNeedsRecaching(stableId)) {
* @return true if the CancerStudy exists, otherwise false
*/
public static boolean doesCancerStudyExistByStableId(String cancerStudyStableId) {
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& studyNeedsRecaching(cancerStudyStableId)) {
System.out.print("Study "+cancerStudyStableId+" updated.");
reCacheAll(System.currentTimeMillis());
}
return byStableId.containsKey(cancerStudyStableId);
}

Expand All @@ -409,11 +393,6 @@ && studyNeedsRecaching(cancerStudyStableId)) {
* @return true if the CancerStudy exists, otherwise false
*/
public static boolean doesCancerStudyExistByInternalId(int internalCancerStudyId) {
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& studyNeedsRecaching(null, internalCancerStudyId)) {
System.out.print("Study with internal ID of "+internalCancerStudyId+" updated.");
reCacheAll(System.currentTimeMillis());
}
return byInternalId.containsKey(internalCancerStudyId);
}

Expand All @@ -423,11 +402,6 @@ && studyNeedsRecaching(null, internalCancerStudyId)) {
* @return ArrayList of all CancerStudy Objects.
*/
public static ArrayList<CancerStudy> getAllCancerStudies() {
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& cacheOutOfSyncWithDb()) {
System.out.print("cache out of sync updated.");
reCacheAll(System.currentTimeMillis());
}
return new ArrayList<CancerStudy>(byStableId.values());
}

Expand All @@ -436,11 +410,6 @@ && cacheOutOfSyncWithDb()) {
* @return number of cancer studies.
*/
public static int getCount() {
if (GlobalProperties.getRecacheStudyAfterUpdate()
&& cacheOutOfSyncWithDb()) {
System.out.print("cache out of sync updated.");
reCacheAll(System.currentTimeMillis());
}
return byStableId.size();
}

Expand Down Expand Up @@ -554,7 +523,6 @@ static void deleteCancerStudy(int internalCancerStudyId) throws DaoException {
JdbcUtil.closeAll(DaoCancerStudy.class, con, pstmt, rs);
}
System.out.print("delete a study "+internalCancerStudyId);
reCacheAll(System.currentTimeMillis());
}

/**
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5 changes: 0 additions & 5 deletions core/src/main/java/org/mskcc/cbio/portal/servlet/CancerStudyView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,11 +103,6 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re

private boolean validate(HttpServletRequest request) throws DaoException {
String cancerStudyID = request.getParameter(QueryBuilder.CANCER_STUDY_ID);

if (DaoCancerStudy.getStatus(cancerStudyID) == DaoCancerStudy.Status.UNAVAILABLE) {
request.setAttribute(ERROR, "The selected cancer study is currently being updated, please try back later.");
return false;
}

CancerStudy cancerStudy = DaoCancerStudy
.getCancerStudyByStableId(cancerStudyID);
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10 changes: 0 additions & 10 deletions core/src/main/java/org/mskcc/cbio/portal/servlet/PatientView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -213,11 +213,6 @@ private boolean validate(HttpServletRequest request) throws DaoException {
request.setAttribute(ERROR, "Please specify cancer study ID. ");
return false;
}

if (cancerStudyUpdating(cancerStudyId)) {
request.setAttribute(ERROR, "The selected cancer study is currently being updated, please try back later.");
return false;
}

CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(cancerStudyId);
if (cancerStudy==null) {
Expand Down Expand Up @@ -309,11 +304,6 @@ private boolean validate(HttpServletRequest request) throws DaoException {
return true;
}

private boolean cancerStudyUpdating(String cancerStudyId) throws DaoException
{
return (DaoCancerStudy.getStatus(cancerStudyId) == DaoCancerStudy.Status.UNAVAILABLE);
}

private void sortSampleIds(int cancerStudyId, int patientId, List<String> sampleIds) {
if (sampleIds.size()==1) {
return;
Expand Down
13 changes: 1 addition & 12 deletions core/src/main/java/org/mskcc/cbio/portal/servlet/QueryBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -250,8 +250,6 @@ protected void doPost(HttpServletRequest httpServletRequest,

httpServletRequest.setAttribute(XDEBUG_OBJECT, xdebug);

checkAndRedirectOnStudyStatus(httpServletRequest, httpServletResponse, cancerTypeId);

boolean errorsExist = validateForm(action, profileList, geneticProfileIdSet, geneList,
patientSetId, patientIds, httpServletRequest);
if (action != null && action.equals(ACTION_SUBMIT) && (!errorsExist)) {
Expand Down Expand Up @@ -334,8 +332,6 @@ private void processData(String cancerStudyStableId,
HttpServletResponse response,
XDebug xdebug) throws IOException, ServletException, DaoException {

checkAndRedirectOnStudyStatus(request, response, cancerStudyStableId);

// parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
double zScore = ZScoreUtil.getZScore(geneticProfileIdSet, profileList, request);
double rppaScore = ZScoreUtil.getRPPAScore(request);
Expand Down Expand Up @@ -551,13 +547,6 @@ private void outputPlainText(HttpServletResponse response, ProfileData mergedPro
writer.close();
}

private void checkAndRedirectOnStudyStatus(HttpServletRequest request, HttpServletResponse response, String cancerStudyId) throws ServletException, IOException, DaoException
{
if (DaoCancerStudy.getStatus(cancerStudyId) == DaoCancerStudy.Status.UNAVAILABLE) {
redirectStudyUnavailable(request, response);
}
}

private void redirectStudyUnavailable(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException
{
request.setAttribute(QueryBuilder.USER_ERROR_MESSAGE, "The selected cancer study is currently being updated, please try back later.");
Expand Down Expand Up @@ -695,4 +684,4 @@ private void forwardToErrorPage(HttpServletRequest request, HttpServletResponse
getServletContext().getRequestDispatcher("/WEB-INF/jsp/error.jsp");
dispatcher.forward(request, response);
}
}
}
7 changes: 5 additions & 2 deletions portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/clinical_timeline.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,18 @@
for (var i=0; i<caseIds.length; i++) {
var caseId = caseIds[i];
var clinicalData = clinicalDataMap[caseId];
var compareAgainstIds = [caseId];
var OtherSampleId = guessClinicalData(clinicalData,["OTHER_SAMPLE_ID"]);
if (!OtherSampleId) OtherSampleId = caseId;
if (OtherSampleId) {
compareAgainstIds = compareAgainstIds.concat(OtherSampleId);
}
var circle = d3.selectAll(".timelineSeries_0").filter(function (x) {
if (x.tooltip_tables.length === 1) {
var specRefNum = x.tooltip_tables[0].filter(function(x) {
return x[0] === "SpecimenReferenceNumber" || x[0] === "SPECIMEN_REFERENCE_NUMBER";
})[0];
if (specRefNum) {
return specRefNum[1] === OtherSampleId;
return compareAgainstIds.indexOf(specRefNum[1]) !== -1;
}
}
return undefined;
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10 changes: 5 additions & 5 deletions portal/src/main/webapp/WEB-INF/jsp/tumormap/patient_view/patient_view.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -457,14 +457,14 @@ function initTabs() {
function fixCytoscapeWebRedraw() {
// to initially hide the network tab
$("#pathways").attr('style', 'display: none !important; height: 0px; width: 0px; visibility: hidden;');
$("#tab_pathways").attr('style', 'display: none !important; height: 0px; width: 0px; visibility: hidden;');
// to fix problem of flash repainting
$("a.patient-tab").click(function(){
if($(this).attr("href")==="#pathways") {
$("#pathways").removeAttr('style');
if($(this).attr("href")==="#tab_pathways") {
$("#tab_pathways").removeAttr('style');
} else {
$("#pathways").attr('style', 'display: block !important; height: 0px; width: 0px; visibility: hidden;');
$("#tab_pathways").attr('style', 'display: block !important; height: 0px; width: 0px; visibility: hidden;');
}
});
}
Expand All @@ -475,7 +475,7 @@ function switchToTab(toTab) {
$('#patient-tabs').tabs("option",
"active",
$('#patient-tabs ul a[href="#'+toTab+'"]').parent().index());
if (toTab==='images') {
if (toTab==='tab_images') {
loadImages();
}
}
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25 changes: 19 additions & 6 deletions portal/src/main/webapp/js/src/study-view/data/StudyViewProxy.js
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,8 @@ var StudyViewProxy = (function() {
_dataLength = _data.length,
_sampleIds = Object.keys(sampleToPatientMapping),
_sequencedSampleIds = [],
_cnaSampleIds = [],
_allSampleIds = [],
_locks=0;

//Keep original data format.
Expand Down Expand Up @@ -219,17 +221,26 @@ var StudyViewProxy = (function() {
var filteredA3 = removeExtraData(_sampleIds,a3[0]);

//Find sequenced sample Ids
// TODO: this is very hacky, we should switch to the cbioportal-client.js
if(a5[0]) {
var _lists = a5[0].split('\n');
for(var i = 0; i < _lists.length; i++) {
if(_lists[i].indexOf('sequenced samples') !== -1) {
var _info = _lists[i].split('\t');
if(_info.length === 5) {
_sequencedSampleIds = _info[4].split(' ');
}
break;
var _parts = _lists[i].split('\t');
if(_parts.length < 5) continue;
if (_parts[0] === parObject.studyId+"_sequenced") {
_sequencedSampleIds = _parts[4].split(' ');
} else if (_parts[0] === parObject.studyId+"_cna") {
_cnaSampleIds = _parts[4].split(' ');
} else if (_parts[0] === parObject.studyId+"_all") {
_allSampleIds = _parts[4].split(' ');
}
}

obtainDataObject.sequencedSampleIds =
_sequencedSampleIds.length>0 ? _sequencedSampleIds : _allSampleIds;
obtainDataObject.cnaSampleIds =
_cnaSampleIds.length>0 ? _cnaSampleIds : _allSampleIds;

}

//Add new attribute MUTATION COUNT for each case if have any
Expand Down Expand Up @@ -616,6 +627,8 @@ var StudyViewProxy = (function() {
getSampleidToPatientidMap: function(){return obtainDataObject.sampleidToPatientidMap;},
getPatientIdsBySampleIds: getPatientIdsBySampleIds,
getSampleIdsByPatientIds: getSampleIdsByPatientIds,
getSequencedSampleIds: function() {return obtainDataObject.sequencedSampleIds;},
getCnaSampleIds: function() {return obtainDataObject.cnaSampleIds;},
getPatientIds: function () {
return Object.keys(patientToSampleMapping);
},
Expand Down
10 changes: 7 additions & 3 deletions portal/src/main/webapp/js/src/study-view/view/StudyViewInitCharts.js
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Original file line number Diff line number Diff line change
Expand Up @@ -303,20 +303,24 @@ var StudyViewInitCharts = (function(){
}

function initTables() {
var initParams = {data: {attr: [], arr: {}}, numOfCases: numOfCases};
var initParams = {data: {attr: [], arr: {}}, numberOfSamples: {}};

if(hasMutation) {
var numberOfSequencedSamples = StudyViewProxy.getSequencedSampleIds().length;
initParams.data.attr.push({
name: 'mutatedGenes',
displayName: 'Mutated Genes'
displayName: 'Mutated Genes (<span id="number-of-selected-sequenced-samples">'+numberOfSequencedSamples+'</span> profiled samples)'
});
initParams.numberOfSamples.numberOfSequencedSamples = numberOfSequencedSamples;
}

if(hasCNA) {
var numberOfCnaSamples = StudyViewProxy.getCnaSampleIds().length;
initParams.data.attr.push({
name: 'cna',
displayName: 'Copy Number Altered Genes'
displayName: 'CNA Genes (<span id="number-of-selected-cna-samples">'+numberOfCnaSamples+'</span> profiled samples)'
});
initParams.numberOfSamples.numberOfCnaSamples = numberOfCnaSamples;
}

StudyViewInitTables.init(initParams);
Expand Down
16 changes: 10 additions & 6 deletions portal/src/main/webapp/js/src/study-view/view/StudyViewInitTables.js
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Original file line number Diff line number Diff line change
Expand Up @@ -85,10 +85,10 @@ var StudyViewInitTables = (function() {
_worker.data.getData = function (callback, workerId){
StudyViewProxy.getMutatedGenesData().then(
function( data ) {
callback(mutatedGenesData(data, numOfCases), workerId);
callback(mutatedGenesData(data, input.numberOfSamples.numberOfSequencedSamples), workerId);
},
function( status ) {
callback(mutatedGenesData(null, numOfCases), workerId);
callback(mutatedGenesData(null, input.numberOfSamples.numberOfSequencedSamples), workerId);
console.log( status + ", you fail this time" );
},
function( status ) {
Expand Down Expand Up @@ -131,10 +131,10 @@ var StudyViewInitTables = (function() {
_worker.data.getData = function (callback, workerId){
StudyViewProxy.getCNAData().then(
function( data ) {
callback(cnaData(data, numOfCases), workerId);
callback(cnaData(data, input.numberOfSamples.numberOfCnaSamples), workerId);
},
function( status ) {
callback(cnaData(null, numOfCases), workerId);
callback(cnaData(null, input.numberOfSamples.numberOfCnaSamples), workerId);
console.log( status + ", you fail this time" );
},
function( status ) {
Expand Down Expand Up @@ -356,6 +356,7 @@ var StudyViewInitTables = (function() {
var genes = [];

if(data) {
$('#number-of-selected-sequenced-samples').html(numOfCases);
for(var i = 0, dataL = data.length; i < dataL; i++){
var datum = {},
caseIds = data[i].caseIds;
Expand Down Expand Up @@ -390,6 +391,7 @@ var StudyViewInitTables = (function() {
var genes = [];

if(data) {
$('#number-of-selected-cna-samples').html(numOfCases);
for(var i = 0, dataL = data.gene.length; i < dataL; i++){
var datum = {},
_altType = '';
Expand Down Expand Up @@ -444,10 +446,12 @@ var StudyViewInitTables = (function() {
if (numSelectedCasesL.length !== 0) {
switch (worker.opts.name) {
case 'mutatedGenes':
worker.data.arr = mutatedGenesData(StudyViewProxy.getMutatedGeneDataBasedOnSampleIds(data.selectedCases), numSelectedCasesL);
var selectedSequencedSamples = _.intersection(StudyViewProxy.getSequencedSampleIds(), data.selectedCases);
worker.data.arr = mutatedGenesData(StudyViewProxy.getMutatedGeneDataBasedOnSampleIds(data.selectedCases), selectedSequencedSamples.length);
break;
case 'cna':
worker.data.arr = cnaData(StudyViewProxy.getCNABasedOnSampleIds(data.selectedCases), numSelectedCasesL);
var selectedCnaSamples = _.intersection(StudyViewProxy.getCnaSampleIds(), data.selectedCases);
worker.data.arr = cnaData(StudyViewProxy.getCNABasedOnSampleIds(data.selectedCases), selectedCnaSamples.length);
break;
default:
break;
Expand Down

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