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organizations: work in progress #TASK-4389
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@pfurio
pfurio committed Sep 8, 2023
1 parent c7866c4 commit 8028603
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Showing 103 changed files with 2,256 additions and 2,082 deletions.
6 changes: 3 additions & 3 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/StorageManager.java
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Expand Up @@ -75,13 +75,13 @@ protected StorageManager(CatalogManager catalogManager, CacheManager cacheManage


public void clearCache(String sessionId) throws CatalogException {
String userId = catalogManager.getUserManager().getUserId(sessionId);
String userId = catalogManager.getUserManager().getUserId(organizationId, sessionId);

}


public void clearCache(String studyId, String sessionId) throws CatalogException {
String userId = catalogManager.getUserManager().getUserId(sessionId);
String userId = catalogManager.getUserManager().getUserId(organizationId, sessionId);

}

Expand All @@ -99,7 +99,7 @@ protected StudyInfo getStudyInfo(@Nullable String studyIdStr, List<String> fileI
throws CatalogException {
StudyInfo studyInfo = new StudyInfo().setSessionId(sessionId);

String userId = catalogManager.getUserManager().getUserId(sessionId);
String userId = catalogManager.getUserManager().getUserId(organizationId, sessionId);
Study study = catalogManager.getStudyManager().get(organizationId, studyIdStr, QueryOptions.empty(), sessionId).first();

List<File> files;
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2 changes: 1 addition & 1 deletion ...a-analysis/src/main/java/org/opencb/opencga/analysis/annotations/TsvAnnotationLoader.java
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Expand Up @@ -71,7 +71,7 @@ public void setStudy(String study) {

@Override
protected void check() throws Exception {
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);

OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(organizationId, study, path, FileManager.INCLUDE_FILE_URI_PATH, token);
if (fileResult.getNumResults() == 0) {
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6 changes: 3 additions & 3 deletions ...sis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationManager.java
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Expand Up @@ -820,8 +820,8 @@ public List<ClinicalVariant> getPrimaryFindings(String clinicalAnalysisId, Query

public ClinicalAnalyst getAnalyst(String token) throws ToolException {
try {
String userId = catalogManager.getUserManager().getUserId(token);
OpenCGAResult<User> userQueryResult = catalogManager.getUserManager().get(userId, new QueryOptions(QueryOptions.INCLUDE,
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
OpenCGAResult<User> userQueryResult = catalogManager.getUserManager().get(organizationId, userId, new QueryOptions(QueryOptions.INCLUDE,
Arrays.asList(UserDBAdaptor.QueryParams.EMAIL.key(), UserDBAdaptor.QueryParams.ORGANIZATION.key())), token);
User user = userQueryResult.first();
return new ClinicalAnalyst(userId, user.getName(), user.getEmail(), "", "");
Expand Down Expand Up @@ -877,7 +877,7 @@ private Query checkQueryPermissions(Query query, String token) throws ClinicalVa
}

// Get userId from token and Study numeric IDs from the query
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
List<String> studyIds = getStudyIds(userId, query);

// If one specific clinical analysis, sample or individual is provided we expect a single valid study as well
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2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcAnalysis.java
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Expand Up @@ -68,7 +68,7 @@ protected void check() throws Exception {
// Check permissions
try {
Study study = catalogManager.getStudyManager().get(organizationId, studyId, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
catalogManager.getAuthorizationManager().checkStudyPermission(study.getUid(), userId, WRITE_FAMILIES);
} catch (CatalogException e) {
throw new ToolException(e);
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2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java
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Expand Up @@ -85,7 +85,7 @@ protected void check() throws Exception {
throw new CatalogException("Parent path " + parents.first().getPath() + " is external. Cannot download to mounted folders");
}

String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
// Check write permissions over the path
catalogManager.getAuthorizationManager()
.checkFilePermission(study.getUid(), parents.first().getUid(), userId, FilePermissions.WRITE);
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2 changes: 1 addition & 1 deletion ...nalysis/src/main/java/org/opencb/opencga/analysis/individual/qc/IndividualQcAnalysis.java
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Expand Up @@ -83,7 +83,7 @@ protected void check() throws Exception {
// Check permissions
try {
Study study = catalogManager.getStudyManager().get(organizationId, studyId, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
catalogManager.getAuthorizationManager().checkStudyPermission(study.getUid(), userId, WRITE_INDIVIDUALS);
} catch (CatalogException e) {
throw new ToolException(e);
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2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/panel/PanelImportTask.java
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Expand Up @@ -30,7 +30,7 @@ protected void check() throws Exception {

@Override
protected void run() throws Exception {
step(() -> catalogManager.getPanelManager().importFromSource(studyFqn, params.getSource(), params.getId(), token));
step(() -> catalogManager.getPanelManager().importFromSource(organizationId, studyFqn, params.getSource(), params.getId(), token));
}

}
30 changes: 15 additions & 15 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/rga/RgaManager.java
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Expand Up @@ -142,7 +142,7 @@ public void index(String studyStr, String fileStr, String token) throws CatalogE
*/
public void index(String study, Path file, String token) throws CatalogException, IOException, RgaException {
checkStorageReadMode();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
Study studyObject = catalogManager.getStudyManager().get(organizationId, study, QueryOptions.empty(), token).first();
try {
catalogManager.getAuthorizationManager().isOwnerOrAdmin(studyObject.getUid(), userId);
Expand Down Expand Up @@ -225,7 +225,7 @@ private void load(String study, Path file, String token) throws RgaException {

public void generateAuxiliarCollection(String studyStr, String token) throws CatalogException, RgaException, IOException {
checkStorageReadMode();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
try {
catalogManager.getAuthorizationManager().isOwnerOrAdmin(study.getUid(), userId);
Expand Down Expand Up @@ -433,7 +433,7 @@ private AuxiliarRgaDataModel getAuxiliarRgaDataModel(String mainCollection, Stri
private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, List<String> sampleIds, RgaIndex.Status status,
String token) throws CatalogException, RgaException {
Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());

catalogManager.getAuthorizationManager().checkIsOwnerOrAdmin(study.getUid(), userId);
Expand All @@ -454,7 +454,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, List<S
for (String sampleId : sampleIds) {
tmpSampleIds.add(sampleId);
if (tmpSampleIds.size() == 100) {
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(study.getFqn(), tmpSampleIds, rgaIndex,
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(organizationId, study.getFqn(), tmpSampleIds, rgaIndex,
token);
updatedSamples += update.getNumUpdated();

Expand All @@ -464,7 +464,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, List<S

if (!tmpSampleIds.isEmpty()) {
// Update last batch
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(study.getFqn(), tmpSampleIds, rgaIndex,
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(organizationId, study.getFqn(), tmpSampleIds, rgaIndex,
token);
updatedSamples += update.getNumUpdated();
}
Expand All @@ -476,7 +476,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, List<S
private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, String token)
throws CatalogException, IOException, RgaException {
Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());

catalogManager.getAuthorizationManager().checkIsOwnerOrAdmin(study.getUid(), userId);
Expand All @@ -497,7 +497,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, String
int updatedSamples = 0;

// Before doing anything, we first reset all the sample rga indexes
OpenCGAResult<Sample> resetResult = catalogManager.getSampleManager().resetRgaIndexes(studyStr, token);
OpenCGAResult<Sample> resetResult = catalogManager.getSampleManager().resetRgaIndexes(organizationId, studyStr, token);
logger.debug("Resetting RGA indexes for " + resetResult.getNumMatches() + " samples took " + resetResult.getTime() + " ms.");

// Update samples in batches of 100
Expand All @@ -507,7 +507,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, String
for (FacetField.Bucket bucket : result.first().getBuckets()) {
sampleIds.add(bucket.getValue());
if (sampleIds.size() == 100) {
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(study.getFqn(), sampleIds, rgaIndex,
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(organizationId, study.getFqn(), sampleIds, rgaIndex,
token);
updatedSamples += update.getNumUpdated();

Expand All @@ -517,7 +517,7 @@ private OpenCGAResult<Long> updateRgaInternalIndexStatus(String studyStr, String

if (!sampleIds.isEmpty()) {
// Update last batch
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(study.getFqn(), sampleIds, rgaIndex, token);
OpenCGAResult<Sample> update = catalogManager.getSampleManager().updateRgaIndexes(organizationId, study.getFqn(), sampleIds, rgaIndex, token);
updatedSamples += update.getNumUpdated();
}

Expand Down Expand Up @@ -619,7 +619,7 @@ public OpenCGAResult<RgaKnockoutByGene> geneQuery(String studyStr, Query query,
}

Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());
if (!rgaEngine.isAlive(collection)) {
throw new RgaException("Missing RGA indexes for study '" + study.getFqn() + "' or solr server not alive");
Expand Down Expand Up @@ -753,7 +753,7 @@ public OpenCGAResult<KnockoutByVariant> variantQuery(String studyStr, Query quer
}

Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());
String auxCollection = getAuxCollectionName(study.getFqn());
if (!rgaEngine.isAlive(collection)) {
Expand Down Expand Up @@ -1048,7 +1048,7 @@ public OpenCGAResult<KnockoutByGeneSummary> geneSummary(String studyStr, Query q
}

Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());
if (!rgaEngine.isAlive(collection)) {
throw new RgaException("Missing RGA indexes for study '" + study.getFqn() + "' or solr server not alive");
Expand Down Expand Up @@ -1132,7 +1132,7 @@ public OpenCGAResult<KnockoutByVariantSummary> variantSummary(String studyStr, Q
}

Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());
String auxCollection = getAuxCollectionName(study.getFqn());
if (!rgaEngine.isAlive(collection)) {
Expand Down Expand Up @@ -1238,7 +1238,7 @@ public OpenCGAResult<KnockoutByVariantSummary> variantSummary(String studyStr, Q
public OpenCGAResult<FacetField> aggregationStats(String studyStr, Query query, QueryOptions options, String fields, String token)
throws CatalogException, IOException, RgaException {
Study study = catalogManager.getStudyManager().get(organizationId, studyStr, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);

catalogManager.getAuthorizationManager().checkCanViewStudy(study.getUid(), userId);

Expand Down Expand Up @@ -1720,7 +1720,7 @@ private Set<String> getAuthorisedSamples(String study, Set<String> sampleIds, Li
private Preprocess individualQueryPreprocess(Study study, Query query, QueryOptions options, String token)
throws RgaException, CatalogException, IOException {

String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
String collection = getMainCollectionName(study.getFqn());
if (!rgaEngine.isAlive(collection)) {
throw new RgaException("Missing RGA indexes for study '" + study.getFqn() + "' or solr server not alive");
Expand Down
2 changes: 1 addition & 1 deletion ...-analysis/src/main/java/org/opencb/opencga/analysis/sample/SampleTsvAnnotationLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,6 @@ public int count(Query query) throws CatalogException {

@Override
public void addAnnotationSet(String entryId, AnnotationSet annotationSet, QueryOptions options) throws CatalogException {
catalogManager.getSampleManager().addAnnotationSet(study, entryId, annotationSet, options, token);
catalogManager.getSampleManager().addAnnotationSet(organizationId, study, entryId, annotationSet, options, token);
}
}
4 changes: 2 additions & 2 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/sample/qc/SampleQcAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ protected void check() throws Exception {
// Check permissions
try {
long studyUid = catalogManager.getStudyManager().get(organizationId, getStudy(), QueryOptions.empty(), token).first().getUid();
String userId = catalogManager.getUserManager().getUserId(token);
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
catalogManager.getAuthorizationManager().checkStudyPermission(studyUid, userId, WRITE_SAMPLES);
} catch (CatalogException e) {
throw new ToolException(e);
Expand Down Expand Up @@ -350,7 +350,7 @@ protected void run() throws ToolException {
if (genomePlot != null) {
qc.getVariant().setGenomePlot(genomePlot);

catalogManager.getSampleManager().update(getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
catalogManager.getSampleManager().update(organizationId, getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
QueryOptions.empty(), getToken());
logger.info("Quality control saved for sample {}", sample.getId());
}
Expand Down
2 changes: 1 addition & 1 deletion ...ysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ protected void run() throws ToolException {
}
qc.getVariant().setGenomePlot(genomePlot);

catalogManager.getSampleManager().update(getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
catalogManager.getSampleManager().update(organizationId, getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
QueryOptions.empty(), getToken());
}
}
Expand Down
2 changes: 1 addition & 1 deletion ...analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -239,7 +239,7 @@ protected void run() throws ToolException {
qc.getVariant().setHrDetects(new ArrayList<>());
}
qc.getVariant().getHrDetects().add(hrDetect);
catalogManager.getSampleManager().update(getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
catalogManager.getSampleManager().update(organizationId, getStudy(), sample.getId(), new SampleUpdateParams().setQualityControl(qc),
QueryOptions.empty(), getToken());
});
}
Expand Down
4 changes: 2 additions & 2 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/julie/JulieTool.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@ protected void check() throws Exception {
String project = getParams().getString(ParamConstants.PROJECT_PARAM);

if (StringUtils.isEmpty(project)) {
String userId = getCatalogManager().getUserManager().getUserId(getToken());
User user = catalogManager.getUserManager().get(userId, null, getToken()).first();
String userId = getCatalogManager().getUserManager().getUserId(organizationId, getToken());
User user = catalogManager.getUserManager().get(organizationId, userId, null, getToken()).first();
if (CollectionUtils.isEmpty(user.getProjects()) || user.getProjects().size() > 1) {
throw new CatalogException("Missing '" + ParamConstants.PROJECT_PARAM + "' parameter");
} else {
Expand Down
6 changes: 3 additions & 3 deletions ...s/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantCatalogQueryUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -279,8 +279,8 @@ public Query parseQuery(Query query, QueryOptions queryOptions, CellBaseUtils ce

if (isValidParam(query, SAVED_FILTER)) {
String savedFilter = query.getString(SAVED_FILTER.key());
String userId = catalogManager.getUserManager().getUserId(token);
UserFilter userFilter = catalogManager.getUserManager().getFilter(userId, savedFilter, token).first();
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
UserFilter userFilter = catalogManager.getUserManager().getFilter(organizationId, userId, savedFilter, token).first();
if (!userFilter.getResource().equals(Enums.Resource.VARIANT)) {
throw VariantQueryException.malformedParam(SAVED_FILTER, savedFilter,
"The selected saved filter is not a filter for '" + Enums.Resource.VARIANT + "'. "
Expand Down Expand Up @@ -1610,7 +1610,7 @@ protected List<String> getValuesToValidate(List<String> rawValues) {
protected List<String> validate(String defaultStudyStr, List<String> values, Integer release, VariantQueryParam param,
String sessionId) throws CatalogException {
if (release == null) {
String userId = catalogManager.getUserManager().getUserId(sessionId);
String userId = catalogManager.getUserManager().getUserId(organizationId, sessionId);
// DataResult<Sample> samples = catalogManager.getSampleManager().get(defaultStudyStr, values,
// SampleManager.INCLUDE_SAMPLE_IDS, sessionId);
long numMatches = catalogManager.getSampleManager()
Expand Down
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