analysis: fix several analysis, #TASK-4389

opencga-analysis/src/main/java/org/opencb/opencga/analysis/ResourceUtils.java

@@ -24,6 +24,8 @@
 import org.opencb.opencga.catalog.db.api.ProjectDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.project.Project;
 import org.opencb.opencga.core.response.OpenCGAResult;
 
@@ -116,6 +118,11 @@ public static DownloadedRefGenome downloadRefGenome(String assembly, Path outDir
     public static String getAssembly(CatalogManager catalogManager, String studyId, String sessionId) throws CatalogException {
         String assembly = "";
         OpenCGAResult<Project> projectQueryResult;
+
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(sessionId);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
+
         projectQueryResult = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyId),
                 new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), sessionId);
         if (CollectionUtils.isNotEmpty(projectQueryResult.getResults())

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentGeneCoverageStatsAnalysis.java

@@ -117,7 +117,7 @@ protected void run() throws ToolException {
                 }
                 qc.getCoverage().setGeneCoverageStats(geneCoverageStats);
 
-                catalogManager.getFileManager().update(organizationId, getStudy(), catalogBamFile.getId(), new FileUpdateParams().setQualityControl(qc),
+                catalogManager.getFileManager().update(getStudy(), catalogBamFile.getId(), new FileUpdateParams().setQualityControl(qc),
                         QueryOptions.empty(), getToken());
             }
         });

opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java

@@ -230,7 +230,7 @@ protected void run() throws ToolException {
             }
 
             if (saveQc) {
-                catalogManager.getFileManager().update(organizationId, getStudy(), catalogBamFile.getId(), new FileUpdateParams().setQualityControl(qc),
+                catalogManager.getFileManager().update(getStudy(), catalogBamFile.getId(), new FileUpdateParams().setQualityControl(qc),
                         QueryOptions.empty(), getToken());
             }
         });

opencga-analysis/src/main/java/org/opencb/opencga/analysis/annotations/TsvAnnotationLoader.java

@@ -26,9 +26,11 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.FileManager;
 import org.opencb.opencga.catalog.utils.AnnotationUtils;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.catalog.utils.Constants;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.AnnotationSet;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.sample.SamplePermissions;
@@ -71,7 +73,9 @@ public void setStudy(String study) {
 
     @Override
     protected void check() throws Exception {
-        String userId = catalogManager.getUserManager().getUserId(organizationId, token);
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(study, jwtPayload);
+        String userId = jwtPayload.getUserId(studyFqn.getOrganizationId());
 
         OpenCGAResult<File> fileResult = catalogManager.getFileManager().get(study, path, FileManager.INCLUDE_FILE_URI_PATH, token);
         if (fileResult.getNumResults() == 0) {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationManager.java

@@ -50,9 +50,11 @@
 import org.opencb.opencga.catalog.managers.ClinicalAnalysisManager;
 import org.opencb.opencga.catalog.managers.FamilyManager;
 import org.opencb.opencga.catalog.managers.StudyManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.clinical.ClinicalAnalysis;
 import org.opencb.opencga.core.models.clinical.Interpretation;
 import org.opencb.opencga.core.models.individual.Individual;
@@ -818,9 +820,13 @@ public List<ClinicalVariant> getPrimaryFindings(String clinicalAnalysisId, Query
         return clinicalVariants;
     }
 
-    public ClinicalAnalyst getAnalyst(String token) throws ToolException {
+    public ClinicalAnalyst getAnalyst(String studyId, String token) throws ToolException {
         try {
-            String userId = catalogManager.getUserManager().getUserId(organizationId, token);
+            JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+            CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+            String organizationId = studyFqn.getOrganizationId();
+            String userId = jwtPayload.getUserId(studyFqn.getOrganizationId());
+
             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();
@@ -831,6 +837,10 @@ public ClinicalAnalyst getAnalyst(String token) throws ToolException {
     }
 
     public String getAssembly(String studyId, String sessionId) throws CatalogException {
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(sessionId);
+        CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+        String organizationId = studyFqn.getOrganizationId();
+
         String assembly = "";
         OpenCGAResult<Project> projectQueryResult;
         projectQueryResult = catalogManager.getProjectManager().search(organizationId, new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), studyId),
@@ -877,7 +887,9 @@ 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(organizationId, token);
+        JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+        String organizationId = jwtPayload.getOrganization();
+        String userId = jwtPayload.getUserId();
         List<String> studyIds = getStudyIds(userId, query);
 
         // If one specific clinical analysis, sample or individual is provided we expect a single valid study as well

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/InterpretationAnalysis.java

@@ -118,7 +118,7 @@ protected void saveInterpretation(String studyId, ClinicalAnalysis clinicalAnaly
                         .setCommit(GitRepositoryState.getInstance().getCommitId())));
 
         // Analyst
-        ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(token);
+        ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(studyId, token);
 
         List<ClinicalVariant> primaryFindings = readClinicalVariants(Paths.get(getOutDir().toString() + "/"
                 + PRIMARY_FINDINGS_FILENAME));

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java

@@ -145,7 +145,7 @@ protected void saveInterpretation(String studyId, ClinicalAnalysis clinicalAnaly
                         .setVersion(ExomiserWrapperAnalysisExecutor.DOCKER_IMAGE_VERSION)));
 
         // Analyst
-        ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(token);
+        ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(studyId, token);
 
         List<ClinicalVariant> primaryFindings = getPrimaryFindings();
 

opencga-analysis/src/main/java/org/opencb/opencga/analysis/cohort/CohortIndexTask.java

@@ -27,6 +27,7 @@
 import org.opencb.opencga.catalog.stats.solr.converters.CatalogCohortToSolrCohortConverter;
 import org.opencb.opencga.catalog.stats.solr.converters.SolrConverterUtil;
 import org.opencb.opencga.core.api.ParamConstants;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.response.OpenCGAResult;

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/PedigreeGraphInitAnalysis.java

@@ -80,7 +80,7 @@ protected void run() throws ToolException {
             for (Family family: familiesToUpdate) {
                 try {
                     logger.info("Updating pedigree graph for family '{}'", family.getId());
-                    catalogManager.getFamilyManager().update(organizationId, study, family.getId(), null,
+                    catalogManager.getFamilyManager().update(study, family.getId(), null,
                             new QueryOptions(ParamConstants.FAMILY_UPDATE_PEDIGREEE_GRAPH_PARAM, true), token);
                     String msg = "Updated pedigree graph for family '" + family.getId() + "'";
                     logger.info(msg);

opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcAnalysis.java

@@ -23,7 +23,9 @@
 import org.opencb.opencga.analysis.tools.OpenCgaTool;
 import org.opencb.opencga.analysis.variant.relatedness.RelatednessAnalysis;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.family.Family;
 import org.opencb.opencga.core.models.family.FamilyQualityControl;
@@ -67,8 +69,12 @@ protected void check() throws Exception {
 
         // Check permissions
         try {
+            JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+            CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyId, jwtPayload);
+            String organizationId = studyFqn.getOrganizationId();
+            String userId = jwtPayload.getUserId(organizationId);
+
             Study study = catalogManager.getStudyManager().get(studyId, QueryOptions.empty(), token).first();
-            String userId = catalogManager.getUserManager().getUserId(organizationId, token);
             catalogManager.getAuthorizationManager().checkStudyPermission(organizationId, study.getUid(), userId, WRITE_FAMILIES);
         } catch (CatalogException e) {
             throw new ToolException(e);
@@ -128,7 +134,7 @@ protected void run() throws ToolException {
         try {
             qualityControl = executor.getQualityControl();
             if (qualityControl != null) {
-                catalogManager.getFamilyManager().update(organizationId, getStudyId(), familyId, new FamilyUpdateParams().setQualityControl(qualityControl),
+                catalogManager.getFamilyManager().update(getStudyId(), familyId, new FamilyUpdateParams().setQualityControl(qualityControl),
                         QueryOptions.empty(), token);
             }
         } catch (CatalogException e) {

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java

@@ -22,8 +22,10 @@
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.exceptions.CatalogIOException;
 import org.opencb.opencga.catalog.managers.StudyManager;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.core.common.UriUtils;
 import org.opencb.opencga.core.exceptions.ToolException;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.file.FileFetch;
@@ -73,9 +75,11 @@ protected void check() throws Exception {
         }
 
         try {
+            JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token);
+            CatalogFqn catalogFqn= CatalogFqn.extractFqnFromStudy(studyFqn, jwtPayload);
             Study study = catalogManager.getStudyManager().get(studyFqn, StudyManager.INCLUDE_STUDY_IDS, token).first();
 
-            OpenCGAResult<File> parents = catalogManager.getFileManager().getParents(studyFqn, toolParams.getPath(), false,
+            OpenCGAResult<File> parents = catalogManager.getFileManager().getParents(study.getFqn(), toolParams.getPath(), false,
                     QueryOptions.empty(), token);
             if (parents.getNumResults() == 0) {
                 throw new ToolException("No parent folders found for " + toolParams.getPath());
@@ -85,10 +89,10 @@ 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(organizationId, token);
+            String userId = jwtPayload.getUserId(catalogFqn.getOrganizationId());
             // Check write permissions over the path
-            catalogManager.getAuthorizationManager()
-                    .checkFilePermission(organizationId, study.getUid(), parents.first().getUid(), userId, FilePermissions.WRITE);
+            catalogManager.getAuthorizationManager().checkFilePermission(catalogFqn.getOrganizationId(), study.getUid(),
+                    parents.first().getUid(), userId, FilePermissions.WRITE);
         } catch (CatalogException e) {
             throw new ToolException(e);
         }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileDeleteTask.java

@@ -112,13 +112,13 @@ protected void run() throws Exception {
                 try {
                     // Update file status to PENDING_DELETE and add tags mark
                     if (catalogFile.getType() == File.Type.FILE) {
-                        fileManager.update(organizationId, studyFqn, file, updateParams, options, token);
+                        fileManager.update(studyFqn, file, updateParams, options, token);
                     } else {
                         // We mark for deletion all the
                         Query query = new Query()
                                 .append(FileDBAdaptor.QueryParams.INTERNAL_STATUS_ID.key(), FileStatus.READY)
                                 .append(FileDBAdaptor.QueryParams.PATH.key(), "~^" + catalogFile.getPath() + "*");
-                        fileManager.update(organizationId, studyFqn, query, updateParams, options, token);
+                        fileManager.update(studyFqn, query, updateParams, options, token);
                     }
                 } catch (Exception e) {
                     logger.error("Error updating status of file '{}' to PENDING_DELETE: {}", file, e.getMessage(), e);
@@ -236,7 +236,7 @@ private void setToMissingFile(File file) {
 
     private void restore(Query query, FileUpdateParams updateParams, QueryOptions options) {
         try {
-            catalogManager.getFileManager().update(organizationId, studyFqn, query, updateParams, options, token);
+            catalogManager.getFileManager().update(studyFqn, query, updateParams, options, token);
         } catch (CatalogException e) {
             addCriticalError(e);
         }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileTsvAnnotationLoader.java

@@ -45,6 +45,6 @@ public int count(Query query) throws CatalogException {
     public void addAnnotationSet(String entryId, AnnotationSet annotationSet, QueryOptions options) throws CatalogException {
         FileUpdateParams fileUpdateParams = new FileUpdateParams().setAnnotationSets(Collections.singletonList(annotationSet));
         options.put(Constants.ACTIONS, new ObjectMap(AnnotationSetManager.ANNOTATION_SETS, ParamUtils.BasicUpdateAction.ADD));
-        catalogManager.getFileManager().update(organizationId, study, entryId, fileUpdateParams, options, token);
+        catalogManager.getFileManager().update(study, entryId, fileUpdateParams, options, token);
     }
 }

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileUnlinkTask.java

@@ -101,13 +101,13 @@ protected void run() throws Exception {
                 try {
                     // Update file status to PENDING_DELETE and add tags mark
                     if (catalogFile.getType() == File.Type.FILE) {
-                        fileManager.update(organizationId, studyFqn, file, updateParams, options, token);
+                        fileManager.update(studyFqn, file, updateParams, options, token);
                     } else {
                         // We mark for deletion all the
                         Query query = new Query()
                                 .append(FileDBAdaptor.QueryParams.INTERNAL_STATUS_ID.key(), FileStatus.READY)
                                 .append(FileDBAdaptor.QueryParams.PATH.key(), "~^" + catalogFile.getPath() + "*");
-                        fileManager.update(organizationId, studyFqn, query, updateParams, options, token);
+                        fileManager.update(studyFqn, query, updateParams, options, token);
                     }
                 } catch (Exception e) {
                     logger.error("Error updating status of file '{}' to PENDING_DELETE: {}", file, e.getMessage(), e);
@@ -176,15 +176,14 @@ private void restoreFiles(Query query) {
 
     private void restore(Query query, FileUpdateParams updateParams, QueryOptions options) {
         try {
-            catalogManager.getFileManager().update(organizationId, studyFqn, query, updateParams, options, token);
+            catalogManager.getFileManager().update(studyFqn, query, updateParams, options, token);
         } catch (CatalogException e) {
             addCriticalError(e);
         }
     }
 
     private void addCriticalError(CatalogException e) {
-        CatalogException exception = new CatalogException("Critical: Could not restore status of pending files to "
-                + FileStatus.READY, e);
+        CatalogException exception = new CatalogException("Critical: Could not restore status of pending files to " + FileStatus.READY, e);
         logger.error("{}", e.getMessage(), e);
         try {
             addError(exception);

opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/PostLinkSampleAssociation.java

@@ -195,7 +195,7 @@ protected void run() throws Exception {
 
                         QueryOptions queryOptions = new QueryOptions(Constants.ACTIONS, actionMap);
 
-                        OpenCGAResult<File> fileUpdateResult = catalogManager.getFileManager().update(organizationId, study, file.getUuid(),
+                        OpenCGAResult<File> fileUpdateResult = catalogManager.getFileManager().update(study, file.getUuid(),
                                 fileUpdateParams, queryOptions, token);
                         if (fileUpdateResult.getNumUpdated() != 1) {
                             throw new CatalogException("Could not update sample list of file '" + file.getPath() + "'.");
@@ -206,7 +206,7 @@ protected void run() throws Exception {
                     FileUpdateParams fileUpdateParams = new FileUpdateParams()
                             .setInternal(new SmallFileInternal(new FileStatus(FileStatus.READY), MissingSamples.initialize()));
 
-                    OpenCGAResult<File> fileUpdateResult = catalogManager.getFileManager().update(organizationId, study, file.getUuid(), fileUpdateParams,
+                    OpenCGAResult<File> fileUpdateResult = catalogManager.getFileManager().update(study, file.getUuid(), fileUpdateParams,
                             QueryOptions.empty(), token);
                     if (fileUpdateResult.getNumUpdated() != 1) {
                         throw new CatalogException("Could not update internal status of file '" + file.getPath() + "'.");