Merge pull request #2343 from opencb/TASK-4210

TASK-4210 - Catalog delete operations may not check if data is used in Clinical Analyses

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/IndividualMongoDBAdaptor.java

@@ -644,7 +644,6 @@ private void updateClinicalAnalysisIndividualReferences(ClientSession clientSess
      */
     private void checkInUseInClinicalAnalysis(ClientSession clientSession, Document individual)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
-        String individualId = individual.getString(QueryParams.ID.key());
         long individualUid = individual.getLong(PRIVATE_UID);
         long studyUid = individual.getLong(PRIVATE_STUDY_UID);
 
@@ -653,8 +652,7 @@ private void checkInUseInClinicalAnalysis(ClientSession clientSession, Document
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.INDIVIDUAL.key(), individualUid);
         OpenCGAResult<Long> count = dbAdaptorFactory.getClinicalAnalysisDBAdaptor().count(clientSession, query);
         if (count.getNumMatches() > 0) {
-            throw new CatalogDBException("Could not delete individual '" + individualId + "'. Individual is in use in "
-                    + count.getNumMatches() + " cases");
+            throw new CatalogDBException("Individual is in use in " + count.getNumMatches() + " cases");
         }
     }
 
@@ -940,7 +938,7 @@ public OpenCGAResult delete(Individual individual) throws CatalogDBException, Ca
             return runTransaction(clientSession -> privateDelete(clientSession, result.first()));
         } catch (CatalogDBException e) {
             logger.error("Could not delete individual {}: {}", individual.getId(), e.getMessage(), e);
-            throw new CatalogDBException("Could not delete individual " + individual.getId() + ": " + e.getMessage(), e.getCause());
+            throw new CatalogDBException("Could not delete individual " + individual.getId() + ": " + e.getMessage(), e);
         }
     }
 
@@ -976,7 +974,7 @@ OpenCGAResult<Object> privateDelete(ClientSession clientSession, Document indivi
         checkInUseInClinicalAnalysis(clientSession, individualDocument);
 
         logger.debug("Deleting individual {} ({})", individualId, individualUid);
-        // Look for all the different family versions
+        // Look for all the different individual versions
         Query individualQuery = new Query()
                 .append(QueryParams.UID.key(), individualUid)
                 .append(QueryParams.STUDY_UID.key(), studyUid);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/SampleMongoDBAdaptor.java

@@ -500,7 +500,6 @@ void updateIndividualIdFromSamples(ClientSession clientSession, long studyUid, S
      */
     private void checkInUseInClinicalAnalysis(ClientSession clientSession, Document sample)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
-        String sampleId = sample.getString(QueryParams.ID.key());
         long sampleUid = sample.getLong(QueryParams.UID.key());
         long studyUid = sample.getLong(QueryParams.STUDY_UID.key());
 
@@ -509,8 +508,7 @@ private void checkInUseInClinicalAnalysis(ClientSession clientSession, Document
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.SAMPLE.key(), sampleUid);
         OpenCGAResult<Long> count = dbAdaptorFactory.getClinicalAnalysisDBAdaptor().count(clientSession, query);
         if (count.getNumMatches() > 0) {
-            throw new CatalogDBException("Could not delete sample '" + sampleId + "'. Sample is in use in "
-                    + count.getNumMatches() + " cases");
+            throw new CatalogDBException("Sample is in use in " + count.getNumMatches() + " cases");
         }
     }
 
@@ -860,7 +858,7 @@ public OpenCGAResult delete(Sample sample) throws CatalogDBException, CatalogPar
             return runTransaction(clientSession -> privateDelete(clientSession, result.first()));
         } catch (CatalogDBException e) {
             logger.error("Could not delete sample {}: {}", sample.getId(), e.getMessage(), e);
-            throw new CatalogDBException("Could not delete sample " + sample.getId() + ": " + e.getMessage(), e.getCause());
+            throw new CatalogDBException("Could not delete sample " + sample.getId() + ": " + e.getMessage(), e);
         }
     }
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FamilyManager.java

@@ -530,7 +530,8 @@ private void checkCanBeDeleted(Study study, Family family) throws CatalogExcepti
         OpenCGAResult<ClinicalAnalysis> result = clinicalDBAdaptor.get(query, ClinicalAnalysisManager.INCLUDE_CLINICAL_IDS);
         if (result.getNumResults() > 0) {
             String clinicalIds = result.getResults().stream().map(ClinicalAnalysis::getId).collect(Collectors.joining(", "));
-            throw new CatalogException("Family {" + family.getId() + "} in use in Clinical Analyses: {" + clinicalIds + "}");
+            throw new CatalogException("Could not delete family '" + family.getId() + "'. Family is in use in Clinical Analyses: '"
+                    + clinicalIds + "'");
         }
     }
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/IndividualManager.java

@@ -710,10 +710,8 @@ private OpenCGAResult delete(Study study, Individual individual, ObjectMap param
         // Check if the individual can be deleted
         if (!params.getBoolean(Constants.FORCE, false)) {
             if (familyDataResult.getNumResults() > 0) {
-                throw new CatalogException("Individual found in the families: " + familyDataResult.getResults()
-                        .stream()
-                        .map(Family::getId)
-                        .collect(Collectors.joining(", ")));
+                throw new CatalogException("Could not delete individual '" + individual.getId() + "'. Individual found in the families: "
+                        + familyDataResult.getResults().stream().map(Family::getId).collect(Collectors.joining(", ")));
             }
         } else {
             logger.info("Forcing deletion of individuals belonging to families");

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/SampleManager.java

@@ -815,6 +815,7 @@ public OpenCGAResult<Sample> resetAnnotations(String studyStr, String sampleStr,
     }
 
     private void checkSampleCanBeDeleted(long studyId, Sample sample, boolean force) throws CatalogException {
+        String msg = "Could not delete sample '" + sample.getId() + "'. ";
         // Look for files related with the sample
         Query query = new Query()
                 .append(FileDBAdaptor.QueryParams.SAMPLE_IDS.key(), sample.getId())
@@ -834,9 +835,9 @@ private void checkSampleCanBeDeleted(long studyId, Sample sample, boolean force)
         }
         if (!errorFiles.isEmpty()) {
             if (force) {
-                throw new CatalogException("Associated files are used in storage: " + StringUtils.join(errorFiles, ", "));
+                throw new CatalogException(msg + "Associated files are used in storage: " + StringUtils.join(errorFiles, ", "));
             } else {
-                throw new CatalogException("Sample associated to the files: " + StringUtils.join(errorFiles, ", "));
+                throw new CatalogException(msg + "Sample associated to the files: " + StringUtils.join(errorFiles, ", "));
             }
         }
 
@@ -865,14 +866,14 @@ private void checkSampleCanBeDeleted(long studyId, Sample sample, boolean force)
             }
         }
         if (associatedToDefaultCohort) {
-            throw new CatalogException("Sample in cohort " + StudyEntry.DEFAULT_COHORT);
+            throw new CatalogException(msg + "Sample in cohort " + StudyEntry.DEFAULT_COHORT);
         }
         if (!errorCohorts.isEmpty()) {
             if (force) {
-                throw new CatalogException("Sample present in cohorts in the process of calculating the stats: "
+                throw new CatalogException(msg + "Sample present in cohorts in the process of calculating the stats: "
                         + StringUtils.join(errorCohorts, ", "));
             } else {
-                throw new CatalogException("Sample present in cohorts: " + StringUtils.join(errorCohorts, ", "));
+                throw new CatalogException(msg + "Sample present in cohorts: " + StringUtils.join(errorCohorts, ", "));
             }
         }
 
@@ -884,8 +885,7 @@ private void checkSampleCanBeDeleted(long studyId, Sample sample, boolean force)
             OpenCGAResult<Individual> individualDataResult = individualDBAdaptor.get(query, new QueryOptions(QueryOptions.INCLUDE,
                     Arrays.asList(IndividualDBAdaptor.QueryParams.UID.key(), IndividualDBAdaptor.QueryParams.ID.key())));
             if (individualDataResult.getNumResults() > 0) {
-                throw new CatalogException("Sample from individual " + individualDataResult.first().getName() + "("
-                        + individualDataResult.first().getUid() + ")");
+                throw new CatalogException(msg + "Sample is associated with individual '" + individualDataResult.first().getId() + "'.");
             }
         }
     }

opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/SampleManagerTest.java

@@ -2786,7 +2786,7 @@ public void deleteInUseInCATest() throws CatalogException {
 
         try {
             catalogManager.getSampleManager().delete(studyFqn, Collections.singletonList(case1.getProband().getSamples().get(0).getId()),
-                    new QueryOptions(ParamConstants.FORCE, true), token);
+                    new QueryOptions(ParamConstants.FORCE, false), token);
         } catch (CatalogException e) {
             assertTrue(e.getMessage().contains("in use in 3 cases"));
         }