TASK-1415 - Fix OpenCGA audit handling

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/metadata/CatalogStorageMetadataSynchronizerTest.java

@@ -158,7 +158,7 @@ public static File create(String resourceName, boolean indexed) throws IOExcepti
             catalogManager.getFileManager().updateFileInternalVariantIndex(file,
                     FileInternalVariantIndex.init().setStatus(new VariantIndexStatus(InternalStatus.READY)), sessionId);
             indexedFiles.add(file.getName());
-            List<String> samples = catalogManager.getCohortManager().getSamples(studyId, cohortId, sessionId).getResults().stream().map(Sample::getId).collect(Collectors.toList());
+            List<String> samples = catalogManager.getCohortManager().get(studyId, cohortId, QueryOptions.empty(), sessionId).first().getSamples().stream().map(Sample::getId).collect(Collectors.toList());
             samples.addAll(file.getSampleIds());
             List<SampleReferenceParam> sampleReferenceParams = samples.stream().map(s -> new SampleReferenceParam().setId(s)).collect(Collectors.toList());
             catalogManager.getCohortManager().update(studyId, cohortId,
@@ -172,8 +172,9 @@ public void updateCatalogFromStorageTest() throws Exception {
 
         StudyMetadata sm = studyConfigurationFactory.getStudyMetadata(studyId);
 
-        List<String> samples = catalogManager.getCohortManager().getSamples(studyId, cohortId, sessionId)
-                .getResults()
+        List<String> samples = catalogManager.getCohortManager().get(studyId, cohortId, QueryOptions.empty(), sessionId)
+                .first()
+                .getSamples()
                 .stream()
                 .map(Sample::getId)
                 .collect(Collectors.toList());

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/CoreDBAdaptor.java

@@ -28,7 +28,7 @@ DBIterator<T> iterator(long studyUid, Query query, QueryOptions options, String
     DBIterator nativeIterator(long studyUid, Query query, QueryOptions options, String user)
             throws CatalogDBException, CatalogAuthorizationException, CatalogParameterException;
 
-    OpenCGAResult<Long> count(Query query, String user) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
+    OpenCGAResult<T> count(Query query, String user) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
     OpenCGAResult<T> groupBy(Query query, List<String> fields, QueryOptions options, String user)
             throws CatalogDBException, CatalogAuthorizationException, CatalogParameterException;

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/DBAdaptor.java

@@ -45,11 +45,11 @@ public interface DBAdaptor<T> extends Iterable<T> {
     @Deprecated
     String FORCE = "force";
 
-    default OpenCGAResult<Long> count() throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    default OpenCGAResult<T> count() throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(new Query());
     }
 
-    OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
+    OpenCGAResult<T> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
     default OpenCGAResult<T> stats() {
         return stats(new Query());

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

@@ -148,23 +148,24 @@ public MongoDBCollection getClinicalCollection() {
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<ClinicalAnalysis> count(Query query)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    OpenCGAResult<ClinicalAnalysis> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query);
         return new OpenCGAResult<>(clinicalCollection.count(clientSession, bson));
     }
 
     @Override
-    public OpenCGAResult<Long> count(final Query query, final String user)
+    public OpenCGAResult<ClinicalAnalysis> count(final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query, user);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, final Query query, final String user)
+    OpenCGAResult<ClinicalAnalysis> count(ClientSession clientSession, final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, user);
         logger.debug("Clinical count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
@@ -300,7 +301,7 @@ UpdateDocument parseAndValidateUpdateParams(ObjectMap parameters, List<ClinicalA
             tmpQuery = new Query()
                     .append(QueryParams.ID.key(), parameters.get(QueryParams.ID.key()))
                     .append(QueryParams.STUDY_UID.key(), studyId);
-            OpenCGAResult<Long> count = count(tmpQuery);
+            OpenCGAResult<ClinicalAnalysis> count = count(tmpQuery);
             if (count.getNumMatches() > 0) {
                 throw new CatalogDBException("Cannot set id for clinical analysis. A clinical analysis with { id: '"
                         + parameters.get(QueryParams.ID.key()) + "'} already exists.");

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

@@ -191,23 +191,23 @@ public OpenCGAResult unmarkPermissionRule(long studyId, String permissionRuleId)
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<Cohort> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    private OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    private OpenCGAResult<Cohort> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         long startTime = startQuery();
         return endQuery(startTime, cohortCollection.count(clientSession, parseQuery(query)));
     }
 
     @Override
-    public OpenCGAResult<Long> count(final Query query, final String user)
+    public OpenCGAResult<Cohort> count(final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query, user);
     }
 
-    private OpenCGAResult<Long> count(ClientSession clientSession, final Query query, final String user)
+    private OpenCGAResult<Cohort> count(ClientSession clientSession, final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, user);
         logger.debug("Cohort count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
@@ -441,8 +441,8 @@ private UpdateDocument parseAndValidateUpdateParams(ClientSession clientSession,
 
             tmpQuery = new Query()
                     .append(QueryParams.ID.key(), parameters.get(QueryParams.ID.key()))
-                    .append(STUDY_UID.key(), studyId);
-            OpenCGAResult<Long> count = count(clientSession, tmpQuery);
+                    .append(QueryParams.STUDY_UID.key(), studyId);
+            OpenCGAResult<Cohort> count = count(clientSession, tmpQuery);
             if (count.getNumMatches() > 0) {
                 throw new CatalogDBException("Cannot update the " + QueryParams.ID.key() + ". Cohort "
                         + parameters.get(QueryParams.ID.key()) + " already exists.");

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

@@ -46,6 +46,7 @@
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.config.Configuration;
+import org.opencb.opencga.core.models.clinical.ClinicalAnalysis;
 import org.opencb.opencga.core.models.cohort.Cohort;
 import org.opencb.opencga.core.models.common.AnnotationSet;
 import org.opencb.opencga.core.models.common.Enums;
@@ -230,23 +231,23 @@ private void createMissingIndividual(ClientSession clientSession, long studyUid,
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<Family> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    OpenCGAResult<Family> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query);
         return new OpenCGAResult<>(familyCollection.count(clientSession, bson));
     }
 
     @Override
-    public OpenCGAResult<Long> count(final Query query, final String user)
+    public OpenCGAResult<Family> count(final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query, user);
     }
 
-    public OpenCGAResult<Long> count(ClientSession clientSession, final Query query, final String user)
+    public OpenCGAResult<Family> count(ClientSession clientSession, final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, user);
         logger.debug("Family count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
@@ -654,7 +655,7 @@ UpdateDocument parseAndValidateUpdateParams(ClientSession clientSession, ObjectM
             tmpQuery = new Query()
                     .append(QueryParams.ID.key(), parameters.get(QueryParams.ID.key()))
                     .append(QueryParams.STUDY_UID.key(), familyDataResult.first().getStudyUid());
-            OpenCGAResult<Long> count = count(clientSession, tmpQuery);
+            OpenCGAResult<Family> count = count(clientSession, tmpQuery);
             if (count.getNumMatches() > 0) {
                 throw new CatalogDBException("Cannot set '" + QueryParams.ID.key() + "' for family. A family with { '"
                         + QueryParams.ID.key() + "': '" + parameters.get(QueryParams.ID.key()) + "'} already exists.");
@@ -731,7 +732,7 @@ OpenCGAResult<Object> privateDelete(ClientSession clientSession, Document family
         Query queryCheck = new Query()
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.FAMILY_UID.key(), familyUid)
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.STUDY_UID.key(), studyUid);
-        OpenCGAResult<Long> count = dbAdaptorFactory.getClinicalAnalysisDBAdaptor().count(clientSession, queryCheck);
+        OpenCGAResult<ClinicalAnalysis> count = dbAdaptorFactory.getClinicalAnalysisDBAdaptor().count(clientSession, queryCheck);
         if (count.getNumMatches() > 0) {
             throw new CatalogDBException("Could not delete family. Family is in use in " + count.getNumMatches() + " cases");
         }

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

@@ -965,18 +965,18 @@ public OpenCGAResult restore(long id, QueryOptions queryOptions) throws CatalogD
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<File> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    OpenCGAResult<File> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query);
         return new OpenCGAResult<>(fileCollection.count(clientSession, bson));
     }
 
     @Override
-    public OpenCGAResult<Long> count(final Query query, final String user)
+    public OpenCGAResult<File> count(final Query query, final String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, user);
         logger.debug("File count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));

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

@@ -275,23 +275,24 @@ public OpenCGAResult unmarkPermissionRule(long studyId, String permissionRuleId)
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<Individual> count(Query query)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    public OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    public OpenCGAResult<Individual> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query);
         return new OpenCGAResult<>(individualCollection.count(clientSession, bson));
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query, String user)
+    public OpenCGAResult<Individual> count(Query query, String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query, user);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, Query query, String user)
+    OpenCGAResult<Individual> count(ClientSession clientSession, Query query, String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, user);
         logger.debug("Individual count: query : {}, dbTime: {}", bson.toBsonDocument(Document.class,
@@ -653,7 +654,7 @@ private void checkInUseInClinicalAnalysis(ClientSession clientSession, Document
         Query query = new Query()
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.STUDY_UID.key(), studyUid)
                 .append(ClinicalAnalysisDBAdaptor.QueryParams.INDIVIDUAL.key(), individualUid);
-        OpenCGAResult<Long> count = dbAdaptorFactory.getClinicalAnalysisDBAdaptor().count(clientSession, query);
+        OpenCGAResult<ClinicalAnalysis> 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");
@@ -675,7 +676,7 @@ UpdateDocument parseAndValidateUpdateParams(ClientSession clientSession, ObjectM
             Query tmpQuery = new Query()
                     .append(QueryParams.ID.key(), parameters.get(QueryParams.ID.key()))
                     .append(QueryParams.STUDY_UID.key(), studyId);
-            OpenCGAResult<Long> count = count(clientSession, tmpQuery);
+            OpenCGAResult<Individual> count = count(clientSession, tmpQuery);
             if (count.getNumMatches() > 0) {
                 throw new CatalogDBException("Cannot set id for individual. An individual with { id: '"
                         + parameters.get(QueryParams.ID.key()) + "'} already exists.");

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

@@ -325,18 +325,18 @@ public OpenCGAResult updateProjectRelease(long studyId, int release)
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException {
+    public OpenCGAResult<Interpretation> count(Query query) throws CatalogDBException {
         return count(null, query);
     }
 
-    public OpenCGAResult<Long> count(ClientSession clientSession, Query query) throws CatalogDBException {
+    public OpenCGAResult<Interpretation> count(ClientSession clientSession, Query query) throws CatalogDBException {
         Bson bson = parseQuery(query);
         logger.debug("Interpretation count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
         return new OpenCGAResult<>(interpretationCollection.count(clientSession, bson));
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query, String user)
+    public OpenCGAResult<Interpretation> count(Query query, String user)
             throws CatalogDBException {
         return count(query);
     }
@@ -415,7 +415,7 @@ private UpdateDocument parseAndValidateUpdateParams(ClientSession clientSession,
                 tmpQuery = new Query()
                         .append(QueryParams.ID.key(), parameters.get(QueryParams.ID.key()))
                         .append(QueryParams.STUDY_UID.key(), studyId);
-                OpenCGAResult<Long> count = count(clientSession, tmpQuery);
+                OpenCGAResult<Interpretation> count = count(clientSession, tmpQuery);
                 if (count.getNumMatches() > 0) {
                     throw new CatalogDBException("Cannot set id for interpretation. A interpretation with { id: '"
                             + parameters.get(QueryParams.ID.key()) + "'} already exists.");

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

@@ -190,22 +190,22 @@ public OpenCGAResult unmarkPermissionRule(long studyId, String permissionRuleId)
     }
 
     @Override
-    public OpenCGAResult<Long> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
+    public OpenCGAResult<Job> count(Query query) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         return count(null, query);
     }
 
-    OpenCGAResult<Long> count(ClientSession clientSession, Query query)
+    OpenCGAResult<Job> count(ClientSession clientSession, Query query)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bsonDocument = parseQuery(query, QueryOptions.empty());
         return new OpenCGAResult<>(jobCollection.count(clientSession, bsonDocument));
     }
 
 
     @Override
-    public OpenCGAResult<Long> count(Query query, String user)
+    public OpenCGAResult<Job> count(Query query, String user)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
         Bson bson = parseQuery(query, QueryOptions.empty(), user);
-        logger.debug("Job count: query : {}, dbTime: {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
+        logger.debug("Job count: query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
         return new OpenCGAResult<>(jobCollection.count(bson));
     }