storage: Fix return annotation from sample data. Fix test. #TASK-6005

opencb · May 15, 2024 · f6b73fe · f6b73fe
1 parent c668143
commit f6b73fe
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git a/...b/opencga/analysis/variant/manager/operations/VariantFileIndexerOperationManagerTest.java b/...b/opencga/analysis/variant/manager/operations/VariantFileIndexerOperationManagerTest.java
@@ -26,7 +26,6 @@
 import org.mockito.Mockito;
 import org.opencb.biodata.models.variant.metadata.Aggregation;
 import org.opencb.biodata.models.variant.metadata.VariantSetStats;
-import org.opencb.commons.datastore.core.DataResult;
 import org.opencb.commons.datastore.core.Event;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
@@ -43,8 +42,8 @@
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.file.FileInternalVariantIndex;
 import org.opencb.opencga.core.models.file.VariantIndexStatus;
-import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.models.operations.variant.VariantIndexParams;
+import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.testclassification.duration.MediumTests;
 import org.opencb.opencga.core.tools.result.ExecutionResult;
 import org.opencb.opencga.storage.core.StorageEngineFactory;
@@ -186,7 +185,7 @@ public void testDeleteIndexedFile() throws Exception {
         Study study = catalogManager.getFileManager().getStudy(inputFile, sessionId);
 
         thrown.expect(CatalogException.class);
-        thrown.expectMessage("The status is READY");
+        thrown.expectMessage("Could not unlink file '" + inputFile.getId() + "'");
         catalogManager.getFileManager().unlink(study.getFqn(), inputFile.getId(), sessionId);
     }
 
@@ -200,7 +199,7 @@ public void testDeleteSampleFromIndexedFile() throws Exception {
         Query query = new Query(SampleDBAdaptor.QueryParams.ID.key(), inputFile.getSampleIds().get(100));
         thrown.expect(CatalogException.class);
         thrown.expectMessage("Sample associated to the files");
-        DataResult delete = catalogManager.getSampleManager().delete(studyFqn, query, null, sessionId);
+        catalogManager.getSampleManager().delete(studyFqn, query, null, sessionId);
     }
 
     @Test

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java
@@ -1832,9 +1832,9 @@ public OpenCGAResult<File> unlink(@Nullable String studyId, String fileId, Strin
                     study.getUuid(), auditParams, new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS));
 
             return result;
-        } catch (CatalogException e) {
+        } catch (Exception e) {
             auditManager.audit(userId, Enums.Action.UNLINK, Enums.Resource.FILE, fileId, "", study.getId(), study.getUuid(),
-                    auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError()));
+                    auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR, new Error(0, "", e.getMessage())));
             throw new CatalogException("Could not unlink file '" + fileId + "'", e);
         }
     }

diff --git a/.../opencb/opencga/storage/hadoop/variant/adaptors/sample/HBaseVariantSampleDataManager.java b/.../opencb/opencga/storage/hadoop/variant/adaptors/sample/HBaseVariantSampleDataManager.java
@@ -51,7 +51,7 @@ public HBaseVariantSampleDataManager(VariantHadoopDBAdaptor dbAdaptor) {
     }
 
     @Override
-    protected DataResult<Variant> getSampleData(Variant variant, String study, QueryOptions options,
+    protected DataResult<Variant> getSampleData(Variant inputVariant, String study, QueryOptions options,
                                                 List<String> includeSamples,
                                                 Set<String> genotypes,
                                                 int sampleLimit) {
@@ -78,14 +78,15 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
 
         int skip = Math.max(0, options.getInt(QueryOptions.SKIP, 0));
         int limit = Math.max(0, options.getInt(QueryOptions.LIMIT, 10));
+        byte[] rowKey = VariantPhoenixKeyFactory.generateVariantRowKey(inputVariant);
 
         try {
             List<Integer> samples = new ArrayList<>(limit);
             List<VariantRow.SampleColumn> sampleDataMap = new ArrayList<>(limit);
 
             dbAdaptor.getHBaseManager().act(dbAdaptor.getVariantTable(), table -> {
                 // Create one GET for samples
-                Get get = new Get(VariantPhoenixKeyFactory.generateVariantRowKey(variant));
+                Get get = new Get(rowKey);
                 LinkedList<Filter> filters = new LinkedList<>();
 
                 filters.add(new QualifierFilter(CompareFilter.CompareOp.EQUAL,
@@ -127,7 +128,7 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
                                     samples.add(sampleColumn.getSampleId());
                                     sampleDataMap.add(sampleColumn);
                                 }
-                            }).walk(variant);
+                            }).walk(inputVariant);
                 }
             });
 
@@ -136,8 +137,9 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
             Set<Integer> fileIdsFromSampleIds = metadataManager.getFileIdsFromSampleIds(studyId, samples);
             HBaseToVariantStatsConverter statsConverter = new HBaseToVariantStatsConverter();
             List<VariantStats> stats = new LinkedList<>();
+            Variant variantResult = new Variant(inputVariant.toString());
             dbAdaptor.getHBaseManager().act(dbAdaptor.getVariantTable(), table -> {
-                Get get = new Get(VariantPhoenixKeyFactory.generateVariantRowKey(variant));
+                Get get = new Get(rowKey);
 
                 // Add file columns
                 for (Integer fileId : fileIdsFromSampleIds) {
@@ -161,7 +163,7 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
                 Result result = table.get(get);
 
                 if (result == null || result.isEmpty()) {
-                    throw VariantQueryException.variantNotFound(variant.toString());
+                    throw VariantQueryException.variantNotFound(variantResult.toString());
                 }
                 // Walk row
                 VariantRow.walker(result)
@@ -175,9 +177,9 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
                         })
                         .onVariantAnnotation(column -> {
                             ImmutableBytesWritable b = column.toBytesWritable();
-                            variant.setAnnotation(new HBaseToVariantAnnotationConverter().convert(b.get(), b.getOffset(), b.getLength()));
+                            variantResult.setAnnotation(new HBaseToVariantAnnotationConverter().convert(b));
                         })
-                        .walk(variant);
+                        .walk(variantResult);
             });
 
             // Convert to VariantSampleData
@@ -193,8 +195,7 @@ protected DataResult<Variant> getSampleData(Variant variant, String study, Query
                                     new ArrayList<>(fileIdsFromSampleIds)))
                     .build());
 
-            Variant variantResult = new Variant(variant.toString());
-            variantResult.setId(variant.toString());
+            variantResult.setId(inputVariant.toString());
             StudyEntry studyEntry = converter.convert(sampleDataMap, filesMap, variantResult, studyId);
 
             variantResult.addStudyEntry(studyEntry);