storage: Fix some tests. #TASK-6596

opencb · Jul 24, 2024 · 5d3c7f4 · 5d3c7f4
1 parent 9a7dd15
commit 5d3c7f4
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Showing 4 changed files with 12 additions and 11 deletions.
diff --git a/...re/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineBNDTest.java b/...re/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineBNDTest.java
@@ -48,6 +48,7 @@ public void before() throws Exception {
         variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
         variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
         variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
+        variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
         if (!loaded) {
             clearDB(DB_NAME);
             loadFiles();
@@ -59,6 +60,7 @@ protected void loadFiles() throws Exception {
         variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
         variantStorageEngine.getConfiguration().getCellbase().setVersion(ParamConstants.CELLBASE_VERSION);
         variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE);
+        variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
         studyMetadata = new StudyMetadata(1, "s1");
 //        variantStorageEngine.getOptions().append(VariantStorageOptions.ANNOTATOR_CELLBASE_EXCLUDE.key(), "expression,clinical");
         input1 = getResourceUri("variant-test-bnd.vcf");

diff --git a/.../test/java/org/opencb/opencga/storage/core/variant/dummy/DummyProjectMetadataAdaptor.java b/.../test/java/org/opencb/opencga/storage/core/variant/dummy/DummyProjectMetadataAdaptor.java
@@ -45,10 +45,9 @@ public void refresh() {
     @Override
     public synchronized DataResult<ProjectMetadata> getProjectMetadata() {
         final DataResult<ProjectMetadata> result = new DataResult<>();
-        if (projectMetadata == null) {
-            projectMetadata = new ProjectMetadata("hsapiens", "grch37", 1);
+        if (projectMetadata != null) {
+            result.setResults(Collections.singletonList(projectMetadata.copy()));
         }
-        result.setResults(Collections.singletonList(projectMetadata.copy()));
         return result;
     }
 

diff --git a/...est/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineBNDTest.java b/...est/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineBNDTest.java
@@ -19,7 +19,7 @@ public class HadoopVariantStorageEngineBNDTest extends VariantStorageEngineBNDTe
     @Override
     protected void loadFiles() throws Exception {
         super.loadFiles();
-        VariantHbaseTestUtils.printVariants(getVariantStorageEngine().getDBAdaptor(), newOutputUri());
+        VariantHbaseTestUtils.printVariants(((HadoopVariantStorageEngine) variantStorageEngine).getDBAdaptor(), newOutputUri());
     }
 
 }
diff --git a/...src/test/java/org/opencb/opencga/storage/hadoop/variant/index/family/FamilyIndexTest.java b/...src/test/java/org/opencb/opencga/storage/hadoop/variant/index/family/FamilyIndexTest.java
@@ -63,13 +63,13 @@ public class FamilyIndexTest extends VariantStorageBaseTest implements HadoopVar
 
     @Before
     public void before() throws Exception {
+        HadoopVariantStorageEngine variantStorageEngine = getVariantStorageEngine();
+        variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
+        variantStorageEngine.getConfiguration().getCellbase().setVersion("v5.2");
+        variantStorageEngine.getConfiguration().getCellbase().setDataRelease("3");
+        variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
+        variantStorageEngine.reloadCellbaseConfiguration();
         if (!loaded) {
-            HadoopVariantStorageEngine variantStorageEngine = getVariantStorageEngine();
-            variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
-            variantStorageEngine.getConfiguration().getCellbase().setVersion("v5.2");
-            variantStorageEngine.getConfiguration().getCellbase().setDataRelease("3");
-            variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
-            variantStorageEngine.reloadCellbaseConfiguration();
             URI outputUri = newOutputUri();
 
             ObjectMap params = new ObjectMap(VariantStorageOptions.ANNOTATE.key(), false)
@@ -91,7 +91,7 @@ public void before() throws Exception {
 
             variantStorageEngine.annotate(outputUri, new ObjectMap());
 
-            VariantHbaseTestUtils.printVariants(getVariantStorageEngine().getDBAdaptor(), newOutputUri(getTestName().getMethodName()));
+            VariantHbaseTestUtils.printVariants(variantStorageEngine.getDBAdaptor(), newOutputUri(getTestName().getMethodName()));
 
             mendelianErrorVariants = new HashSet<>();
             deNovoVariants = new HashSet<>();