Merge pull request #2242 from opencb/TASK-3836

TASK-3836 - Fix CellBase data release usage
opencb · Jan 27, 2023 · ae04f6c · ae04f6c
2 parents 3c06f5a + bff2e12
commit ae04f6c
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Showing 7 changed files with 12 additions and 8 deletions.
diff --git a/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java b/...analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java
@@ -439,7 +439,9 @@ public List<Region> mergeRegions(List<Region> regions, List<String> genes, boole
         // Get species and assembly from catalog
         OpenCGAResult<Project> projectQueryResult = catalogManager.getProjectManager().search(
                 new Query(ProjectDBAdaptor.QueryParams.STUDY.key(), study),
-                new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ORGANISM.key()), token);
+                new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
+                        ProjectDBAdaptor.QueryParams.ORGANISM.key(),
+                        ProjectDBAdaptor.QueryParams.CELLBASE.key())), token);
         if (projectQueryResult.getNumResults() != 1) {
             throw new CatalogException("Error getting species and assembly from catalog");
         }

diff --git a/...opencb/opencga/analysis/variant/manager/operations/VariantAnnotationOperationManager.java b/...opencb/opencga/analysis/variant/manager/operations/VariantAnnotationOperationManager.java
@@ -121,7 +121,7 @@ private void annotate(String projectStr, List<String> studies, String loadFileSt
     }
 
     private void synchronizeProjectMetadata(String projectStr, String token) throws CatalogException, StorageEngineException {
-        Project project = catalogManager.getProjectManager().get(projectStr, null, token).first();
+        Project project = catalogManager.getProjectManager().get(projectStr, QueryOptions.empty(), token).first();
         ProjectOrganism organism = project.getOrganism();
         int currentRelease = project.getCurrentRelease();
         CatalogStorageMetadataSynchronizer.updateProjectMetadata(variantStorageEngine.getMetadataManager(), organism, currentRelease,

diff --git a/...pencb/opencga/analysis/variant/manager/operations/VariantFileIndexerOperationManager.java b/...pencb/opencga/analysis/variant/manager/operations/VariantFileIndexerOperationManager.java
@@ -61,8 +61,7 @@
 
 import static org.opencb.opencga.catalog.db.api.FileDBAdaptor.QueryParams.ID;
 import static org.opencb.opencga.catalog.db.api.FileDBAdaptor.QueryParams.UID;
-import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.CURRENT_RELEASE;
-import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.ORGANISM;
+import static org.opencb.opencga.catalog.db.api.ProjectDBAdaptor.QueryParams.*;
 
 /**
  * Created by imedina on 17/08/16.
@@ -163,7 +162,8 @@ private void updateProject(String studyFqn, String token) throws CatalogExceptio
         Project project = catalogManager
                 .getProjectManager()
                 .get(projectFqn,
-                        new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(CURRENT_RELEASE.key(), ORGANISM.key())), token).first();
+                        new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(CURRENT_RELEASE.key(), ORGANISM.key(), CELLBASE.key())),
+                        token).first();
         release = project.getCurrentRelease();
 
         // Add species, assembly and release

diff --git a/...java/org/opencb/opencga/analysis/variant/metadata/CatalogStorageMetadataSynchronizer.java b/...java/org/opencb/opencga/analysis/variant/metadata/CatalogStorageMetadataSynchronizer.java
@@ -110,7 +110,8 @@ public static void updateProjectMetadata(CatalogManager catalog, VariantStorageM
             throws CatalogException, StorageEngineException {
         final Project p = catalog.getProjectManager().get(project,
                         new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
-                                ProjectDBAdaptor.QueryParams.ORGANISM.key(), ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key())),
+                                ProjectDBAdaptor.QueryParams.ORGANISM.key(), ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key(),
+                                ProjectDBAdaptor.QueryParams.CELLBASE.key())),
                         sessionId)
                 .first();
 

diff --git a/...a/org/opencb/opencga/app/migrations/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/...a/org/opencb/opencga/app/migrations/v2_1_0/storage/AddCellbaseConfigurationToProject.java
@@ -23,7 +23,7 @@ protected void run() throws Exception {
 //        StorageEngineFactory engineFactory = StorageEngineFactory.get(storageConfiguration);
 //        VariantStorageManager variantStorageManager = new VariantStorageManager(catalogManager, engineFactory);
 
-        for (Project project : catalogManager.getProjectManager().search(new Query(), new QueryOptions(), token).getResults()) {
+        for (Project project : catalogManager.getProjectManager().search(new Query(), QueryOptions.empty(), token).getResults()) {
             if (project.getInternal() == null || project.getCellbase() == null) {
                 String userToken = catalogManager.getUserManager()
                         .getNonExpiringToken(project.getFqn().split(USER_PROJECT_SEPARATOR)[0], token);

diff --git a/...rc/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java b/...rc/main/java/org/opencb/opencga/app/migrations/v2_6_0/storage/AddCellbaseDataRelease.java
@@ -22,7 +22,7 @@ public class AddCellbaseDataRelease extends StorageMigrationTool {
     protected void run() throws Exception {
         VariantStorageManager variantStorageManager = getVariantStorageManager();
         for (String projectFqn : getVariantStorageProjects()) {
-            Project project = catalogManager.getProjectManager().get(projectFqn, new QueryOptions(), token).first();
+            Project project = catalogManager.getProjectManager().get(projectFqn, QueryOptions.empty(), token).first();
             CellBaseConfiguration cellbase = project.getCellbase();
             CellBaseUtils cellBaseUtils = getVariantStorageEngineByProject(projectFqn).getCellBaseUtils();
             boolean updateCellbase = false;

diff --git a/...ore/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java b/...ore/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
@@ -57,6 +57,7 @@ public void before() throws Exception {
     protected void loadFiles() throws Exception {
         variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL);
         variantStorageEngine.getConfiguration().getCellbase().setVersion("v5.1");
+        variantStorageEngine.getConfiguration().getCellbase().setDataRelease("2");
         variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
         variantStorageEngine.reloadCellbaseConfiguration();