catalog: fix project include issues, #TASK-4851

opencb · Aug 9, 2023 · b176eb7 · b176eb7
1 parent 41b33a1
commit b176eb7
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java
@@ -318,10 +318,10 @@ Study insert(ClientSession clientSession, Project project, Study study)
     }
 
     @Override
-    public OpenCGAResult<Study> getAllStudiesInProject(long projectId, QueryOptions options) throws CatalogDBException {
+    public OpenCGAResult<Study> getAllStudiesInProject(long projectUid, QueryOptions options) throws CatalogDBException {
         long startTime = startQuery();
-        dbAdaptorFactory.getCatalogProjectDbAdaptor().checkId(projectId);
-        Query query = new Query(QueryParams.PROJECT_ID.key(), projectId);
+        dbAdaptorFactory.getCatalogProjectDbAdaptor().checkId(projectUid);
+        Query query = new Query(QueryParams.PROJECT_UID.key(), projectUid);
         return endQuery(startTime, get(query, options));
     }
 

diff --git a/...n/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java b/...n/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java
@@ -146,8 +146,8 @@ private boolean includeStudyInfo() {
             return true;
         } else if (options.containsKey(QueryOptions.INCLUDE)) {
             List<String> list = options.getAsStringList(QueryOptions.INCLUDE);
-            for (String exclude : list) {
-                if (exclude.equals("studies") || exclude.equals("projects.studies")) {
+            for (String include : list) {
+                if (include.startsWith("studies") || include.startsWith("projects.studies")) {
                     return true;
                 }
             }

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java
@@ -610,7 +610,9 @@ public OpenCGAResult<Integer> incrementRelease(String projectStr, String session
             int currentRelease = project.getCurrentRelease();
 
             // Check current release has been used at least in one study or file or cohort or individual...
-            List<Study> allStudiesInProject = project.getStudies();
+            QueryOptions studyOptions = keepFieldInQueryOptions(StudyManager.INCLUDE_STUDY_IDS, StudyDBAdaptor.QueryParams.RELEASE.key());
+            OpenCGAResult<Study> studyResult = studyDBAdaptor.getAllStudiesInProject(projectUid, studyOptions);
+            List<Study> allStudiesInProject = studyResult.getResults();
             if (allStudiesInProject.isEmpty()) {
                 throw new CatalogException("Cannot increment current release number. No studies found for release " + currentRelease);
             }