master: add required params for sample index, #TASK-6219

opencb · Feb 24, 2025 · 5cf2620 · 5cf2620
1 parent d9c2655
commit 5cf2620
Showing 1 changed file with 11 additions and 0 deletions.
diff --git a/...ster/src/main/java/org/opencb/opencga/master/monitor/daemons/VariantOperationJanitor.java b/...ster/src/main/java/org/opencb/opencga/master/monitor/daemons/VariantOperationJanitor.java
@@ -185,6 +185,7 @@ private void checkPendingChore(OperationChore operationChore, Project project, S
                 paramsMap = new HashMap<>();
             }
             paramsMap.put(ParamConstants.PROJECT_PARAM, project.getFqn());
+            operationChore.addSpecificParams(paramsMap);
             catalogManager.getJobManager().submit(studyFqns.get(0), toolId, Enums.Priority.HIGH, paramsMap, null,
                     generateJobDescription(config, operationChore, attributes), null,
                     Collections.singletonList(TAG), null, null, null, attributes, ownerToken);
@@ -223,6 +224,7 @@ private void checkPendingChore(OperationChore operationChore, Project project, S
                 paramsMap = new HashMap<>();
             }
             paramsMap.put(ParamConstants.STUDY_PARAM, study.getFqn());
+            operationChore.addSpecificParams(paramsMap);
             catalogManager.getJobManager().submit(study.getFqn(), toolId, Enums.Priority.HIGH, paramsMap, null,
                     generateJobDescription(config, operationChore, attributes), null,
                     Collections.singletonList(TAG), null, null, null, attributes, ownerToken);
@@ -251,6 +253,9 @@ private interface OperationChore {
 
         OperationExecutionConfig getConfig();
 
+        default void addSpecificParams(Map<String, Object> params) {
+        }
+
     }
 
     private static class VariantSecondarySampleIndexOperationChore implements OperationChore {
@@ -306,6 +311,12 @@ public List<String> dependantTools() {
         public OperationExecutionConfig getConfig() {
             return operationConfig;
         }
+
+        @Override
+        public void addSpecificParams(Map<String, Object> params) {
+            params.put("sample", Collections.singletonList(ParamConstants.ALL));
+            params.put("familyIndex", true);
+        }
     }
 
     private static class VariantSecondaryAnnotationIndexOperationChore implements OperationChore {