catalog: allow updating the workflow system, #TASK-6445

opencb · Sep 19, 2024 · 49ec23e · 49ec23e
1 parent 2da90f8
commit 49ec23e
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Showing 3 changed files with 23 additions and 10 deletions.
diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/WorkflowDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/WorkflowDBAdaptor.java
@@ -28,6 +28,7 @@ enum QueryParams implements QueryParam {
         TYPE("type", TEXT, ""),
         TAGS("tags", TEXT_ARRAY, ""),
         COMMAND_LINE("commandLine", TEXT, ""),
+        MANAGER("manager", OBJECT, ""),
         SCRIPTS("scripts", OBJECT, ""),
         VARIABLES("variables", OBJECT, ""),
         INTERNAL_REGISTRATION_USER_ID("internal.registrationUserId", TEXT, ""),

diff --git a/...a-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/WorkflowMongoDBAdaptor.java b/...a-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/WorkflowMongoDBAdaptor.java
@@ -330,7 +330,7 @@ private UpdateDocument parseAndValidateUpdateParams(ObjectMap parameters, QueryO
         final String[] acceptedMapParams = {QueryParams.ATTRIBUTES.key()};
         filterMapParams(parameters, document.getSet(), acceptedMapParams);
 
-        final String[] acceptedListParams = {QueryParams.SCRIPTS.key(), QueryParams.VARIABLES.key()};
+        final String[] acceptedListParams = {QueryParams.MANAGER.key(), QueryParams.SCRIPTS.key(), QueryParams.VARIABLES.key()};
         filterObjectParams(parameters, document.getSet(), acceptedListParams);
 
 //        // Check if the scripts exist.

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/WorkflowManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/WorkflowManager.java
@@ -173,18 +173,10 @@ public OpenCGAResult<Workflow> update(String studyStr, String workflowId, Workfl
 
         JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
         CatalogFqn studyFqn = CatalogFqn.extractFqnFromStudy(studyStr, tokenPayload);
-        ObjectMap updateMap = null;
-        try {
-            if (updateParams != null) {
-                updateMap = new ObjectMap(getUpdateObjectMapper().writeValueAsString(updateParams));
-            }
-        } catch (JsonProcessingException e) {
-            throw new CatalogException("Could not parse WorkflowUpdateParams object: " + e.getMessage(), e);
-        }
 
         ObjectMap auditParams = new ObjectMap()
                 .append("workflowId", workflowId)
-                .append("updateParams", updateMap)
+                .append("updateParams", updateParams)
                 .append("options", options)
                 .append("token", token);
 
@@ -208,6 +200,26 @@ public OpenCGAResult<Workflow> update(String studyStr, String workflowId, Workfl
             id = workflow.getId();
             uuid = workflow.getUuid();
 
+            if (updateParams == null) {
+                throw new CatalogException("Missing parameters to update the workflow.");
+            }
+
+            if (updateParams.getManager() != null) {
+                if (updateParams.getManager().getId() == null) {
+                    throw new CatalogException("Manager id cannot be left empty.");
+                }
+                if (StringUtils.isEmpty(updateParams.getManager().getVersion())) {
+                    throw new CatalogException("Manager version cannot be left empty.");
+                }
+            }
+
+            ObjectMap updateMap;
+            try {
+                updateMap = new ObjectMap(getUpdateObjectMapper().writeValueAsString(updateParams));
+            } catch (JsonProcessingException e) {
+                throw new CatalogException("Could not parse WorkflowUpdateParams object: " + e.getMessage(), e);
+            }
+
             // 2. Update workflow object
             OpenCGAResult<Workflow> insert = getWorkflowDBAdaptor(organizationId).update(workflow.getUid(), updateMap, options);
             if (options.getBoolean(ParamConstants.INCLUDE_RESULT_PARAM)) {