Merge pull request #655 from sennetconsortium/maxsibilla/fix-metadata…

…-write Maxsibilla/fix metadata write
sennetconsortium · Feb 13, 2025 · e314c71 · e314c71
2 parents f673c63 + 6ce7e7d
commit e314c71
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Showing 3 changed files with 9 additions and 7 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.4.23
+1.4.24
diff --git a/ingest-api-spec.yaml b/ingest-api-spec.yaml
@@ -2,7 +2,7 @@ openapi: 3.0.0
 info:
   description: |
     A RESTful web service exposing calls needed for the SenNet Data Sharing Portal.
-  version: 1.4.23
+  version: 1.4.24
   title: SenNet Ingest API
   contact:
     name: SenNet Help Desk

diff --git a/src/routes/entity_CRUD/__init__.py b/src/routes/entity_CRUD/__init__.py
@@ -867,8 +867,6 @@ def publish_datastage(identifier):
                     abort_bad_req(f"{dataset_uuid} missing contacts or contributors. Must have at least one of each")
 
             ingest_helper = IngestFileHelper(current_app.config)
-            ds_path = ingest_helper.dataset_directory_absolute_path(dataset_data_access_level, dataset_group_uuid,
-                                                                    dataset_uuid, False)
             is_component = entity_dict.get('creation_action') == 'Multi-Assay Split'
 
             data_access_level = dataset_data_access_level
@@ -888,9 +886,6 @@ def publish_datastage(identifier):
                 if asset_dir_exists:
                     ingest_helper.relink_to_public(dataset_uuid)
 
-            acls_cmd = ingest_helper.set_dataset_permissions(dataset_uuid, dataset_group_uuid, data_access_level,
-                                                             True, no_indexing_and_acls)
-
             doi_info = None
             # Generating DOI's for lab processed/derived data as well as IEC/pipeline/airflow processed/derived data).
             if is_primary or has_entity_lab_processed_dataset_type:
@@ -962,6 +957,9 @@ def publish_datastage(identifier):
                 for e_id in uuids_for_public:
                     entity_instance.clear_cache(e_id)
 
+        # Write metadata.json into directory
+        ds_path = ingest_helper.dataset_directory_absolute_path(dataset_data_access_level, dataset_group_uuid,
+                                                                dataset_uuid, True)
         if is_primary or is_component is False:
             md_file = os.path.join(ds_path, "metadata.json")
             json_object = entity_json_dumps(entity, auth_tokens, EntitySdk(service_url=current_app.config['ENTITY_WEBSERVICE_URL']), True)
@@ -973,6 +971,10 @@ def publish_datastage(identifier):
                 logger.exception(f"Fatal error while writing md_file {md_file}; {str(e)}")
                 return jsonify({"error": f"{dataset_uuid} problem writing metadata.json file."}), 500
 
+        # Change the directory permissions to prevent user from writing to published folder
+        acls_cmd = ingest_helper.set_dataset_permissions(dataset_uuid, dataset_group_uuid, data_access_level,
+                                                         True, no_indexing_and_acls)
+
         if no_indexing_and_acls:
             r_val = {'acl_cmd': acls_cmd, 'sources_for_indexing': sources_to_reindex}
         else: