Merge pull request #497 from hubmapconsortium/datasets_publish_move_j…

…son_dump_to_end

Move writing of metadata.json to the end of dataset publish endpoint

src/app.py

@@ -945,19 +945,8 @@ def publish_datastage(identifier):
                 dataset_contributors = dataset_contributors.replace("'", '"')
                 if len(json.loads(dataset_contacts)) < 1 or len(json.loads(dataset_contributors)) < 1:
                     return jsonify({"error": f"{dataset_uuid} missing contacts or contributors. Must have at least one of each"}), 400
+
             ingest_helper: IngestFileHelper = IngestFileHelper(app.config)
-            ds_path = ingest_helper.dataset_directory_absolute_path(dataset_data_access_level,
-                                                                    dataset_group_uuid, dataset_uuid, False)
-            md_file = os.path.join(ds_path, "metadata.json")
-            json_object = entity_json_dumps(entity_instance, dataset_uuid)
-            logger.info(f"publish_datastage; writing metadata.json file: '{md_file}'; "
-                        f"containing: '{json_object}'")
-            try:
-                with open(md_file, "w") as outfile:
-                    outfile.write(json_object)
-            except Exception as e:
-                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
 
             data_access_level = dataset_data_access_level
             #if consortium access level convert to public dataset, if protected access leave it protected
@@ -1038,6 +1027,20 @@ def publish_datastage(identifier):
                 for e_id in uuids_for_public:
                     out = entity_instance.clear_cache(e_id)
 
+            # Write out the metadata.json file after all processing has been done...
+            ds_path = ingest_helper.dataset_directory_absolute_path(dataset_data_access_level,
+                                                                    dataset_group_uuid, dataset_uuid, False)
+            md_file = os.path.join(ds_path, "metadata.json")
+            json_object = entity_json_dumps(entity_instance, dataset_uuid)
+            logger.info(f"publish_datastage; writing metadata.json file: '{md_file}'; "
+                        f"containing: '{json_object}'")
+            try:
+                with open(md_file, "w") as outfile:
+                    outfile.write(json_object)
+            except Exception as e:
+                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
+
         if no_indexing_and_acls:
             r_val = {'acl_cmd': acls_cmd, 'donors_for_indexing': donors_to_reindex}
         else: