Reverting changes to get absolute path

sennetconsortium · Feb 13, 2024 · 02b754d · 02b754d
1 parent 8d4b812
commit 02b754d
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/src/routes/entity_CRUD/__init__.py b/src/routes/entity_CRUD/__init__.py
@@ -843,7 +843,7 @@ 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.get_dataset_directory_absolute_path(entity_dict, dataset_group_uuid, dataset_uuid, False)
+            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, auth_tokens, entity_instance)

diff --git a/src/routes/entity_CRUD/ingest_file_helper.py b/src/routes/entity_CRUD/ingest_file_helper.py
@@ -28,7 +28,7 @@ def make_directory(new_file_path, symbolic_file_path=None):
     def dataset_asset_directory_absolute_path(self, dataset_uuid):
         return file_helper.ensureTrailingSlashURL(self.appconfig['SENNET_WEBSERVICE_FILEPATH']) + dataset_uuid
 
-    def get_dataset_directory_absolute_path(self, dataset_record, group_uuid, dataset_uuid, published=False):
+    def get_dataset_directory_absolute_path(self, dataset_record, group_uuid, dataset_uuid):
         if dataset_record['contains_human_genetic_sequences']:
             access_level = self.appconfig['ACCESS_LEVEL_PROTECTED']
         elif not 'data_access_level' in dataset_record:
@@ -40,9 +40,9 @@ def get_dataset_directory_absolute_path(self, dataset_record, group_uuid, datase
         if 'status' in dataset_record and dataset_record['status'] == 'Published':
             published = True
 
-        return self.__dataset_directory_absolute_path(access_level, group_uuid, dataset_uuid, published)
+        return self.dataset_directory_absolute_path(access_level, group_uuid, dataset_uuid, published)
 
-    def __dataset_directory_absolute_path(self, access_level, group_uuid, dataset_uuid, published):
+    def dataset_directory_absolute_path(self, access_level, group_uuid, dataset_uuid, published):
         grp_name = AuthHelper.getGroupDisplayName(group_uuid)
         if access_level == 'protected':
             base_dir = self.appconfig['GLOBUS_PROTECTED_ENDPOINT_FILEPATH']
@@ -175,12 +175,12 @@ def set_dir_permissions(self, access_level, file_path, published=False, trial_ru
             self.logger.error(e, exc_info=True)
 
     def move_dataset_files_for_publishing(self, uuid, group_uuid, dataset_access_level, trial_run=False):
-        from_path = self.__dataset_directory_absolute_path(dataset_access_level, group_uuid, uuid, False)
+        from_path = self.dataset_directory_absolute_path(dataset_access_level, group_uuid, uuid, False)
         if not os.path.isdir(from_path):
             raise HTTPException(f"{uuid}: path not found to dataset will not publish, path is {from_path}", 500)
         data_access_level = 'protected'
         if not dataset_access_level == 'protected': data_access_level = 'public'
-        to_path = self.__dataset_directory_absolute_path(data_access_level, group_uuid, uuid, True)
+        to_path = self.dataset_directory_absolute_path(data_access_level, group_uuid, uuid, True)
         if not trial_run:
             shutil.move(from_path, to_path)
         else:
@@ -204,7 +204,7 @@ def create_upload_directory(self, group_uuid, upload_uuid):
             self.logger.error(e, exc_info=True)
 
     def set_dataset_permissions(self, dataset_uuid, group_uuid, dataset_access_level, published, trial_run=False):
-        file_path = self.__dataset_directory_absolute_path(dataset_access_level, group_uuid, dataset_uuid, published)
+        file_path = self.dataset_directory_absolute_path(dataset_access_level, group_uuid, dataset_uuid, published)
         return self.set_dir_permissions(dataset_access_level, file_path, published, trial_run=trial_run)
 
     def relink_to_public(self, dataset_uuid):