fix: Fixes for changes introdueced when switching pull functions to q…

…uery (#188)
bihealth · Jul 11, 2023 · 5fcc369 · 5fcc369
1 parent e4f46d4
commit 5fcc369
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/cubi_tk/snappy/pull_processed_data.py b/cubi_tk/snappy/pull_processed_data.py
@@ -207,14 +207,13 @@ def execute(self) -> typing.Optional[int]:
 
         # Find all remote files (iRODS)
         pseudo_args = SimpleNamespace(hash_scheme=DEFAULT_HASH_SCHEME)
-        extensions_tuple = self.file_type_to_extensions_dict.get(self.args.file_type)
         remote_files_dict = RetrieveIrodsCollection(
             pseudo_args,
             self.args.sodar_url,
             self.args.sodar_api_token,
             self.args.assay_uuid,
             self.args.project_uuid,
-        ).perform(identifiers=selected_identifiers, extensions_tuple=extensions_tuple)
+        ).perform()
 
         # Filter based on identifiers and file type
         filtered_remote_files_dict = self.filter_irods_collection(

diff --git a/cubi_tk/snappy/retrieve_irods_collection.py b/cubi_tk/snappy/retrieve_irods_collection.py
@@ -141,7 +141,7 @@ def parse_irods_collection(irods_data_objs) -> typing.Dict[str, typing.List[iROD
         # Initialise variables
         output_dict = defaultdict(list)
 
-        for obj in irods_data_objs["files"].values():
+        for obj in irods_data_objs["files"]:
             output_dict[obj.name].append(obj)
 
         return output_dict