Unverified Commit f5c511be authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #13768 from kxk302/main_irods_fixes 

[22.01] Fix race condition in object store dir creation
parents 518bf3f1 5dcb1294

lib/galaxy/objectstore/irods.py

+3 −3
Original line number Diff line number Diff line
@@ -336,7 +336,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin): 
        # Ensure the cache directory structure exists (e.g., dataset_#_files/)

        rel_path_dir = os.path.dirname(rel_path)

        if not os.path.exists(self._get_cache_path(rel_path_dir)):

            os.makedirs(self._get_cache_path(rel_path_dir))

            os.makedirs(self._get_cache_path(rel_path_dir), exist_ok=True)

        # Now pull in the file

        file_ok = self._download(rel_path)

        self._fix_permissions(self._get_cache_path(rel_path_dir))
@@ -461,7 +461,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin): 
        if dir_only and base_dir:

            # for JOB_WORK directory

            if not os.path.exists(rel_path):

                os.makedirs(rel_path)

                os.makedirs(rel_path, exist_ok=True)

            log.debug("irods_pt _exists: %s", ipt_timer)

            return True

        log.debug("irods_pt _exists: %s", ipt_timer)
@@ -489,7 +489,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin): 
            # Create given directory in cache

            cache_dir = os.path.join(self.staging_path, rel_path)

            if not os.path.exists(cache_dir):

                os.makedirs(cache_dir)

                os.makedirs(cache_dir, exist_ok=True)



            if not dir_only:

                rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")