mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-31 02:28:09 +08:00
mvdbeek
a6ce0d666c
Data managers can record absolute paths below $out_file.extra_files_path, while bundle writing runs on the job handler after that directory has been collected into the object store. Relativizing against dataset.extra_files_path then escapes with '..' and leaves the compute-side path in the bundle index. The job working directory is already known. For outputs_to_working_directory, reconstruct the exact compute-side extra-files root with the same uuid-keyed output-path rule used during command construction, then pass that per-output root to bundle writing. For other outputs, retain the dataset extra-files path. This restores ordinary os.path.relpath containment checks, including '.' for the extra-files root itself, instead of inferring the root from a matching directory component. It handles split job/object-store prefixes and id-keyed object stores without changing the bundle format or sending anything to the compute node. Regression tests cover the split-prefix case, uuid-keyed compute paths on id-keyed stores, the root directory, and nested dataset-like directory names.