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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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Remote metadata doesn't work with globs in from_work_dir outputs #285

Closed natefoo closed 2 years ago

natefoo commented 2 years ago

e.g. from cutadapt:

Traceback (most recent call last):
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/metadata/set_metadata.py", line 276, in set_metadata_portable
    set_meta(dataset, file_dict)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/metadata/set_metadata.py", line 133, in set_meta
    set_meta_with_tool_provided(new_dataset_instance, file_dict, set_meta_kwds, datatypes_registry, max_metadata_value_size)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/metadata/set_metadata.py", line 97, in set_meta_with_tool_provided
    dataset_instance.datatype.set_meta(dataset_instance, **set_meta_kwds)
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/datatypes/sequence.py", line 660, in set_meta
    with compression_utils.get_fileobj(dataset.file_name) as in_file:
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/compression_utils.py", line 28, in get_fileobj
    return get_fileobj_raw(filename, mode, compressed_formats)[1]
  File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/compression_utils.py", line 59, in get_fileobj_raw
    return compressed_format, open(filename, mode, encoding='utf-8')
FileNotFoundError: [Errno 2] No such file or directory: '/jetstream/scratch0/test/jobs/1460118/working/out1*'