AttributeError: '_io.TextIOWrapper' object has no attribute 'startswith'

[gawbul]

Getting the following error when I'm trying to use a package that depends on fsspec:

INFO:root:<_io.TextIOWrapper name='/Users/stephenmoss/.astropy/cache/download/url/141581d04d4001254d07601dfa7d983b/contents' encoding='UTF-8'>
Traceback (most recent call last):
  File "openomics_test.py", line 34, in <module>
    gencode = GENCODE(path="ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/",
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/database/sequence.py", line 67, in __init__
    super(GENCODE, self).__init__(path=path, file_resources=file_resources, col_rename=col_rename,
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/database/sequence.py", line 17, in __init__
    super(SequenceDataset, self).__init__(**kwargs)
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/database/base.py", line 39, in __init__
    self.data = self.load_dataframe(file_resources, npartitions=npartitions)
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/database/sequence.py", line 74, in load_dataframe
    df = read_gtf(file_resources[gtf_file], npartitions=npartitions)
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/utils/read_gtf.py", line 349, in read_gtf
    result_df = parse_gtf_and_expand_attributes(
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/utils/read_gtf.py", line 290, in parse_gtf_and_expand_attributes
    result = parse_gtf(
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/openomics/utils/read_gtf.py", line 195, in parse_gtf
    chunk_iterator = dd.read_table(
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/dask/dataframe/io/csv.py", line 659, in read
    return read_pandas(
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/dask/dataframe/io/csv.py", line 464, in read_pandas
    paths = get_fs_token_paths(urlpath, mode="rb", storage_options=storage_options)[
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/fsspec/core.py", line 619, in get_fs_token_paths
    path = cls._strip_protocol(urlpath)
  File "/Users/stephenmoss/.pyenv/versions/3.8.7/lib/python3.8/site-packages/fsspec/implementations/local.py", line 148, in _strip_protocol
    if path.startswith("file://"):
AttributeError: '_io.TextIOWrapper' object has no attribute 'startswith'

[andersy005]

@gawbul, it appears that your script is passing a stream wrapped in io.TextIOWrapper as path to fsspec and fsspec is expecting the path to be a string. Could you provide a reproducible example or share more details about the contents of openomics_test.py?

[gawbul]

Hi, @andersy005 👋

Thanks for the swift reply 🙏

Yeah, I was just thinking the same myself. I'm doing a code review of the OpenOmics package and just trying to get to the bottom of things at present. I think this is likely an issue with the package or one of its dependencies?

I'll let you know how I get on, but might be able to close this. Just trying to do some debugging to understand where it is setting it to a stream object?

I think it is somewhere in here https://github.com/BioMeCIS-Lab/OpenOmics/blob/master/openomics/database/base.py.

[gawbul]

Yeah, it appears to be here https://github.com/BioMeCIS-Lab/OpenOmics/blob/master/openomics/database/base.py#L89-L90.

As per https://docs.python.org/3/library/gzip.html:

For text mode, a GzipFile object is created, and wrapped in an io.TextIOWrapper instance with the specified encoding, error handling behavior, and line ending(s).

I think it was expecting it to be returned as a standard file object, but the gzip library is behaving unexpectedly.

[gawbul]

Happy to close. Thanks for your help 👍