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bibsnet fails #127

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dnkennedy opened this issue Jul 18, 2024 · 0 comments
Open

bibsnet fails #127

dnkennedy opened this issue Jul 18, 2024 · 0 comments

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@dnkennedy
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$ datalad containers-run -n bids-bibsnet --input sourcedata         --output derivatives/bibsnet-3.3.2/         '{inputs}' '{outputs}' participant -w workdir
[INFO   ] Making sure inputs are available (this may take some time) 
[INFO   ] == Command start (output follows) ===== 
"uname": executable file not found in $PATH
Traceback (most recent call last):
  File "/home/bibsnet//bibsnet", line 48, in <module>
    main()
  File "/home/bibsnet//bibsnet", line 33, in main
    json_args, sub_ses_IDs = get_params([get_stage_name(stg) for stg in STAGES])
  File "/home/bibsnet/src/get_args.py", line 177, in get_params
    return validate_cli_args(vars(parser.parse_args()), stage_names,
  File "/home/bibsnet/src/get_args.py", line 270, in validate_cli_args
    ) if cli_args["brain_z_size"] else get_brain_z_size(
  File "/home/bibsnet/src/get_args.py", line 399, in get_brain_z_size
    age2headradius = pd.read_csv(AGE_TO_HEAD_RADIUS_TABLE)
  File "/opt/conda/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in __init__
    self._open_handles(src, kwds)
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/parsers/base_parser.py", line 222, in _open_handles
    self.handles = get_handle(
  File "/opt/conda/lib/python3.8/site-packages/pandas/io/common.py", line 702, in get_handle
    handle = open(
PermissionError: [Errno 13] Permission denied: '/home/bibsnet/data/age_to_avg_head_radius_BCP.csv'
[INFO   ] == Command exit (modification check follows) ===== 
run(error): /mnt/DATA/data/dnkennedy/my_experiments/ds000003-qcsing24 (dataset) [./code/containers/scripts/singularity_cm...]
action summary:
  get (notneeded: 3)
  run (error: 1)
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