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datalad / datalad-neuroimaging

DataLad extension for neuroimaging research
http://datalad.org
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crash while running on a datalad-fuse'd dataset #95

Open yarikoptic opened 2 years ago

yarikoptic commented 2 years ago 
(git-annex)lena:/tmp/mnt/ds000001[master]git-annex
$> datalad meta-extract bids
[ERROR  ] TypeError('PosixPath' object is not subscriptable) (TypeError) 
(dev3) 1 35958 ->1.....................................:Tue 01 Feb 2022 09:32:42 AM EST:.
(git-annex)lena:/tmp/mnt/ds000001[master]git-annex
$> datalad --dbg meta-extract bids
Traceback (most recent call last):
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/bin/datalad", line 8, in <module>
    sys.exit(main())
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/datalad/cmdline/main.py", line 211, in main
    ret = cmdlineargs.func(cmdlineargs)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/datalad/interface/base.py", line 786, in call_from_parser
    ret = list(ret)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/datalad/interface/utils.py", line 396, in generator_func
    for r in _process_results(
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/datalad/interface/utils.py", line 579, in _process_results
    for res in results:
  File "/home/yoh/proj/datalad/datalad-metalad/datalad_metalad/extract.py", line 297, in __call__
    yield from do_dataset_extraction(extraction_parameters)
  File "/home/yoh/proj/datalad/datalad-metalad/datalad_metalad/extract.py", line 341, in do_dataset_extraction
    yield from legacy_extract_dataset(ep)
  File "/home/yoh/proj/datalad/datalad-metalad/datalad_metalad/extract.py", line 678, in legacy_extract_dataset
    dataset_result, _ = extractor.get_metadata(True, False)
  File "/home/yoh/proj/datalad/datalad-neuroimaging/datalad_neuroimaging/extractors/bids.py", line 72, in get_metadata
    bids = BIDSLayout(self.ds.path, derivatives=derivative_exist)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/layout.py", line 145, in __init__
    indexer(self)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/index.py", line 109, in __call__
    self._index_dir(self._layout._root, self._config)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/index.py", line 193, in _index_dir
    self._index_dir(d, list(config), default_action=default)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/index.py", line 193, in _index_dir
    self._index_dir(d, list(config), default_action=default)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/index.py", line 164, in _index_dir
    cfg = Config.load(config_file, session=self.session)
  File "/home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/models.py", line 156, in load
    result = session.query(Config).filter_by(name=config['name']).first()
TypeError: 'PosixPath' object is not subscriptable

> /home/yoh/proj/datalad/datalad-metalad/venvs/dev3/lib/python3.9/site-packages/bids/layout/models.py(156)load()
-> result = session.query(Config).filter_by(name=config['name']).first()
(Pdb) import bids
*(Pdb) print(bids.__version__)
0.14.0