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datalad / datalad-neuroimaging

DataLad extension for neuroimaging research
http://datalad.org
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ds000174 participants is problematic for pybids #47

Open yarikoptic opened 5 years ago

yarikoptic commented 5 years ago

just want to file to check in detail later

$> DATALAD_EXC_STR_TBLIMIT=10 datalad --dbg aggregate-metadata --force-extraction --incremental $PWD
[INFO   ] Aggregate metadata for dataset /mnt/btrfs/datasets/datalad/crawl/openfmri/ds000174
Metadata extraction:  60%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▊                                                                                                   | 3.00/5.00 [00:01<00:01, 1.63 extractors/s]/usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
Metadata extraction: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 5.00/5.00 [00:03<00:00, 1.43 extractors/s]/home/yoh/proj/datalad/datalad-neuroimaging/venvs/dev/local/lib/python2.7/site-packages/grabbit/core.py:448: UserWarning: Domain with name 'bids' already exists; returning existing Domain configuration.
  warnings.warn(msg)
[WARNING] Failed to load participants info due to: Can only use .str accessor with string values, which use np.object_ dtype in pandas [bids.py:_get_cnmeta:123,bids.py:yield_participant_info:197,bids_layout.py:get_collections:317,io.py:load_variables:76,io.py:_load_tsv_variables:364,generic.py:__getattr__:4372,accessor.py:__get__:133,strings.py:__init__:1895,strings.py:_validate:1917]. Skipping the rest of file
                                                                                                                                                                                                                                                                                                                              [INFO   ] Update aggregate metadata in dataset at: /mnt/btrfs/datasets/datalad/crawl/openfmri/ds000174
aggregate_metadata(ok): /mnt/btrfs/datasets/datalad/crawl/openfmri/ds000174 (dataset)
[INFO   ] Attempting to save 6 files/datasets
action summary:
  aggregate_metadata (ok: 1)
  save (notneeded: 1)
DATALAD_EXC_STR_TBLIMIT=10 datalad --dbg aggregate-metadata --force-extractio  5.35s user 3.58s system 137% cpu 6.496 total
yarikoptic commented 5 years ago

FTR: the same in ds001720. pybids is still an elderly '0.6.4'