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psychoinformatics-de / datalad-hirni

DataLad extension for (semi-)automated, reproducible processing of (medical/neuro)imaging data
http://datalad.org
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`spec4anything()` misinterprets relative path #118

Open mih opened 5 years ago

mih commented 5 years ago

Demo:

(datalad3-dev) mih@meiner /tmp % datalad hirni-spec4anything -d raw raw/acq2/events.tsv --properties '{"procedures": {"procedure-name": "copy-converter", "procedure-call": "bash {script} {{location}} {ds}/sub-{{bids-subject}}/func/sub-{{bids-subject}}_task-{{bids-task}}_run-{{bids-run}}_events.tsv"}, "type": "events_file"}' 
hirni spec4anything(impossible): raw/acq2/events.tsv
[ERROR  ] list index out of range [spec4anything.py:__call__:294] (IndexError)

It should not take the given path as relative to the dataset, but relative to PWD.

Also, it should not crash.

This works:

(datalad3-dev) 1 mih@meiner /tmp % datalad hirni-spec4anything -d raw acq2/events.tsv --properties '{"procedures": {"procedure-name": "copy-converter", "procedure-call": "bash {script} {{location}} {ds}/sub-{{bids-subject}}/func/sub-{{bids-subject}}_task-{{bids-task}}_run-{{bids-run}}_events.tsv"}, "type": "events_file"}' 
hirni spec4anything(ok): acq2/events.tsv (file)
add(ok): acq2/studyspec.json (file)
save(ok): . (dataset)
action summary:
  add (ok: 1)
  hirni spec4anything (ok: 1)
  save (ok: 1)