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bids-standard / pybids-reports

A subpackage of pyBIDS, implementing automatic report generation from BIDS datasets.
http://pybids-reports.readthedocs.io/
MIT License
1 stars 2 forks source link

test pybids_reports CLI on all bids examples #70

Open Remi-Gau opened 7 months ago

Remi-Gau commented 7 months ago

Tried and it started to fail pretty quickly

Remi-Gau commented 7 months ago

the current test we have only runs on a subset of datasets

so we may miss things like this

pybids_reports bids-examples/7t_trt /home/remi/github/bids/pybids-reports 
[16:04:52] WARNING  File not found or empty:                                                                                                        parsing.py:395
                     ['sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz']                                                                                                
           WARNING  File not found or empty:                                                                                                        parsing.py:395
                     ['sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz']                                                                                    
Traceback (most recent call last):
  File "/home/remi/github/bids/pybids-reports/env/bin/pybids_reports", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/cli.py", line 124, in cli
    counter = report.generate()
              ^^^^^^^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/report.py", line 179, in generate
    descriptions.append(self._report_subject(subject=sub, **kwargs))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/report.py", line 226, in _report_subject
    ses_description = parsing.parse_files(
                      ^^^^^^^^^^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/parsing.py", line 349, in parse_files
    group_description = fmap_info(layout, group, config)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/parsing.py", line 235, in fmap_info
    "intended_for": parameters.intendedfor_targets(metadata, layout),
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/ext/reports/parameters.py", line 196, in intendedfor_targets
    run_num = int(if_file.run)
                  ^^^^^^^^^^^
  File "/home/remi/github/bids/pybids-reports/env/lib/python3.11/site-packages/bids/layout/models.py", line 234, in __getattr__
    raise AttributeError("%s object has no attribute named %r" %
AttributeError: BIDSImageFile object has no attribute named 'run'
Remi-Gau commented 5 months ago

can currently run with no crash on dataset starting with: asl ds00 eeg meg ieeg pet

running on dataset bids-examples/asl004
pybids_reports bids-examples/asl004 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/asl003
pybids_reports bids-examples/asl003 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/asl001
pybids_reports bids-examples/asl001 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/asl005
pybids_reports bids-examples/asl005 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/asl002
pybids_reports bids-examples/asl002 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds003
pybids_reports bids-examples/ds003 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds000248
pybids_reports bids-examples/ds000248 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds007
pybids_reports bids-examples/ds007 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds001
pybids_reports bids-examples/ds001 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds006
pybids_reports bids-examples/ds006 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds005
pybids_reports bids-examples/ds005 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds002
pybids_reports bids-examples/ds002 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds004332
pybids_reports bids-examples/ds004332 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds000117
pybids_reports bids-examples/ds000117 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds000247
pybids_reports bids-examples/ds000247 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds000246
pybids_reports bids-examples/ds000246 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds008
pybids_reports bids-examples/ds008 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds000001-fmriprep
pybids_reports bids-examples/ds000001-fmriprep /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ds009
pybids_reports bids-examples/ds009 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_ds003645s_hed_demo
pybids_reports bids-examples/eeg_ds003645s_hed_demo /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_matchingpennies
pybids_reports bids-examples/eeg_matchingpennies /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_face13
pybids_reports bids-examples/eeg_face13 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_ds003645s_hed_library
pybids_reports bids-examples/eeg_ds003645s_hed_library /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_cbm
pybids_reports bids-examples/eeg_cbm /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_rest_fmri
pybids_reports bids-examples/eeg_rest_fmri /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_rishikesh
pybids_reports bids-examples/eeg_rishikesh /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/eeg_ds000117
pybids_reports bids-examples/eeg_ds000117 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_epilepsy
pybids_reports bids-examples/ieeg_epilepsy /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_epilepsyNWB
pybids_reports bids-examples/ieeg_epilepsyNWB /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_visual_multimodal
pybids_reports bids-examples/ieeg_visual_multimodal /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_visual
pybids_reports bids-examples/ieeg_visual /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_filtered_speech
pybids_reports bids-examples/ieeg_filtered_speech /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_epilepsy_ecog
pybids_reports bids-examples/ieeg_epilepsy_ecog /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/ieeg_motorMiller2007
pybids_reports bids-examples/ieeg_motorMiller2007 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/pet003
pybids_reports bids-examples/pet003 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/pet001
pybids_reports bids-examples/pet001 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/pet004
pybids_reports bids-examples/pet004 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/pet002
pybids_reports bids-examples/pet002 /home/remi/github/bids/pybids-reports/tools --verbosity 0

running on dataset bids-examples/pet005
pybids_reports bids-examples/pet005 /home/remi/github/bids/pybids-reports/tools --verbosity 0