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SCHEMA: Fix diffusion and NIRS rules #1650

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merged 4 commits into from
Nov 10, 2023

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effigies
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@effigies effigies commented Nov 9, 2023

Only one schema rule fix for today.

Edit: Okay, a couple more.

@effigies effigies added schema Issues related to the YAML schema representation of the specification. Patch version release. exclude-from-changelog This item will not feature in the automatically generated changelog labels Nov 9, 2023
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codecov bot commented Nov 9, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (bf015e6) 87.97% compared to head (641a12b) 87.97%.

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1650   +/-   ##
=======================================
  Coverage   87.97%   87.97%           
=======================================
  Files          16       16           
  Lines        1356     1356           
=======================================
  Hits         1193     1193           
  Misses        163      163           

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@rwblair This gets us down to:

    issue key                 filename                                   schema path                               
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ds000248                                                                                                      │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    MISSING_REQUIRED_ENTITY   sub-01_acq-crosstalk_meg.fif               task missing from rule                    
                                                                         rules.files.deriv.preprocessed_data.m     
                                                                         eg_meg_common                             
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ genetics_ukbb                                                                                                 │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    NOT_INCLUDED              .bids-validator-config.json                                                          
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_epilepsy                                                                                                 │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-01_ses-postimp_space-IXI549Space_ele   Columns cited as index columns not in     
                              ctrodes.tsv                                file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_epilepsy_ecog                                                                                            │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-ecog01_ses-postimp_space-IXI549Space   Columns cited as index columns not in     
                              _electrodes.tsv                            file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_epilepsyNWB                                                                                              │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-01_ses-postimp_space-IXI549Space_ele   Columns cited as index columns not in     
                              ctrodes.tsv                                file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_filtered_speech                                                                                          │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-cm4_electrodes.tsv                     Columns cited as index columns not in     
                                                                         file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_motorMiller2007                                                                                          │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-bp_ses-01_space-ACPC_electrodes.tsv    Columns cited as index columns not in     
                                                                         file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_visual                                                                                                   │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-01_ses-01_electrodes.tsv               Columns cited as index columns not in     
                                                                         file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_visual_multimodal                                                                                        │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    TSV_COLUMN_MISSING        sub-som682_ses-somecog01_electrodes.tsv    Columns cited as index columns not in     
                                                                         file: name.                               
                                                                         schema.rules.tabular_data.ieeg.iEEGEl     
                                                                         ectrodes                                  

Most of these are bids-standard/bids-validator#1842.

@effigies effigies changed the title SCHEMA: Check for three bvec rows SCHEMA: Fix diffusion and NIRS rules Nov 10, 2023
@effigies effigies merged commit 426de56 into bids-standard:master Nov 10, 2023
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@effigies effigies deleted the schema/rule-fixes branch November 10, 2023 17:24
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