Add regexps for space entity: EEG and iEEG

[adam2392]

Closes: #743
closes #1164

Adding regex pattern for iEEG space entity.

TODO

• Add regex for MEG space not in their entities currently, although probably would be applicable (headshape + markers)?
• Add regex for EEG
• Update unit tests

Questions

• How does one include the optional fields like MNI152NLin2009[a-c][Sym|Asym] (a-c and Sym/Asym) in regex?
• Anyone have an idea where the tests are to fix for this PR?

[sappelhoff]

I think tests are not in place yet for the space entity 😬

this would be a proper place:

bids-validator/bids-validator/tests/type.spec.js

Lines 373 to 390 in 4c1be20

	describe('utils.type.file.isIEEG', function() {
	const goodFilenames = [
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_ieeg.json',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.edf',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.vhdr',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.vmrk',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.eeg',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.set',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.fdt',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.nwb',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.mefd/sub-01_ses-001_task-rest_run-01_ieeg.rdat',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.mefd/sub-01_ses-001_task-rest_run-01_ieeg.ridx',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.mefd/CH1.timd/CH1-000000.segd/sub-01_ses-001_task-rest_run-01_ieeg.tdat',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.mefd/CH1.timd/CH1-000000.segd/sub-01_ses-001_task-rest_run-01_ieeg.idx',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_split-01_ieeg.mefd/CH1.timd/CH1-000000.segd/sub-01_ses-001_task-rest_run-01_ieeg.tmet',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_channels.tsv',
	'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_electrodes.tsv',
	]

How does one include the optional fields like MNI152NLin2009[a-c][Sym|Asym] (a-c and Sym/Asym) in regex?

You could write it all out, like I did in the JSON schema:

bids-validator/bids-validator/validators/json/schemas/common_definitions.json

Lines 21 to 28 in 4c1be20

	"MNI152NLin2009aSym",
	"MNI152NLin2009bSym",
	"MNI152NLin2009cSym",
	"MNI152NLin2009aAsym",
	"MNI152NLin2009bAsym",
	"MNI152NLin2009cAsym",
	"MNI152NLin6Sym",
	"MNI152NLin6ASym",

Or you go over to https://regex101.com/ and check what regexp works. But I suggest the former, not the latter.

[sappelhoff]

please also check the session level rules, etc.

[codecov]

Codecov Report

Merging #1190 (e5fed90) into master (4c1be20) will increase coverage by 3.43%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1190      +/-   ##
==========================================
+ Coverage   79.09%   82.53%   +3.43%     
==========================================
  Files          78       78              
  Lines        2622     2622              
  Branches      598      598              
==========================================
+ Hits         2074     2164      +90     
+ Misses        407      369      -38     
+ Partials      141       89      -52     

Impacted Files	Coverage Δ
bids-validator/utils/type.js	98.94% <100.00%> (ø)
bids-validator/tests/env/FileList.js	63.33% <0.00%> (-10.01%)	⬇️
bids-validator/validators/json/json.js	100.00% <0.00%> (+1.40%)	⬆️
bids-validator/utils/bids_files.js	92.59% <0.00%> (+3.70%)	⬆️
bids-validator/validators/bids/start.js	93.33% <0.00%> (+20.00%)	⬆️
bids-validator/validators/nifti/nii.js	64.75% <0.00%> (+23.19%)	⬆️
bids-validator/validators/bids/quickTestError.js	93.33% <0.00%> (+73.33%)	⬆️

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[sappelhoff]

@adam2392 I added some commits (including a force push for rebasing, sorry), so please before you continue to work, do:

• git stash (in case you have any non committed changes)
• git pull and then
• git reset --hard origin/space
• git stash apply (in case you had previous non committed changes that you now want to bring back)

In particular I:

• added a CI job to test against bids-examples, because there are several datasets that make use of space ... fixes test bids-examples as part of bids-validator CI #1164
• fixed your regexp
• made a style linebreak the circleci CI script

[sappelhoff]

@adam2392 is something holding you back from finishing this PR? Or is it more of a "finding time to do it" issue (which is absolutely fine)?

[adam2392]

Yeah sorry didn't have time, but procrastinated a bit this morning and hopefully this is closer to being done / done. LMk.

FYI: currently the validator allows other entities into the *_electrodes.tsv and *coordsystem.json files even though they are not technically allowed in the spec.

[sappelhoff]

FYI: currently the validator allows other entities into the *_electrodes.tsv and *coordsystem.json files even though they are not technically allowed in the spec.

yes, thanks for the note, see also: bids-standard/bids-examples#244

[sappelhoff]

I added the regexps and tests for EEG.

hopefully this is closer to being done / done

I think it's done