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Update MEG regexps and testsuite to comply with father level specification #789

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merged 7 commits into from
Jun 25, 2019
Merged

Update MEG regexps and testsuite to comply with father level specification #789

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619e49b
gitignore yarn error log
sappelhoff Jun 21, 2019
dadf1b0
add hed validator to yarn lock
sappelhoff Jun 21, 2019
561fb2c
allow KIT markers for MEG regexp
sappelhoff Jun 21, 2019
801491f
add tests
sappelhoff Jun 21, 2019
5b6e9f4
add big test suite
sappelhoff Jun 24, 2019
4a65be7
fix CTF regexp
sappelhoff Jun 24, 2019
8cd2462
add _digitizer.txt
sappelhoff Jun 25, 2019
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
yarn-error.log
node_modules/
.DS_Store
bids-validator/tests/data/bids-examples-*
Expand All @@ -16,4 +17,4 @@ bids-validator-web/.next/

# Only use global yarn.lock
bids-validator/yarn.lock
bids-validator-web/yarn.lock
bids-validator-web/yarn.lock
43 changes: 22 additions & 21 deletions bids-validator/bids_validator/rules/file_level_rules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -85,24 +85,6 @@
}
},

"eeg": {
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?eeg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))$",
"tokens": {
"@@@_eeg_type_@@@": ["vhdr", "vmrk", "eeg", "edf", "bdf", "set", "fdt"],
"@@@_eeg_ext_@@@": [
"_events\\.json",
"_events\\.tsv",
"_electrodes\\.json",
"_electrodes\\.tsv",
"_channels\\.json",
"_channels\\.tsv",
"_eeg\\.json",
"_coordsystem\\.json",
"_photo\\.jpg"
]
}
},

"field_map": {
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?fmap\\/\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_dir-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(?:@@@_field_map_type_@@@)\\.(@@@_field_map_ext_@@@)$",
"tokens": {
Expand Down Expand Up @@ -170,6 +152,24 @@
}
},

"eeg": {
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?eeg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))$",
"tokens": {
"@@@_eeg_type_@@@": ["vhdr", "vmrk", "eeg", "edf", "bdf", "set", "fdt"],
"@@@_eeg_ext_@@@": [
"_events\\.json",
"_events\\.tsv",
"_electrodes\\.json",
"_electrodes\\.tsv",
"_channels\\.json",
"_channels\\.tsv",
"_eeg\\.json",
"_coordsystem\\.json",
"_photo\\.jpg"
]
}
},

"ieeg": {
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?ieeg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(?:_space-[a-zA-Z0-9]+)?(_ieeg\\.(@@@_ieeg_type_@@@)|(@@@_ieeg_ext_@@@))$",
"tokens": {
Expand Down Expand Up @@ -198,9 +198,9 @@
},

"meg": {
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?meg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_meg(@@@_meg_type_@@@\\/.*|\\/.*)|(@@@_meg_ext_@@@))$",
"regexp": "^\\/(sub-[a-zA-Z0-9]+)\\/(?:(ses-[a-zA-Z0-9]+)\\/)?meg\\/\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_part-[0-9]+)?(_digitizer.txt|_meg(@@@_meg_type_@@@\\/(.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*|\\/(.(?!\\.(sqd|con|fif|raw|raw\\.mhd|trg|kdf|chn)$))*)|(@@@_meg_ext_@@@))$",
"tokens": {
"@@@_meg_type_@@@": ["\\.fif", "\\.ds"],
"@@@_meg_type_@@@": ["\\.ds/.*", "\\.(?:chn|kdf|trg)", "\\.(?:raw|raw\\.mhd)", "\\.fif", "\\.(?:con|sqd)", "\\.(?:kdf|chn|trg)"],
"@@@_meg_ext_@@@": [
"_events\\.json",
"_events\\.tsv",
Expand All @@ -209,7 +209,8 @@
"_meg\\.json",
"_coordsystem\\.json",
"_photo\\.jpg",
"_headshape\\.pos"
"_headshape\\.pos",
"_markers\\.(?:mrk|sqd)"
]
}
},
Expand Down
52 changes: 45 additions & 7 deletions bids-validator/tests/type.spec.js
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Expand Up @@ -172,13 +172,33 @@ describe('utils.type.file.isDWI', function() {

describe('utils.type.file.isMEG', function() {
const goodFilenames = [
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.sqd',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.raw.mhd',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/xyz', // for e.g., BTi files
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_markers.sqd',
// Metadata MEG files
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.json',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_part-01_meg.fif',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_channels.tsv',
// Father directory files are fine for some file formats:
// Father dir: CTF data with a .ds ... the contents within .ds are not checked
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.ds/catch-alp-good-f.meg4',
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the contents within the CTF .ds must be checked, otherwise it is not a valid dataset and standard software (e..g that of CTF itself) will not be able to read it.

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I agree, but this is not something I break in this PR ... it's never been there :-)

Also, I have opened an issue on this several months ago: https://github.com/bids-standard/bids-validator/issues/692

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agreed

'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.ds/xyz',
// Father dir: BTi/4D ... again: within contents not checked
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/config',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/hs_file',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/e,rfhp1.0Hz.COH',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/c,rfDC',
// NO father dir: KRISS data
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_run-01_meg.chn',
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_run-01_meg.kdf',
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_run-01_meg.trg',
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_digitizer.txt',
// NO father dir: KIT data
'/sub-01/ses-001/meg/sub-01_ses-001_markers.sqd',
'/sub-01/ses-001/meg/sub-01_ses-001_markers.mrk',
'/sub-01/ses-001/meg/sub-01_ses-001_meg.sqd',
'/sub-01/ses-001/meg/sub-01_ses-001_meg.con',
// NO father dir: ITAB data
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_run-01_meg.raw',
'/sub-control01/ses-001/meg/sub-control01_ses-001_task-rest_run-01_meg.raw.mhd',
// NO father dir: fif data
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_part-01_meg.fif',
]

goodFilenames.forEach(function(path) {
Expand All @@ -189,11 +209,29 @@ describe('utils.type.file.isMEG', function() {
})

const badFilenames = [
// only parent directory name matters for KIT/BTi systems
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_megggg/sub-01_ses-001_task-rest_run-01_meg.sqd',
// missing session directory
'/sub-01/meg/sub-01_ses-001_task-rest_run-01_meg.json',
// subject not matching
'/sub-01/ses-001/meg/sub-12_ses-001_task-rest_run-01_part-01_meg.fif',
// invalid file endings
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.tsv',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.bogus',
// only parent directory name matters for BTi and CTF systems
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meggg/config',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg.dd/xyz',
// KIT with a father dir ... should not have a father dir
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_markers.sqd',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_markers.con',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.sqd',
// FIF with a father dir ... should not have a father dir
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_meg.fif',
// ITAB with a father dir ... should not have a father dir
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.raw',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.raw.mhd',
// KRISS with a father dir ... should not have a father dir
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.kdf',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.trg',
'/sub-01/ses-001/meg/sub-01_ses-001_task-rest_run-01_meg/sub-01_ses-001_task-rest_run-01_meg.chn',
]

badFilenames.forEach(function(path) {
Expand Down
5 changes: 5 additions & 0 deletions yarn.lock
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Expand Up @@ -3697,6 +3697,11 @@ hasha@^3.0.0:
dependencies:
is-stream "^1.0.1"

hed-validator@^0.3.0:
version "0.3.0"
resolved "https://registry.yarnpkg.com/hed-validator/-/hed-validator-0.3.0.tgz#53e80420c3e24209e5fbcd45156b29be429b6a99"
integrity sha512-yQLR+S2HPtb9dMQQISBamdcYa+0ShJl2vf/0D5xDqjFM6QrAmtXZYBsBwnPRy1HR0RCiBubRoBUG92veqRl54w==

hmac-drbg@^1.0.0:
version "1.0.1"
resolved "https://registry.yarnpkg.com/hmac-drbg/-/hmac-drbg-1.0.1.tgz#d2745701025a6c775a6c545793ed502fc0c649a1"
Expand Down