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Add regexps for space entity: EEG and iEEG #1190

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merged 9 commits into from
Feb 23, 2021
Merged

Add regexps for space entity: EEG and iEEG #1190

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b7a71b8
Adding regex for space entity.
adam2392 Feb 15, 2021
45246af
Adding regex for space entity.
adam2392 Feb 15, 2021
b7ca891
test ALL bids examples in separate CI flow
sappelhoff Feb 16, 2021
ed873d3
debug ci
sappelhoff Feb 16, 2021
6de6624
do not use gh action checkout, use shallow clone
sappelhoff Feb 16, 2021
c279846
fix regexp
sappelhoff Feb 16, 2021
56fe88e
Merging .
adam2392 Feb 16, 2021
d117298
Updating unit test.
adam2392 Feb 22, 2021
e5fed90
add space regexp for EEG
sappelhoff Feb 22, 2021
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6 changes: 4 additions & 2 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ jobs:
name: Eslint
command: yarn lint
- run:
name: Test Data
name: Get bids-examples data
command: git submodule update --init
- run:
name: Jest tests
Expand All @@ -52,7 +52,9 @@ jobs:
command: yarn codecov
- run:
name: Smoke tests
command: bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders && bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json
command: |
bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders
bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json
test_docker:
machine:
# Ubuntu 16.04, docker 18.09.3, docker-compose 1.23.1
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53 changes: 53 additions & 0 deletions .github/workflows/test-bids-examples.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
name: test-bids-examples

on:
push:
branches: ['**']
pull_request:
branches: ['**']

jobs:
build:
strategy:
fail-fast: false
matrix:
platform: [ubuntu-latest]
bids-validator-branch: [master]
bids-examples-branch: [bep001_qmri]

runs-on: ${{ matrix.platform }}

env:
TZ: Europe/Berlin
FORCE_COLOR: 1

steps:
- name: Set up Node.js
uses: actions/setup-node@v1
with:
node-version: 12

- name: Install bids-validator
run: |
git clone --depth 1 https://github.com/bids-standard/bids-validator -b ${{ matrix.bids-validator-branch }}
npm install -g bids-validator/bids-validator

- name: Get bids-examples data
run: |
git clone --depth 1 https://github.com/bids-standard/bids-examples -b ${{ matrix.bids-examples-branch }}

- name: Display versions and environment information
run: |
echo $TZ
date
echo "npm"; npm --version
echo "node"; node --version
echo "bids-validator"; bids-validator --version

- name: Validate all BIDS datasets using bids-validator
run: |
pushd ./bids-examples
cat ./run_tests.sh
bash ./run_tests.sh
popd
shell: bash
91 changes: 88 additions & 3 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 @@ -356,8 +356,53 @@
},

"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]+)?(?:_split-[0-9]+)?((_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?eeg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(?:_space-(@@@_eeg_space_@@@))?((_eeg\\.(@@@_eeg_type_@@@)|(@@@_eeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
"tokens": {
"@@@_eeg_space_@@@": [
"Other",
"CapTrak",
"CTF",
"ElektaNeuromag",
"4DBti",
"KitYokogawa",
"ChietiItab",
"ICBM452AirSpace",
"ICBM452Warp5Space",
"IXI549Space",
"fsaverage",
"fsaverageSym",
"fsLR",
"MNIColin27",
"MNI152Lin",
"MNI152NLin2009aSym",
"MNI152NLin2009bSym",
"MNI152NLin2009cSym",
"MNI152NLin2009aAsym",
"MNI152NLin2009bAsym",
"MNI152NLin2009cAsym",
"MNI152NLin6Sym",
"MNI152NLin6ASym",
"MNI305",
"NIHPD",
"OASIS30AntsOASISAnts",
"OASIS30Atropos",
"Talairach",
"UNCInfant",
"fsaverage3",
"fsaverage4",
"fsaverage5",
"fsaverage6",
"fsaveragesym",
"UNCInfant0V21",
"UNCInfant1V21",
"UNCInfant2V21",
"UNCInfant0V22",
"UNCInfant1V22",
"UNCInfant2V22",
"UNCInfant0V23",
"UNCInfant1V23",
"UNCInfant2V23"
],
"@@@_eeg_type_@@@": ["vhdr", "vmrk", "eeg", "edf", "bdf", "set", "fdt"],
"@@@_eeg_ext_@@@": [
"_events\\.json",
Expand All @@ -378,10 +423,50 @@
]
}
},

"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]+)?(?:_split-[0-9]+)?(?:_space-[a-zA-Z0-9]+)?((_ieeg\\.(@@@_ieeg_type_@@@)|(@@@_ieeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?ieeg[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_split-[0-9]+)?(?:_space-(@@@_ieeg_space_@@@))?((_ieeg\\.(@@@_ieeg_type_@@@)|(@@@_ieeg_ext_@@@))|(?:_recording-[a-zA-Z0-9]+)?(?:@@@_cont_ext_@@@))$",
"tokens": {
"@@@_ieeg_space_@@@": [
"Other",
"Pixels",
"ACPC",
"ICBM452AirSpace",
"ICBM452Warp5Space",
"IXI549Space",
"fsaverage",
"fsaverageSym",
"fsLR",
"MNIColin27",
"MNI152Lin",
"MNI152NLin2009aSym",
"MNI152NLin2009bSym",
"MNI152NLin2009cSym",
"MNI152NLin2009aAsym",
"MNI152NLin2009bAsym",
"MNI152NLin2009cAsym",
"MNI152NLin6Sym",
"MNI152NLin6ASym",
"MNI305",
"NIHPD",
"OASIS30AntsOASISAnts",
"OASIS30Atropos",
"Talairach",
"UNCInfant",
"fsaverage3",
"fsaverage4",
"fsaverage5",
"fsaverage6",
"fsaveragesym",
"UNCInfant0V21",
"UNCInfant1V21",
"UNCInfant2V21",
"UNCInfant0V22",
"UNCInfant1V22",
"UNCInfant2V22",
"UNCInfant0V23",
"UNCInfant1V23",
"UNCInfant2V23"
],
"@@@_ieeg_type_@@@": [
"edf",
"vhdr",
Expand Down
90 changes: 88 additions & 2 deletions bids-validator/bids_validator/rules/session_level_rules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@
},

"eeg_ses": {
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(@@@_eeg_ses_type_@@@)$",
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_eeg_space_@@@))?(@@@_eeg_ses_type_@@@)$",
"tokens": {
"@@@_eeg_ses_type_@@@": [
"_events.tsv",
Expand All @@ -87,12 +87,57 @@
"_eeg.json",
"_coordsystem.json",
"_photo.jpg"
],
"@@@_eeg_space_@@@": [
"Other",
"CapTrak",
"CTF",
"ElektaNeuromag",
"4DBti",
"KitYokogawa",
"ChietiItab",
"ICBM452AirSpace",
"ICBM452Warp5Space",
"IXI549Space",
"fsaverage",
"fsaverageSym",
"fsLR",
"MNIColin27",
"MNI152Lin",
"MNI152NLin2009aSym",
"MNI152NLin2009bSym",
"MNI152NLin2009cSym",
"MNI152NLin2009aAsym",
"MNI152NLin2009bAsym",
"MNI152NLin2009cAsym",
"MNI152NLin6Sym",
"MNI152NLin6ASym",
"MNI305",
"NIHPD",
"OASIS30AntsOASISAnts",
"OASIS30Atropos",
"Talairach",
"UNCInfant",
"fsaverage3",
"fsaverage4",
"fsaverage5",
"fsaverage6",
"fsaveragesym",
"UNCInfant0V21",
"UNCInfant1V21",
"UNCInfant2V21",
"UNCInfant0V22",
"UNCInfant1V22",
"UNCInfant2V22",
"UNCInfant0V23",
"UNCInfant1V23",
"UNCInfant2V23"
]
}
},

"ieeg_ses": {
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-[a-zA-Z0-9]+)?(@@@_ieeg_ses_type_@@@)$",
"regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_proc-[a-zA-Z0-9]+)?(?:_space-(@@@_ieeg_space_@@@))?(@@@_ieeg_ses_type_@@@)$",
"tokens": {
"@@@_ieeg_ses_type_@@@": [
"_events.tsv",
Expand All @@ -103,6 +148,47 @@
"_ieeg.json",
"_coordsystem.json",
"_photo.jpg"
],
"@@@_ieeg_space_@@@": [
"Other",
"Pixels",
"ACPC",
"ICBM452AirSpace",
"ICBM452Warp5Space",
"IXI549Space",
"fsaverage",
"fsaverageSym",
"fsLR",
"MNIColin27",
"MNI152Lin",
"MNI152NLin2009aSym",
"MNI152NLin2009bSym",
"MNI152NLin2009cSym",
"MNI152NLin2009aAsym",
"MNI152NLin2009bAsym",
"MNI152NLin2009cAsym",
"MNI152NLin6Sym",
"MNI152NLin6ASym",
"MNI305",
"NIHPD",
"OASIS30AntsOASISAnts",
"OASIS30Atropos",
"Talairach",
"UNCInfant",
"fsaverage3",
"fsaverage4",
"fsaverage5",
"fsaverage6",
"fsaveragesym",
"UNCInfant0V21",
"UNCInfant1V21",
"UNCInfant2V21",
"UNCInfant0V22",
"UNCInfant1V22",
"UNCInfant2V22",
"UNCInfant0V23",
"UNCInfant1V23",
"UNCInfant2V23"
]
}
}
Expand Down
2 changes: 1 addition & 1 deletion bids-validator/tests/data/bids-examples
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Submodule bids-examples updated 2917 files
9 changes: 8 additions & 1 deletion bids-validator/tests/type.spec.js
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -345,7 +345,9 @@ describe('utils.type.file.isEEG', function() {
'/sub-01/ses-001/eeg/sub-01_ses-001_task-rest_run-01_eeg.fdt',
'/sub-01/ses-001/eeg/sub-01_ses-001_task-rest_run-01_channels.tsv',
'/sub-01/ses-001/eeg/sub-01_ses-001_electrodes.tsv',
'/sub-01/ses-001/eeg/sub-01_ses-001_space-CapTrak_electrodes.tsv',
'/sub-01/ses-001/eeg/sub-01_ses-001_coordsystem.json',
'/sub-01/ses-001/eeg/sub-01_ses-001_space-CapTrak_coordsystem.json',
'/sub-01/ses-001/eeg/sub-01_ses-001_photo.jpg',
]

Expand All @@ -360,6 +362,8 @@ describe('utils.type.file.isEEG', function() {
'/sub-01/eeg/sub-01_ses-001_task-rest_run-01_eeg.json',
'/sub-01/ses-001/eeg/sub-12_ses-001_task-rest_run-01_split-01_eeg.edf',
'/sub-01/ses-001/eeg/sub-01_ses-001_task-rest_run-01_eeg.tsv',
'/sub-01/ses-001/eeg/sub-01_ses-001_space-BOGUS_electrodes.tsv',
'/sub-01/ses-001/eeg/sub-01_ses-001_space-BOGUS_coordsystem.json',
]

badFilenames.forEach(function(path) {
Expand All @@ -386,7 +390,8 @@ describe('utils.type.file.isIEEG', function() {
'/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',
'/sub-01/ses-001/ieeg/sub-01_ses-001_space-fsaverage_electrodes.tsv',
'/sub-01/ses-001/ieeg/sub-01_ses-001_space-fsaverage_coordsystem.json',
]

goodFilenames.forEach(function(path) {
Expand All @@ -400,6 +405,8 @@ describe('utils.type.file.isIEEG', function() {
'/sub-01/ieeg/sub-01_ses-001_task-rest_run-01_ieeg.json',
'/sub-01/ses-001/ieeg/sub-12_ses-001_task-rest_run-01_split-01_ieeg.fif',
'/sub-01/ses-001/ieeg/sub-01_ses-001_task-rest_run-01_ieeg.tsv',
'/sub-01/ses-001/ieeg/sub-01_ses-001_space-fsavg_electrodes.tsv',
'/sub-01/ses-001/ieeg/sub-01_ses-001_space-fsavg_coordsystem.json',
]

badFilenames.forEach(function(path) {
Expand Down