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Merge pull request #1932 from nellh/schema-cleanup
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chore: Remove schema experiment from legacy validator
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@rwblair
rwblair authored Apr 16, 2024
2 parents eec8aa9 + bb645b8 commit a6f0756
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Showing 6 changed files with 64 additions and 334 deletions.
1 change: 0 additions & 1 deletion bids-validator/utils/options.js
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@ export default {
remoteFiles: Boolean(options.remoteFiles),
gitRef: options.gitRef || 'HEAD',
config: options.config || {},
schema: options.schema !== 'disable' ? options.schema : false,
}
if (options.config && typeof options.config !== 'boolean') {
this.parseConfig(dir, options.config, function (issues, config) {
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201 changes: 61 additions & 140 deletions bids-validator/utils/type.js
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,6 @@ import session_level_rules from '../bids_validator/rules/session_level_rules.jso
import subject_level_rules from '../bids_validator/rules/subject_level_rules.json'
import top_level_rules from '../bids_validator/rules/top_level_rules.json'

let bids_schema

// Alternative method of loading from bids-specification schema
export function schemaSetup(schema) {
bids_schema = schema
}

// Associated data
const associatedData = buildRegExp(associated_data_rules.associated_data)
// File level
Expand Down Expand Up @@ -146,57 +139,30 @@ export default {
* Check if the file has appropriate name for a top level file
*/
isTopLevel: function (path) {
if (bids_schema) {
return (
bids_schema.top_level_files.some((regex) => regex.exec(path)) ||
funcTop.test(path) ||
aslTop.test(path) ||
dwiTop.test(path) ||
anatTop.test(path) ||
vfaTop.test(path) ||
megreTop.test(path) ||
irt1Top.test(path) ||
mpmTop.test(path) ||
mtsTop.test(path) ||
mtrTop.test(path) ||
mp2rageTop.test(path) ||
fmapEpiTop.test(path) ||
fmapGreTop.test(path) ||
otherTopFiles.test(path) ||
megTop.test(path) ||
eegTop.test(path) ||
ieegTop.test(path) ||
petTop.test(path) ||
motionTop.test(path) ||
nirsTop.test(path) ||
microscopyTop.test(path)
)
} else {
return (
rootTop.test(path) ||
funcTop.test(path) ||
aslTop.test(path) ||
dwiTop.test(path) ||
anatTop.test(path) ||
vfaTop.test(path) ||
megreTop.test(path) ||
irt1Top.test(path) ||
mpmTop.test(path) ||
mtsTop.test(path) ||
mtrTop.test(path) ||
mp2rageTop.test(path) ||
fmapEpiTop.test(path) ||
fmapGreTop.test(path) ||
otherTopFiles.test(path) ||
megTop.test(path) ||
eegTop.test(path) ||
ieegTop.test(path) ||
petTop.test(path) ||
motionTop.test(path) ||
nirsTop.test(path) ||
microscopyTop.test(path)
)
}
return (
rootTop.test(path) ||
funcTop.test(path) ||
aslTop.test(path) ||
dwiTop.test(path) ||
anatTop.test(path) ||
vfaTop.test(path) ||
megreTop.test(path) ||
irt1Top.test(path) ||
mpmTop.test(path) ||
mtsTop.test(path) ||
mtrTop.test(path) ||
mp2rageTop.test(path) ||
fmapEpiTop.test(path) ||
fmapGreTop.test(path) ||
otherTopFiles.test(path) ||
megTop.test(path) ||
eegTop.test(path) ||
ieegTop.test(path) ||
petTop.test(path) ||
motionTop.test(path) ||
nirsTop.test(path) ||
microscopyTop.test(path)
)
},

/**
Expand Down Expand Up @@ -267,51 +233,39 @@ export default {
* Check if the file has a name appropriate for an anatomical scan
*/
isAnat: function (path) {
if (bids_schema) {
return bids_schema.datatypes['anat'].some((regex) => regex.exec(path))
} else {
return (
conditionalMatch(anatNonparametric, path) ||
conditionalMatch(anatParametric, path) ||
conditionalMatch(anatDefacemask, path) ||
conditionalMatch(anatMultiEcho, path) ||
conditionalMatch(anatMultiFlip, path) ||
conditionalMatch(anatMultiInv, path) ||
conditionalMatch(anatMP2RAGE, path) ||
conditionalMatch(anatVFAMT, path) ||
conditionalMatch(anatMTR, path)
)
}
return (
conditionalMatch(anatNonparametric, path) ||
conditionalMatch(anatParametric, path) ||
conditionalMatch(anatDefacemask, path) ||
conditionalMatch(anatMultiEcho, path) ||
conditionalMatch(anatMultiFlip, path) ||
conditionalMatch(anatMultiInv, path) ||
conditionalMatch(anatMP2RAGE, path) ||
conditionalMatch(anatVFAMT, path) ||
conditionalMatch(anatMTR, path)
)
},

/**
* Check if the file has a name appropriate for a diffusion scan
*/
isDWI: function (path) {
if (bids_schema) {
return bids_schema.datatypes['dwi'].some((regex) => regex.exec(path))
} else {
return conditionalMatch(dwiData, path)
}
return conditionalMatch(dwiData, path)
},

/**
* Check if the file has a name appropriate for a fieldmap scan
*/
isFieldMap: function (path) {
if (bids_schema) {
return bids_schema.datatypes['fmap'].some((regex) => regex.exec(path))
} else {
return (
conditionalMatch(fmapGre, path) ||
conditionalMatch(fmapPepolarAsl, path) ||
conditionalMatch(fmapTB1DAM, path) ||
conditionalMatch(fmapTB1EPI, path) ||
conditionalMatch(fmapTB1SRGE, path) ||
conditionalMatch(fmapRF, path) ||
conditionalMatch(fmapParametric, path)
)
}
return (
conditionalMatch(fmapGre, path) ||
conditionalMatch(fmapPepolarAsl, path) ||
conditionalMatch(fmapTB1DAM, path) ||
conditionalMatch(fmapTB1EPI, path) ||
conditionalMatch(fmapTB1SRGE, path) ||
conditionalMatch(fmapRF, path) ||
conditionalMatch(fmapParametric, path)
)
},

isFieldMapMainNii: function (path) {
Expand All @@ -332,73 +286,47 @@ export default {
* Check if the file has a name appropriate for a functional scan
*/
isFunc: function (path) {
if (bids_schema) {
return bids_schema.datatypes['func'].some((regex) => regex.exec(path))
} else {
return (
conditionalMatch(func, path) ||
conditionalMatch(funcPhaseDeprecated, path) ||
conditionalMatch(funcEvents, path) ||
conditionalMatch(funcTimeseries, path)
)
}
return (
conditionalMatch(func, path) ||
conditionalMatch(funcPhaseDeprecated, path) ||
conditionalMatch(funcEvents, path) ||
conditionalMatch(funcTimeseries, path)
)
},

isAsl: function (path) {
return conditionalMatch(aslData, path)
},

isPET: function (path) {
if (bids_schema) {
return bids_schema.datatypes['pet'].some((regex) => regex.exec(path))
} else {
return conditionalMatch(petData, path)
}
return conditionalMatch(petData, path)
},

isPETBlood: function (path) {
return conditionalMatch(petBlood, path)
},

isMeg: function (path) {
if (bids_schema) {
return bids_schema.datatypes['meg'].some((regex) => regex.exec(path))
} else {
return (
conditionalMatch(megData, path) ||
conditionalMatch(megCalibrationData, path) ||
conditionalMatch(megCrosstalkData, path)
)
}
return (
conditionalMatch(megData, path) ||
conditionalMatch(megCalibrationData, path) ||
conditionalMatch(megCrosstalkData, path)
)
},
isNIRS: function (path) {
return conditionalMatch(nirsData, path)
},

isEEG: function (path) {
if (bids_schema) {
return bids_schema.datatypes['eeg'].some((regex) => regex.exec(path))
} else {
return conditionalMatch(eegData, path)
}
return conditionalMatch(eegData, path)
},

isIEEG: function (path) {
if (bids_schema) {
return bids_schema.datatypes['ieeg'].some((regex) => regex.exec(path))
} else {
return conditionalMatch(ieegData, path)
}
return conditionalMatch(ieegData, path)
},

isMOTION: function (path) {
if (bids_schema) {
// Motion not currently in schema
// return bids_schema.datatypes['motion'].some(regex => regex.exec(path))
return conditionalMatch(motion, path)
} else {
return conditionalMatch(motion, path)
}
return conditionalMatch(motion, path)
},

isMicroscopy: function (path) {
Expand All @@ -414,11 +342,7 @@ export default {
},

isBehavioral: function (path) {
if (bids_schema) {
return bids_schema.datatypes['beh'].some((regex) => regex.exec(path))
} else {
return conditionalMatch(behavioralData, path)
}
return conditionalMatch(behavioralData, path)
},

isFuncBold: function (path) {
Expand Down Expand Up @@ -479,9 +403,6 @@ export default {

return values
},

// CommonJS default export
schemaSetup,
}

function conditionalMatch(expression, path) {
Expand Down
4 changes: 2 additions & 2 deletions bids-validator/validators/bids/fullTest.js
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ import collectModalities from '../../utils/summary/collectModalities'
* Takes on an array of files, callback, and boolean indicating if git-annex is used.
* Starts the validation process for a BIDS package.
*/
const fullTest = (fileList, options, annexed, dir, schema, callback) => {
const fullTest = (fileList, options, annexed, dir, callback) => {
const self = BIDS
self.options = options

Expand Down Expand Up @@ -64,7 +64,7 @@ const fullTest = (fileList, options, annexed, dir, schema, callback) => {
})
}

const summary = utils.collectSummary(fileList, self.options, schema)
const summary = utils.collectSummary(fileList, self.options)

// remove size redundancies
for (const key in fileList) {
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10 changes: 1 addition & 9 deletions bids-validator/validators/bids/start.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,6 @@ import quickTest from './quickTest'
import quickTestError from './quickTestError'
import fullTest from './fullTest'
import utils from '../../utils'
import { schemaRegex } from '../../validators/schemaTypes'
import { schemaSetup } from '../../utils/type'

/**
* Start
Expand All @@ -31,17 +29,11 @@ const start = (dir, options, callback) => {
} else {
BIDS.options = options
reset(BIDS)
// Load the bids-spec schema ahead of any validation
let schema
if (options.schema) {
schema = await schemaRegex(options.schema)
schemaSetup(schema)
}
const files = await utils.files.readDir(dir, options)
if (quickTest(files)) {
// Is the dir using git-annex?
const annexed = utils.files.remoteFiles.isGitAnnex(dir)
fullTest(files, BIDS.options, annexed, dir, schema, callback)
fullTest(files, BIDS.options, annexed, dir, callback)
} else {
// Return an error immediately if quickTest fails
const issue = quickTestError(dir)
Expand Down
7 changes: 0 additions & 7 deletions bids-validator/validators/options.js
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Original file line number Diff line number Diff line change
Expand Up @@ -66,13 +66,6 @@ export function parseOptions(argumentOverride) {
'A less accurate check that reads filenames one per line from stdin.',
)
.hide('filenames')
.option('schema', {
alias: 's',
describe:
'BIDS specification schema version to use for validation, e.g. "v1.6.0" (beta)',
default: 'disable',
choices: ['disable', 'v1.6.0', 'v1.7.0', 'master'],
})
.epilogue(
'This tool checks if a dataset in a given directory is \
compatible with the Brain Imaging Data Structure specification. To learn \
Expand Down
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