diff --git a/docs/html/BidsFile.html b/docs/html/BidsFile.html
index b9a5ce8a..05e307ad 100644
--- a/docs/html/BidsFile.html
+++ b/docs/html/BidsFile.html
@@ -367,7 +367,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Type:
Methods
- () parse() → {Array}
@@ -452,7 +452,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Source: bids/types/json.js
import isPlainObject from 'lodash/isPlainObject'
import { sidecarValueHasHed } from '../utils'
-import { parseHedString } from '../../parser/parser'
+import { parse } from '../../parser/parser'
import ParsedHedString from '../../parser/parsedHedString'
import { BidsFile } from './file'
import BidsHedSidecarValidator from '../validator/sidecarValidator'
@@ -359,7 +359,7 @@ Source: bids/types/json.js
* The value strings cannot contain definitions.
*/
_parseValueString(hedSchemas) {
- const [parsedString, parsingIssues] = parseHedString(this.valueString, hedSchemas, false, true)
+ const [parsedString, parsingIssues] = parse(this.valueString, hedSchemas, false, true)
this.parsedValueString = parsedString
return parsingIssues
}
@@ -383,7 +383,7 @@ Source: bids/types/json.js
file: this.sidecar?.file?.relativePath,
})
}
- const [parsedString, parsingIssues] = parseHedString(string, hedSchemas, true, true)
+ const [parsedString, parsingIssues] = parse(string, hedSchemas, true, true)
this.parsedCategoryMap.set(value, parsedString)
issues.push(...parsingIssues)
if (parsingIssues.length === 0) {
@@ -525,7 +525,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Source: bids/validator/tsvValidator.js
import { BidsHedIssue, BidsIssue } from '../types/issues'
import { BidsTsvElement, BidsTsvRow } from '../types/tsv'
import { BidsValidator } from './validator'
-import { parseHedString } from '../../parser/parser'
+import { parse } from '../../parser/parser'
import ParsedHedString from '../../parser/parsedHedString'
import { generateIssue } from '../../issues/issues'
import { ReservedChecker } from '../../parser/reservedChecker'
@@ -111,7 +111,7 @@ Source: bids/validator/tsvValidator.js
// Find basic parsing issues and return if unable to parse the string. (Warnings are okay.)
const issues = []
- const [parsedString, parsingIssues] = parseHedString(hedString, this.hedSchemas, false, false)
+ const [parsedString, parsingIssues] = parse(hedString, this.hedSchemas, false, false)
issues.push(...BidsHedIssue.fromHedIssues(parsingIssues, this.bidsFile.file, { tsvLine: rowIndex }))
if (parsedString === null) {
return issues
@@ -203,7 +203,7 @@ Source: bids/validator/tsvValidator.js
}
// Assemble the HED strings associated with same onset into single string. Use the parse duplicate detection.
const rowString = elementList.map((element) => element.hedString).join(',')
- const [parsedString, parsingIssues] = parseHedString(rowString, this.hedSchemas, false, false)
+ const [parsedString, parsingIssues] = parse(rowString, this.hedSchemas, false, false)
if (parsingIssues.length > 0) {
const tsvLines = BidsTsvElement.getTsvLines(elementList)
issues.push(...BidsHedIssue.fromHedIssues(parsingIssues, this.bidsFile.file, { tsvLine: tsvLines }))
@@ -339,7 +339,7 @@ Source: bids/validator/tsvValidator.js
// Add the parsed HED strings to the elements and quite if there are serious errors
const cummulativeIssues = []
for (const element of elements) {
- const [parsedHedString, parsingIssues] = parseHedString(element.hedString, this.hedSchemas, false, false)
+ const [parsedHedString, parsingIssues] = parse(element.hedString, this.hedSchemas, false, false)
element.parsedHedString = parsedHedString
if (parsingIssues.length > 0) {
cummulativeIssues.push(
@@ -630,7 +630,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Returns:
- (hedString, hedSchemas, definitionsAllowed, placeholdersAllowed) → {Array}
@@ -3752,7 +3752,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV
- Classes Global
+ Classes Global
Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Source: parser/definitionManager.js
import { generateIssue, IssueError } from '../issues/issues'
-import { parseHedString } from './parser'
+import { parse } from './parser'
import { filterByTagName } from './parseUtils'
export class Definition {
@@ -91,7 +91,7 @@ Source: parser/definitionManager.js
return [this.defContents.normalized, []]
}
const evalString = this.defContents.originalTag.replace('#', tag._splitValue)
- const [normalizedValue, issues] = parseHedString(evalString, hedSchema, false, false)
+ const [normalizedValue, issues] = parse(evalString, hedSchema, false, false)
if (issues.length > 0) {
return [null, issues]
}
@@ -130,7 +130,7 @@ Source: parser/definitionManager.js
* @returns {Array} - Returns [Definition, Issue[]] with the definition and any issues.
*/
static createDefinition(hedString, hedSchemas) {
- const [parsedString, issues] = parseHedString(hedString, hedSchemas, true, true)
+ const [parsedString, issues] = parse(hedString, hedSchemas, true, true)
if (issues.length > 0) {
return [null, issues]
}
@@ -442,7 +442,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Source: parser/parser.js
* Parse a full HED string.
* @returns {Array} - [ParsedHedString|null, Issue[]] representing the parsed HED string and any parsing issues.
*/
- parseHedString() {
+ parse() {
if (this.hedString === null || this.hedString === undefined) {
return [null, [generateIssue('invalidTagString', {})]]
}
@@ -151,7 +151,7 @@ Source: parser/parser.js
hedSchemas,
definitionsAllowed,
placeholdersAllowed,
- ).parseHedString()
+ ).parse()
parsedStrings.push(parsedString)
cumulativeIssues.push(...currentIssues)
}
@@ -169,8 +169,8 @@ Source: parser/parser.js
* @param {boolean} placeholdersAllowed - True if placeholders are allowed.
* @returns {Array} - [ParsedHedString, Issue[]] representing the parsed HED string and any issues found.
*/
-export function parseHedString(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed) {
- return new HedStringParser(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed).parseHedString()
+export function parse(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed) {
+ return new HedStringParser(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed).parse()
}
/**
@@ -292,7 +292,7 @@ Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV Global
localSchemaList mergeSchemas normalized parseHedString parse parseHedStrings parseSchemaXML parseTSV }
*/
categoryMap
+
/**
* The parsed category mapping.
* @type {Map}
*/
parsedCategoryMap
+
/**
* The unparsed value string.
* @type {string}
*/
valueString
+
/**
* The parsed value string.
* @type {ParsedHedString}
*/
parsedValueString
+
/**
* Weak reference to the bidsFile.
* @type {BidsSidecar}
*/
sidecar
+ /**
+ * Indication of whether this key is for definitions.
+ * @type {Boolean}
+ */
hasDefinitions
/**
@@ -328,8 +340,10 @@ export class BidsSidecarKey {
/**
* Parse the HED data for this key.
*
+ * ###Note: This sets the parsedHedData as a side effect.
+ *
* @param {Schemas} hedSchemas The HED schema collection.
- * @returns {Issue[]} Any issues found.
+ * @returns {Array} - [Issue[], Issues[]] Errors and warnings that result from parsing.
*/
parseHed(hedSchemas) {
if (this.isValueKey) {
@@ -345,24 +359,25 @@ export class BidsSidecarKey {
* The value strings cannot contain definitions.
*
* @param {Schemas} hedSchemas - The HED schemas to use.
- * @returns {Issue[]}
+ * @returns {Array} - [Issue[], Issue[]] - Errors due for the value.
* @private
*/
_parseValueString(hedSchemas) {
- const [parsedString, parsingIssues] = parseHedString(this.valueString, hedSchemas, false, true)
+ const [parsedString, errors, warnings] = parseHedString(this.valueString, hedSchemas, false, true)
this.parsedValueString = parsedString
- return parsingIssues
+ return [errors, warnings]
}
/**
* Parse the categorical values associated with this key.
* @param {Schemas} hedSchemas - The HED schemas used to check against.
- * @returns {Issue[]} - A list of issues if any
+ * @returns {Array} - Array[Issue[], Issue[]] A list of error issues and warning issues.
* @private
*/
_parseCategory(hedSchemas) {
- const issues = []
this.parsedCategoryMap = new Map()
+ const errors = []
+ const warnings = []
for (const [value, string] of Object.entries(this.categoryMap)) {
const trimmedValue = value.trim()
if (ILLEGAL_SIDECAR_KEYS.has(trimmedValue.toLowerCase())) {
@@ -373,18 +388,25 @@ export class BidsSidecarKey {
file: this.sidecar?.file?.relativePath,
})
}
- const [parsedString, parsingIssues] = parseHedString(string, hedSchemas, true, true)
+ const [parsedString, errorIssues, warningIssues] = parseHedString(string, hedSchemas, true, true)
this.parsedCategoryMap.set(value, parsedString)
- issues.push(...parsingIssues)
- if (parsingIssues.length === 0) {
- issues.push(...this._checkDefinitions(parsedString))
+ warnings.push(...warningIssues)
+ errors.push(...errorIssues)
+ if (errorIssues.length === 0) {
+ errors.push(...this._checkDefinitions(parsedString))
}
}
- return issues
+ return [errors, warnings]
}
+ /**
+ * Check for definitions in the HED string.
+ * @param {ParsedHedString} parsedString - The string to check for definitions.
+ * @returns {Issue[]} - Errors that occur.
+ * @private
+ */
_checkDefinitions(parsedString) {
- const issues = []
+ const errors = []
for (const group of parsedString.tagGroups) {
if (!group.isDefinitionGroup) {
continue
@@ -392,12 +414,12 @@ export class BidsSidecarKey {
this.hasDefinitions = true
const [def, defIssues] = Definition.createDefinitionFromGroup(group)
if (defIssues.length > 0) {
- issues.push(...defIssues)
+ errors.push(...defIssues)
} else {
- issues.push(...this.sidecar.definitions.addDefinition(def))
+ errors.push(...this.sidecar.definitions.addDefinition(def))
}
}
- return issues
+ return errors
}
/**
diff --git a/src/bids/validator/sidecarValidator.js b/src/bids/validator/sidecarValidator.js
index 8f594553..189d3f5b 100644
--- a/src/bids/validator/sidecarValidator.js
+++ b/src/bids/validator/sidecarValidator.js
@@ -19,22 +19,19 @@ export class BidsHedSidecarValidator extends BidsValidator {
}
/**
- * Validate a BIDS JSON bidsFile file. This method returns the complete issue list for convenience.
+ * Validate a BIDS JSON bidsFile file. Errors and warnings are stored.
*
- * @returns {BidsHedIssue[]} - Any issues found during validation of this bidsFile file.
*/
validate() {
// Allow schema to be set a validation time -- this is checked by the superclass of BIDS file
- const sidecarParsingIssues = BidsHedIssue.fromHedIssues(
- this.bidsFile.parseHedStrings(this.hedSchemas),
- this.bidsFile.file,
- )
- this.issues.push(...sidecarParsingIssues)
- if (sidecarParsingIssues.length > 0) {
- return this.issues
+ const [errorIssues, warningIssues] = this.bidsFile.parseHed(this.hedSchemas)
+ this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file))
+ this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file))
+ if (errorIssues.length > 0) {
+ return
}
- this.issues.push(...this._validateStrings(), ...this._validateCurlyBraces())
- return this.issues
+
+ this.errors.push(...this._validateStrings(), ...this._validateCurlyBraces())
}
/**
diff --git a/src/bids/validator/tsvValidator.js b/src/bids/validator/tsvValidator.js
index 91eac32a..4b0fba80 100644
--- a/src/bids/validator/tsvValidator.js
+++ b/src/bids/validator/tsvValidator.js
@@ -32,47 +32,49 @@ export class BidsHedTsvValidator extends BidsValidator {
/**
* Validate a BIDS TSV file. This method returns the complete issue list for convenience.
*
- * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file.
*/
validate() {
- // Validate the BIDS bidsFile if it exists.
+ // Validate the BIDS bidsFile if it exists and return if there are errors
if (this.bidsFile.mergedSidecar) {
- const sidecarIssues = this.bidsFile.mergedSidecar.validate(this.hedSchemas)
- this.issues.push(...sidecarIssues)
- if (BidsHedIssue.anyAreErrors(sidecarIssues)) {
- return this.issues
+ const issues = this.bidsFile.mergedSidecar.validate(this.hedSchemas)
+ const [errorIssues, warningIssues] = BidsHedIssue.splitErrors(issues)
+ this.errors.push(...errorIssues)
+ this.warnings.push(...warningIssues)
+ if (this.errors.length > 0) {
+ return
}
}
// Valid the HED column by itself.
- const hedColumnIssues = this._validateHedColumn()
- this.issues.push(...hedColumnIssues)
- if (BidsHedIssue.anyAreErrors(this.issues)) {
- return this.issues
+ this._validateHedColumn()
+ if (this.errors.length > 0) {
+ return
}
// Now do a full validation
const bidsHedTsvParser = new BidsHedTsvParser(this.bidsFile, this.hedSchemas)
- const [bidsEvents, parsingIssues] = bidsHedTsvParser.parse()
- this.issues.push(...parsingIssues)
- if (!BidsHedIssue.anyAreErrors(this.issues)) {
- this.issues.push(...this.validateDataset(bidsEvents))
+ const [bidsEvents, errorIssues, warningIssues] = bidsHedTsvParser.parse()
+ this.errors.push(...errorIssues)
+ this.warnings.push(...warningIssues)
+ if (this.errors.length > 0) {
+ return
+ }
+ this.validateDataset(bidsEvents)
+ if (this.errors.length === 0) {
+ //this.issues.push(...this.check_missing_keys())
}
- return this.issues
}
/**
* Validate this TSV file's HED column.
*
- * @returns {BidsHedIssue[]} - Issues found in validating the HED column without sidecar information.
* @private
*/
_validateHedColumn() {
- if (this.bidsFile.hedColumnHedStrings.length === 0) {
- return []
+ if (this.bidsFile.hedColumnHedStrings.length > 0) {
+ this.bidsFile.hedColumnHedStrings.flatMap((hedString, rowIndexMinusTwo) =>
+ this._validateHedColumnString(hedString, rowIndexMinusTwo + 2),
+ )
}
- return this.bidsFile.hedColumnHedStrings.flatMap((hedString, rowIndexMinusTwo) =>
- this._validateHedColumnString(hedString, rowIndexMinusTwo + 2),
- )
}
/**
@@ -80,25 +82,24 @@ export class BidsHedTsvValidator extends BidsValidator {
*
* @param {string} hedString - The string to be validated.
* @param {number} rowIndex - The index of this row in the TSV file.
- * @returns {BidsHedIssue[]} - Specific issues found in validating the HED column
* @private
*/
_validateHedColumnString(hedString, rowIndex) {
if (!hedString) {
- return []
+ return
}
// Find basic parsing issues and return if unable to parse the string. (Warnings are okay.)
- const issues = []
- const [parsedString, parsingIssues] = parseHedString(hedString, this.hedSchemas, false, false)
- issues.push(...BidsHedIssue.fromHedIssues(parsingIssues, this.bidsFile.file, { tsvLine: rowIndex }))
+ const [parsedString, errorIssues, warningIssues] = parseHedString(hedString, this.hedSchemas, false, false)
+ this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file, { tsvLine: rowIndex }))
+ this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file, { tsvLine: rowIndex }))
if (parsedString === null) {
- return issues
+ return
}
// The HED column is not allowed to have column splices.
if (parsedString.columnSplices.length > 0) {
- issues.push(
+ this.errors.push(
BidsHedIssue.fromHedIssue(
generateIssue('curlyBracesInHedColumn', {
string: parsedString.hedString,
@@ -107,7 +108,7 @@ export class BidsHedTsvValidator extends BidsValidator {
this.bidsFile.file,
),
)
- return issues
+ return
}
// Check whether definitions used exist and are used correctly.
@@ -115,36 +116,31 @@ export class BidsHedTsvValidator extends BidsValidator {
...this.bidsFile.mergedSidecar.definitions.validateDefs(parsedString, this.hedSchemas, false),
...this.bidsFile.mergedSidecar.definitions.validateDefExpands(parsedString, this.hedSchemas, false),
]
- const convertedIssues = BidsHedIssue.fromHedIssues(defIssues, this.bidsFile.file, { tsvLine: rowIndex })
- issues.push(...convertedIssues)
- return issues
+ this.errors.push(...BidsHedIssue.fromHedIssues(defIssues, this.bidsFile.file, { tsvLine: rowIndex }))
}
/**
* Validate the HED data in a combined event TSV file/bidsFile BIDS data collection.
- *
- * @param {BidsTsvElement[]} elements - The element objects, which include the strings and row information.
- * @returns {BidsHedIssue[]} - The errors resulting from final validation, including dataset-level checks.
*/
validateDataset(elements) {
// Final top-tag detection cannot be done until the strings are fully assembled and finalized.
- const issues = this._checkNoTopTags(elements)
- if (issues.length > 0) {
- return issues
+ this._checkNoTopTags(elements)
+ if (this.errors.length > 0) {
+ return
}
// Temporal files have to check Onset, Inset, Offset consistency.
if (this.bidsFile.isTimelineFile) {
- return this._validateTemporal(elements)
+ this._validateTemporal(elements)
+ } else {
+ // Non-temporal files cannot have temporal tags.
+ this._checkNoTime(elements)
}
- // Non-temporal files cannot have temporal tags.
- return this._checkNoTime(elements)
}
/**
* Check the temporal relationships among events.
*
* @param {BidsTsvElement[]} elements - The elements representing the tsv file.
- * @returns {BidsHedIssue[]} - Errors in temporal relationships among events.
* @private
*/
_validateTemporal(elements) {
@@ -152,14 +148,14 @@ export class BidsHedTsvValidator extends BidsValidator {
const eventManager = new EventManager()
const [eventList, temporalIssues] = eventManager.parseEvents(elements)
if (temporalIssues.length > 0) {
- return temporalIssues
+ this.errors.push(...temporalIssues)
+ return
}
// There still may be non-temporal duplicates when multiple rows with the same onset.
- const duplicateErrors = this._checkDuplicatesAcrossRows(elements)
- if (duplicateErrors.length > 0) {
- return duplicateErrors
+ this._checkDuplicatesAcrossRows(elements)
+ if (this.errors.length === 0) {
+ this.errors.push(...eventManager.validate(eventList))
}
- return eventManager.validate(eventList)
}
/**
@@ -175,20 +171,17 @@ export class BidsHedTsvValidator extends BidsValidator {
*/
_checkDuplicatesAcrossRows(elements) {
const duplicateMap = this._getOnsetMap(elements)
- const issues = []
for (const elementList of duplicateMap.values()) {
if (elementList.length === 1) {
continue
}
// Assemble the HED strings associated with same onset into single string. Use the parse duplicate detection.
const rowString = elementList.map((element) => element.hedString).join(',')
- const [parsedString, parsingIssues] = parseHedString(rowString, this.hedSchemas, false, false)
- if (parsingIssues.length > 0) {
- const tsvLines = BidsTsvElement.getTsvLines(elementList)
- issues.push(...BidsHedIssue.fromHedIssues(parsingIssues, this.bidsFile.file, { tsvLine: tsvLines }))
- }
+ const [parsedString, errorIssues, warningIssues] = parseHedString(rowString, this.hedSchemas, false, false)
+ const tsvLines = BidsTsvElement.getTsvLines(elementList)
+ this.errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.bidsFile.file, { tsvLine: tsvLines }))
+ this.warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.bidsFile.file, { tsvLine: tsvLines }))
}
- return issues
}
/**
@@ -217,16 +210,14 @@ export class BidsHedTsvValidator extends BidsValidator {
* Top group tag requirements may not be satisfied until all splices have been done.
*
* @param {BidsTsvElement[]} elements - The elements to be checked.
- * @returns {BidsHedIssue[]} - Issues from final check of top groups.
* @private
*/
_checkNoTopTags(elements) {
- const topGroupIssues = []
for (const element of elements) {
const topTags = element.parsedHedString ? element.parsedHedString.topLevelTags : []
const badTags = topTags.filter((tag) => ReservedChecker.hasTopLevelTagGroupAttribute(tag))
if (badTags.length > 0) {
- topGroupIssues.push(
+ this.errors.push(
BidsHedIssue.fromHedIssue(
generateIssue('invalidTopLevelTag', { tag: getTagListString(badTags), string: element.hedString }),
element.file,
@@ -235,20 +226,17 @@ export class BidsHedTsvValidator extends BidsValidator {
)
}
}
- return topGroupIssues
}
/**
* Verify that this non-temporal file does not contain any temporal tags.
*
* @param {BidsTsvElement[]} elements - The elements representing a tsv file (with HED string parsed).
- * @returns {BidsHedIssue[]} - Issues from checking non-temporal files for temporal tags.
*/
_checkNoTime(elements) {
- const timeIssues = []
for (const element of elements) {
if (element.parsedHedString.tags.some((tag) => this.reserved.timelineTags.has(tag.schemaTag.name))) {
- timeIssues.push(
+ this.errors.push(
BidsHedIssue.fromHedIssue(
generateIssue('temporalTagInNonTemporalContext', { string: element.hedString, tsvLine: element.tsvLine }),
this.bidsFile.file,
@@ -256,7 +244,6 @@ export class BidsHedTsvValidator extends BidsValidator {
)
}
}
- return timeIssues
}
}
@@ -295,44 +282,47 @@ export class BidsHedTsvParser {
/**
* Combine the BIDS bidsFile HED data into a BIDS TSV file's HED data.
*
- * @returns {Array} - Returns a two-element array [BidsTsvElement[], BidsHedIssue[]].
+ * @returns {Array} - Returns a two-element array [BidsTsvElement[], BidsHedIssue[], BidsHedIssue[]].
*/
parse() {
const tsvHedRows = this._generateHedRows()
const tsvElements = this._parseHedRows(tsvHedRows)
- const parsingIssues = this._parseElementStrings(tsvElements)
- return [tsvElements, parsingIssues]
+ const [errors, warnings] = this._parseElementStrings(tsvElements)
+ return [tsvElements, errors, warnings]
}
/**
* Parse element HED strings.
*
* @param {BidsTsvElement[]} elements - The objects representing tsv rows with their parsed HEd strings.
- * @returns {BidsHedIssue[]} - The issues resulting in creating the parsed HED strings.
+ * @returns {Array} - [BidsHedIssue[], BidsHedIssue[]] The errors and warnings resulting in creating the parsed HED strings.
*/
_parseElementStrings(elements) {
if (elements.length === 0) {
- return []
+ return [[], []]
}
// Add the parsed HED strings to the elements and quite if there are serious errors
- const cummulativeIssues = []
+ const errors = []
+ const warnings = []
for (const element of elements) {
- const [parsedHedString, parsingIssues] = parseHedString(element.hedString, this.hedSchemas, false, false)
+ const [parsedHedString, errorIssues, warningIssues] = parseHedString(
+ element.hedString,
+ this.hedSchemas,
+ false,
+ false,
+ )
element.parsedHedString = parsedHedString
- if (parsingIssues.length > 0) {
- cummulativeIssues.push(
- ...BidsHedIssue.fromHedIssues(parsingIssues, this.tsvFile.file, { tsvLine: element.tsvLine }),
- )
- }
+ errors.push(...BidsHedIssue.fromHedIssues(errorIssues, this.tsvFile.file, { tsvLine: element.tsvLine }))
+ warnings.push(...BidsHedIssue.fromHedIssues(warningIssues, this.tsvFile.file, { tsvLine: element.tsvLine }))
}
- return cummulativeIssues
+ return [errors, warnings]
}
/**
* Generate a list of rows with column-to-value mappings.
*
- * @returns {Array.Map} A list of single-row column-to-value mappings.
+ * @returns {Array} A list of single-row column-to-value mappings.
* @private
*/
_generateHedRows() {
diff --git a/src/bids/validator/validator.js b/src/bids/validator/validator.js
index 18ac2713..98f523ae 100644
--- a/src/bids/validator/validator.js
+++ b/src/bids/validator/validator.js
@@ -16,7 +16,13 @@ export class BidsValidator {
* The issues found during validation.
* @type {BidsHedIssue[]}
*/
- issues
+ errors
+
+ /**
+ * The warnings found during validation.
+ * @type {BidsHedIssue[]}
+ */
+ warnings
/**
* Bids validator base class.
@@ -27,15 +33,15 @@ export class BidsValidator {
constructor(bidsFile, hedSchemas) {
this.bidsFile = bidsFile
this.hedSchemas = hedSchemas // Will be set when the file is validated
- this.issues = []
+ this.errors = []
+ this.warnings = []
}
/**
- * Validate a BIDS TSV file. This method returns the complete issue list for convenience.
+ * Validate a BIDS file. Overridden by particular types of BIDS files.
*
- * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file.
*/
validate() {
- return this.issues
+ return
}
}
diff --git a/src/parser/parser.js b/src/parser/parser.js
index bb357333..aca64589 100644
--- a/src/parser/parser.js
+++ b/src/parser/parser.js
@@ -49,48 +49,51 @@ class HedStringParser {
/**
* Parse a full HED string.
- * @returns {Array} - [ParsedHedString|null, Issue[]] representing the parsed HED string and any parsing issues.
+ *
+ * ###Note: now separates errors and warnings for easier handling.
+ *
+ * @returns {Array} - [ParsedHedString|null, Issue[], Issue[]] representing the parsed HED string and any parsing issues.
*/
- parseHedString() {
+ parse() {
if (this.hedString === null || this.hedString === undefined) {
- return [null, [generateIssue('invalidTagString', {})]]
+ return [null, [generateIssue('invalidTagString', {})], []]
}
const placeholderIssues = this._getPlaceholderCountIssues()
if (placeholderIssues.length > 0) {
- return [null, placeholderIssues]
+ return [null, placeholderIssues, []]
}
if (this.hedString instanceof ParsedHedString) {
- return [this.hedString, []]
+ return [this.hedString, [], []]
}
if (!this.hedSchemas) {
- return [null, [generateIssue('missingSchemaSpecification', {})]]
+ return [null, [generateIssue('missingSchemaSpecification', {})], []]
}
// This assumes that splitter errors are only errors and not warnings
const [parsedTags, parsingIssues] = new HedStringSplitter(this.hedString, this.hedSchemas).splitHedString()
if (parsedTags === null || parsingIssues.length > 0) {
- return [null, parsingIssues]
+ return [null, parsingIssues, []]
}
// Returns a parsed HED string unless empty
const parsedString = new ParsedHedString(this.hedString, parsedTags)
if (!parsedString) {
- return [null, null]
+ return [null, null, []]
}
// Check the definition syntax issues
const definitionIssues = new DefinitionChecker(parsedString).check(this.definitionsAllowed)
if (definitionIssues.length > 0) {
- return [null, definitionIssues]
+ return [null, definitionIssues, []]
}
// Check the other reserved tags requirements
const checkIssues = ReservedChecker.getInstance().checkHedString(parsedString)
if (checkIssues.length > 0) {
- return [null, checkIssues]
+ return [null, checkIssues, []]
}
- return [parsedString, []]
+ return [parsedString, [], []]
}
/**
@@ -116,50 +119,56 @@ class HedStringParser {
* @param {Schemas} hedSchemas The collection of HED schemas.
* @param {boolean} definitionsAllowed - True if definitions are allowed
* @param {boolean} placeholdersAllowed - True if placeholders are allowed
- * @returns {Array} - [ParsedHedString[], Issue[]] representing the parsed HED strings and any issues found.
+ * @returns {Array} - [ParsedHedString[], Issue[], Issue[]] representing the parsed HED strings and any errors and warnings.
*/
static parseHedStrings(hedStrings, hedSchemas, definitionsAllowed, placeholdersAllowed) {
if (!hedSchemas) {
- return [null, [generateIssue('missingSchemaSpecification', {})]]
+ return [null, [generateIssue('missingSchemaSpecification', {})], []]
}
const parsedStrings = []
- const cumulativeIssues = []
+ const errors = []
+ const warnings = []
for (const hedString of hedStrings) {
- const [parsedString, currentIssues] = new HedStringParser(
+ const [parsedString, errorIssues, warningIssues] = new HedStringParser(
hedString,
hedSchemas,
definitionsAllowed,
placeholdersAllowed,
- ).parseHedString()
+ ).parse()
parsedStrings.push(parsedString)
- cumulativeIssues.push(...currentIssues)
+ errors.push(...errorIssues)
+ warnings.push(...warningIssues)
}
- return [parsedStrings, cumulativeIssues]
+ return [parsedStrings, errors, warnings]
}
}
/**
* Parse a HED string.
*
+ * ###Note: now separates errors and warnings for easier handling.
+ *
* @param {string|ParsedHedString} hedString A (possibly already parsed) HED string.
* @param {Schemas} hedSchemas - The collection of HED schemas.
* @param {boolean} definitionsAllowed - True if definitions are allowed.
* @param {boolean} placeholdersAllowed - True if placeholders are allowed.
- * @returns {Array} - [ParsedHedString, Issue[]] representing the parsed HED string and any issues found.
+ * @returns {Array} - [ParsedHedString, Issue[], Issue[]] representing the parsed HED string and any issues found.
*/
export function parseHedString(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed) {
- return new HedStringParser(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed).parseHedString()
+ return new HedStringParser(hedString, hedSchemas, definitionsAllowed, placeholdersAllowed).parse()
}
/**
* Parse a list of HED strings.
*
+ * ###Note: now separates errors and warnings for easier handling.
+ *
* @param {string[]|ParsedHedString[]} hedStrings - A list of HED strings.
* @param {Schemas} hedSchemas - The collection of HED schemas.
* @param {boolean} definitionsAllowed - True if definitions are allowed
* @param {boolean} placeholdersAllowed - True if placeholders are allowed
- * @returns {Array} - [ParsedHedString[], Issue[]] representing the parsed HED strings and any issues found.
+ * @returns {Array} - [ParsedHedString[], Issue[], Issue[]] representing the parsed HED strings and any issues found.
*/
export function parseHedStrings(hedStrings, hedSchemas, definitionsAllowed, placeholdersAllowed) {
return HedStringParser.parseHedStrings(hedStrings, hedSchemas, definitionsAllowed, placeholdersAllowed)
diff --git a/tests/bidsTests.spec.js b/tests/bidsTests.spec.js
index 992c2ffe..a0664752 100644
--- a/tests/bidsTests.spec.js
+++ b/tests/bidsTests.spec.js
@@ -14,7 +14,7 @@ import { DefinitionManager } from '../src/parser/definitionManager'
//const skipMap = new Map([['definition-tests', ['invalid-missing-definition-for-def', 'invalid-nested-definition']]])
const skipMap = new Map()
const runAll = true
-const runMap = new Map([['temporal-tests', ['valid-offset-after-onset']]])
+const runMap = new Map([['curly-brace-tests', ['valid-HED-column-splice-with-n/a']]])
describe('BIDS validation', () => {
const schemaMap = new Map([['8.3.0', undefined]])
diff --git a/tests/stringParserTests.spec.js b/tests/stringParserTests.spec.js
index b2625b89..a67badce 100644
--- a/tests/stringParserTests.spec.js
+++ b/tests/stringParserTests.spec.js
@@ -42,9 +42,10 @@ describe('Null schema objects should cause parsing to bail', () => {
it('Should not proceed if no schema and valid array of strings', () => {
const arrayIn = ['Item, Red', 'Blue']
const expectedIssues = [generateIssue('missingSchemaSpecification', {})]
- const [directParsed, directIssues] = parseHedStrings(arrayIn, null, true, false, false)
+ const [directParsed, directIssues, warningIssues] = parseHedStrings(arrayIn, null, true, false)
assert.isNull(directParsed, `Parsed HED string of ${arrayIn} is null for invalid string`)
assert.deepStrictEqual(directIssues, expectedIssues)
+ assert.equal(warningIssues.length, 0)
})
})
diff --git a/tests/testData/bidsTests.data.js b/tests/testData/bidsTests.data.js
index 0143a38e..4e566cd7 100644
--- a/tests/testData/bidsTests.data.js
+++ b/tests/testData/bidsTests.data.js
@@ -146,7 +146,7 @@ export const bidsTestData = [
],
},
{
- testname: 'invalid-bad-tag-in-JSON',
+ testname: 'invalid-bad-tag-in-JSON-no-use',
explanation: 'Bad tag in JSON',
schemaVersion: '8.3.0',
definitions: ['(Definition/Acc/#, (Acceleration/# m-per-s^2, Red))', '(Definition/MyColor, (Label/Pie))'],
@@ -160,15 +160,15 @@ export const bidsTestData = [
eventsString: 'onset\tduration\tHED\n' + '7\t4\tGreen',
sidecarErrors: [
BidsHedIssue.fromHedIssue(generateIssue('invalidTag', { tag: 'Baloney' }), {
- path: 'invalid-bad-tag-in-JSON.json',
- relativePath: 'invalid-bad-tag-in-JSON.json',
+ path: 'invalid-bad-tag-in-JSON-no-use.json',
+ relativePath: 'invalid-bad-tag-in-JSON-no-use.json',
}),
],
tsvErrors: [],
comboErrors: [
BidsHedIssue.fromHedIssue(generateIssue('invalidTag', { tag: 'Baloney' }), {
- path: 'invalid-bad-tag-in-JSON.tsv',
- relativePath: 'invalid-bad-tag-in-JSON.tsv',
+ path: 'invalid-bad-tag-in-JSON-no-use.tsv',
+ relativePath: 'invalid-bad-tag-in-JSON-no-use.tsv',
}),
],
},