bids-validator-deno 2.0.8__tar.gz → 2.0.10__tar.gz

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.0.8
+Version: 2.0.10
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.0.8",
+  "version": "2.0.10",
   "exports": {
     ".": "./src/bids-validator.ts",
     "./main": "./src/main.ts",
@@ -28,7 +28,7 @@
   },
   "imports": {
     "@ajv": "npm:ajv@8.17.1",
-    "@bids/schema": "jsr:@bids/schema@1.0.4",
+    "@bids/schema": "jsr:@bids/schema@~1.0.14",
     "@cliffy/command": "jsr:@effigies/cliffy-command@1.0.0-dev.8",
     "@cliffy/table": "jsr:@effigies/cliffy-table@1.0.0-dev.5",
     "@hed/validator": "npm:hed-validator@4.0.1",

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.0.8"
+version = "2.0.10"
 
 [project.license]
 text = "MIT"

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/inheritance.ts

@@ -1,7 +1,6 @@
 import type { BIDSFile, FileTree } from '../types/filetree.ts'
 import { readEntities } from '../schema/entities.ts'
 
-
 type Ret<T> = T extends [string, ...string[]] ? (BIDSFile | BIDSFile[]) : BIDSFile
 
 /** Find associated files in order of proximity to a source file.

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/json.test.ts

@@ -40,7 +40,7 @@ Deno.test('Test JSON error conditions', async (t) => {
     await loadJSON(BOMfile).catch((e) => {
       error = e
     })
-    assertObjectMatch(error, { key: 'INVALID_JSON_ENCODING' })
+    assertObjectMatch(error, { code: 'INVALID_JSON_ENCODING' })
   })
 
   await t.step('Error on UTF-16', async () => {
@@ -49,7 +49,7 @@ Deno.test('Test JSON error conditions', async (t) => {
     await loadJSON(UTF16file).catch((e) => {
       error = e
     })
-    assertObjectMatch(error, { key: 'INVALID_JSON_ENCODING' })
+    assertObjectMatch(error, { code: 'INVALID_JSON_ENCODING' })
   })
 
   await t.step('Error on invalid JSON syntax', async () => {
@@ -58,6 +58,6 @@ Deno.test('Test JSON error conditions', async (t) => {
     await loadJSON(badJSON).catch((e) => {
       error = e
     })
-    assertObjectMatch(error, { key: 'JSON_INVALID' })
+    assertObjectMatch(error, { code: 'JSON_INVALID' })
   })
 })

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/json.ts

@@ -14,7 +14,7 @@ async function readJSONText(file: BIDSFile): Promise<string> {
     }
     return text
   } catch (error) {
-    throw { key: 'INVALID_JSON_ENCODING' }
+    throw { code: 'INVALID_JSON_ENCODING' }
   } finally {
     decoder.decode() // Reset decoder
   }
@@ -22,9 +22,17 @@ async function readJSONText(file: BIDSFile): Promise<string> {
 
 export async function loadJSON(file: BIDSFile): Promise<Record<string, unknown>> {
   const text = await readJSONText(file) // Raise encoding errors
+  let parsedText
   try {
-    return JSON.parse(text)
+    parsedText = JSON.parse(text)
   } catch (error) {
-    throw { key: 'JSON_INVALID' } // Raise syntax errors
+    throw { code: 'JSON_INVALID' } // Raise syntax errors
   }
+  if (Array.isArray(parsedText) || typeof parsedText !== 'object') {
+    throw {
+      code: 'JSON_NOT_AN_OBJECT',
+      issueMessage: text.substring(0, 10) + (text.length > 10 ? '...' : ''),
+    }
+  }
+  return parsedText
 }

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/nifti.test.ts

@@ -51,7 +51,7 @@ Deno.test('Test loading nifti header', async (t) => {
     const header = await loadHeader(file).catch((e) => {
       error = e
     })
-    assertObjectMatch(error, { key: 'NIFTI_HEADER_UNREADABLE' })
+    assertObjectMatch(error, { code: 'NIFTI_HEADER_UNREADABLE' })
   })
 
   await t.step('Tolerate big headers', async () => {

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/nifti.ts

@@ -45,7 +45,7 @@ export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
       header.readHeader(data.buffer)
     }
     if (!header) {
-      throw { key: 'NIFTI_HEADER_UNREADABLE' }
+      throw { code: 'NIFTI_HEADER_UNREADABLE' }
     }
     const ndim = header.dims[0]
     return {
@@ -67,6 +67,6 @@ export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
       sform_code: header.sform_code,
     } as NiftiHeader
   } catch (err) {
-    throw { key: 'NIFTI_HEADER_UNREADABLE' }
+    throw { code: 'NIFTI_HEADER_UNREADABLE' }
   }
 }

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/tsv.test.ts

@@ -53,7 +53,7 @@ Deno.test('TSV loading', async (t) => {
     try {
       await loadTSV(file)
     } catch (e: any) {
-      assertObjectMatch(e, { key: 'TSV_EMPTY_LINE', line: 3 })
+      assertObjectMatch(e, { code: 'TSV_EMPTY_LINE', line: 3 })
     }
   })
 
@@ -64,7 +64,7 @@ Deno.test('TSV loading', async (t) => {
     try {
       await loadTSV(file)
     } catch (e: any) {
-      assertObjectMatch(e, { key: 'TSV_EQUAL_ROWS', line: 3 })
+      assertObjectMatch(e, { code: 'TSV_EQUAL_ROWS', location: '/mismatched_row.tsv', line: 3 })
     }
   })
 
@@ -171,7 +171,7 @@ Deno.test('TSV loading', async (t) => {
       await loadTSV(file)
       assert(false, 'Expected error')
     } catch (e: any) {
-      assertObjectMatch(e, { key: 'TSV_COLUMN_HEADER_DUPLICATE', evidence: 'a, a' })
+      assertObjectMatch(e, { code: 'TSV_COLUMN_HEADER_DUPLICATE', issueMessage: 'a, a' })
     }
   })
 

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/files/tsv.ts

@@ -19,7 +19,11 @@ async function _loadTSV(file: BIDSFile, maxRows: number = -1): Promise<ColumnsMa
     const headers = (headerRow.done || !headerRow.value) ? [] : headerRow.value.split('\t')
 
     if (new Set(headers).size !== headers.length) {
-      throw { key: 'TSV_COLUMN_HEADER_DUPLICATE', evidence: headers.join(', ') }
+      throw {
+        code: 'TSV_COLUMN_HEADER_DUPLICATE',
+        location: file.path,
+        issueMessage: headers.join(', '),
+      }
     }
 
     // Initialize columns in array for construction efficiency
@@ -36,12 +40,12 @@ async function _loadTSV(file: BIDSFile, maxRows: number = -1): Promise<ColumnsMa
       if (!value) {
         const nextRow = await reader.read()
         if (nextRow.done) break
-        throw { key: 'TSV_EMPTY_LINE', line: rowIndex + 2 }
+        throw { code: 'TSV_EMPTY_LINE', location: file.path, line: rowIndex + 2 }
       }
 
       const values = value.split('\t')
       if (values.length !== headers.length) {
-        throw { key: 'TSV_EQUAL_ROWS', line: rowIndex + 2 }
+        throw { code: 'TSV_EQUAL_ROWS', location: file.path, line: rowIndex + 2 }
       }
       columns.forEach((column, columnIndex) => {
         // Double array size if we exceed the current capacity

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/issues/list.ts

@@ -9,6 +9,10 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'Not a valid JSON file.',
   },
+  JSON_NOT_AN_OBJECT: {
+    severity: 'error',
+    reason: 'Parsed JSON file does not contain an object.',
+  },
   MISSING_DATASET_DESCRIPTION: {
     severity: 'error',
     reason: 'A dataset_description.json file is required in the root of the dataset',
@@ -166,6 +170,10 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'A json sidecar file was found without a corresponding data file',
   },
+  UNSUPPORTED_DATASET_TYPE: {
+    severity: 'error',
+    reason: 'This DatasetType is not supported by the application.',
+  },
   BLACKLISTED_MODALITY: {
     severity: 'error',
     reason: 'The modality in this file is blacklisted through validator configuration.',

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/main.ts

@@ -10,6 +10,7 @@ import { consoleFormat, resultToJSONStr } from './utils/output.ts'
 import { setupLogging } from './utils/logger.ts'
 import type { ValidationResult } from './types/validation-result.ts'
 export type { ValidationResult } from './types/validation-result.ts'
+export { getVersion } from './version.ts'
 
 /**
  * Validation entrypoint intended for command line usage with Deno

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/schema/applyRules.ts

@@ -94,7 +94,6 @@ export function evalCheck(src: string, context: BIDSContext) {
  * We associate theys keys from a rule object to a function adds an
  * issue to the context if the rule evaluation fails.
  */
-// @ts-expect-error
 const evalMap: Record<
   keyof GenericRule,
   (
@@ -105,9 +104,13 @@ const evalMap: Record<
   ) => boolean | void
 > = {
   checks: evalRuleChecks,
+  // @ts-expect-error
   columns: evalColumns,
+  // @ts-expect-error
   additional_columns: evalAdditionalColumns,
+  // @ts-expect-error
   initial_columns: evalInitialColumns,
+  // @ts-expect-error
   index_columns: evalIndexColumns,
   fields: evalJsonCheck,
 }
@@ -183,7 +186,9 @@ function evalJsonCheck(
   // Count on other JSON rules to use selectors to match the correct files
   // Text files at the root do not have sidecars. We might want a cleaner
   // or more schematic way to identify them in the future.
-  if (sidecarRule && (['.json', '', '.md', '.txt', '.rst', '.cff'].includes(context.extension))) return
+  if (sidecarRule && (['.json', '', '.md', '.txt', '.rst', '.cff'].includes(context.extension))) {
+    return
+  }
 
   const json: Record<string, any> = sidecarRule ? context.sidecar : context.json
   for (const [key, requirement] of Object.entries(rule.fields)) {

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/schema/associations.ts

@@ -143,8 +143,8 @@ export async function buildAssociations(
       // @ts-expect-error
       associations[key] = await load(file, { maxRows: context.dataset.options?.maxRows }).catch(
         (error: any) => {
-          if (key in error) {
-            context.dataset.issues.add({ code: error.key, location: file.path })
+          if (error.code) {
+            context.dataset.issues.add({ ...error, location: file.path })
           }
         },
       )

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/schema/context.ts

@@ -9,6 +9,7 @@ import type {
   Subjects,
   Tiff,
 } from '@bids/schema/context'
+import type { Schemas as HedSchemas } from '@hed/validator'
 import type { Schema } from '../types/schema.ts'
 import type { BIDSFile } from '../types/filetree.ts'
 import { FileTree } from '../types/filetree.ts'
@@ -41,7 +42,7 @@ export class BIDSContextDataset implements Dataset {
   opaqueDirectories: Set<string>
 
   // Opaque object for HED validator
-  hedSchemas: object | undefined | null = undefined
+  hedSchemas: HedSchemas | undefined | null = undefined
 
   constructor(
     args: Partial<BIDSContextDataset>,
@@ -209,8 +210,8 @@ export class BIDSContext implements Context {
     }
     for (const file of sidecars) {
       const json = await loadJSON(file).catch((error) => {
-        if (error.key) {
-          this.dataset.issues.add({ code: error.key, location: file.path })
+        if (error.code) {
+          this.dataset.issues.add({ ...error, location: file.path })
           return {}
         } else {
           throw error
@@ -231,8 +232,8 @@ export class BIDSContext implements Context {
     ) return
 
     this.nifti_header = await loadHeader(this.file).catch((error) => {
-      if (error.key) {
-        this.dataset.issues.add({ code: error.key, location: this.file.path })
+      if (error.code) {
+        this.dataset.issues.add({ ...error, location: this.file.path })
         return undefined
       } else {
         throw error
@@ -247,8 +248,8 @@ export class BIDSContext implements Context {
 
     this.columns = await loadTSV(this.file, this.dataset.options?.maxRows)
       .catch((error) => {
-        if (error.key) {
-          this.dataset.issues.add({ code: error.key, location: this.file.path })
+        if (error.code) {
+          this.dataset.issues.add({ ...error, location: this.file.path })
         }
         logger.warn(
           `tsv file could not be opened by loadColumns '${this.file.path}'`,
@@ -271,8 +272,8 @@ export class BIDSContext implements Context {
       return
     }
     this.json = await loadJSON(this.file).catch((error) => {
-      if (error.key) {
-        this.dataset.issues.add({ code: error.key, location: this.file.path })
+      if (error.code) {
+        this.dataset.issues.add({ ...error, location: this.file.path })
         return {}
       } else {
         throw error
@@ -319,9 +320,10 @@ export class BIDSContext implements Context {
     const participants_tsv = this.dataset.tree.get('participants.tsv') as BIDSFile
     if (participants_tsv) {
       const participantsData = await loadTSV(participants_tsv)
-      this.dataset.subjects.participant_id = participantsData[
-        'participant_id'
-      ] as string[]
+        .catch((error) => {
+          return new Map()
+        }) as Record<string, string[]>
+      this.dataset.subjects.participant_id = participantsData['participant_id']
     }
 
     // Load phenotype from phenotype/*.tsv
@@ -332,7 +334,10 @@ export class BIDSContext implements Context {
       const seen = new Set() as Set<string>
       for (const file of phenotypeFiles) {
         const phenotypeData = await loadTSV(file)
-        const participant_id = phenotypeData['participant_id'] as string[]
+          .catch((error) => {
+            return new Map()
+          }) as Record<string, string[]>
+        const participant_id = phenotypeData['participant_id']
         if (participant_id) {
           participant_id.forEach((id) => seen.add(id))
         }

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.10}/src/schema/tables.test.ts

@@ -26,6 +26,18 @@ const schemaDefs = {
           index_columns: ['filename'],
           additional_columns: 'allowed',
         },
+        Participants: {
+          selectors: ['path == "/participants.tsv"'],
+          initial_columns: ['participant_id'],
+          columns: {
+            participant_id: 'required',
+            age: 'recommended',
+            sex: 'recommended',
+            strain_rrid: 'recommended',
+          },
+          index_columns: ['participant_id'],
+          additional_columns: 'allowed',
+        },
       },
       made_up: {
         MadeUp: {
@@ -93,6 +105,67 @@ Deno.test('tables eval* tests', async (t) => {
     assertEquals(context.dataset.issues.size, 0)
   })
 
+  await t.step('verify column override behavior', () => {
+    const context = {
+      path: '/participants.tsv',
+      extension: '.tsv',
+      sidecar: {
+        participant_id: {
+          Description: 'A participant identifier',
+          Format: 'string',
+        },
+        age: {
+          Description: 'Age in weeks',
+          Format: 'number',
+        },
+        sex: {
+          Description: 'Phenotypic sex',
+          Format: 'string',
+          Levels: {
+            'F': { Description: 'Female' },
+            'M': { Description: 'Male' },
+            'O': { Description: 'Other' },
+          },
+        },
+        strain_rrid: {
+          Description: 'Invalid override',
+          Format: 'integer',
+        },
+      },
+      sidecarKeyOrigin: {
+        participant_id: '/participants.json',
+        age: '/participants.json',
+        sex: '/participants.json',
+        strain_rrid: '/participants.json',
+      },
+      columns: {
+        participant_id: ['sub-01', 'sub-02', 'sub-03'],
+        age: ['10', '20', '30'],
+        sex: ['M', 'F', 'f'],
+        strain_rrid: ['RRID:SCR_012345', 'RRID:SCR_012345', 'n/a'],
+      },
+      dataset: { issues: new DatasetIssues() },
+    }
+    const rule = schemaDefs.rules.tabular_data.modality_agnostic.Participants
+    evalColumns(rule, context, schema, 'rules.tabular_data.modality_agnostic.Participants')
+
+    // participant_id column definition is compatible with schema
+    // age and sex may be overridden
+    // strain_rrid can't be redefined to numeric
+    let issues = context.dataset.issues.get({ code: 'TSV_COLUMN_TYPE_REDEFINED' })
+    assertEquals(issues.length, 1)
+    assertEquals(issues[0].subCode, 'strain_rrid')
+    assertEquals(issues[0].issueMessage, 'Format "integer" must be rrid')
+
+    // Overriding the default sex definition uses the provided values
+    // Values in the default definition may raise issues
+    issues = context.dataset.issues.get({ code: 'TSV_VALUE_INCORRECT_TYPE_NONREQUIRED' })
+    assertEquals(issues.length, 1)
+    assertEquals(issues[0].subCode, 'sex')
+    assertEquals(issues[0].line, 4)
+    assertEquals(issues[0].issueMessage, "'f'")
+  })
+
   await t.step('verify column ordering', () => {
     const context = {
       path: '/sub-01/sub-01_scans.tsv',