bids-validator-deno 2.0.8__tar.gz → 2.0.9__tar.gz

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.0.8
+Version: 2.0.9
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.0.8",
+  "version": "2.0.9",
   "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-2.0.9}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.0.8"
+version = "2.0.9"
 
 [project.license]
 text = "MIT"

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/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-2.0.9}/src/files/json.ts

@@ -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
   }
+  if (Array.isArray(parsedText) || typeof parsedText !== 'object') {
+    throw {
+      key: 'JSON_NOT_AN_OBJECT',
+      evidence: text.substring(0, 10) + (text.length > 10 ? '...' : ''),
+    }
+  }
+  return parsedText
 }

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/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-2.0.9}/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-2.0.9}/src/schema/applyRules.ts

@@ -183,7 +183,9 @@ 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-2.0.9}/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>,

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/schema/tables.ts

@@ -239,7 +239,7 @@ export function evalAdditionalColumns(
   if (context.extension !== '.tsv') return
   const headers = Object.keys(context?.columns)
   if (rule.columns) {
-    if (!rule.additional_columns || rule.additional_columns === 'n/a' ) {
+    if (!rule.additional_columns || rule.additional_columns === 'n/a') {
       // Old schemas might be missing the field, so be permissive.
       // New schemas indicate it is not applicable with 'n/a'.
       return

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/setup/options.test.ts

@@ -10,6 +10,7 @@ Deno.test('options parsing', async (t) => {
       json: true,
       color: false,
       blacklistModalities: [],
+      datasetTypes: [],
       maxRows: 1000,
     })
   })

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/setup/options.ts

@@ -28,11 +28,16 @@ export type ValidatorOptions = {
   color?: boolean
   recursive?: boolean
   outfile?: string
+  datasetTypes: string[]
   blacklistModalities: string[]
   prune?: boolean
   maxRows?: number
 }
 
+const datasetType = new EnumType<string>(
+  schema.objects.metadata.DatasetType.enum as string[],
+)
+
 const modalityType = new EnumType<string>(
   Object.keys(schema.rules.modalities),
 )
@@ -69,6 +74,12 @@ export const validateCommand: Command<void, void, any, string[], void> = new Com
     '--filenameMode',
     'Enable filename checks for newline separated filenames read from stdin',
   )
+  .type('datasetType', datasetType)
+  .option(
+    '--datasetTypes <...datasetTypes:datasetType>',
+    'Permitted dataset types to validate against (default: all)',
+    { default: [] as string[] },
+  )
   .type('modality', modalityType)
   .option(
     '--blacklistModalities <...modalities:modality>',

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/summary/collectSubjectMetadata.ts

@@ -54,8 +54,8 @@ export const collectSubjectMetadata = (
         )
         // make age an integer
         if (ageKey) {
-          if(data[ageKey.index] === "89+") {
-            data[ageKey.index] = "89+"
+          if (data[ageKey.index] === '89+') {
+            data[ageKey.index] = '89+'
           } else {
             // @ts-expect-error
             data[ageKey.index] = parseFloat(data[ageKey.index])

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/tests/regression.test.ts

@@ -24,6 +24,7 @@ Deno.test('Regression tests', async (t) => {
       debug: 'ERROR',
       ignoreNiftiHeaders: true,
       blacklistModalities: [],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'NOT_INCLUDED' }).length == 1)
     assert(result.issues.get({ code: 'SCANS_FILENAME_NOT_MATCH_DATASET' }).length == 0)
@@ -37,6 +38,7 @@ Deno.test('Regression tests', async (t) => {
       debug: 'ERROR',
       ignoreNiftiHeaders: true,
       blacklistModalities: [],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'NOT_INCLUDED' }).length == 0)
     assert(result.issues.get({ code: 'SCANS_FILENAME_NOT_MATCH_DATASET' }).length == 0)

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/types/validation-result.ts

@@ -2,7 +2,7 @@ import type { DatasetIssues } from '../issues/datasetIssues.ts'
 
 export interface SubjectMetadata {
   participantId: string
-  age?: number | null | "89+"
+  age?: number | null | '89+'
   sex?: string
 }
 /*

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/validators/bids.test.ts

@@ -14,6 +14,7 @@ Deno.test('Smoke tests of main validation function', async (t) => {
       debug: 'INFO',
       ignoreNiftiHeaders: true,
       blacklistModalities: [],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'BLACKLISTED_MODALITY' }).length === 0)
 
@@ -22,6 +23,7 @@ Deno.test('Smoke tests of main validation function', async (t) => {
       debug: 'INFO',
       ignoreNiftiHeaders: true,
       blacklistModalities: ['MRI'],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'BLACKLISTED_MODALITY' }).length === 1)
 
@@ -30,6 +32,7 @@ Deno.test('Smoke tests of main validation function', async (t) => {
       debug: 'INFO',
       ignoreNiftiHeaders: true,
       blacklistModalities: ['MEG'],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'BLACKLISTED_MODALITY' }).length === 0)
 
@@ -38,6 +41,7 @@ Deno.test('Smoke tests of main validation function', async (t) => {
       debug: 'INFO',
       ignoreNiftiHeaders: true,
       blacklistModalities: ['MEG', 'MRI'],
+      datasetTypes: [],
     })
     assert(result.issues.get({ code: 'BLACKLISTED_MODALITY' }).length === 1)
   })
@@ -48,6 +52,7 @@ Deno.test('Smoke tests of main validation function', async (t) => {
         datasetPath: '/dataset',
         debug: 'INFO',
         blacklistModalities: [],
+        datasetTypes: [],
       },
       {
         ignore: [{ location: '/dataset_description.json' }],

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/validators/bids.ts

@@ -72,6 +72,18 @@ export async function validate(
     })
   }
 
+  // Empty list defaults to allow all
+  if (options.datasetTypes.length) {
+    const datasetType = (dsContext.dataset_description.DatasetType ?? 'raw') as string
+    if (!options.datasetTypes.includes(datasetType)) {
+      dsContext.issues.add({
+        code: 'UNSUPPORTED_DATASET_TYPE',
+        location: '/dataset_description.json',
+        issueMessage: `"DatasetType": "${datasetType}"`,
+      })
+    }
+  }
+
   const bidsDerivatives: FileTree[] = []
   const nonstdDerivatives: FileTree[] = []
   fileTree.directories = fileTree.directories.filter((dir) => {

{bids_validator_deno-2.0.8 → bids_validator_deno-2.0.9}/src/validators/hed.ts

@@ -30,8 +30,14 @@ async function setHedSchemas(dataset: BIDSContextDataset): Promise<HedIssue[]> {
       datasetDescriptionData,
     )
     return [] as HedIssue[]
-  } catch (issueError) {
+  } catch (error) {
     dataset.hedSchemas = null
+    let issueError: Error
+    if (error instanceof Error) {
+      issueError = error
+    } else {
+      issueError = new Error('unknown error')
+    }
     return hedValidator.BidsHedIssue.fromHedIssues(
       issueError,
       datasetDescriptionData.file,