bids-validator-deno 2.2.10__tar.gz → 2.3.1.dev0__tar.gz

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.2.10
+Version: 2.3.1.dev0
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.2.10",
+  "version": "2.3.1-dev",
   "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@~1.1.3",
+    "@bids/schema": "jsr:@bids/schema@~1.1.6",
     "@bradenmacdonald/s3-lite-client": "jsr:@bradenmacdonald/s3-lite-client@^0.9.4",
     "@cliffy/command": "jsr:@effigies/cliffy-command@1.0.0-dev.8",
     "@cliffy/table": "jsr:@effigies/cliffy-table@1.0.0-dev.5",
@@ -38,16 +38,18 @@
     "@mango/nifti": "npm:@bids/nifti-reader-js@^0.6.9",
     "@std/assert": "jsr:@std/assert@^1.0.16",
     "@std/fmt": "jsr:@std/fmt@^1.0.8",
-    "@std/fs": "jsr:@std/fs@^1.0.20",
+    "@std/fs": "jsr:@std/fs@^1.0.21",
     "@std/io": "jsr:@std/io@^0.225.2",
     "@std/log": "jsr:@std/log@^0.224.14",
-    "@std/path": "jsr:@std/path@^1.1.3",
-    "@std/streams": "jsr:@std/streams@^1.0.14",
+    "@std/path": "jsr:@std/path@^1.1.4",
+    "@std/streams": "jsr:@std/streams@^1.0.16",
     "@std/testing": "jsr:@std/testing@^1.0.16",
     "@std/yaml": "jsr:@std/yaml@^1.0.10",
-    "isomorphic-git": "npm:isomorphic-git@^1.35.1",
+    "ansi-escapes": "npm:ansi-escapes@^7.2.0",
+    "isomorphic-git": "npm:isomorphic-git@^1.36.1",
     "hash-wasm": "npm:hash-wasm@^4.12.0",
-    "marked": "npm:marked@^15.0.4"
+    "marked": "npm:marked@^15.0.12",
+    "supports-hyperlinks": "npm:supports-hyperlinks@^4.4.0"
   },
   "nodeModulesDir": "auto",
   "tasks": {

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/pdm_build.py

@@ -21,12 +21,27 @@ def pdm_build_initialize(context):
     if deno is None:
         raise OSError("Deno is not installed or not in PATH")
 
+    permissions = [
+        # Access filesystem for reading BIDS datasets
+        "--allow-read",
+        # Accept environment variables
+        "--allow-env",
+        # Access network for fetching remote schemas
+        "--allow-net",
+        # Allow writing results to file
+        "--allow-write",
+        # Run git to get version info
+        "--allow-run=git",
+    ]
+    if sysconfig.get_platform().startswith("win"):
+        # Terminal detection code in supports-hyperlinks calls osRelease
+        permissions.append("--allow-sys=osRelease")
+
     subprocess.run(
         [
             deno,
             "compile",
-            "-ERNW",
-            "--allow-run",
+            *permissions,
             # Types are checked elsewhere. Type checking at wheel build
             # is painful if some platforms have newer typescript than others.
             "--no-check",

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.2.10"
+version = "2.3.1-dev"
 
 [project.license]
 text = "MIT"

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/bids-validator.ts

@@ -1,9 +1,9 @@
 import { main } from './main.ts'
+import { detectErrors } from './summary/summary.ts'
 
 const result = await main()
 
-const errors = result.issues.get({ severity: 'error' })
-if (errors.length) {
+if (detectErrors(result)) {
   Deno.exit(16)
 }
 Deno.exit(0)

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/files/filetree.ts

@@ -45,7 +45,7 @@ function rerootTree({
 }: RerootTreeOptions): FileTree {
   const tree = new FileTree(
     oldTree.path.substr(newRoot.length) || '/',
-    parent ? oldTree.name : `${oldTree.path}/`,  // Set the name of the root to its full path
+    parent ? oldTree.name : `${oldTree.path}/`, // Set the name of the root to its full path
     parent,
     ignore,
   )
@@ -60,7 +60,7 @@ function rerootTree({
 
 export async function subtree(filetree: FileTree): Promise<FileTree> {
   const ignore = new FileIgnoreRules([])
-  const tree = rerootTree({oldTree: filetree, newRoot: filetree.path, ignore})
+  const tree = rerootTree({ oldTree: filetree, newRoot: filetree.path, ignore })
   const bidsignore = tree.get('.bidsignore')
   if (bidsignore) {
     try {

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/files/openers.test.ts

@@ -2,13 +2,12 @@
  * File openers for use in testing
  */
 import { assertEquals, assertRejects } from '@std/assert'
-import { resolvesNext, stub } from "@std/testing/mock";
+import { resolvesNext, stub } from '@std/testing/mock'
 import { type FileOpener } from '../types/filetree.ts'
 import { streamFromString } from '../tests/utils.ts'
 import { createUTF8Stream } from './streams.ts'
 import { HTTPOpener } from './openers.ts'
 
-
 const textEncoder = new TextEncoder()
 const textDecoder = new TextDecoder()
 
@@ -157,25 +156,25 @@ Deno.test('Validate CompressedStringOpener', async (t) => {
 })
 
 Deno.test('Validate HTTPOpener', async (t) => {
-  const url = "http://example.com"
+  const url = 'http://example.com'
   await t.step('Use successful fetch stub', async () => {
     using _fetchStub = stub(
       globalThis,
-      "fetch",
-      resolvesNext([new Response("Hello, world!")]),
-    );
+      'fetch',
+      resolvesNext([new Response('Hello, world!')]),
+    )
     const httpOpener = new HTTPOpener(url, 1)
-    assertEquals(await httpOpener.text(), "Hello, world!");
+    assertEquals(await httpOpener.text(), 'Hello, world!')
   })
   await t.step('Use failed fetch stub', async () => {
     using _fetchStub = stub(
       globalThis,
-      "fetch",
-      resolvesNext([new Response("Not Found", { status: 404, statusText: "Not Found" })])
-    );
+      'fetch',
+      resolvesNext([new Response('Not Found', { status: 404, statusText: 'Not Found' })]),
+    )
     const httpOpener = new HTTPOpener(url, 1)
-    assertRejects(httpOpener.text);
-    assertRejects(httpOpener.stream);
-    assertRejects(() => httpOpener.readBytes(1, 0));
+    assertRejects(httpOpener.text)
+    assertRejects(httpOpener.stream)
+    assertRejects(() => httpOpener.readBytes(1, 0))
   })
-});
+})

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/files/openers.ts

@@ -106,8 +106,8 @@ export class HTTPOpener implements FileOpener {
     this.size = size
   }
 
-  async _fetch(headers={}): Promise<Response> {
-    return fetch(this.url, {headers}).then((response) => {
+  async _fetch(headers = {}): Promise<Response> {
+    return fetch(this.url, { headers }).then((response) => {
       if (!response.ok || !response.body) {
         throw new Error(`Failed to fetch ${this.url}: ${response.status} ${response.statusText}`)
       }
@@ -116,11 +116,11 @@ export class HTTPOpener implements FileOpener {
   }
 
   async stream(): Promise<ReadableStream<Uint8Array<ArrayBuffer>>> {
-    return this._fetch().then(response => response.body!)
+    return this._fetch().then((response) => response.body!)
   }
 
   async text(): Promise<string> {
-    return this._fetch().then(response => response.text())
+    return this._fetch().then((response) => response.text())
   }
 
   async readBytes(size: number, offset = 0): Promise<Uint8Array<ArrayBuffer>> {

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/files/repo.ts

@@ -38,8 +38,8 @@ class NonSigningClient {
   async presignedGetObject(
     objectName: string,
     options: {
-      versionId: string,
-    }
+      versionId: string
+    },
   ): Promise<string> {
     return `${this.endPoint}/${this.bucket}/${objectName}?versionId=${options.versionId}`
   }
@@ -215,7 +215,7 @@ export async function resolveAnnexedFile(
 
   const metadata = rmet[uuid]
   const client = await createS3Client({ endPoint: `https://${host}`, bucket, region })
-  const url = await client.presignedGetObject(metadata.path, {versionId: metadata.version})
+  const url = await client.presignedGetObject(metadata.path, { versionId: metadata.version })
 
   return { url }
 }

bids_validator_deno-2.3.1.dev0/src/summary/summary.test.ts

@@ -0,0 +1,142 @@
+import { computeModalities, modalityPrettyLookup, Summary } from './summary.ts'
+import { assertEquals, type assertObjectMatch } from '@std/assert'
+import { detectErrors } from './summary.ts'
+import { ValidationResult } from '../types/validation-result.ts'
+import { DatasetIssues } from '../issues/datasetIssues.ts'
+import type { Issue } from '../types/issues.ts'
+
+Deno.test('Summary class and helper functions', async (t) => {
+  await t.step('Constructor succeeds', () => {
+    new Summary()
+  })
+  await t.step('computeModalities properly sorts modality counts', () => {
+    const modalitiesIn = { eeg: 5, pet: 6, mri: 6, ieeg: 6 }
+    const modalitiesOut = ['pet', 'ieeg', 'mri', 'eeg'].map(
+      (x) => modalityPrettyLookup[x],
+    )
+    assertEquals(computeModalities(modalitiesIn), modalitiesOut)
+  })
+})
+
+const json_mock_validation_result = {
+  'issues': {
+    'issues': [],
+    'codeMessages': {},
+  },
+  'summary': {
+    'sessions': [],
+    'subjects': [
+      '01',
+    ],
+    'subjectMetadata': [],
+    'tasks': [],
+    'modalities': [
+      'MRI',
+    ],
+    'secondaryModalities': [
+      'MRI_Structural',
+    ],
+    'totalFiles': 14,
+    'size': 1513,
+    'dataProcessed': false,
+    'pet': {},
+    'dataTypes': [
+      'fmap',
+      'anat',
+    ],
+    'schemaVersion': '1.1.3',
+  },
+  'derivativesSummary': {
+    '/derivatives/mock/': {
+      'issues': {
+        'issues': [
+          {
+            'code': 'EMPTY_FILE',
+            'severity': 'error',
+            'location': '/README',
+          },
+        ],
+      },
+      'summary': {
+        'sessions': [],
+        'subjects': [
+          '01',
+        ],
+        'subjectMetadata': [],
+        'tasks': [],
+        'modalities': [
+          'MRI',
+        ],
+        'secondaryModalities': [
+          'MRI_Structural',
+        ],
+        'totalFiles': 12,
+        'size': 3715,
+        'dataProcessed': true,
+        'pet': {},
+        'dataTypes': [
+          'fmap',
+          'anat',
+        ],
+        'schemaVersion': '1.1.3',
+      },
+    },
+  },
+}
+
+const mockValidationResultBadDerivatives: ValidationResult = {
+  issues: new DatasetIssues({
+    issues: json_mock_validation_result.issues.issues as Issue[],
+    codeMessages: new Map(Object.entries(json_mock_validation_result.issues.codeMessages)),
+  }),
+  summary: json_mock_validation_result.summary,
+  derivativesSummary: {
+    '/derivatives/mock/': {
+      issues: new DatasetIssues({
+        issues: json_mock_validation_result.derivativesSummary['/derivatives/mock/'].issues
+          .issues as Issue[],
+      }),
+      summary: json_mock_validation_result.derivativesSummary['/derivatives/mock/'].summary,
+    },
+  },
+}
+
+const mockValidationResultBadRawData: ValidationResult = {
+  issues: new DatasetIssues({
+    issues: json_mock_validation_result.derivativesSummary['/derivatives/mock/'].issues
+      .issues as Issue[],
+  }),
+  summary: json_mock_validation_result.summary,
+}
+
+Deno.test('detectErrors properly collects errors', () => {
+  const errors = detectErrors(mockValidationResultBadDerivatives)
+  assertEquals(errors, true)
+})
+
+Deno.test('detectErrors properly collects errors from raw data', () => {
+  const errors = detectErrors(mockValidationResultBadRawData)
+  assertEquals(errors, true)
+})
+
+const mockValidationResultNoErrors: ValidationResult = {
+  issues: new DatasetIssues({
+    issues: [],
+    codeMessages: new Map(),
+  }),
+  summary: json_mock_validation_result.summary,
+  derivativesSummary: {
+    '/derivatives/mock/': {
+      issues: new DatasetIssues({
+        issues: [],
+        codeMessages: new Map(),
+      }),
+      summary: json_mock_validation_result.derivativesSummary['/derivatives/mock/'].summary,
+    },
+  },
+}
+
+Deno.test('detectErrors returns false when no errors found', () => {
+  const errors = detectErrors(mockValidationResultNoErrors)
+  assertEquals(errors, false)
+})

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/summary/summary.ts

@@ -1,6 +1,8 @@
 import { collectSubjectMetadata } from './collectSubjectMetadata.ts'
 import type { SubjectMetadata, SummaryOutput } from '../types/validation-result.ts'
 import type { BIDSContext } from '../schema/context.ts'
+import type { ValidationResult } from '../types/validation-result.ts'
+import type { Issue } from '../types/issues.ts'
 
 export const modalityPrettyLookup: Record<string, string> = {
   mri: 'MRI',
@@ -169,3 +171,8 @@ export class Summary {
     }
   }
 }
+
+export function detectErrors(result: ValidationResult): boolean {
+  return result.issues.get({ severity: 'error' }).length > 0 ||
+    Object.values(result.derivativesSummary ?? {}).some((res) => detectErrors(res))
+}

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/utils/output.ts

@@ -5,6 +5,8 @@ import { Table } from '@cliffy/table'
 import * as colors from '@std/fmt/colors'
 import { format as prettyBytes } from '@std/fmt/bytes'
 import { marked } from 'marked'
+import supportsHyperlinks from 'supports-hyperlinks'
+import ansiEscapes from 'ansi-escapes'
 import type { SummaryOutput, ValidationResult } from '../types/validation-result.ts'
 import type { Issue, Severity } from '../types/issues.ts'
 import type { DatasetIssues } from '../issues/datasetIssues.ts'
@@ -36,7 +38,7 @@ export function consoleFormat(
   if (result.derivativesSummary) {
     for (const [key, derivResult] of Object.entries(result.derivativesSummary)) {
       output.push(colors.blue(`Derivative: ${key}`))
-      
+
       if (derivResult.issues.size === 0) {
         output.push(colors.green('\tThis derivative appears to be BIDS compatible.'))
       } else {
@@ -48,7 +50,7 @@ export function consoleFormat(
       output.push('')
     }
   }
-  
+
   return output.join('\n')
 }
 
@@ -59,32 +61,35 @@ function renderTokens(tokenList: any[]): string {
   if (!tokenList) return ''
 
   return tokenList.map((token) => {
-    if (token.type === 'paragraph') {
-      return renderTokens(token.tokens)
-    }
+    switch (token.type) {
+      case 'paragraph':
+        return renderTokens(token.tokens)
 
-    if (token.type === 'strong') {
-      return colors.bold(renderTokens(token.tokens))
-    }
+      case 'strong':
+        return colors.bold(renderTokens(token.tokens))
 
-    if (token.type === 'em') {
-      return colors.italic(renderTokens(token.tokens))
-    }
+      case 'em':
+        return colors.italic(renderTokens(token.tokens))
 
-    if (token.type === 'codespan') {
-      return colors.cyan(token.text)
-    }
+      case 'codespan':
+        return colors.cyan(token.text)
 
-    if (token.type === 'link') {
-      return `${colors.blue(token.text)} (${colors.gray(token.href)})`
-    }
+      case 'link':
+        // Using the library to check for stdout support
+        if (supportsHyperlinks.stdout) {
+          return ansiEscapes.link(token.text, token.href)
+        } else {
+          // Fallback for terminals without support
+          return `${colors.blue(token.text)} (${colors.gray(token.href)})`
+        }
 
-    if (token.type === 'text') {
-      return token.text
-    }
+      case 'text':
+        return token.text
 
-    // Render children or return raw text
-    return renderTokens(token.tokens || []) || token.raw || ''
+      default:
+        // Render children or return raw text
+        return renderTokens(token.tokens || []) || token.raw || ''
+    }
   }).join('')
 }
 

{bids_validator_deno-2.2.10 → bids_validator_deno-2.3.1.dev0}/src/validators/hed.ts

@@ -13,7 +13,7 @@ function sidecarHasHed(sidecarData: BIDSContext['sidecar']): boolean {
 }
 
 function sidecarValueHasHed(sidecarValue: { HED?: string }): boolean {
-  return typeof sidecarValue.HED !== 'undefined'
+  return typeof sidecarValue?.HED !== 'undefined'
 }
 
 async function setHedSchemas(dataset: BIDSContextDataset): Promise<HedIssue[]> {

bids_validator_deno-2.2.10/src/summary/summary.test.ts

@@ -1,15 +0,0 @@
-import { computeModalities, modalityPrettyLookup, Summary } from './summary.ts'
-import { assertEquals, type assertObjectMatch } from '@std/assert'
-
-Deno.test('Summary class and helper functions', async (t) => {
-  await t.step('Constructor succeeds', () => {
-    new Summary()
-  })
-  await t.step('computeModalities properly sorts modality counts', () => {
-    const modalitiesIn = { eeg: 5, pet: 6, mri: 6, ieeg: 6 }
-    const modalitiesOut = ['pet', 'ieeg', 'mri', 'eeg'].map(
-      (x) => modalityPrettyLookup[x],
-    )
-    assertEquals(computeModalities(modalitiesIn), modalitiesOut)
-  })
-})