bids-validator-deno 2.2.1__tar.gz → 2.2.3__tar.gz

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.2.1
+Version: 2.2.3
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.2.1",
+  "version": "2.2.3",
   "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@~1.1.0",
+    "@bids/schema": "jsr:@bids/schema@~1.1.1",
     "@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@~4.1.4",

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.2.1"
+version = "2.2.3"
 
 [project.license]
 text = "MIT"

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/files/deno.ts

@@ -6,8 +6,8 @@ import * as posix from '@std/path/posix'
 import { BIDSFile, type FileOpener, FileTree } from '../types/filetree.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
 import { FileIgnoreRules, readBidsIgnore } from './ignore.ts'
-import { FsFileOpener, HTTPOpener } from './openers.ts'
-import { resolveAnnexedFile } from './repo.ts'
+import { FsFileOpener, HTTPOpener, NullFileOpener } from './openers.ts'
+import { parseAnnexedFile, resolveAnnexedFile } from './repo.ts'
 import fs from 'node:fs'
 
 export class BIDSFileDeno extends BIDSFile {
@@ -51,12 +51,13 @@ async function _readFileTree({
       try {
         const fileInfo = await Deno.stat(fullPath)
         opener = new FsFileOpener(rootPath, thisPath, fileInfo)
-      } catch (error) {
+      } catch (_) {
+        const { key, size, gitdir } = await parseAnnexedFile(fullPath)
         try {
-          const { url, size } = await resolveAnnexedFile(fullPath, preferredRemote, { cache, fs })
+          const { url } = await resolveAnnexedFile(key, preferredRemote, { cache, fs, gitdir })
           opener = new HTTPOpener(url, size)
         } catch (_) {
-          throw error
+          opener = new NullFileOpener(size)
         }
       }
       tree.files.push(new BIDSFile(thisPath, opener, ignore, tree))

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/files/nifti.test.ts

@@ -96,6 +96,10 @@ Deno.test('Test extracting axis codes', async (t) => {
     const affine = [[0, 0, 1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]]
     assertEquals(axisCodes(affine), ['A', 'S', 'R'])
   })
+  await t.step('Fail gracefully on NaNs', async () => {
+    const affine = [[Number.NaN, 0, 1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]]
+    assertEquals(axisCodes(affine), null)
+  })
 })
 
 testAsyncFileAccess('Test file access errors for loadHeader', loadHeader)

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/files/nifti.ts

@@ -34,9 +34,9 @@ async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array<A
 
 export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
   const buf = await readBytes(file, 1024)
+  let header
   try {
     const data = isCompressed(buf.buffer) ? await extract(buf, 540) : buf.slice(0, 540)
-    let header
     if (isNIFTI1(data.buffer)) {
       header = new NIFTI1()
       // Truncate to 348 bytes to avoid attempting to parse extensions
@@ -48,29 +48,30 @@ export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
     if (!header) {
       throw { code: 'NIFTI_HEADER_UNREADABLE' }
     }
-    const ndim = header.dims[0]
-    return {
-      dim: header.dims,
-      // Hack: round pixdim to 3 decimal places; schema should add rounding function
-      pixdim: header.pixDims.map((pixdim) => Math.round(pixdim * 1000) / 1000),
-      shape: header.dims.slice(1, ndim + 1),
-      voxel_sizes: header.pixDims.slice(1, ndim + 1),
-      dim_info: {
-        freq: header.dim_info & 0x03,
-        phase: (header.dim_info >> 2) & 0x03,
-        slice: (header.dim_info >> 4) & 0x03,
-      },
-      xyzt_units: {
-        xyz: ['unknown', 'meter', 'mm', 'um'][header.xyzt_units & 0x03],
-        t: ['unknown', 'sec', 'msec', 'usec'][(header.xyzt_units >> 3) & 0x03],
-      },
-      qform_code: header.qform_code,
-      sform_code: header.sform_code,
-      axis_codes: axisCodes(header.affine),
-    } as NiftiHeader
   } catch (err) {
     throw { code: 'NIFTI_HEADER_UNREADABLE' }
   }
+
+  const ndim = header.dims[0]
+  return {
+    dim: header.dims,
+    // Hack: round pixdim to 3 decimal places; schema should add rounding function
+    pixdim: header.pixDims.map((pixdim) => Math.round(pixdim * 1000) / 1000),
+    shape: header.dims.slice(1, ndim + 1),
+    voxel_sizes: header.pixDims.slice(1, ndim + 1),
+    dim_info: {
+      freq: header.dim_info & 0x03,
+      phase: (header.dim_info >> 2) & 0x03,
+      slice: (header.dim_info >> 4) & 0x03,
+    },
+    xyzt_units: {
+      xyz: ['unknown', 'meter', 'mm', 'um'][header.xyzt_units & 0x03],
+      t: ['unknown', 'sec', 'msec', 'usec'][(header.xyzt_units >> 3) & 0x03],
+    },
+    qform_code: header.qform_code,
+    sform_code: header.sform_code,
+    axis_codes: axisCodes(header.affine),
+  } as NiftiHeader
 }
 
 /** Vector addition */
@@ -124,13 +125,18 @@ function argMax(arr: number[]): number {
  *
  * @returns character codes describing the orientation of an image affine.
  */
-export function axisCodes(affine: number[][]): string[] {
+export function axisCodes(affine: number[][]): string[] | null {
   // This function is an extract of the Python function transforms3d.affines.decompose44
   // (https://github.com/matthew-brett/transforms3d/blob/6a43a98/transforms3d/affines.py#L10-L153)
   //
   // As an optimization, this only orthogonalizes the basis,
   // and does not normalize to unit vectors.
 
+  // Bad qforms result in NaNs in the rotation matrix
+  if (affine.some((row) => row.some((val) => !Number.isFinite(val)))) {
+    return null
+  }
+
   // Operate on columns, which are the cosines that project input coordinates onto output axes
   const [cosX, cosY, cosZ] = [0, 1, 2].map((j) => [0, 1, 2].map((i) => affine[i][j]))
 
@@ -148,7 +154,7 @@ export function axisCodes(affine: number[][]): string[] {
 
   // Check that indices are 0, 1 and 2 in some order
   if (maxIndices.toSorted().some((idx, i) => idx !== i)) {
-    throw { key: 'AMBIGUOUS_AFFINE' }
+    throw { code: 'AMBIGUOUS_AFFINE' }
   }
 
   // Positive/negative codes for each world axis

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/files/openers.ts

@@ -126,3 +126,18 @@ export class HTTPOpener implements FileOpener {
     return new Uint8Array(await response.arrayBuffer())
   }
 }
+
+export class NullFileOpener implements FileOpener {
+  size: number
+  constructor(size = 0) {
+    this.size = size
+  }
+  stream = async () =>
+    new ReadableStream({
+      start(controller) {
+        controller.close()
+      },
+    })
+  text = async () => ''
+  readBytes = async (size: number, offset?: number) => new Uint8Array()
+}

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/files/repo.ts

@@ -84,27 +84,29 @@ export async function readRemotes(options: any): Promise<Record<string, Record<s
   return byUUID
 }
 
-/**
- * Resolve an annexed file location to an HTTP URL, if a public S3 remote is available
- */
-export async function resolveAnnexedFile(
+export async function parseAnnexedFile(
   path: string,
-  remote?: string,
-  options?: any,
-): Promise<{ url: string; size: number }> {
-  // path is known to be a symlink
+): Promise<{ key: string; size: number; gitdir: string }> {
   const target = await Deno.readLink(path)
   const { dir, base } = parse(target)
 
-  if (!options?.gitdir) {
-    const dirs = dir.split(SEPARATOR_PATTERN)
-    const gitdir = join(dirname(path), ...dirs.slice(0, dirs.indexOf('.git') + 1))
-    options = { ...options, gitdir }
-  }
+  const dirs = dir.split(SEPARATOR_PATTERN)
+  const gitdir = join(dirname(path), ...dirs.slice(0, dirs.indexOf('.git') + 1))
 
   const size = +base.match(annexKeyRegex)?.groups?.size!
 
-  const rmet = await readRmet(base, options)
+  return { key: base, size, gitdir }
+}
+
+/**
+ * Resolve an annexed file location to an HTTP URL, if a public S3 remote is available
+ */
+export async function resolveAnnexedFile(
+  key: string,
+  remote?: string,
+  options?: any,
+): Promise<{ url: string }> {
+  const rmet = await readRmet(key, options)
   const remotes = await readRemotes(options)
   let uuid: string
   if (remote) {
@@ -137,5 +139,5 @@ export async function resolveAnnexedFile(
   const metadata = rmet[uuid]
   const url = `${publicurl}/${metadata.path}?versionId=${metadata.version}`
 
-  return { url, size }
+  return { url }
 }

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/issues/list.ts

@@ -203,6 +203,10 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'Files with the same name but different casing have been found.',
   },
+  INVALID_FILE_ENCODING: {
+    severity: 'error',
+    reason: 'File encoding is not valid UTF-8.',
+  },
 }
 
 export const nonSchemaIssues = { ...bidsIssues }

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/schema/expressionLanguage.ts

@@ -79,11 +79,23 @@ export const expressionFunctions = {
     }
     return typeof operand
   },
-  min: (list: number[]): number | null => {
-    return list != null ? Math.min(...list.map(Number).filter((x) => !isNaN(x))) : null
+  min: (list: number | number[]): number | null => {
+    if (list == null) {
+      return null
+    }
+    if (!Array.isArray(list)) {
+      list = [list]
+    }
+    return Math.min(...list.map(Number).filter((x) => !isNaN(x)))
   },
-  max: (list: number[]): number | null => {
-    return list != null ? Math.max(...list.map(Number).filter((x) => !isNaN(x))) : null
+  max: (list: number | number[]): number | null => {
+    if (list == null) {
+      return null
+    }
+    if (!Array.isArray(list)) {
+      list = [list]
+    }
+    return Math.max(...list.map(Number).filter((x) => !isNaN(x)))
   },
   length: <T>(list: T[]): number | null => {
     if (Array.isArray(list) || typeof list == 'string') {

{bids_validator_deno-2.2.1 → bids_validator_deno-2.2.3}/src/schema/walk.ts

@@ -1,6 +1,7 @@
 import { BIDSContext, type BIDSContextDataset } from './context.ts'
-import { BIDSFile, FileOpener, FileTree } from '../types/filetree.ts'
+import { BIDSFile, type FileTree } from '../types/filetree.ts'
 import type { DatasetIssues } from '../issues/datasetIssues.ts'
+import { NullFileOpener } from '../files/openers.ts'
 import { loadTSV } from '../files/tsv.ts'
 import { loadJSON } from '../files/json.ts'
 import { queuedAsyncIterator } from '../utils/queue.ts'
@@ -14,21 +15,6 @@ function* quickWalk(dir: FileTree): Generator<BIDSFile> {
   }
 }
 
-class NullFileOpener implements FileOpener {
-  size: number
-  constructor(size = 0) {
-    this.size = size
-  }
-  stream = async () =>
-    new ReadableStream({
-      start(controller) {
-        controller.close()
-      },
-    })
-  text = async () => ''
-  readBytes = async (size: number, offset?: number) => new Uint8Array()
-}
-
 function pseudoFile(dir: FileTree, opaque: boolean): BIDSFile {
   return new BIDSFile(
     // Use a trailing slash to indicate directory