bids-validator-deno 2.2.2__tar.gz → 2.2.4__tar.gz

{bids_validator_deno-2.2.2 → bids_validator_deno-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bids-validator-deno
-Version: 2.2.2
+Version: 2.2.4
 Summary: Typescript implementation of the BIDS validator
 Keywords: BIDS,BIDS validator
 Author: bids-standard developers

{bids_validator_deno-2.2.2 → bids_validator_deno-2.2.4}/deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.2.2",
+  "version": "2.2.4",
   "exports": {
     ".": "./src/bids-validator.ts",
     "./main": "./src/main.ts",
@@ -28,22 +28,22 @@
   },
   "imports": {
     "@ajv": "npm:ajv@^8.17.1",
-    "@bids/schema": "jsr:@bids/schema@~1.1.1",
+    "@bids/schema": "jsr:@bids/schema@~1.1.3",
     "@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",
     "@ignore": "npm:ignore@^7.0.5",
-    "@libs/xml": "jsr:@libs/xml@^6.0.8",
+    "@libs/xml": "jsr:@libs/xml@^7.0.3",
     "@mango/nifti": "npm:@bids/nifti-reader-js@^0.6.9",
-    "@std/assert": "jsr:@std/assert@^1.0.14",
+    "@std/assert": "jsr:@std/assert@^1.0.16",
     "@std/fmt": "jsr:@std/fmt@^1.0.8",
-    "@std/fs": "jsr:@std/fs@^1.0.19",
+    "@std/fs": "jsr:@std/fs@^1.0.20",
     "@std/io": "jsr:@std/io@^0.225.2",
     "@std/log": "jsr:@std/log@^0.224.14",
-    "@std/path": "jsr:@std/path@^1.1.2",
-    "@std/streams": "jsr:@std/streams@^1.0.12",
-    "@std/yaml": "jsr:@std/yaml@^1.0.9",
-    "isomorphic-git": "npm:isomorphic-git@^1.27.1",
+    "@std/path": "jsr:@std/path@^1.1.3",
+    "@std/streams": "jsr:@std/streams@^1.0.14",
+    "@std/yaml": "jsr:@std/yaml@^1.0.10",
+    "isomorphic-git": "npm:isomorphic-git@^1.35.1",
     "hash-wasm": "npm:hash-wasm@^4.12.0"
   },
   "tasks": {

{bids_validator_deno-2.2.2 → bids_validator_deno-2.2.4}/pyproject.toml

@@ -18,7 +18,7 @@ keywords = [
     "BIDS validator",
 ]
 dynamic = []
-version = "2.2.2"
+version = "2.2.4"
 
 [project.license]
 text = "MIT"

{bids_validator_deno-2.2.2 → bids_validator_deno-2.2.4}/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-2.2.2 → bids_validator_deno-2.2.4}/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-2.2.4/src/files/repo.test.ts

@@ -0,0 +1,28 @@
+import { assert, assertArrayIncludes, assertObjectMatch } from '@std/assert'
+import { parseRmetLine } from './repo.ts'
+
+Deno.test('parseRmetLine', async (t) => {
+  await t.step('parses valid rmet line', () => {
+    const line =
+      '1590213748.042921433s 57894849-d0c8-4c62-8418-3627be18a196:V +iVcEk18e3J2WQys4zr_ANaTPfpUufW4Y#ds002778/dataset_description.json'
+    const entry = parseRmetLine(line)
+    assertObjectMatch(entry!, {
+      timestamp: 1590213748.042921433,
+      uuid: '57894849-d0c8-4c62-8418-3627be18a196',
+      version: 'iVcEk18e3J2WQys4zr_ANaTPfpUufW4Y',
+      path: 'ds002778/dataset_description.json',
+    })
+  })
+  await t.step('parses base64-encoded rmet line', () => {
+    // Real example from OpenNeuro, has a unicode apostrophe in the filename
+    const line =
+      '1714730995.499196097s 51d08fb4-c58a-4fd7-a171-e5ff8226ca2f:V +!aG1NM2VqYWRxdFgxR18uc1VRNmJzd0FMLnhUcFJFeG8jZHMwMDQxOTQvZGVyaXZhdGl2ZXMvQnJhbmRzZXRhbDIwMjRUZW1wb3JhbEFkYXB0YXRpb25FQ29HL2RhdGFfc3ViamVjdHMvc3ViLXAxMS9lcG9jaHNfYi9lcG9jaHNfYl9jaGFubmVsMzItQW1iZXLigJlzIE1hY0Jvb2sgUHJvLnR4dA=='
+    const entry = parseRmetLine(line)
+    assertObjectMatch(entry!, {
+      timestamp: 1714730995.499196097,
+      uuid: '51d08fb4-c58a-4fd7-a171-e5ff8226ca2f',
+      version: 'hmM3ejadqtX1G_.sUQ6bswAL.xTpRExo',
+      path: 'ds004194/derivatives/Brandsetal2024TemporalAdaptationECoG/data_subjects/sub-p11/epochs_b/epochs_b_channel32-Amber’s MacBook Pro.txt'
+    })
+  })
+})

{bids_validator_deno-2.2.2 → bids_validator_deno-2.2.4}/src/files/repo.ts

@@ -9,7 +9,8 @@ const textDecoder = new TextDecoder('utf-8')
 export const annexKeyRegex =
   /^(?<hashname>[A-Z0-9]+)-s(?<size>\d+)--(?<digest>[0-9a-fA-F]+)(?<ext>\.[\w\-. ]*)?/
 export const rmetLineRegex =
-  /^(?<timestamp>\d+(\.\d+)?)s (?<uuid>[0-9a-fA-F-]+):V \+(?<version>[^#]+)#(?<path>.+)/
+  /^(?<timestamp>\d+(\.\d+)?)s (?<uuid>[0-9a-fA-F-]+):V \+(?<version_str>.+)/
+export const versionRegex = /^(?<version>[^#]+)#(?<path>.+)/
 
 type Rmet = {
   timestamp: number
@@ -39,6 +40,33 @@ export async function hashDirLower(annexKey: string): Promise<[string, string]>
   return [digest.slice(0, 3), digest.slice(3, 6)]
 }
 
+export function parseRmetLine(line: string): Rmet | null {
+  const match = line.match(rmetLineRegex)
+  if (!match) {
+    return null
+  }
+  const uuid = match!.groups!.uuid
+  const timestamp = parseFloat(match!.groups!.timestamp)
+  let versionStr = match!.groups!.version_str as string
+  // Base64 encoded version strings are prefixed with '!'
+  if (versionStr.startsWith('!')) {
+    versionStr = b64toUtf8(versionStr.slice(1))
+  }
+  const versionMatch = versionStr.match(versionRegex)
+  return {
+    timestamp,
+    uuid,
+    version: versionMatch!.groups!.version,
+    path: versionMatch!.groups!.path,
+  }
+}
+
+function b64toUtf8(str: string): string {
+  const decoded = atob(str)
+  const bytes = Uint8Array.from({ length: decoded.length }, (_, i) => decoded.charCodeAt(i))
+  return textDecoder.decode(bytes)
+}
+
 /**
  * Read remote metadata entries for a given annex key
  *
@@ -55,9 +83,9 @@ async function readRmet(key: string, options: any): Promise<Record<string, Rmet>
   const rmet = await readAnnexPath(join(...hashDirs, `${key}.log.rmet`), options)
   const ret: Record<string, Rmet> = {}
   for (const line of rmet.split('\n')) {
-    const match = line.match(rmetLineRegex)
-    if (match) {
-      ret[match!.groups!.uuid] = match!.groups as unknown as Rmet
+    const entry = parseRmetLine(line)
+    if (entry) {
+      ret[entry.uuid] = entry
     }
   }
   return ret