fix: Guard file openings

Author: effigies

src/files/gzip.test.ts

@@ -1,6 +1,7 @@
 import { assert, assertObjectMatch } from '@std/assert'
 import { parseGzip } from './gzip.ts'
 import { BIDSFileDeno } from './deno.ts'
+import { testAsyncFileAccess } from './access.test.ts'
 
 Deno.test('parseGzip', async (t) => {
   await t.step('parses anonymized file', async () => {
@@ -40,3 +41,5 @@ Deno.test('parseGzip', async (t) => {
     assert(!gzip)
   })
 })
+
+testAsyncFileAccess('Test file access errors for parseGzip', parseGzip)

src/files/gzip.ts

@@ -4,6 +4,7 @@
  */
 import type { Gzip } from '@bids/schema/context'
 import type { BIDSFile } from '../types/filetree.ts'
+import { readBytes } from './access.ts'
 
 /**
  * Parse a gzip header from a file
@@ -19,7 +20,7 @@ export async function parseGzip(
   file: BIDSFile,
   maxBytes: number = 512,
 ): Promise<Gzip | undefined> {
-  const buf = await file.readBytes(maxBytes)
+  const buf = await readBytes(file, maxBytes)
   const view = new DataView(buf.buffer, buf.byteOffset, buf.byteLength)
   if (view.byteLength < 2 || view.getUint16(0, false) !== 0x1f8b) return undefined
 

src/files/json.test.ts

@@ -1,6 +1,7 @@
 import { type assert, assertObjectMatch } from '@std/assert'
 import type { BIDSFile } from '../types/filetree.ts'
 import type { FileIgnoreRules } from './ignore.ts'
+import { testAsyncFileAccess } from './access.test.ts'
 
 import { loadJSON } from './json.ts'
 
@@ -61,3 +62,5 @@ Deno.test('Test JSON error conditions', async (t) => {
     assertObjectMatch(error, { code: 'JSON_INVALID' })
   })
 })
+
+testAsyncFileAccess('Test file access errors for loadJSON', loadJSON)

src/files/json.ts

@@ -1,12 +1,13 @@
 import type { BIDSFile } from '../types/filetree.ts'
+import { readBytes } from './access.ts'
 
 async function readJSONText(file: BIDSFile): Promise<string> {
   // Read JSON text from a file
   // JSON must be encoded in UTF-8 without a byte order mark (BOM)
   const decoder = new TextDecoder('utf-8', { fatal: true, ignoreBOM: true })
   // Streaming TextDecoders are buggy in Deno and Chrome, so read the
   // entire file into memory before decoding and parsing
-  const data = await file.readBytes(file.size)
+  const data = await readBytes(file, file.size)
   try {
     const text = decoder.decode(data)
     if (text.startsWith('\uFEFF')) {

src/files/nifti.test.ts

@@ -1,6 +1,7 @@
 import { assert, assertEquals, assertObjectMatch } from '@std/assert'
 import { FileIgnoreRules } from './ignore.ts'
 import { BIDSFileDeno } from './deno.ts'
+import { testAsyncFileAccess } from './access.test.ts'
 
 import { axisCodes, loadHeader } from './nifti.ts'
 
@@ -96,3 +97,5 @@ Deno.test('Test extracting axis codes', async (t) => {
     assertEquals(axisCodes(affine), ['A', 'S', 'R'])
   })
 })
+
+testAsyncFileAccess('Test file access errors for loadHeader', loadHeader)

src/files/nifti.ts

@@ -2,6 +2,7 @@ import { isCompressed, isNIFTI1, isNIFTI2, NIFTI1, NIFTI2 } from '@mango/nifti'
 import type { BIDSFile } from '../types/filetree.ts'
 import { logger } from '../utils/logger.ts'
 import type { NiftiHeader } from '@bids/schema/context'
+import { readBytes } from './access.ts'
 
 async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array<ArrayBuffer>> {
   // The fflate decompression that is used in nifti-reader does not like
@@ -32,8 +33,8 @@ async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array<A
 }
 
 export async function loadHeader(file: BIDSFile): Promise<NiftiHeader> {
+  const buf = await readBytes(file, 1024)
   try {
-    const buf = await file.readBytes(1024)
     const data = isCompressed(buf.buffer) ? await extract(buf, 540) : buf.slice(0, 540)
     let header
     if (isNIFTI1(data.buffer)) {

src/files/tiff.test.ts

@@ -1,6 +1,7 @@
 import { assert, assertObjectMatch } from '@std/assert'
 import { parseTIFF } from './tiff.ts'
 import { BIDSFileDeno } from './deno.ts'
+import { testAsyncFileAccess } from './access.test.ts'
 
 Deno.test('parseTIFF', async (t) => {
   await t.step('parse example file as TIFF', async () => {
@@ -53,3 +54,5 @@ Deno.test('parseTIFF', async (t) => {
     })
   })
 })
+
+testAsyncFileAccess('Test file access errors for parseTIFF', parseTIFF)

src/files/tiff.ts

@@ -5,6 +5,7 @@
 import type { Ome, Tiff } from '@bids/schema/context'
 import * as XML from '@libs/xml'
 import type { BIDSFile } from '../types/filetree.ts'
+import { readBytes } from './access.ts'
 
 function getImageDescription(
   dataview: DataView<ArrayBuffer>,
@@ -44,7 +45,7 @@ export async function parseTIFF(
   file: BIDSFile,
   OME: boolean,
 ): Promise<{ tiff?: Tiff; ome?: Ome }> {
-  const buf = await file.readBytes(4096)
+  const buf = await readBytes(file, 4096)
   const dataview = new DataView(buf.buffer, buf.byteOffset, buf.byteLength)
   const magic = dataview.getUint16(0, true)
   const littleEndian = magic === 0x4949

src/files/tsv.test.ts

@@ -9,6 +9,7 @@ import { pathToFile } from './filetree.ts'
 import { loadTSV, loadTSVGZ } from './tsv.ts'
 import { streamFromString } from '../tests/utils.ts'
 import { ColumnsMap } from '../types/columns.ts'
+import { testAsyncFileAccess } from './access.test.ts'
 
 function compressedStreamFromString(str: string): ReadableStream<Uint8Array<ArrayBuffer>> {
   return streamFromString(str).pipeThrough(new CompressionStream('gzip')) as ReadableStream<
@@ -292,3 +293,5 @@ Deno.test('TSVGZ loading', async (t) => {
     assertEquals(map.c, ['3', '6', '9'])
   })
 })
+
+testAsyncFileAccess('Test file access errors for loadTSV', loadTSV)

src/files/tsv.ts

@@ -7,6 +7,7 @@ import { ColumnsMap } from '../types/columns.ts'
 import type { BIDSFile } from '../types/filetree.ts'
 import { filememoizeAsync } from '../utils/memoize.ts'
 import { createUTF8Stream } from './streams.ts'
+import { openStream } from './access.ts'
 
 async function loadColumns(
   reader: ReadableStreamDefaultReader<string>,
@@ -55,7 +56,7 @@ export async function loadTSVGZ(
   headers: string[],
   maxRows: number = -1,
 ): Promise<ColumnsMap> {
-  const reader = file.stream
+  const reader = openStream(file)
     .pipeThrough(new DecompressionStream('gzip'))
     .pipeThrough(createUTF8Stream())
     .pipeThrough(new TextLineStream())
@@ -75,7 +76,7 @@ export async function loadTSVGZ(
 }
 
 async function _loadTSV(file: BIDSFile, maxRows: number = -1): Promise<ColumnsMap> {
-  const reader = file.stream
+  const reader = openStream(file)
     .pipeThrough(createUTF8Stream())
     .pipeThrough(new TextLineStream())
     .getReader()