fix: OSX and Windows tests

bids-validator/src/deps/fs.ts

@@ -1 +1 @@
-export { walk } from 'https://deno.land/[email protected]/fs/walk.ts'
+export { walk, EOL } from 'https://deno.land/[email protected]/fs/mod.ts'

bids-validator/src/deps/path.ts

@@ -5,9 +5,10 @@ export {
   basename,
   dirname,
   extname,
+  posix,
   fromFileUrl,
   parse,
-  SEPARATOR,
+  SEPARATOR_PATTERN,
 } from 'https://deno.land/[email protected]/path/mod.ts'
 export {
   globToRegExp,

bids-validator/src/files/browser.ts

@@ -1,7 +1,7 @@
 import { BIDSFile } from '../types/file.ts'
 import { FileTree } from '../types/filetree.ts'
 import { FileIgnoreRules } from './ignore.ts'
-import { parse, join, SEPARATOR } from '../deps/path.ts'
+import { parse, posix, SEPARATOR_PATTERN } from '../deps/path.ts'
 
 /**
  * Browser implement of BIDSFile wrapping native File/FileList types
@@ -56,7 +56,7 @@ export function fileListToTree(files: File[]): Promise<FileTree> {
       // Top level file
       tree.files.push(file)
     } else {
-      const levels = fPath.dir.split(SEPARATOR).slice(1)
+      const levels = fPath.dir.split(SEPARATOR_PATTERN).slice(1)
       let currentLevelTree = tree
       for (const level of levels) {
         const exists = currentLevelTree.directories.find(
@@ -68,7 +68,7 @@ export function fileListToTree(files: File[]): Promise<FileTree> {
         } else {
           // Otherwise make a new level and continue if needed
           const newTree = new FileTree(
-            join(currentLevelTree.path, level),
+            posix.join(currentLevelTree.path, level),
             level,
             currentLevelTree,
           )

bids-validator/src/files/deno.test.ts

@@ -1,15 +1,16 @@
-import { assertEquals, assertRejects } from '../deps/asserts.ts'
+import { assert, assertEquals, assertRejects } from '../deps/asserts.ts'
 import { readAll, readerFromStreamReader } from '../deps/stream.ts'
-import { dirname, basename, join } from '../deps/path.ts'
-import { BIDSFileDeno, UnicodeDecodeError } from './deno.ts'
+import { dirname, basename, join, fromFileUrl } from '../deps/path.ts'
+import { EOL } from '../deps/fs.ts'
+import { BIDSFileDeno, readFileTree, UnicodeDecodeError } from './deno.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
 import { FileIgnoreRules } from './ignore.ts'
 
 await requestReadPermission()
 
 // Use this file for testing file behavior
 const testUrl = import.meta.url
-const testPath = testUrl.slice('file://'.length)
+const testPath = fromFileUrl(testUrl)
 const testDir = dirname(testPath)
 const testFilename = basename(testPath)
 const ignore = new FileIgnoreRules([])
@@ -55,7 +56,22 @@ Deno.test('Deno implementation of BIDSFile', async (t) => {
       const bomFilename = 'bom-utf8.json'
       const file = new BIDSFileDeno(bomDir, bomFilename, ignore)
       const text = await file.text()
-      assertEquals(text, '{\n  "example": "JSON for test suite"\n}\n')
+      assertEquals(text, ['{', '  "example": "JSON for test suite"', '}', ''].join(EOL))
     },
   )
 })
+
+Deno.test('Deno implementation of FileTree', async (t) => {
+  const srcdir = dirname(testDir)
+  const parent = basename(testDir)
+  const tree = await readFileTree(srcdir)
+  await t.step('uses POSIX relative paths', async () => {
+    assertEquals(tree.path, '/')
+    const parentObj = tree.directories.find((dir) => dir.name === parent)
+    assert(parentObj !== undefined)
+    assertEquals(parentObj.path, `/${parent}`)
+    const testObj = parentObj.files.find((file) => file.name === testFilename)
+    assert(testObj !== undefined)
+    assertEquals(testObj.path, `/${parent}/${testFilename}`)
+  })
+})

bids-validator/src/files/deno.ts

@@ -1,7 +1,7 @@
 /**
  * Deno specific implementation for reading files
  */
-import { join, basename } from '../deps/path.ts'
+import { posix, join, basename } from '../deps/path.ts'
 import { BIDSFile } from '../types/file.ts'
 import { FileTree } from '../types/filetree.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
@@ -122,7 +122,7 @@ export async function _readFileTree(
     if (dirEntry.isFile || dirEntry.isSymlink) {
       const file = new BIDSFileDeno(
         rootPath,
-        join(relativePath, dirEntry.name),
+        posix.join(relativePath, dirEntry.name),
         ignore,
       )
       // For .bidsignore, read in immediately and add the rules
@@ -134,7 +134,7 @@ export async function _readFileTree(
     if (dirEntry.isDirectory) {
       const dirTree = await _readFileTree(
         rootPath,
-        join(relativePath, dirEntry.name),
+        posix.join(relativePath, dirEntry.name),
         ignore,
         tree,
       )

bids-validator/src/validators/filenameIdentify.test.ts

@@ -75,8 +75,13 @@ Deno.test('test hasMatch', async (t) => {
   })
 
   await t.step('No match', async () => {
-    const fileName = Deno.makeTempFileSync().split('/')[2]
-    const file = new BIDSFileDeno('/tmp', fileName, ignore)
+    const tmpFile = Deno.makeTempFileSync()
+    const parts = tmpFile.split('/')
+    const file = new BIDSFileDeno(
+      parts.slice(0, parts.length - 1).join('/'),
+      parts[parts.length - 1],
+      ignore,
+    )
 
     const context = new BIDSContext(fileTree, file, issues)
     await hasMatch(schema, context)
@@ -86,6 +91,7 @@ Deno.test('test hasMatch', async (t) => {
         .includes('NOT_INCLUDED'),
       true,
     )
+    Deno.removeSync(tmpFile)
   })
   await t.step('2 matches, no pruning', async () => {
     const path = `${PATH}/../bids-examples/fnirs_automaticity`

bids-validator/src/validators/filenameIdentify.ts

@@ -12,7 +12,7 @@
  * object in the schema for reference.
  */
 // @ts-nocheck
-import { SEPARATOR, globToRegExp } from '../deps/path.ts'
+import { SEPARATOR_PATTERN, globToRegExp } from '../deps/path.ts'
 import { GenericSchema, Schema } from '../types/schema.ts'
 import { BIDSContext } from '../schema/context.ts'
 import { lookupModality } from '../schema/modalities.ts'
@@ -75,7 +75,7 @@ export function _findRuleMatches(node, path, context) {
 export async function datatypeFromDirectory(schema, context) {
   const subEntity = schema.objects.entities.subject.name
   const sesEntity = schema.objects.entities.session.name
-  const parts = context.file.path.split(SEPARATOR)
+  const parts = context.file.path.split(SEPARATOR_PATTERN)
   let datatypeIndex = parts.length - 2
   if (datatypeIndex < 1) {
     return Promise.resolve()

bids-validator/src/validators/filenameValidate.test.ts

@@ -13,40 +13,52 @@ const fileTree = new FileTree('/tmp', '/')
 const issues = new DatasetIssues()
 const ignore = new FileIgnoreRules([])
 
+const splitFile = (path: string) => {
+  const parts = path.split('/')
+  return {
+    dirname: parts.slice(0, parts.length - 1).join('/'),
+    basename: parts[parts.length - 1],
+  }
+}
+
 Deno.test('test missingLabel', async (t) => {
   await t.step('File with underscore and no hyphens errors out.', async () => {
-    const fileName = Deno.makeTempFileSync({
+    const tmpFile = Deno.makeTempFileSync({
       prefix: 'no_labels_',
       suffix: '_entities.wav',
-    }).split('/')[2]
-    let file = new BIDSFileDeno('/tmp', fileName, ignore)
+    })
+    const { dirname, basename } = splitFile(tmpFile)
+    const file = new BIDSFileDeno(dirname, basename, ignore)
 
-    let context = new BIDSContext(fileTree, file, issues)
+    const context = new BIDSContext(fileTree, file, issues)
     await missingLabel(schema, context)
     assertEquals(
       context.issues
         .getFileIssueKeys(context.file.path)
         .includes('ENTITY_WITH_NO_LABEL'),
       true,
     )
+    Deno.removeSync(tmpFile)
   })
 
   await t.step(
     "File with underscores and hyphens doesn't error out.",
     async () => {
-      const fileName = Deno.makeTempFileSync({
+      const tmpFile = Deno.makeTempFileSync({
         prefix: 'we-do_have-',
         suffix: '_entities.wav',
-      }).split('/')[2]
-      let file = new BIDSFileDeno('/tmp', fileName, ignore)
-      let context = new BIDSContext(fileTree, file, issues)
+      })
+      const { dirname, basename } = splitFile(tmpFile)
+      const file = new BIDSFileDeno(dirname, basename, ignore)
+      const context = new BIDSContext(fileTree, file, issues)
       await missingLabel(schema, context)
       assertEquals(
         context.issues
           .getFileIssueKeys(context.file.path)
           .includes('ENTITY_WITH_NO_LABEL'),
         false,
       )
+      Deno.removeSync(tmpFile)
     },
   )
 })

bids-validator/src/validators/filenameValidate.ts

@@ -2,7 +2,7 @@ import { CheckFunction, RuleCheckFunction } from '../types/check.ts'
 import { DatasetIssues } from '../issues/datasetIssues.ts'
 import { BIDSContext } from '../schema/context.ts'
 import { GenericSchema, Schema, Entity, Format } from '../types/schema.ts'
-import { SEPARATOR } from '../deps/path.ts'
+import { SEPARATOR_PATTERN } from '../deps/path.ts'
 import { hasProp } from '../utils/objectPathHandler.ts'
 
 const sidecarExtensions = ['.json', '.tsv', '.bvec', '.bval']
@@ -25,7 +25,7 @@ export async function filenameValidate(
 }
 
 export function isAtRoot(context: BIDSContext) {
-  if (context.file.path.split(SEPARATOR).length !== 2) {
+  if (context.file.path.split(SEPARATOR_PATTERN).length !== 2) {
     return false
   }
   return true

bids-validator/src/validators/isBidsy.ts

@@ -3,7 +3,6 @@
  * derivatives to have the lowest common denomenator of bids like file names.
  */
 // @ts-nocheck
-import { SEPARATOR } from '../deps/path.ts'
 import { BIDSContext } from '../schema/context.ts'
 import { CheckFunction } from '../../types/check.ts'
 import { BIDSFile } from '../types/file.ts'