Merge remote-tracking branch 'upstream/main' into dev

Author: effigies

README.md

@@ -27,12 +27,12 @@ The BIDS Validator can be run with the [Deno][] runtime
 (see [Deno - Installation][] for detailed installation instructions):
 
 ```shell
-deno run -ERN jsr:@bids/validator
+deno run -ERWN jsr:@bids/validator
 ```
 
 Deno by default sandboxes applications like a web browser.
-`-E`, `-R` and `-N` allow the validator to read environment variables,
-local files, and network locations.
+`-E`, `-R`, '-W', and `-N` allow the validator to read environment variables,
+read/write local files, and read network locations.
 
 ### Configuration file
 

docs/user_guide/command-line.md

@@ -10,19 +10,19 @@ In general, there is no need to install Deno applications.
 `deno run` allows running from the Javascript Repository:
 
 ```sh
-deno run -ERN jsr:@bids/validator <dataset>
+deno run -ERWN jsr:@bids/validator <dataset>
 ```
 
 However, you can also install a lightweight script (into `$HOME/.deno/bin`):
 
 ```sh
-deno install -ERN -g -n bids-validator jsr:@bids/validator
+deno install -ERWN -g -n bids-validator jsr:@bids/validator
 ```
 
 Or compile a bundled binary:
 
 ```sh
-deno compile -ERN -o bids-validator jsr:@bids/validator
+deno compile -ERWN -o bids-validator jsr:@bids/validator
 ```
 
 ## Usage
@@ -36,7 +36,7 @@ The BIDS Validator takes a single dataset as input:
 :sync: run
 
 ```sh
-deno run -ERN jsr:@bids/validator <dataset>
+deno run -ERWN jsr:@bids/validator <dataset>
 ```
 
 :::

src/files/filetree.ts

@@ -8,7 +8,7 @@ const nullFile = {
   stream: new ReadableStream({
     start(controller) {
       controller.close()
-    }
+    },
   }),
   text: () => Promise.resolve(''),
   readBytes: async (size: number, offset?: number) => new Uint8Array(),

src/files/streams.test.ts

@@ -1,6 +1,6 @@
 import { assert, assertEquals } from '@std/assert'
 import { createUTF8Stream, UnicodeDecodeError } from './streams.ts'
-import { streamFromUint8Array, streamFromString } from '../tests/utils.ts'
+import { streamFromString, streamFromUint8Array } from '../tests/utils.ts'
 
 Deno.test('createUTF8Stream', async (t) => {
   await t.step('should return a TransformStream with UTF8StreamTransformer', () => {

src/files/tsv.test.ts

@@ -1,4 +1,10 @@
-import { assert, assertEquals, assertNotStrictEquals, assertObjectMatch, assertStrictEquals } from '@std/assert'
+import {
+  assert,
+  assertEquals,
+  assertNotStrictEquals,
+  assertObjectMatch,
+  assertStrictEquals,
+} from '@std/assert'
 import { pathToFile } from './filetree.ts'
 import { loadTSV } from './tsv.ts'
 import { streamFromString } from '../tests/utils.ts'

src/issues/datasetIssues.ts

@@ -42,7 +42,7 @@ export class DatasetIssues {
       if (!value) {
         continue
       }
-      if (key === 'location' && typeof value === "string" && !value.startsWith('/')){
+      if (key === 'location' && typeof value === 'string' && !value.startsWith('/')) {
         const key_ignore = ignore().add(value as string)
         found = found.filter((x) => x[key] && key_ignore.ignores(x[key].slice(1, x[key].length)))
       } else {

src/types/columns.test.ts

@@ -37,6 +37,13 @@ Deno.test('ColumnsMap', async (t) => {
     // @ts-expect-error ibid
     assertEquals(columns.size, ['0'])
   })
+  await t.step('set columns are permissible', () => {
+    const columns = new ColumnsMap()
+    // @ts-expect-error ts thinks size is protected property
+    columns['set'] = ['0']
+    // @ts-expect-error ibid
+    assertEquals(columns.set, ['0'])
+  })
   await t.step('missing columns are undefined', () => {
     const columns = new ColumnsMap()
     columns['a'] = ['0']

src/types/columns.ts

@@ -15,8 +15,14 @@ const columnMapAccessorProxy = {
     prop: symbol | string,
     receiver: ColumnsMap,
   ) {
-    // Map.size exists, so we need to shadow it with the column contents
-    if (prop === 'size') return target.get('size')
+    // Map instance methods/properties that could plasubily be column names:
+    if (
+      ['clear', 'delete', 'keys', 'set', 'values', 'size'].includes(
+        prop as string,
+      )
+    ) {
+      return target.get(prop as string)
+    }
     const value = Reflect.get(target, prop, receiver)
     if (typeof value === 'function') return value.bind(target)
     if (prop === Symbol.iterator) return target[Symbol.iterator].bind(target)

src/utils/memoize.ts

@@ -1,6 +1,6 @@
 export type WithCache<T> = T & { cache: Map<string, any> }
 interface FileLike {
-  path: string,
+  path: string
   parent: { path: string }
 }
 

src/validators/filenameIdentify.test.ts

@@ -68,7 +68,7 @@ Deno.test('test hasMatch', async (t) => {
 
   await t.step('No match', async () => {
     const tmpFile = Deno.makeTempFileSync()
-    const [ dir, base ]  = tmpFile.split(SEPARATOR_PATTERN)
+    const [dir, base] = tmpFile.split(SEPARATOR_PATTERN)
     const file = new BIDSFileDeno(dir, `/${base}`, ignore)
 
     const context = new BIDSContext(file)