Merge pull request #134 from bpinsard/enh/config_wildcards

enable wildcards in paths for config files

Author: rwblair

deno.json

@@ -32,7 +32,7 @@
     "@cliffy/command": "jsr:@effigies/[email protected]",
     "@cliffy/table": "jsr:@effigies/[email protected]",
     "@hed/validator": "npm:[email protected]",
-    "@ignore": "npm:ignore@6.0.2",
+    "@ignore": "npm:ignore@7.0.3",
     "@libs/xml": "jsr:@libs/[email protected]",
     "@mango/nifti": "npm:@bids/[email protected]",
     "@std/assert": "jsr:@std/[email protected]",

deno.lock

@@ -84,6 +84,8 @@ warnings, errors or ignored.
 }
 ```
 
+When a configuration specifies `location` without leading `/` it is interpreted
+as a glob pattern following gitignore syntax.
 The issues are partial matches of the [Issues] that the validator accumulates.
 Pass the `--json` flag to see the issues in detail.
 

docs/user_guide/command-line.md

@@ -31,7 +31,6 @@ export class FileIgnoreRules {
     config: string[],
     addDefaults: boolean = true,
   ) {
-    // @ts-expect-error
     this.#ignore = ignore()
     if (addDefaults) {
       this.#ignore.add(defaultIgnores)

src/files/ignore.ts

@@ -25,6 +25,16 @@ Deno.test('DatasetIssues management class', async (t) => {
     assertEquals(foundIssue[0].code, 'TEST_FILES_ERROR')
   })
 
+  await t.step('get issues with glob pattern', () => {
+    const issues = new DatasetIssues()
+    issues.add({ code: 'TEST_FILES_ERROR', location: '/acq-mprage_T1w.json' }, 'Test issue')
+    issues.add({ code: 'TEST_FILES_ERROR', location: '/acq-memprage_T1w.json' }, 'Test issue')
+    issues.add({ code: 'TEST_FILES_ERROR', location: '/acq-mb1_bold.json' }, 'Test issue')
+    issues.add({ code: 'TEST_FILES_ERROR', location: '/acq-mb4_bold.json' }, 'Test issue')
+    const foundIssue = issues.get({ location: '*_bold.json' })
+    assertEquals(foundIssue.length, 2)
+  })
+
   await t.step('test groupBy', () => {
     const issues = new DatasetIssues()
     issues.add({ code: 'NOT_INCLUDED', location: '/file_1' })

src/issues/datasetIssues.test.ts

@@ -1,3 +1,4 @@
+import { default as ignore } from '@ignore'
 import { nonSchemaIssues } from './list.ts'
 import type { Issue, IssueDefinition, IssueFile, Severity } from '../types/issues.ts'
 export type { Issue, IssueDefinition, IssueFile, Severity }
@@ -41,7 +42,12 @@ export class DatasetIssues {
       if (!value) {
         continue
       }
-      found = found.filter((x) => x[key as keyof Issue] === value)
+      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 {
+        found = found.filter((x) => x[key as keyof Issue] === value)
+      }
     }
     return found
   }

src/issues/datasetIssues.ts

@@ -1,4 +1,5 @@
 import { assertEquals } from '@std/assert'
+import { SEPARATOR_PATTERN } from '@std/path'
 import { BIDSContext } from '../schema/context.ts'
 import { _findRuleMatches, datatypeFromDirectory, hasMatch } from './filenameIdentify.ts'
 import { BIDSFileDeno } from '../files/deno.ts'
@@ -67,12 +68,8 @@ Deno.test('test hasMatch', async (t) => {
 
   await t.step('No match', async () => {
     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 [ dir, base ]  = tmpFile.split(SEPARATOR_PATTERN)
+    const file = new BIDSFileDeno(dir, `/${base}`, ignore)
 
     const context = new BIDSContext(file)
     await hasMatch(schema, context)