use logger on bidsignore failure. update logger warning to warn, deno…

…land/std#4258
bids-standard · Oct 9, 2024 · 2052938 · 2052938
1 parent bc01649
commit 2052938
Show file tree

Hide file tree

Showing 5 changed files with 12 additions and 7 deletions.
diff --git a/bids-validator/src/files/browser.ts b/bids-validator/src/files/browser.ts
@@ -55,7 +55,11 @@ export async function fileListToTree(files: File[]): Promise<FileTree> {
   const tree = filesToTree(files.map((f) => new BIDSFileBrowser(f, ignore, root)))
   const bidsignore = tree.get('.bidsignore')
   if (bidsignore) {
-    ignore.add(await readBidsIgnore(bidsignore as BIDSFile))
+    try {
+      ignore.add(await readBidsIgnore(bidsignore as BIDSFile))
+    } catch(err) {
+      console.log(`Failed to read '.bidsignore' file with the following error:\n${err}`)
+    }
   }
   return tree
 }
diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts
@@ -6,6 +6,7 @@ import * as posix from '@std/path/posix'
 import { type BIDSFile, FileTree } from '../types/filetree.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
 import { FileIgnoreRules, readBidsIgnore } from './ignore.ts'
+import { logger } from '../utils/logger.ts'
 
 /**
  * Thrown when a text file is decoded as UTF-8 but contains UTF-16 characters
@@ -157,8 +158,8 @@ export async function readFileTree(rootPath: string): Promise<FileTree> {
         )
         ignore.add(await readBidsIgnore(ignoreFile))
   } catch (err) {
-    if (!(Object.hasOwn(err, 'code') && err.code === "ENOENT")) {
-      throw err
+    if (!Object.hasOwn(err, 'code') || err.code !== "ENOENT") {
+      logger.error(`Failed to read '.bidsignore' file with the following error:\n${err}`)
     }
   }
   return _readFileTree(rootPath, '/', ignore)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
@@ -221,7 +221,7 @@ function evalJsonCheck(
     }
 
     if (sidecarRule && !(keyName in context.sidecarKeyOrigin)) {
-      logger.warning(
+      logger.warn(
         `sidecarKeyOrigin map failed to initialize for ${context.path} on key ${keyName}. Validation caching not active for this key.`,
       )
     }

diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
@@ -225,7 +225,7 @@ export class BIDSContext implements Context {
         if (error.key) {
           this.dataset.issues.add({ code: error.key, location: this.file.path })
         }
-        logger.warning(
+        logger.warn(
           `tsv file could not be opened by loadColumns '${this.file.path}'`,
         )
         logger.debug(error)

diff --git a/bids-validator/src/validators/json.ts b/bids-validator/src/validators/json.ts
@@ -10,7 +10,7 @@ export const compile = memoize(metadataValidator.compile.bind(metadataValidator)
 
 export function setCustomMetadataFormats(schema: Schema): void {
   if (typeof schema.objects.formats !== 'object') {
-    logger.warning(
+    logger.warn(
       `schema.objects.formats missing from schema, format validation disabled.`,
     )
     return
@@ -19,7 +19,7 @@ export function setCustomMetadataFormats(schema: Schema): void {
   for (const key of Object.keys(schemaFormats)) {
     const pattern = schemaFormats[key]['pattern']
     if (typeof pattern !== 'string') {
-      logger.warning(
+      logger.warn(
         `schema.objects.formats.${key} pattern missing or invalid. Skipping this format for addition to context json validator`,
       )
       continue