Merge branch 'bids-standard:master' into bep029_motion

bids-standard · Aug 25, 2023 · 16fd80b · 16fd80b
2 parents c6810aa + 6677c9a
commit 16fd80b
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Showing 4 changed files with 27 additions and 13 deletions.
diff --git a/bids-validator/bids_validator/rules/file_level_rules.json b/bids-validator/bids_validator/rules/file_level_rules.json
@@ -488,6 +488,8 @@
         "_events\\.tsv",
         "_channels\\.json",
         "_channels\\.tsv",
+        "_electrodes\\.json",
+        "_electrodes\\.tsv",
         "_meg\\.json",
         "_coordsystem\\.json",
         "_photo\\.jpg",

diff --git a/bids-validator/src/README.md b/bids-validator/src/README.md
@@ -8,9 +8,19 @@ Deno is a JavaScript and TypeScript runtime that is used to run the schema based
 
 At the root of the repository there are two directories, `bids-validator` and `bids-validator-web`. These are separate npm packages, the Deno validator lives within the bids-validator package within the `src` directory.
 
-## Schema validator examples
+## Usage
 
-Deno by default sandboxes applications like a web browser. To validate datasets located on your local system, you need to use the --allow-read flag to read local files. --allow-env is also required to allow for detection of OS specific features. These flags are included in the script line of the `./bids-validator-deno` script.
+To use the latest validator hosted at https://deno.land/x/bids_validator, use the following command:
+
+```console
+$ deno run --allow-read --allow-env https://deno.land/x/bids_validator/bids-validator.ts path/to/dataset
+```
+
+Deno by default sandboxes applications like a web browser. `--allow-read` allows the validator to read local files, and `--allow-env` enables OS-specific features.
+
+### Development tools
+
+From the repository root, use `bids-validator/bids-validator-deno` to run with all permissions enabled by default:
 
 ```shell
 # Run from within the /bids-validator directory
@@ -19,12 +29,6 @@ cd bids-validator
 ./bids-validator-deno path/to/dataset
 ```
 
-By default only schema derived validation rules are run. The legacy validator can be run at the same time with `--legacy` and this may improve coverage for issues not yet implemented in the schema variant.
-
-```shell
-./bids-validator-deno --legacy path/to/dataset
-```
-
 ## Schema validator test suite
 
 ```shell

diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts
@@ -25,10 +25,10 @@ export class BIDSFileDeno implements BIDSFile {
   name: string
   path: string
   #fileInfo?: Deno.FileInfo
-  private _datasetAbsPath: string
+  #datasetAbsPath: string
 
   constructor(datasetPath: string, path: string, ignore: FileIgnoreRules) {
-    this._datasetAbsPath = datasetPath
+    this.#datasetAbsPath = datasetPath
     this.path = path
     this.name = basename(path)
     this.#ignore = ignore
@@ -42,7 +42,7 @@ export class BIDSFileDeno implements BIDSFile {
   }
 
   private _getPath(): string {
-    return join(this._datasetAbsPath, this.path)
+    return join(this.#datasetAbsPath, this.path)
   }
 
   get size(): number {

diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
@@ -131,8 +131,16 @@ export class BIDSContext implements Context {
     })
 
     if (validSidecars.length > 1) {
-      // two matching in one dir not allowed
-    } else if (validSidecars.length === 1) {
+      const exactMatch = validSidecars.find(sidecar => sidecar.path == this.file.path.replace(this.extension, ".json"));
+      if (exactMatch) {
+        validSidecars.splice(1);
+        validSidecars[0] = exactMatch;
+      } else {
+        logger.warning(`Multiple sidecar files detected for '${this.file.path}'`)
+      }
+    }
+
+    if (validSidecars.length === 1) {
       const json = await validSidecars[0]
         .text()
         .then((text) => JSON.parse(text))