Merge pull request #231 from bids-standard/fix/truncate_opaque_trees

fix: Do not descend into pseudo-files or opaque directories when checking for unused files

Author: effigies

changelog.d/20250822_091529_markiewicz_truncate_opaque_trees.md

@@ -0,0 +1,50 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+For top level release notes, leave all the headers commented out.
+-->
+
+<!--
+### Added
+
+- A bullet item for the Added category.
+
+-->
+<!--
+### Changed
+
+- A bullet item for the Changed category.
+
+-->
+### Fixed
+
+- Avoid descending into opaque directories (such as `*.zarr/`) when checking
+  for unused sidecars. ([#227])
+
+[#227]: https://github.com/bids-standard/bids-validator/issues/227
+
+<!--
+### Deprecated
+
+- A bullet item for the Deprecated category.
+
+-->
+<!--
+### Removed
+
+- A bullet item for the Removed category.
+
+-->
+<!--
+### Security
+
+- A bullet item for the Security category.
+
+-->
+<!--
+### Infrastructure
+
+- A bullet item for the Infrastructure category.
+
+-->

src/bids-validator.ts

@@ -6,3 +6,4 @@ const errors = result.issues.get({ severity: 'error' })
 if (errors.length) {
   Deno.exit(16)
 }
+Deno.exit(0)

src/validators/bids.ts

@@ -124,6 +124,7 @@ export async function validate(
     }
     await summary.update(context)
   }
+
   for (const check of perDSChecks) {
     await check(schema as unknown as GenericSchema, dsContext)
   }

src/validators/internal/unusedFile.ts

@@ -2,18 +2,20 @@ import type { GenericSchema } from '../../types/schema.ts'
 import type { BIDSFile, FileTree } from '../../types/filetree.ts'
 import type { BIDSContextDataset } from '../../schema/context.ts'
 
-function* walkFileTree(fileTree?: FileTree): Generator<BIDSFile> {
+function* walkFileTree(fileTree: FileTree, dsContext: BIDSContextDataset): Generator<BIDSFile> {
   if (!fileTree) {
     return
   }
+
   for (const file of fileTree.files) {
     if (!file.ignored) {
       yield file
     }
   }
+
   for (const dir of fileTree.directories) {
-    if (!dir.ignored) {
-      yield* walkFileTree(dir)
+    if (!dir.ignored && !dsContext.isPseudoFile(dir) && !dsContext.isOpaqueDirectory(dir)) {
+      yield* walkFileTree(dir, dsContext)
     }
   }
 }
@@ -23,7 +25,9 @@ export async function unusedStimulus(
   dsContext: BIDSContextDataset,
 ) {
   const stimDir = dsContext.tree.get('stimuli') as FileTree
-  const unusedStimuli = [...walkFileTree(stimDir)].filter((stimulus) => !stimulus.viewed)
+  const unusedStimuli = [...walkFileTree(stimDir, dsContext)].filter((stimulus) =>
+    !stimulus.viewed
+  )
   if (unusedStimuli.length) {
     dsContext.issues.add({ code: 'UNUSED_STIMULUS', affects: unusedStimuli.map((s) => s.path) })
   }
@@ -35,7 +39,7 @@ export async function sidecarWithoutDatafile(
   schema: GenericSchema,
   dsContext: BIDSContextDataset,
 ) {
-  const unusedSidecars = [...walkFileTree(dsContext.tree)].filter(
+  const unusedSidecars = [...walkFileTree(dsContext.tree, dsContext)].filter(
     (file) => (!file.viewed && file.name.endsWith('.json') &&
       !standalone_json.includes(file.name)),
   )