BEP042 patches

.github/workflows/deno_tests.yml

@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  BIDS_SCHEMA: https://bids-specification--1998.org.readthedocs.build/en/1998/schema.json
+
 jobs:
   debug_info:
     runs-on: ubuntu-latest
@@ -52,7 +55,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        allow-net: [true, false]
+        allow-net: [true] # , false]
       fail-fast: false
     defaults:
       run:

changelog.d/20250919_172910_dan_add_keys_to_assoc_coordsys.md

@@ -0,0 +1,49 @@
+<!--
+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
+
+- Implement `associations.coordsystems` to collate multiple `coordsystem.json` files,
+  as required by BEP 042 (EMG).
+
+<!--
+### Changed
+
+- A bullet item for the Changed category.
+
+-->
+<!--
+### Fixed
+
+- A bullet item for the Fixed category.
+
+-->
+<!--
+### 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/schema/associations.ts

@@ -3,14 +3,19 @@ import type { Schema as MetaSchema } from '@bids/schema/metaschema'
 
 import type { BIDSFile } from '../types/filetree.ts'
 import type { BIDSContext } from './context.ts'
+import { loadJSON } from '../files/json.ts'
 import { loadTSV } from '../files/tsv.ts'
 import { parseBvalBvec } from '../files/dwi.ts'
 import { walkBack } from '../files/inheritance.ts'
 import { evalCheck } from './applyRules.ts'
 import { expressionFunctions } from './expressionLanguage.ts'
+import { readEntities } from './entities.ts'
 
 import { readText } from '../files/access.ts'
 
+type LoadFunction = (file: BIDSFile, options: any) => Promise<any>
+type MultiLoadFunction = (files: BIDSFile[], options: any) => Promise<any>
+
 function defaultAssociation(file: BIDSFile, _options: any): Promise<{ path: string }> {
   return Promise.resolve({ path: file.path })
 }
@@ -23,7 +28,7 @@ function defaultAssociation(file: BIDSFile, _options: any): Promise<{ path: stri
  *
  * Many associations only consist of a path; this object is for more complex associations.
  */
-const associationLookup = {
+const associationLookup: Record<string, LoadFunction> = {
   events: async (file: BIDSFile, options: { maxRows: number }): Promise<Events> => {
     const columns = await loadTSV(file, options.maxRows)
       .catch((e) => {
@@ -86,6 +91,24 @@ const associationLookup = {
     }
   },
 }
+const multiAssociationLookup: Record<string, MultiLoadFunction> = {
+  coordsystems: async (
+    files: BIDSFile[],
+    options: any,
+  ): Promise<{ paths: string[]; spaces: string[]; ParentCoordinateSystems: string[] }> => {
+    const jsons = await Promise.allSettled(
+      files.map((f) => loadJSON(f).catch(() => ({} as Record<string, unknown>))),
+    )
+    const parents = jsons.map((j) =>
+      j.status === 'fulfilled' ? j.value?.ParentCoordinateSystem : undefined
+    ).filter((p) => p) as string[]
+    return {
+      paths: files.map((f) => f.path),
+      spaces: files.map((f) => readEntities(f.name).entities?.space),
+      ParentCoordinateSystems: parents,
+    }
+  },
+}
 
 export async function buildAssociations(
   context: BIDSContext,
@@ -123,33 +146,37 @@ export async function buildAssociations(
         rule.target.suffix,
         rule.target?.entities ?? [],
       ).next().value
-      if (Array.isArray(file)) {
-        file = file[0]
-      }
-    } catch (error) {
-      if (
-        error && typeof error === 'object' && 'code' in error &&
-        error.code === 'MULTIPLE_INHERITABLE_FILES'
-      ) {
-        // @ts-expect-error
+    } catch (error: any) {
+      if (error?.code === 'MULTIPLE_INHERITABLE_FILES') {
         context.dataset.issues.add(error)
-        break
+        continue
       } else {
         throw error
       }
     }
 
-    if (file) {
-      // @ts-expect-error
-      const load = associationLookup[key] ?? defaultAssociation
-      // @ts-expect-error
-      associations[key] = await load(file, { maxRows: context.dataset.options?.maxRows }).catch(
-        (error: any) => {
-          if (error.code) {
-            context.dataset.issues.add({ ...error, location: file.path })
-          }
-        },
-      )
+    if (file && !(Array.isArray(file) && file.length === 0)) {
+      const options = { maxRows: context.dataset.options?.maxRows }
+      if (key in multiAssociationLookup) {
+        const load = multiAssociationLookup[key]
+        if (!Array.isArray(file)) {
+          file = [file]
+        }
+        associations[key as keyof Associations] = await load(file, options).catch((e: any) => {})
+      } else {
+        const load = associationLookup[key] ?? defaultAssociation
+        if (Array.isArray(file)) {
+          file = file[0]
+        }
+        const location = file.path
+        associations[key as keyof Associations] = await load(file, options).catch(
+          (error: any) => {
+            if (error.code) {
+              context.dataset.issues.add({ ...error, location })
+            }
+          },
+        )
+      }
     }
   }
   return Promise.resolve(associations)