RF(schema): harmonize into dirs, ids, ids_phenotype

Current names duplicate their "domain" (subject_ or session_), inconsistent in
plurality (_id although for all ids), and not clear really what
'phenotype' corresponds to without reading the description.

With proposed change there is no duplication of the domain, consistency
in plurality (albeit 'id' is an abbreviation so 'ids' is a non-word), and
IMHO clearer meaning in `ids_phenotype`.

This would also allow for generalization across other entities in a perspective
bids-standard/bids-2-devel#54 - where then any entity
with folders for its level could have `dirs`. Also it could come handy to
determine `ids` for some other entities in tests.

Ref: bids-standard/bids-validator#94 (comment)

TODOs
- [ ] introduce corresponding changes to bids-validator

Author: yarikoptic

src/schema/meta/context.yaml

@@ -67,20 +67,20 @@ properties:
         description: 'Collections of subjects in dataset'
         type: object
         required:
-          - sub_dirs
+          - dirs
         additionalProperties: false
         properties:
-          sub_dirs:
+          dirs:
             description: 'Subjects as determined by sub-* directories'
             type: array
             items:
               type: string
-          participant_id:
+          ids:
             description: 'The participant_id column of participants.tsv'
             type: array
             items:
               type: string
-          phenotype:
+          ids_phenotype:
             description: 'The union of participant_id columns in phenotype files'
             type: array
             items:
@@ -96,20 +96,20 @@ properties:
         description: 'Collections of sessions in subject'
         type: object
         required:
-          - ses_dirs
+          - dirs
         additionalProperties: false
         properties:
-          ses_dirs:
+          dirs:
             description: 'Sessions as determined by ses-* directories'
             type: array
             items:
               type: string
-          session_id:
+          ids:
             description: 'The session_id column of sessions.tsv'
             type: array
             items:
               type: string
-          phenotype:
+          ids_phenotype:
             description: 'The union of session_id columns in phenotype files'
             type: array
             items:

src/schema/rules/checks/dataset.yaml

@@ -11,7 +11,7 @@ SubjectFolders:
   selectors:
     - path == '/dataset_description.json'
   checks:
-    - length(dataset.subjects.sub_dirs) > 0
+    - length(dataset.subjects.dirs) > 0
 
 # 49
 ParticipantIDMismatch:
@@ -24,7 +24,7 @@ ParticipantIDMismatch:
   selectors:
     - path == '/participants.tsv'
   checks:
-    - allequal(sorted(columns.participant_id), sorted(dataset.subjects.sub_dirs))
+    - allequal(sorted(columns.participant_id), sorted(dataset.subjects.dirs))
 
 # 51
 PhenotypeSubjectsMissing:
@@ -35,9 +35,9 @@ PhenotypeSubjectsMissing:
     level: error
   selectors:
     - path == '/dataset_description.json'
-    - type(dataset.subjects.phenotype) != 'null'
+    - type(dataset.subjects.ids_phenotype) != 'null'
   checks:
-    - allequal(sorted(dataset.subjects.phenotype), sorted(dataset.subjects.sub_dirs))
+    - allequal(sorted(dataset.subjects.ids_phenotype), sorted(dataset.subjects.dirs))
 
 # 214
 SamplesTSVMissing:

tools/typescript/generate.test.ts

@@ -53,14 +53,14 @@ Deno.test('generateTypes() supports generic array type', () => {
 Deno.test('generateTypes() supports typed array type', () => {
   const file = createSourceFile('test.ts')
   file.statements = generateTypes({
-    sub_dirs: {
+    dirs: {
       description: 'Subjects as determined by sub-*/ directories',
       type: 'array',
       items: { type: 'string' },
     },
   })
 
-  assertEquals(print(file), 'sub_dirs: string[];\n')
+  assertEquals(print(file), 'dirs: string[];\n')
 })
 
 // Object without defined properties
@@ -134,7 +134,7 @@ Deno.test('generateTypes() supports object trees', () => {
           description: 'Collections of subjects in dataset',
           type: 'object',
           properties: {
-            sub_dirs: {
+            dirs: {
               description: 'Subjects as determined by sub-*/ directories',
               type: 'array',
               items: { type: 'string' },
@@ -148,7 +148,7 @@ Deno.test('generateTypes() supports object trees', () => {
   assertEquals(
     print(file),
     `export interface DatasetSubjects {
-    sub_dirs: string[];
+    dirs: string[];
 }
 export interface Dataset {
     dataset_description: object;