[SCHEMA] harmonize into dirs, ids, ids_phenotype for "subjects" and "sessions"

src/schema/SCHEMA_VERSION

@@ -1 +1 @@
-0.11.4-dev
+0.12.0-dev

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;