Merge pull request #1 from ericearl/bep036

Arshitha · web-flow · commit c4f06d706b91 · 2025-09-23T21:45:44.000+05:30
Update pheno00* examples
diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml
@@ -107,7 +107,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pet006 pheno00* volume_timing; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -119,7 +119,7 @@ jobs:
     - name: Skip main validation for datasets with unreleased spec features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a spec release
-      run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in dwi_deriv pheno00*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -128,7 +128,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--2123.org.readthedocs.build/en/2123/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |
diff --git a/pheno001/dataset_description.json b/pheno001/dataset_description.json
@@ -1,12 +1,13 @@
 {
 	"Name": "Phenotype guidelines example dataset 1",
-	"BIDSVersion": "1.9.0",
+	"BIDSVersion": "1.10.1",
 	"DatasetType": "raw",
 	"License": "CC0",
 	"Authors": [
 		"Arshitha Basavaraj",
 		"Eric Earl",
 		"Sebastian Urchs",
 		"Samuel Guay"
-	]
+	],
+	"AdditionalValidation": "Phenotype"
 }
diff --git a/pheno002/README.md b/pheno002/README.md
@@ -32,5 +32,4 @@ pheno002
             `-- sub-02_ses-02_T1w.nii.gz
 
 12 directories, 15 files
-
 ```
diff --git a/pheno002/dataset_description.json b/pheno002/dataset_description.json
@@ -1,6 +1,6 @@
 {
 	"Name": "Phenotype guidelines example dataset 2",
-	"BIDSVersion": "1.10.0",
+	"BIDSVersion": "1.10.1",
 	"DatasetType": "raw",
 	"License": "CC0",
 	"Authors": [
diff --git a/pheno002/phenotype/ace.json b/pheno002/phenotype/ace.json
@@ -5,8 +5,8 @@
   "session_id": {
     "Description": "ID assigned to participant's visit.",
     "Levels": {
-      "01": "First phenotype assessment and imaging visit.",
-      "02": "Second imaging only visit."
+      "ses-01": "First phenotype assessment and imaging visit.",
+      "ses-02": "Second imaging only visit."
     }
   },
   "b_ace_q1": {
diff --git a/pheno002/phenotype/ace.tsv b/pheno002/phenotype/ace.tsv
@@ -1,3 +1,3 @@
 participant_id	session_id	b_ace_q1	b_ace_q2	b_ace_q3	b_ace_q4	b_ace_q5	tesi_s_165	b_ace_q7	b_ace_q8	b_ace_q9	ceahd15
-sub-01	01	0	0	0	0	0	0	1	0	0	0
-sub-02	01	0	0	0	0	1	0	0	0	0	0
+sub-01	ses-01	0	0	0	0	0	0	1	0	0	0
+sub-02	ses-01	0	0	0	0	1	0	0	0	0	0
diff --git a/pheno002/sessions.json b/pheno002/sessions.json
@@ -5,8 +5,8 @@
 	"session_id": {
 		"Description": "ID assigned to participant's visit.",
 		"Levels": {
-			"01": "First phenotype assessment and imaging visit.",
-			"02": "Second imaging only visit."
+			"ses-01": "First phenotype assessment and imaging visit.",
+			"ses-02": "Second imaging only visit."
 		}
 	},
 	"age": {
diff --git a/pheno002/sessions.tsv b/pheno002/sessions.tsv
@@ -1,5 +1,5 @@
-participant_id	session_id	age	acq_time
-sub-01	01	22	1975-02-08 11:37:09
-sub-01	02	24	1977-04-01 09:00:57
-sub-02	01	63	1975-02-09 13:50:30
-sub-02	02	65	1977-03-29 10:25:04
+participant_id	session_id	acq_time
+sub-01	ses-01	1975-02-08 11:37:09
+sub-01	ses-02	1977-04-01 09:00:57
+sub-02	ses-01	1975-02-09 13:50:30
+sub-02	ses-02	1977-03-29 10:25:04
diff --git a/pheno003/README.md b/pheno003/README.md
@@ -10,8 +10,6 @@ pheno003
 |-- phenotype
 |   |-- ace.json
 |   `-- ace.tsv
-|-- sessions.json
-|-- sessions.tsv
 |-- sub-01
 |   `-- ses-baseline
 |       `-- anat
@@ -23,6 +21,6 @@ pheno003
             |-- sub-02_ses-baseline_T1w.json
             `-- sub-02_ses-baseline_T1w.nii.gz
 
-8 directories, 11 files
+8 directories, 9 files
 
 ```
diff --git a/pheno003/dataset_description.json b/pheno003/dataset_description.json
@@ -1,6 +1,6 @@
 {
 	"Name": "Phenotype guidelines example dataset 3",
-	"BIDSVersion": "1.10.0",
+	"BIDSVersion": "1.10.1",
 	"DatasetType": "raw",
 	"License": "CC0",
 	"Authors": [
diff --git a/pheno003/participants.json b/pheno003/participants.json
@@ -2,6 +2,13 @@
 	"participant_id": {
 		"Description": "Unique participant identifier."
 	},
+	"session_id": {
+		"Description": "ID assigned to participant's visit.",
+		"Levels": {
+			"ses-baseline": "First imaging and phenotype data collection visit.",
+			"ses-followup": "Second phenotype data collection visit."
+		}
+	},
 	"sex": {
 		"Description": "Sex assigned at birth.",
 		"Levels": {
diff --git a/pheno003/participants.tsv b/pheno003/participants.tsv
@@ -1,3 +1,4 @@
-participant_id	sex	age
-sub-01	m	22
-sub-02	f	63
+participant_id	session_id	sex	age
+sub-01	ses-baseline	m	22
+sub-01	ses-followup	m	24
+sub-02	ses-baseline	f	63
diff --git a/pheno003/phenotype/ace.json b/pheno003/phenotype/ace.json
@@ -5,8 +5,8 @@
   "session_id": {
     "Description": "ID assigned to participant's visit.",
     "Levels": {
-      "baseline": "First imaging and phenotype data collection visit.",
-      "followup": "Second phenotype data collection visit."
+      "ses-baseline": "First imaging and phenotype data collection visit.",
+      "ses-followup": "Second phenotype data collection visit."
     }
   },
   "b_ace_q1": {
diff --git a/pheno003/phenotype/ace.tsv b/pheno003/phenotype/ace.tsv
@@ -1,4 +1,4 @@
 participant_id	session_id	b_ace_q1	b_ace_q2	b_ace_q3	b_ace_q4	b_ace_q5	tesi_s_165	b_ace_q7	b_ace_q8	b_ace_q9	ceahd15
-sub-01	baseline	0	0	0	0	0	0	1	0	0	0
-sub-01	followup	1	0	0	1	0	1	0	0	0	0
-sub-02	baseline	0	0	0	0	0	0	0	0	0	0
+sub-01	ses-baseline	0	0	0	0	0	0	1	0	0	0
+sub-01	ses-followup	1	0	0	1	0	1	0	0	0	0
+sub-02	ses-baseline	0	0	0	0	0	0	0	0	0	0
diff --git a/pheno003/sessions.json b/pheno003/sessions.json
diff --git a/pheno003/sessions.tsv b/pheno003/sessions.tsv
diff --git a/pheno004/dataset_description.json b/pheno004/dataset_description.json
@@ -1,6 +1,6 @@
 {
 	"Name": "Mixed Phenotype+Participants",
-	"BIDSVersion": "1.11.0",
+	"BIDSVersion": "1.10.1",
 	"License": "CC0",
 	"Authors": [
 		"Eric Earl",
diff --git a/pheno005/dataset_description.json b/pheno005/dataset_description.json
@@ -1,6 +1,6 @@
 {
 	"Name": "BEP036 example dataset 05: Two multi-run sessions with one imaging-only session.",
-	"BIDSVersion": "1.10.0",
+	"BIDSVersion": "1.10.1",
 	"DatasetType": "raw",
 	"License": "CC0",
 	"Authors": [
diff --git a/pheno005/participants.json b/pheno005/participants.json
@@ -2,6 +2,13 @@
 	"participant_id": {
 		"Description": "Unique participant identifier."
 	},
+	"session_id": {
+		"Description": "ID assigned to participant's visit.",
+		"Levels": {
+			"ses-baseline": "First imaging and phenotype data collection visit.",
+			"ses-followup": "Second phenotype data collection visit."
+		}
+	},
 	"sex": {
 		"Description": "Sex assigned at birth.",
 		"Levels": {
diff --git a/pheno005/participants.tsv b/pheno005/participants.tsv
@@ -1,3 +1,4 @@
-participant_id	age	sex	race	ethnicity	education	marital_status
-sub-01	22	m	3	0	4	1
-sub-02	63	f	6	0	3	2
+participant_id	session_id	sex	age	race	ethnicity	education	marital_status
+sub-01	ses-baseline	m	22	3	0	4	1
+sub-01	ses-followup	m	24	3	0	4	1
+sub-02	ses-baseline	f	63	6	0	3	2
diff --git a/pheno005/sessions.json b/pheno005/sessions.json
@@ -9,17 +9,13 @@
 			"ses-followup": "Second phenotype data collection visit."
 		}
 	},
-	"run": {
+	"run_id": {
 		"Description": "Run index assigned to a given session.",
 		"Levels": {
 			"run-01": "First run of the session.",
 			"run-02": "Second run of the session."
 		}
 	},
-	"age": {
-		"Description": "Age of the participant at the time of the visit.",
-		"Units": "years"
-	},
 	"acq_time": {
 		"Description": "Date and time of data acquisition in YYYY-MM-DD HH:MM:SS format."
 	}
diff --git a/pheno005/sessions.tsv b/pheno005/sessions.tsv
@@ -1,6 +1,6 @@
-participant_id	session_id	run	age	acq_time
-sub-01	ses-baseline	run-01	22	2001-01-05 10:05:23
-sub-01	ses-baseline	run-02	22	2001-01-05 14:15:59
-sub-01	ses-followup	run-01	24	2003-02-06 09:45:00
-sub-02	ses-baseline	run-01	63	2001-01-13 12:04:08
-sub-02	ses-baseline	run-02	63	2001-01-13 16:20:17
+participant_id	session_id	run_id	acq_time
+sub-01	ses-baseline	run-01	2001-01-05 10:05:23
+sub-01	ses-baseline	run-02	2001-01-05 14:15:59
+sub-01	ses-followup	run-01	2003-02-06 09:45:00
+sub-02	ses-baseline	run-01	2001-01-13 12:04:08
+sub-02	ses-baseline	run-02	2001-01-13 16:20:17

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"Name": "Phenotype guidelines example dataset 2",`
`3`		`- "BIDSVersion": "1.10.0",`
	`3`	`+ "BIDSVersion": "1.10.1",`
`4`	`4`	`"DatasetType": "raw",`
`5`	`5`	`"License": "CC0",`
`6`	`6`	`"Authors": [`