Add examples with DatasetType = "project"

proj-nipoppy/.recreate_hierarchy

@@ -0,0 +1,83 @@
+#!/bin/bash
+
+set -eu
+
+git rm --ignore-unmatch -fr [a-zA-Z]*
+mkdir -p {code,derivatives{,/fmriprep-{20.2.7,23.1.3},/mriqc-23.1.0,/neurobagel-0.0.1},sourcedata{,/tabular{,/demographics,/assesments},/raw/sub-001/ses-A,/dicoms}}
+
+cat >| dataset_description.json <<EOF
+{
+    "Name": "Example how nipoppy dataset could be presented as 'study'-type BIDS dataset",
+    "Description": "Demonstration for the https://github.com/bids-standard/bids-specification/pull/1972",
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "study",
+    "Authors": [
+        "Yaroslav O. Halchenko", "Samuel Nastase"
+    ],
+    "GeneratedBy": [
+       {
+         "Name": "Script to produce this dataset",
+         "CodeURL": "file://./recreate-hierarchy"
+       }
+    ],
+    "License": "PDDL"
+}
+EOF
+
+cat >| CHANGES << EOF
+0.0.3 2024-10-28
+
+  -  Changed to use "study" instead of "project".
+  -  Refer to https://github.com/bids-standard/bids-specification/pull/1972 .
+
+0.0.2 2024-10-28
+
+  -  Updated to reflect addressed in bids-validator issues and
+     to merge "master" branch of the bids-examples project.
+     Added GeneratedBy and License.
+
+0.0.1 2024-06-20
+
+  -  Started to work on this support of the DatasetType project
+
+EOF
+
+cat >| README.md << EOF
+This is an example of an entire study level BIDS dataset.
+Built taking a hierarchy depicted on
+https://github.com/neurodatascience/nipoppy?tab=readme-ov-file#nipoppy
+and turning it into a valid BIDS layout.
+
+Some files (e.g. bagel.csv) are specific to nipoppy etc projects, but since
+located under folders where bids layout is not enforced -- should be just fine. 
+
+Some outstanding issues with validator(s) which were ran into while trying to
+get "proper" validation working using deno bids-validator (mark when solved)
+
+- [x] https://github.com/bids-standard/bids-validator/issues/2007
+
+EOF
+
+cat >| derivatives/bagel.csv << EOF
+bids_id,participant_id,session,has_mri_data,pipeline_name,pipeline_version,pipeline_starttime,pipeline_complete
+sub-MNI001,MNI001,1,TRUE,freesurfer,6.0.1,2022-05-24 13:43,SUCCESS
+sub-MNI001,MNI001,2,TRUE,freesurfer,6.0.1,2022-05-24 13:46,SUCCESS
+sub-MNI001,MNI001,3,TRUE,freesurfer,6.0.1,UNAVAILABLE,INCOMPLETE
+EOF
+
+cat >| sourcedata/tabular/bagel.csv << EOF
+bids_id,participant_id,session,assessment_name,assessment_score
+sub-MNI001,MNI001,1,group,Patient
+sub-MNI001,MNI001,2,group,Patient
+EOF
+
+touch sourcedata/tabular/manifest.csv
+echo '{}' > code/global_config.json
+
+# populate empty folders with some placeholder .dotfile
+find * -type d  | while read d; do
+    if ! /bin/ls -a "$d" | grep -q '[a-z]'; then
+        touch $d/.fill
+    fi
+done
+git add *

proj-nipoppy/CHANGES

@@ -0,0 +1,15 @@
+0.0.3 2024-10-28
+
+  -  Changed to use "study" instead of "project".
+  -  Refer to https://github.com/bids-standard/bids-specification/pull/1972 .
+
+0.0.2 2024-10-28
+
+  -  Updated to reflect addressed in bids-validator issues and
+     to merge "master" branch of the bids-examples project.
+     Added GeneratedBy and License.
+
+0.0.1 2024-06-20
+
+  -  Started to work on this support of the DatasetType project
+

proj-nipoppy/README.md

@@ -0,0 +1,13 @@
+This is an example of an entire study level BIDS dataset.
+Built taking a hierarchy depicted on
+https://github.com/neurodatascience/nipoppy?tab=readme-ov-file#nipoppy
+and turning it into a valid BIDS layout.
+
+Some files (e.g. bagel.csv) are specific to nipoppy etc projects, but since
+located under folders where bids layout is not enforced -- should be just fine. 
+
+Some outstanding issues with validator(s) which were ran into while trying to
+get "proper" validation working using deno bids-validator (mark when solved)
+
+- [x] https://github.com/bids-standard/bids-validator/issues/2007
+

proj-nipoppy/code/global_config.json

@@ -0,0 +1 @@
+{}

proj-nipoppy/dataset_description.json

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+{
+    "Name": "Example how nipoppy dataset could be presented as 'study'-type BIDS dataset",
+    "Description": "Demonstration for the https://github.com/bids-standard/bids-specification/pull/1972",
+    "BIDSVersion": "1.11.0",
+    "DatasetType": "study",
+    "Authors": [
+        "Yaroslav O. Halchenko", "Samuel Nastase"
+    ],
+    "GeneratedBy": [
+       {
+         "Name": "Script to produce this dataset",
+         "CodeURL": "file://./recreate-hierarchy"
+       }
+    ],
+    "License": "PDDL"
+}

proj-nipoppy/derivatives/bagel.csv

@@ -0,0 +1,4 @@
+bids_id,participant_id,session,has_mri_data,pipeline_name,pipeline_version,pipeline_starttime,pipeline_complete
+sub-MNI001,MNI001,1,TRUE,freesurfer,6.0.1,2022-05-24 13:43,SUCCESS
+sub-MNI001,MNI001,2,TRUE,freesurfer,6.0.1,2022-05-24 13:46,SUCCESS
+sub-MNI001,MNI001,3,TRUE,freesurfer,6.0.1,UNAVAILABLE,INCOMPLETE

proj-nipoppy/sourcedata/tabular/bagel.csv

@@ -0,0 +1,3 @@
+bids_id,participant_id,session,assessment_name,assessment_score
+sub-MNI001,MNI001,1,group,Patient
+sub-MNI001,MNI001,2,group,Patient