From fb9553f8495a19d968e4aaaf5a4201acbe9564bb Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Sat, 22 Jun 2024 16:22:00 +0900
Subject: [PATCH] Script construction of the nipoppy-inpsired project dataset

---
 proj-nipoppy/.recreate_hierarchy | 65 ++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100755 proj-nipoppy/.recreate_hierarchy

diff --git a/proj-nipoppy/.recreate_hierarchy b/proj-nipoppy/.recreate_hierarchy
new file mode 100755
index 000000000..9395ba031
--- /dev/null
+++ b/proj-nipoppy/.recreate_hierarchy
@@ -0,0 +1,65 @@
+#!/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 project-type BIDS dataset",
+	"Description": "Demonstration for the https://github.com/bids-standard/bids-specification/pull/1861",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "project",
+    "Authors": [
+        "Yaroslav O. Halchenko", "Samuel Nastase"
+    ]
+}
+EOF
+
+cat >| CHANGES << EOF
+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 project/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)
+
+- [ ] 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 *