From 0bb33cd4e8a73db4d570687aa41f817504050dc4 Mon Sep 17 00:00:00 2001
From: "omar.elrifai" <omar.void@gmail.com>
Date: Tue, 9 Nov 2021 14:37:46 +0100
Subject: [PATCH] Add Clinica example

---
 examples/clinica_pipelines/readme.md          | 21 +++++++++
 .../clinica_pipelines/t1linear_mat.jsonld     | 44 +++++++++++++++++++
 .../clinica_pipelines/t1linear_nii.jsonld     | 44 +++++++++++++++++++
 3 files changed, 109 insertions(+)
 create mode 100644 examples/clinica_pipelines/readme.md
 create mode 100644 examples/clinica_pipelines/t1linear_mat.jsonld
 create mode 100644 examples/clinica_pipelines/t1linear_nii.jsonld

diff --git a/examples/clinica_pipelines/readme.md b/examples/clinica_pipelines/readme.md
new file mode 100644
index 000000000..1daf26b2a
--- /dev/null
+++ b/examples/clinica_pipelines/readme.md
@@ -0,0 +1,21 @@
+## 2-step workflow using Clinica (https://github.com/aramis-lab/clinica)
+
+---
+
+### Workflow
+
+<center>
+<img src="clinica_pipelines.png" width="90%" position="center">
+</center>
+
+---
+
+### Generate a graph
+
+from the root of this project
+
+```bash
+python bids_prov/visualize.py examples/clinica_pipelines/adni-to-bids.json examples/clinica_pipelines/t1linear-mat.json examples/clinica_pipelines/t1linear-nii.json -o clinica_pipelines.png
+```
+
+generates the graph illustrating the provenance of files related to two Clinica pipelines (adni-to-bids and t1-linear) 
diff --git a/examples/clinica_pipelines/t1linear_mat.jsonld b/examples/clinica_pipelines/t1linear_mat.jsonld
new file mode 100644
index 000000000..5b1930bc2
--- /dev/null
+++ b/examples/clinica_pipelines/t1linear_mat.jsonld
@@ -0,0 +1,44 @@
+{
+    "@context": "https://raw.githubusercontent.com/omar-rifai/Provenance/main/context.json",
+    "records":{
+	"prov:Agent" : [{
+	    "@id": "RRID:Clinica",
+	    "@type": "prov:SoftwareAgent",
+	    "label": "Clinica"
+	}],
+	"prov:Activity": [
+	    {
+		"@id": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13",
+		"label": "t1-linear",
+		"command": [
+                    [
+			"run",
+			"t1-linear",
+			"/path/to/bids",
+			"ws/CAPS_t1linear",
+			"-np",
+			"4",
+			"-tsv",
+			"subjects.tsv",
+			"-ui"
+                    ]
+		],
+		"parameters": {
+                    "uncropped_image": true
+		},
+		"wasAssociatedWith": "RRID:Clinica",
+		"used": [
+		    "uuid:6cada670-8bf2-44ef-80ae-71796eb5ecd7"
+		]
+            }
+	],
+	"prov:Entity": [
+	    {
+		"@id": "uuid:696a079c-3618-4e0d-87aa-b60965c86127",
+		"label": "sub-ADN..-MNI152NLin2009cSym_res-1x1x1_affine.mat",
+		"wasGeneratedBy": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13"
+	    }
+
+	]
+    }
+}
diff --git a/examples/clinica_pipelines/t1linear_nii.jsonld b/examples/clinica_pipelines/t1linear_nii.jsonld
new file mode 100644
index 000000000..6c06ed0ee
--- /dev/null
+++ b/examples/clinica_pipelines/t1linear_nii.jsonld
@@ -0,0 +1,44 @@
+{
+    "@context": "https://raw.githubusercontent.com/omar-rifai/Provenance/main/context.json",
+    "records":{
+	"prov:Agent" : [{
+	    "@id": "RRID:Clinica",
+	    "@type": "prov:SoftwareAgent",
+	    "label": "Clinica"
+	}],
+	"prov:Activity": [
+	    {
+		"@id": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13",
+		"label": "t1-linear",
+		"command": [
+                    [
+			"run",
+			"t1-linear",
+			"/path/to/bids",
+			"ws/CAPS_t1linear",
+			"-np",
+			"4",
+			"-tsv",
+			"subjects.tsv",
+			"-ui"
+                    ]
+		],
+		"parameters": {
+                    "uncropped_image": true
+		},
+		"wasAssociatedWith": "RRID:Clinica",
+		"used": [
+		    "uuid:6cada670-8bf2-44ef-80ae-71796eb5ecd7"
+		]
+            }
+	],
+	"prov:Entity": [
+	    {
+		"@id": "uuid:5ebd15a4-0051-46e1-ada0-d718f39b2e2c",
+		"label": "sub-ADN..-MNI152NLin2009cSym_res-1x1x1_affine.nii",
+		"wasGeneratedBy": "uuid:2c2964f2-f865-41cc-a4e9-5d4f4ecaec13"
+	    }
+
+	]
+    }
+}