From 2621d9e835a1d59a4bceb3234ed00d123b813afc Mon Sep 17 00:00:00 2001
From: James Scherer <jscherer@uab.edu>
Date: Wed, 18 Oct 2023 15:49:04 -0500
Subject: [PATCH] First push of the animal model systems script to insert
 sections into the analysis for the intercenter meeting

---
 .../migrate-insert-animal-model-systems.js    | 133 ++++++++++++++++++
 1 file changed, 133 insertions(+)
 create mode 100644 etc/fixtures/migrations/migrate-insert-animal-model-systems.js

diff --git a/etc/fixtures/migrations/migrate-insert-animal-model-systems.js b/etc/fixtures/migrations/migrate-insert-animal-model-systems.js
new file mode 100644
index 00000000..9cb2b6df
--- /dev/null
+++ b/etc/fixtures/migrations/migrate-insert-animal-model-systems.js
@@ -0,0 +1,133 @@
+const usage = `
+mongosh --eval 'var cpamAnalysis="";var modelSystem=""' /tmp/fixtures/migrations/migrate-insert-animal-model-systems.js
+
+    Script Options:
+        help : Bool : Optional
+            - If True print this help message
+        cpamAnalysis : String : Required
+        modelSystem : String : Required
+            - Mus musculus (Mouse) Model System
+            - Danio rerio (Zebrafish) Model System
+            - Rattus norvegicus (Rat) Model System
+            - Xenopus laevis (Frog) Model System
+            - C. elegans (Roundworm) Model System
+    
+    Run mongosh help for mongosh connection and authentication usage.
+
+    Example:
+
+    mongosh --host localhost --port 27017 --eval 'var help=True;' /tmp/fixtures/migrations/migrate-insert-animal-model-systems.js
+
+    docker exec -it <rosalution_db_container> mongosh --eval 'var cpamAnalysis="CPAM0002";var modelSystem="Mus musculus (Mouse) Model System"' /tmp/fixtures/migrations/migrate-insert-animal-model-systems.js
+`
+
+if (help === true) {
+    print(usage);
+    quit(1);
+}
+
+if (typeof databaseName === 'undefined') {
+    databaseName = 'rosalution_db';
+} else if (typeof databaseName !== 'string') {
+    print('databaseName must be a string');
+    print(usage);
+    quit(1);
+}
+
+if(typeof cpamAnalysis === 'undefined' || typeof cpamAnalysis !== 'string' || cpamAnalysis == '') {
+    print('cpamAnalysis needs to be defined and must be a string');
+    print(usage);
+    quit(1);
+}
+
+if(typeof modelSystem === 'undefined' || typeof modelSystem !== 'string' || modelSystem == '') {
+    print('modelSystem needs to be defined and must be a string');
+    print(usage);
+    quit(1);
+}
+
+print(`Adding ${modelSystem} to ${cpamAnalysis}...`)
+
+db = db.getSiblingDB(databaseName)
+
+const animalModelSystemSection = {
+    "header": modelSystem,
+    "content": [
+        {
+            "type": "section-text",
+            "field": "Mutation",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Pathogenicity Test",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Design",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Founder Screening/Expansion",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Screening",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "History",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Diagnoses",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Remarks",
+            "value": []
+        },
+        {
+            "type": "supporting-evidence",
+            "field": "Vetrinary Pathology Imaging",
+            "value": {}
+        },          
+        {
+            "type": "supporting-evidence",
+            "field": "Vetrinary Pathology Report",
+            "value": {}
+        }
+    ]
+}
+
+try {
+    var analysis = db.analyses.findOne({name: cpamAnalysis})
+    print(`Found ${cpamAnalysis} in mongodb...`)
+    var index = 0;
+
+    for(section in analysis.sections) {
+        if(analysis.sections[section].header == 'Pedigree') {
+            index = section
+            break;
+        }
+    }
+
+    print(`Inserting '${modelSystem}' section into the analysis...`)
+    analysis.sections.splice(index, 0, animalModelSystemSection)
+
+    print(`Writing to mongodb...`)
+    db.analyses.updateOne({'_id': analysis._id}, {'$set': analysis})
+
+    print(`Success! Done.`)
+} catch(e) {
+    console.log(e.stack);
+    console.log(usage);
+    quit(1);
+}
+