From 0531fba123dcbcf72cab162ce792a9f8048a5ab4 Mon Sep 17 00:00:00 2001
From: James Scherer <jscherer@uab.edu>
Date: Thu, 19 Sep 2024 09:07:48 -0500
Subject: [PATCH] Draft script to run on every Cilipathies case to update
 landing page with new sections and fields (#181)

* cpam to ciliopathies migration script

* Updated the name of the script to migrate-cpam-to-ciliopathies-landing-page.js in the documentation

* Adding a ciliopathy analysis json for reference for how a different analysis can be used in Rosalution
---
 .../import/CILI_2_5K_ARMC9_L510V.json         |  19 +++
 ...grate-cpam-to-ciliopathies-landing-page.js | 129 ++++++++++++++++++
 2 files changed, 148 insertions(+)
 create mode 100644 etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json
 create mode 100644 etc/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js

diff --git a/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json b/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json
new file mode 100644
index 00000000..089c3ad8
--- /dev/null
+++ b/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json
@@ -0,0 +1,19 @@
+{
+  "date": "2022-07-16T16:07:38.000Z",
+  "external_id": "CILI_2_5K ARMC9_L510V",
+  "variants": [
+      {
+          "transcript": "NM_025139.6",
+          "gene": "ENSG00000135931",
+          "reference_genome": "GRCh37",
+          "protein": "p.Leu510Val",
+          "cdna": "c.1528C>G"
+      }
+  ],
+  "genes": [
+      {
+          "gene": "ARMC9",
+          "id": "ENSG00000135931"
+      }
+  ]
+}
\ No newline at end of file
diff --git a/etc/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js b/etc/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js
new file mode 100644
index 00000000..2d7b1847
--- /dev/null
+++ b/etc/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js
@@ -0,0 +1,129 @@
+const usage = `
+mongosh --eval 'var ciliAnalysis=""' /tmp/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js
+
+Script Options:
+    help : Bool : Optional
+        - If True print this help message
+    ciliAnalysis : String : Required
+
+Run mongosh help for mongosh connection and authentication usage.
+
+Example:
+
+    mongosh --host localhost --port 27017 --eval 'var help=True;' /tmp/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.js
+
+    docker exec -it <rosalution_db_container> mongosh --eval 'var ciliAnalysis="CILI_2_5K ARMC9_L510V"' /tmp/fixtures/migrations/migrate-cpam-to-ciliopathies-landing-page.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 ciliAnalysis === 'undefined' || typeof ciliAnalysis !== 'string' || ciliAnalysis == '') {
+    print('ciliAnalysis needs to be defined and must be a string');
+    print(usage);
+    quit(1);
+}
+
+print(`Converting ${ciliAnalysis}'s Analysis View from CPAM to Ciliopathies...`)
+
+// New Ciliopathy specific fields
+
+const databaseTextField = {
+    "type":"section-text",
+    "field":"Database",
+    "value":[]
+}
+
+const patientRelatedVariantEvidenceField = {
+    "type": "section-supporting-evidence",
+    "field": "Patient Related Variants",
+    "value": []
+}
+
+const resourcesSection = {
+    "header": "Resources",
+    "content": [
+        {
+            "type": "section-text",
+            "field": "Purchased Antibody Catalog #",
+            "value": []
+        },
+        {
+            "type": "section-text",
+            "field": "Physical Resources",
+            "value": []
+        }
+    ]
+}
+
+const reportingSection = {
+    "header": "Reporting",
+    "content": [
+        {
+            "type": "section-supporting-evidence",
+            "field": "Benchling",
+            "value": []
+        }
+    ]
+}
+
+// Getting the database driver for mongo
+db = db.getSiblingDB(databaseName)
+
+// Getting the analysis and inserting the new sections
+// Note: This will insert the fields twice if run twice
+try {
+    var analysis = db.analyses.findOne({name: ciliAnalysis})
+    print(`Found ${ciliAnalysis} in mongodb...`)
+
+    var index = 0;
+
+    console.log(analysis.sections)
+
+    for(section in analysis.sections) {        
+        if(analysis.sections[section].header == 'Brief') {
+            print(`Inserting the Database text field into the Brief section...`)
+            analysis.sections[section]['content'].splice(1, 0, databaseTextField);
+
+            print(`Inserting the Patient Related Variants Evidence field into the Brief section...`)
+            analysis.sections[section]['content'].push(patientRelatedVariantEvidenceField)
+        }
+    }
+
+    for(section in analysis.sections) {
+        if(analysis.sections[section].header == 'Pedigree') {
+            console.log(`Section #: ${section}, Header: ${analysis.sections[section].header}`)
+            print(`Inserting the Resources section into the analysis...`)
+            analysis.sections.splice(section, 0, resourcesSection)
+            break;
+        }
+    }
+
+    for(section in analysis.sections) {
+        if(analysis.sections[section].header == 'Model Goals') {
+            console.log(`Section #: ${section}, Header: ${analysis.sections[section].header}`)
+            print(`Inserting the Reporting section into the analysis...`)
+            analysis.sections.splice(section + 1, 0, reportingSection)
+            break;
+        }
+    }
+
+    print(`Writing to mongodb...`)
+    db.analyses.updateOne({'_id': analysis._id}, {'$set': analysis})
+
+    print(`Success! Done.`)
+} catch(e) {
+    console.log(e.stack);
+    console.log(usage);
+    quit(1);
+}