From ddb014b4134c33302527b4b95a17ce34fbd80a21 Mon Sep 17 00:00:00 2001
From: Steven Weaver <sweaver@temple.edu>
Date: Wed, 13 Nov 2024 16:19:35 -0500
Subject: [PATCH] adding error sink option

---
 app/models/busted.js                |  4 ++++
 app/routes/busted.js                |  4 +++-
 app/templates/busted/upload_msa.ejs | 10 +++++++++-
 public/assets/js/busted/form.js     |  1 +
 4 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/app/models/busted.js b/app/models/busted.js
index 74001743..746d605d 100644
--- a/app/models/busted.js
+++ b/app/models/busted.js
@@ -13,6 +13,7 @@ var Busted = AnalysisSchema.extend({
   multihit: String,
   results: Object,
   ds_variation: Number,
+  error_protection: String,
 });
 
 Busted.virtual("analysistype").get(function () {
@@ -62,6 +63,7 @@ Busted.statics.spawn = function (fn, options, callback) {
     datatype = 0,
     gencodeid = options.gencodeid,
     ds_variation = options.ds_variation,
+    error_protection = options.error_protection,
     multihit = options.multihit;
 
   busted.tagged_nwk_tree = options.nwk_tree;
@@ -93,6 +95,8 @@ Busted.statics.spawn = function (fn, options, callback) {
 
     busted.msa = msa;
     busted.ds_variation = ds_variation;
+    busted.error_protection = error_protection;
+
     busted.multihit = multihit;
 
     busted.save((err, busted_result) => {
diff --git a/app/routes/busted.js b/app/routes/busted.js
index b1337c9d..b37e6343 100644
--- a/app/routes/busted.js
+++ b/app/routes/busted.js
@@ -24,7 +24,8 @@ exports.uploadFile = function (req, res) {
     postdata = req.body,
     datatype = 0,
     gencodeid = data.gencodeid,
-    ds_variation = postdata.ds_variation;
+    ds_variation = postdata.ds_variation,
+    error_protection = postdata.error_protection;
   multihit = postdata.multihit;
 
   busted.mail = postdata.mail;
@@ -54,6 +55,7 @@ exports.uploadFile = function (req, res) {
 
     busted.msa = msa;
     busted.ds_variation = ds_variation;
+    busted.error_protection = error_protection;
     busted.multihit = multihit;
 
     busted.save(function (err, busted_result) {
diff --git a/app/templates/busted/upload_msa.ejs b/app/templates/busted/upload_msa.ejs
index 3a1d68cf..308e7f6b 100644
--- a/app/templates/busted/upload_msa.ejs
+++ b/app/templates/busted/upload_msa.ejs
@@ -75,7 +75,7 @@
       </div>
 
       <div class="ds-variation-div pt-2 pb-2">
-        <label>Synonymous rate variation (recommended)?</label>
+        <label>BUSTED-S : Synonymous rate variation (recommended)?</label>
         <select id="ds-variation">
           <option value="1">
             Yes
@@ -86,6 +86,14 @@
         </select>
       </div>
 
+      <div class="error-protection-div pt-2 pb-2">
+        <label>BUSTED-E : Error-protection component?</label>
+        <select id="error-protection" name="error_protection">
+          <option value="No" selected>No</option>
+          <option value="Yes">Yes</option>
+        </select>
+      </div>
+
       <div class="multihit-div pt-3 pb-3 pl-2 bg-light rounded">
         <label><span class="badge rounded-pill text-bg-info">Advanced</span> Include support for multiple nucleotide substitutions? </label>
         <select id="multihit">
diff --git a/public/assets/js/busted/form.js b/public/assets/js/busted/form.js
index 2ba1e309..a8f42fff 100644
--- a/public/assets/js/busted/form.js
+++ b/public/assets/js/busted/form.js
@@ -12,6 +12,7 @@ $(function () {
     formData.append("datatype", $("select[name='datatype']").val());
     formData.append("gencodeid", $("select[name='gencodeid']").val());
     formData.append("ds_variation", $("#ds-variation").val());
+    formData.append("error_protection", $("#error-protection").val());
     formData.append("mail", $("input[name='mail']").val());
     formData.append("multihit", $("#multihit").val());