Allow PCR eff update of target

RDML-consortium · May 11, 2022 · 65d342a · 65d342a
1 parent 5ea4d22
commit 65d342a
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Showing 6 changed files with 37 additions and 13 deletions.
diff --git a/client/.babelrc b/client/.babelrc
@@ -1,6 +1,7 @@
 {
   "plugins": [
-    ["@babel/plugin-transform-runtime",
+    [
+      "@babel/plugin-transform-runtime",
       {
         "regenerator": true
       }

diff --git a/client/.gitignore b/client/.gitignore
@@ -2,4 +2,5 @@
 /.cache/
 /.parcel-cache/
 /dist/
+/dist_*
 /.env.production
diff --git a/client/src/linregpcr.html b/client/src/linregpcr.html
@@ -157,21 +157,15 @@ <h5 class="card-title">Load RDML file</h5>
               </select>
             </td>
             <td style="width:3%;background-color: #e6e6e6;"></td>
-            <td style="width:4%;"></td>
-            <td style="width:14%;">Include Annotations:</td>
-            <td style="width:6%;">
-              <select class="form-control" id="choiceIncludeAnnotations">
+            <td style="width:4%;background-color: #e6e6e6;"></td>
+            <td style="width:18%;background-color: #e6e6e6;">Update Target PCR Efficiency:</td>
+            <td style="width:20%;background-color: #e6e6e6;">
+              <select class="form-control" id="choiceUpdateTarget">
                 <option value="y">yes</option>
                 <option value="n" selected>no</option>
               </select>
             </td>
-            <td style="width:18%;text-align: right;">
-              <button type="submit" class="btn btn-outline-primary" id="btn-rdml-linregpcr">
-                <i class="far fa-save" style="margin-right: 5px;"></i>
-                Save RDML
-              </button>
-            </td>
-            <td style="width:1%;"></td>
+            <td style="width:1%;background-color: #e6e6e6;"></td>
           </tr>
         </table>
         <table style="width:100%;">
@@ -194,6 +188,24 @@ <h5 class="card-title">Load RDML file</h5>
               </select>
             </td>
             <td style="width:5%;"></td>
+            <td style="width:14%;">Include Annotations:</td>
+            <td style="width:6%;">
+              <select class="form-control" id="choiceIncludeAnnotations">
+                <option value="y">yes</option>
+                <option value="n" selected>no</option>
+              </select>
+            </td>
+            <td style="width:18%;text-align: right;">
+              <button type="submit" class="btn btn-outline-primary" id="btn-rdml-linregpcr">
+                <i class="far fa-save" style="margin-right: 5px;"></i>
+                Save RDML
+              </button>
+            </td>
+            <td style="width:1%;"></td>
+          </tr>
+        </table>
+        <table style="width:100%;">
+            <td style="width:61%;"></td>
             <td style="width:38%;text-align: right;">
               <button type="submit" class="btn btn-outline-primary" id="btn-copy-linregpcr">
                 <i class="fas fa-paste" style="margin-right: 5px;"></i>

diff --git a/client/src/static/js/rdml_linregpcr.js b/client/src/static/js/rdml_linregpcr.js
@@ -125,6 +125,7 @@ window.maxLogRange = 10000;
 window.exNoPlateau = true;
 window.exUnstBase  = true;
 window.exDiffMean = "outlier";
+window.updateTargets = false;
 window.decimalSepPoint = true;
 
 window.sampSelFirst = "7s8e45-Show-All"  // To avoid conflicts with existing values
@@ -469,6 +470,7 @@ function runLinRegPCR() {
     window.exNoPlateau = true
     window.exUnstBase = true
     window.exDiffMean = "outlier"
+    window.updateTargets = false
     hideElement(resultError)
 
     window.sampSelFirst = "7s8e45-Show-All"  // To avoid conflicts with existing values
@@ -496,6 +498,10 @@ function runLinRegPCR() {
     if ((bbExcludeUnstBase) && (bbExcludeUnstBase.value == "n")) {
         window.exUnstBase = false
     }
+    var bbUpdateTarget = document.getElementById('choiceUpdateTarget')
+    if (bbUpdateTarget) {
+        window.updateTargets = bbUpdateTarget.value
+    }
 
     window.yScale = "log"
     window.curveSource = "bas"
@@ -505,6 +511,7 @@ function runLinRegPCR() {
     ret["sel-experiment"] = window.selExperiment
     ret["sel-run"] = window.selRun
     ret["pcr-eff-range"] = rPCREffRange
+    ret["update-target-efficiency"] = window.updateTargets
     ret["update-RDML-data"] = rUpdateRDML
     ret["exclude-no-plateau"] = window.exNoPlateau
     ret["exclude-efficiency"] = window.exDiffMean

diff --git a/server/rdmlpython b/server/rdmlpython
diff --git a/server/server.py b/server/server.py
@@ -2162,6 +2162,8 @@ def handle_data():
                 return jsonify(errors=[{"title": "Invalid server request - sel-run id missing!"}]), 400
             if "pcr-eff-range" not in reqdata:
                 return jsonify(errors=[{"title": "Invalid server request - pcr-eff-range missing!"}]), 400
+            if "update-target-efficiency" not in reqdata:
+                return jsonify(errors=[{"title": "Invalid server request - update-target-efficiency missing!"}]), 400
             if "update-RDML-data" not in reqdata:
                 return jsonify(errors=[{"title": "Invalid server request - update-RDML-data missing!"}]), 400
             if "exclude-no-plateau" not in reqdata:
@@ -2179,6 +2181,7 @@ def handle_data():
                 if s_run is None:
                     return jsonify(errors=[{"title": "Invalid server request - run id not found!"}]), 400
                 data["reactsdata"] = s_run.webAppLinRegPCR(pcrEfficiencyExl=reqdata["pcr-eff-range"],
+                                                           updateTargetEfficiency=reqdata["update-target-efficiency"],
                                                            updateRDML=reqdata["update-RDML-data"],
                                                            excludeNoPlateau=reqdata["exclude-no-plateau"],
                                                            excludeEfficiency=reqdata["exclude-efficiency"],