Merge e0e7533 into 7c84d90

Clinical-Genomics · Nov 16, 2020 · e6fa630 · e6fa630
2 parents 7c84d90 + e0e7533
commit e6fa630
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Showing 17 changed files with 264 additions and 134 deletions.
diff --git a/...erver/templates/batch/fetal_fraction.html → NIPTool/server/templates/batch/plots/FF.html b/...erver/templates/batch/fetal_fraction.html → NIPTool/server/templates/batch/plots/FF.html
@@ -1,26 +1,3 @@
-{% extends 'layout/layout.html' %}
-
-
-
-{% block body %}
-{% include 'layout/navigation.html' %}
-<div class="container-fluid">
-    {% include 'batch/header.html' %}
-    <div class="tab-content">
-        <div class="tab-pane active" id='NCV_XY'>
-            <div class="panel panel-default">
-                <div class="panel-body">
-                    <div id="FFY" style="min-width:400px; height:800px; ">
-                    </div>
-                    <div id="FFX" style="min-width:400px; height:800px; ">
-                    </div>
-                </div>
-            </div>
-        </div>
-    </div>
-</div>
-{% endblock %}
-
 {% block scripts %}
 <script>
     var XY_plot = document.getElementById('FFY')

diff --git a/...er/templates/batch/fetal_fraction_XY.html → ...l/server/templates/batch/plots/FF_XY.html b/...er/templates/batch/fetal_fraction_XY.html → ...l/server/templates/batch/plots/FF_XY.html
@@ -1,23 +1,3 @@
-{% extends 'layout/layout.html' %}
-
-
-
-{% block body %}
-{% include 'layout/navigation.html' %}
-<div class="container-fluid">
-    {% include 'batch/header.html' %}
-    <div class="tab-content">
-        <div class="tab-pane active" id='NCV_XY'>
-            <div class="panel panel-default">
-                <div class="panel-body">
-                    <div id="FFXY" style="min-width:400px; height:800px; ">
-                    </div>
-                </div>
-            </div>
-        </div>
-    </div>
-</div>
-{% endblock %}
 {% block scripts %}
 <script>
     var XY_plot = document.getElementById('FFXY')
@@ -89,7 +69,4 @@
 
     Plotly.newPlot('FFXY', data, layout);
 </script>
-{% endblock %}
-
-
-
+{% endblock %}
diff --git a/NIPTool/server/templates/batch/NCV.html → ...ool/server/templates/batch/plots/NCV.html b/NIPTool/server/templates/batch/NCV.html → ...ool/server/templates/batch/plots/NCV.html
@@ -1,20 +1,6 @@
-{% extends 'layout/layout.html' %}
-{% block body %}
-{% include 'layout/navigation.html' %}
-<div class="container-fluid">
-    {% include 'batch/header.html' %}
-    <div class="tab-pane active" id='NCV_{{chrom}}'>
-        <div class="panel panel-default">
-            <div class="panel-body">
-                <div id="NCV_plot" style="min-width:400px; height:800px; "></div><br><br>
-            </div>
-        </div>
-    </div>
-</div>
-{% endblock %}
-
 {% block scripts %}
 <script>
+    {% for chrom, cases  in ncv_chrom_data.items() %}
     $(function chrom_plot() {
     var data = []
     var layout = {
@@ -73,8 +59,9 @@
     {% endfor %}
 
 
-    Plotly.newPlot('NCV_plot', data, layout);
+    Plotly.newPlot('NCV{{chrom}}_plot', data, layout);
     });
+    {% endfor %}
 </script>
 
 

diff --git a/NIPTool/server/templates/batch/coverage.html → ...erver/templates/batch/plots/coverage.html b/NIPTool/server/templates/batch/coverage.html → ...erver/templates/batch/plots/coverage.html
@@ -1,19 +1,3 @@
-{% extends 'layout/layout.html' %}
-
-{% block body %}
-{% include 'layout/navigation.html' %}
-<div class="container-fluid">
-    {% include 'batch/header.html' %}
-    <div class="tab-pane active" id='norm_cov'>
-        <div class="panel panel-default">
-            <div class="panel-body">
-                <div id="cov_plot" style="min-width:400px; height:800px; "></div>
-            </div>
-        </div>
-    </div>
-</div>
-{% endblock %}
-
 {% block scripts %}
 <script>
         var XY_plot = document.getElementById('cov_plot')

diff --git a/NIPTool/server/templates/batch/report.html b/NIPTool/server/templates/batch/report.html
@@ -1,7 +1,88 @@
 {% extends 'layout/layout.html' %}
 
 
-
 {% block body %}
-{% include 'layout/navigation.html' %}
+<div class="container-fluid">
+    <div class="tab-pane active" id='NCV_{{chrom}}'>
+        <div class="panel panel-default">
+            <div class="panel-body">
+                <h2 class="page-header"><strong>NIPT Results </strong><br><small>Batch:
+                        {{batch._id}}</small><small>
+                        <p align="right" id="demo"></p>
+                    </small></h2>
+                <footer>
+                    <table id="batch_table" class="table table-bordered">
+                        <thead>
+                            <tr>
+                                <th>Sample Name</th>
+                                <th>NCV13</th>
+                                <th>NCV18</th>
+                                <th>NCV21</th>
+                                <th>NCVX</th>
+                                <th>FF(%)</th>
+                                <th>FFX(%)</th>
+                                <th>FFY(%)</th>
+                                <th>CNVSegment</th>
+                                <th>Warning</th>
+                                <th>Status</th>
+                                <th>Comment</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for sample in sample_info %}
+                            <input type=text name="samples" value="{{ sample.sample_id }}" hidden>
+                            <tr>
+                                <td width="20%">{{ sample.sample_id }}</td>
+                                <td width="4%" class="{{ sample.Zscore_13.warn}}">{{ sample.Zscore_13.value }}</td>
+                                <td width="4%" class="{{ sample.Zscore_18.warn}}">{{ sample.Zscore_18.value }}</td>
+                                <td width="4%" class="{{ sample.Zscore_21.warn}}">{{ sample.Zscore_21.value }}</td>
+                                <td width="4%" class="{{ sample.Zscore_X.warn}}">{{ sample.Zscore_X.value }}</td>
+                                <td width="4%" class="{{sample.FF.warn}}">{{sample.FF.value}}</td>
+                                <td width="4%" class="{{sample.FFX.warn}}">{{sample.FFX.value}}</td>
+                                <td width="4%" class="{{sample.FFY.warn}}">{{sample.FFY.value}}</td>
+                                <td width="4%" class="{{sample.CNVSegment.warn}}">{{sample.CNVSegment.value}}</td>
+                                <th>
+                                    <p> <small></small></p>
+                                </th>
+                                <th>
+                                    <p> <small>{{ sample.Status }}</small></p>
+                                </th>
+                                <td width="18%">{{sample.Comment}}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>
+                </footer>
+                <footer>
+                    <div id="cov_plot" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="NCV13_plot" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="NCV18_plot" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="NCV21_plot" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="FFXY" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="FFY" style="min-width:400px; height:800px; "></div>
+                </footer>
+                <footer>
+                    <div id="FFX" style="min-width:400px; height:800px; "></div>
+                </footer>
+            </div>
+        </div>
+    </div>
+</div>
 {% endblock %}
+{% block scripts %}
+{% include 'batch/plots/NCV.html' %}
+{% include 'batch/plots/FF_XY.html' %}
+{% include 'batch/plots/FF.html' %}
+{% include 'batch/plots/coverage.html' %}
+
+{% endblock %}
diff --git a/NIPTool/server/templates/batch/tabs/FF.html b/NIPTool/server/templates/batch/tabs/FF.html
@@ -0,0 +1,25 @@
+{% extends 'layout/layout.html' %}
+
+
+
+{% block body %}
+<div class="container-fluid">
+    {% include 'batch/header.html' %}
+    <div class="tab-content">
+        <div class="tab-pane active" id='NCV_XY'>
+            <div class="panel panel-default">
+                <div class="panel-body">
+                    <div id="FFY" style="min-width:400px; height:800px; ">
+                    </div>
+                    <div id="FFX" style="min-width:400px; height:800px; ">
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}
+
+{% block scripts %}
+{% include 'batch/plots/FF.html' %}
+{% endblock %}
diff --git a/NIPTool/server/templates/batch/tabs/FF_XY.html b/NIPTool/server/templates/batch/tabs/FF_XY.html
@@ -0,0 +1,22 @@
+{% extends 'layout/layout.html' %}
+{% block body %}
+<div class="container-fluid">
+    {% include 'batch/header.html' %}
+    <div class="tab-content">
+        <div class="tab-pane active" id='NCV_XY'>
+            <div class="panel panel-default">
+                <div class="panel-body">
+                    <div id="FFXY" style="min-width:400px; height:800px; ">
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}
+{% block scripts %}
+{% include 'batch/plots/FF_XY.html' %}
+{% endblock %}
+
+
+
diff --git a/NIPTool/server/templates/batch/tabs/NCV.html b/NIPTool/server/templates/batch/tabs/NCV.html
@@ -0,0 +1,17 @@
+{% extends 'layout/layout.html' %}
+{% block body %}
+<div class="container-fluid">
+    {% include 'batch/header.html' %}
+    <div class="tab-pane active" id='NCV_{{chr}}'>
+        <div class="panel panel-default">
+            <div class="panel-body">
+                <div id="NCV{{chr}}_plot" style="min-width:400px; height:800px; "></div><br><br>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}
+
+{% block scripts %}
+{% include 'batch/plots/NCV.html' %}
+{% endblock %}
diff --git a/NIPTool/server/templates/batch/tabs/coverage.html b/NIPTool/server/templates/batch/tabs/coverage.html
@@ -0,0 +1,18 @@
+{% extends 'layout/layout.html' %}
+
+{% block body %}
+<div class="container-fluid">
+    {% include 'batch/header.html' %}
+    <div class="tab-pane active" id='norm_cov'>
+        <div class="panel panel-default">
+            <div class="panel-body">
+                <div id="cov_plot" style="min-width:400px; height:800px; "></div>
+            </div>
+        </div>
+    </div>
+</div>
+{% endblock %}
+
+{% block scripts %}
+{% include 'batch/plots/coverage.html' %}
+{% endblock %}
diff --git a/NIPTool/server/templates/batch/batch.html → ...ol/server/templates/batch/tabs/table.html b/NIPTool/server/templates/batch/batch.html → ...ol/server/templates/batch/tabs/table.html
@@ -3,7 +3,7 @@
 
 
 {% block body %}
-{% include 'layout/navigation.html' %}
+
 <div class="container-fluid">
     {% include 'batch/header.html' %}
     <div class="tab-content">
@@ -28,7 +28,6 @@
                                 </tr>
                             </tbody>
                         </table>
-                        <div class="table-responsive">
 
                                 <table id="batch_table" class="table table-bordered table-hover table-wrapper-scroll-y" >
                                     <thead>

diff --git a/NIPTool/server/templates/batches.html b/NIPTool/server/templates/batches.html
@@ -1,6 +1,5 @@
 {% extends 'layout/layout.html' %}
 {% block body %}
-{% include 'layout/navigation.html' %}
 <div class="container-fluid">
     <div class="jumbotron vertical-center">
         <div class="row">

diff --git a/NIPTool/server/templates/layout/layout.html b/NIPTool/server/templates/layout/layout.html
@@ -50,7 +50,9 @@
 
 <body>
 <div id="wrapper">
-  {% block body %}{% endblock %}
+  {% include 'layout/navigation.html' %}
+  {% block body %}
+  {% endblock %}
 </div>  <!--wrapper-->
 
 

diff --git a/NIPTool/server/templates/sample/sample.html b/NIPTool/server/templates/sample/sample.html
@@ -1,6 +1,5 @@
 {% extends 'layout/layout.html' %}
 {% block body %}
-{% include 'layout/navigation.html' %}
 <div class="container-fluid">
     {% include 'sample/header.html' %}
     <ul class="nav nav-tabs" id="myTab">

diff --git a/NIPTool/server/templates/sample/sample_tris.html b/NIPTool/server/templates/sample/sample_tris.html
@@ -1,7 +1,6 @@
 {% extends 'layout/layout.html' %}
 
 {% block body %}
-{% include 'layout/navigation.html' %}
 <div class="container-fluid">
     {% include 'sample/header.html' %}
     <ul class="nav nav-tabs" id="myTab">

diff --git a/NIPTool/server/templates/statistics.html b/NIPTool/server/templates/statistics.html
@@ -1,6 +1,5 @@
 {% extends 'layout/layout.html' %}
 {% block body %}
-{% include 'layout/navigation.html' %}
 <div class="container-fluid">
     <div class="jumbotron vertical-center">
         <div class="row">

diff --git a/NIPTool/server/utils.py b/NIPTool/server/utils.py
@@ -350,6 +350,8 @@ def get_last_batches(adapter, nr: int) -> list:
     return(sorted_batches)
 
 
+# Statistics
+
 def get_statistics_for_scatter_plot(batches: list, fields: list)-> dict:
     """Formating data for scatter plot"""