From 4c364826767c6ac0b80de9e6c6978fed5c1621e7 Mon Sep 17 00:00:00 2001
From: mayabrandi <maya.brandi@scilifelab.se>
Date: Wed, 11 Nov 2020 15:55:39 +0100
Subject: [PATCH 1/3] building report view

---
 .../{fetal_fraction.html => plots/FF.html}    |  23 ---
 .../FF_XY.html}                               |  25 +---
 .../templates/batch/{ => plots}/NCV.html      |  19 +--
 .../templates/batch/{ => plots}/coverage.html |  16 ---
 NIPTool/server/templates/batch/report.html    |  85 ++++++++++-
 NIPTool/server/templates/batch/tabs/FF.html   |  25 ++++
 .../server/templates/batch/tabs/FF_XY.html    |  22 +++
 NIPTool/server/templates/batch/tabs/NCV.html  |  17 +++
 .../server/templates/batch/tabs/coverage.html |  18 +++
 .../batch/{batch.html => tabs/table.html}     |   3 +-
 NIPTool/server/templates/batches.html         |   1 -
 NIPTool/server/templates/layout/layout.html   |   4 +-
 NIPTool/server/templates/sample/sample.html   |   1 -
 .../server/templates/sample/sample_tris.html  |   1 -
 NIPTool/server/templates/statistics.html      |   1 -
 NIPTool/server/utils.py                       |   2 +
 NIPTool/server/views.py                       | 135 ++++++++++++------
 17 files changed, 264 insertions(+), 134 deletions(-)
 rename NIPTool/server/templates/batch/{fetal_fraction.html => plots/FF.html} (79%)
 rename NIPTool/server/templates/batch/{fetal_fraction_XY.html => plots/FF_XY.html} (81%)
 rename NIPTool/server/templates/batch/{ => plots}/NCV.html (81%)
 rename NIPTool/server/templates/batch/{ => plots}/coverage.html (76%)
 create mode 100644 NIPTool/server/templates/batch/tabs/FF.html
 create mode 100644 NIPTool/server/templates/batch/tabs/FF_XY.html
 create mode 100644 NIPTool/server/templates/batch/tabs/NCV.html
 create mode 100644 NIPTool/server/templates/batch/tabs/coverage.html
 rename NIPTool/server/templates/batch/{batch.html => tabs/table.html} (98%)

diff --git a/NIPTool/server/templates/batch/fetal_fraction.html b/NIPTool/server/templates/batch/plots/FF.html
similarity index 79%
rename from NIPTool/server/templates/batch/fetal_fraction.html
rename to NIPTool/server/templates/batch/plots/FF.html
index c586e921..96525a9c 100644
--- a/NIPTool/server/templates/batch/fetal_fraction.html
+++ b/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/NIPTool/server/templates/batch/fetal_fraction_XY.html b/NIPTool/server/templates/batch/plots/FF_XY.html
similarity index 81%
rename from NIPTool/server/templates/batch/fetal_fraction_XY.html
rename to NIPTool/server/templates/batch/plots/FF_XY.html
index a81ad295..bf119a60 100644
--- a/NIPTool/server/templates/batch/fetal_fraction_XY.html
+++ b/NIPTool/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 %}
\ No newline at end of file
diff --git a/NIPTool/server/templates/batch/NCV.html b/NIPTool/server/templates/batch/plots/NCV.html
similarity index 81%
rename from NIPTool/server/templates/batch/NCV.html
rename to NIPTool/server/templates/batch/plots/NCV.html
index fd232712..0d8d3b22 100644
--- a/NIPTool/server/templates/batch/NCV.html
+++ b/NIPTool/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 b/NIPTool/server/templates/batch/plots/coverage.html
similarity index 76%
rename from NIPTool/server/templates/batch/coverage.html
rename to NIPTool/server/templates/batch/plots/coverage.html
index b9b6ecbb..2f44eb6c 100644
--- a/NIPTool/server/templates/batch/coverage.html
+++ b/NIPTool/server/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
index 241ba6e7..676d7f76 100644
--- 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.SampleProject}}</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 %}
\ No newline at end of file
diff --git a/NIPTool/server/templates/batch/tabs/FF.html b/NIPTool/server/templates/batch/tabs/FF.html
new file mode 100644
index 00000000..dd8e8e89
--- /dev/null
+++ 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 %}
\ No newline at end of file
diff --git a/NIPTool/server/templates/batch/tabs/FF_XY.html b/NIPTool/server/templates/batch/tabs/FF_XY.html
new file mode 100644
index 00000000..415ef8e0
--- /dev/null
+++ 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
new file mode 100644
index 00000000..cc71c56c
--- /dev/null
+++ 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 %}
\ No newline at end of file
diff --git a/NIPTool/server/templates/batch/tabs/coverage.html b/NIPTool/server/templates/batch/tabs/coverage.html
new file mode 100644
index 00000000..2e5a3e41
--- /dev/null
+++ 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 %}
\ No newline at end of file
diff --git a/NIPTool/server/templates/batch/batch.html b/NIPTool/server/templates/batch/tabs/table.html
similarity index 98%
rename from NIPTool/server/templates/batch/batch.html
rename to NIPTool/server/templates/batch/tabs/table.html
index 8094452b..6d97da74 100644
--- a/NIPTool/server/templates/batch/batch.html
+++ b/NIPTool/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
index 063e5482..57156656 100644
--- 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
index 7ff64ad4..afe9d23b 100644
--- 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
index 500b32d7..cf302624 100644
--- 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
index 68e579a6..67a04fe4 100644
--- 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
index 4b9703af..ecbe3fd6 100644
--- 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
index 4eb213b9..cb5254c4 100644
--- 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"""
 
diff --git a/NIPTool/server/views.py b/NIPTool/server/views.py
index c427a2e2..a6561b45 100644
--- a/NIPTool/server/views.py
+++ b/NIPTool/server/views.py
@@ -36,34 +36,7 @@ def batches():
     return render_template("batches.html", batches=all_batches)
 
 
-@server_bp.route("/statistics")
-@login_required
-def statistics():
-    """Statistics view."""
-
-    nr_batches = 3
-    scatter_plots = ['Stdev_13', 'Stdev_18', 'Stdev_21']
-    box_plots = ['Chr13_Ratio', 'Chr18_Ratio', 'Chr21_Ratio','FF_Formatted', 
-                'DuplicationRate', 'MappedReads', 'GC_Dropout']
-
-    batches = get_last_batches(adapter=app.adapter, nr=nr_batches)
-    batch_ids = [batch.get('_id') for batch in batches]
-    box_stat = get_statistics_for_box_plot(adapter=app.adapter, batches=batch_ids, fields=box_plots)
-    scatter_stat = get_statistics_for_scatter_plot(batches=batches, fields=scatter_plots)
-    return render_template("statistics.html",
-        ticks = list(range(1, nr_batches+1)),
-        nr_batches = nr_batches,
-        batch_ids = batch_ids,
-        box_stat = box_stat,
-        box_plots = box_plots,
-        scatter_stat = scatter_stat,
-        scatter_plots = scatter_plots
-        )
-
-
-
-### Batch Views
-
+### Batch tabs
 
 @server_bp.route("/batches/<batch_id>/")
 @login_required
@@ -71,11 +44,9 @@ def batch(batch_id):
     """Batch view with table of all samples in the batch."""
     samples = app.adapter.batch_samples(batch_id)
     return render_template(
-        "batch/batch.html",
-        batch = app.adapter.batch(batch_id),
+        "batch/tabs/table.html",
+        batch=app.adapter.batch(batch_id),
         sample_info=[get_sample_info(sample) for sample in samples],
-        # warnings = ...,
-        # sample_ids = ",".join(sample.get("_id") for sample in samples),
         page_id="batches",
     )
 
@@ -85,10 +56,10 @@ def batch(batch_id):
 def NCV13(batch_id):
     """Batch view with with NCV-13 plot"""
     return render_template(
-        "batch/NCV.html",
+        "batch/tabs/NCV.html",
         batch=app.adapter.batch(batch_id),
-        chrom="13",
-        cases=get_tris_cases(app.adapter, "13", batch_id),
+        chr="13",
+        ncv_chrom_data={"13": get_tris_cases(app.adapter, "13", batch_id)},
         normal_data=get_tris_control_normal(app.adapter, "13"),
         abnormal_data=get_tris_control_abnormal(app.adapter, "13", 0),
         page_id="batches_NCV13",
@@ -100,10 +71,10 @@ def NCV13(batch_id):
 def NCV18(batch_id):
     """Batch view with with NCV-18 plot"""
     return render_template(
-        "batch/NCV.html",
+        "batch/tabs/NCV.html",
         batch=app.adapter.batch(batch_id),
-        chrom="18",
-        cases=get_tris_cases(app.adapter, "18", batch_id),
+        chr="18",
+        ncv_chrom_data={"18": get_tris_cases(app.adapter, "18", batch_id)},
         normal_data=get_tris_control_normal(app.adapter, "18"),
         abnormal_data=get_tris_control_abnormal(app.adapter, "18", 0),
         page_id="batches_NCV18",
@@ -115,10 +86,10 @@ def NCV18(batch_id):
 def NCV21(batch_id):
     """Batch view with NCV-21 plot"""
     return render_template(
-        "batch/NCV.html",
+        "batch/tabs/NCV.html",
         batch=app.adapter.batch(batch_id),
-        chrom="21",
-        cases=get_tris_cases(app.adapter, "21", batch_id),
+        chr="21",
+        ncv_chrom_data={"21": get_tris_cases(app.adapter, "21", batch_id)},
         normal_data=get_tris_control_normal(app.adapter, "21"),
         abnormal_data=get_tris_control_abnormal(app.adapter, "21", 0),
         page_id="batches_NCV21",
@@ -133,7 +104,7 @@ def fetal_fraction_XY(batch_id):
     control = get_ff_control_normal(app.adapter)
     abnormal = get_ff_control_abnormal(app.adapter)
     return render_template(
-        "batch/fetal_fraction_XY.html",
+        "batch/tabs/FF_XY.html",
         control=control,
         abnormal=abnormal,
         cases=get_ff_cases(app.adapter, batch_id),
@@ -150,7 +121,7 @@ def fetal_fraction(batch_id):
     """Batch view with fetal fraction plot"""
     batch = app.adapter.batch(batch_id)
     return render_template(
-        "batch/fetal_fraction.html",
+        "batch/tabs/FF.html",
         control=get_ff_control_normal(app.adapter),
         cases=get_ff_cases(app.adapter, batch_id),
         batch=batch,
@@ -167,20 +138,52 @@ def coverage(batch_id):
     scatter_data = get_scatter_data_for_coverage_plot(samples)
     box_data = get_box_data_for_coverage_plot(samples)
     return render_template(
-        "batch/coverage.html",
+        "batch/tabs/coverage.html",
         batch=batch,
         x_axis=list(range(1, 23)),
         scatter_data=scatter_data,
-        box_data = box_data,
+        box_data=box_data,
         page_id="batches_cov",
     )
 
 
+# Report
+
 @server_bp.route("/batches/<batch_id>/report/<coverage>")
 @login_required
 def report(batch_id, coverage):
     """Report view, collecting all tables and plots from one batch."""
-    return render_template("batch/report.html", batch_id=batch_id)
+
+    batch = app.adapter.batch(batch_id)
+    samples = list(app.adapter.batch_samples(batch_id))
+    scatter_data = get_scatter_data_for_coverage_plot(samples)
+    box_data = get_box_data_for_coverage_plot(samples)
+    control = get_ff_control_normal(app.adapter)
+    return render_template(
+        "batch/report.html",
+        batch=batch,
+        # NCV
+        ncv_chrom_data={
+            "13": get_tris_cases(app.adapter, "13", batch_id),
+            "18": get_tris_cases(app.adapter, "18", batch_id),
+            "21": get_tris_cases(app.adapter, "21", batch_id),
+        },
+        normal_data=get_tris_control_normal(app.adapter, "21"),
+        abnormal_data=get_tris_control_abnormal(app.adapter, "21", 0),
+        # FF
+        control=control,
+        cases=get_ff_cases(app.adapter, batch_id),
+        abnormal=get_ff_control_abnormal(app.adapter),
+        max_x=max(control["FFX"]) + 1,
+        min_x=min(control["FFX"]) - 1,
+        # table
+        sample_info=[get_sample_info(sample) for sample in samples],
+        # coverage
+        x_axis=list(range(1, 23)),
+        scatter_data=scatter_data,
+        box_data=box_data,
+        page_id="batches",
+    )
 
 
 ### Sample Views
@@ -224,6 +227,46 @@ def sample_tris(sample_id):
     )
 
 
+# Statistics
+
+
+@server_bp.route("/statistics")
+@login_required
+def statistics():
+    """Statistics view."""
+
+    nr_batches = 3
+    scatter_plots = ["Stdev_13", "Stdev_18", "Stdev_21"]
+    box_plots = [
+        "Chr13_Ratio",
+        "Chr18_Ratio",
+        "Chr21_Ratio",
+        "FF_Formatted",
+        "DuplicationRate",
+        "MappedReads",
+        "GC_Dropout",
+    ]
+
+    batches = get_last_batches(adapter=app.adapter, nr=nr_batches)
+    batch_ids = [batch.get("_id") for batch in batches]
+    box_stat = get_statistics_for_box_plot(
+        adapter=app.adapter, batches=batch_ids, fields=box_plots
+    )
+    scatter_stat = get_statistics_for_scatter_plot(
+        batches=batches, fields=scatter_plots
+    )
+    return render_template(
+        "statistics.html",
+        ticks=list(range(1, nr_batches + 1)),
+        nr_batches=nr_batches,
+        batch_ids=batch_ids,
+        box_stat=box_stat,
+        box_plots=box_plots,
+        scatter_stat=scatter_stat,
+        scatter_plots=scatter_plots,
+    )
+
+
 ### Udate
 
 

From a2fcacbcdadec313ec95f847865f8a3ff5325c5a Mon Sep 17 00:00:00 2001
From: mayabrandi <maya.brandi@scilifelab.se>
Date: Fri, 13 Nov 2020 14:05:05 +0100
Subject: [PATCH 2/3] sample project and ratio corection

---
 NIPTool/server/templates/batch/report.html | 2 +-
 NIPTool/server/utils.py                    | 4 ++--
 NIPTool/server/views.py                    | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/NIPTool/server/templates/batch/report.html b/NIPTool/server/templates/batch/report.html
index 676d7f76..fa8a7f02 100644
--- a/NIPTool/server/templates/batch/report.html
+++ b/NIPTool/server/templates/batch/report.html
@@ -7,7 +7,7 @@
         <div class="panel panel-default">
             <div class="panel-body">
                 <h2 class="page-header"><strong>NIPT Results </strong><br><small>Batch:
-                        {{batch.SampleProject}}</small><small>
+                        {{batch._id}}</small><small>
                         <p align="right" id="demo"></p>
                     </small></h2>
                 <footer>
diff --git a/NIPTool/server/utils.py b/NIPTool/server/utils.py
index 5e01527e..830c37a0 100644
--- a/NIPTool/server/utils.py
+++ b/NIPTool/server/utils.py
@@ -105,7 +105,7 @@ def get_scatter_data_for_coverage_plot(samples):
         sample_id = sample["_id"]
         data[sample_id] = {"x": [], "y": []}
         for chr in range(1, 23):
-            ratio = sample.get(f"chr{str(chr)}_Ratio")
+            ratio = sample.get(f"Chr{str(chr)}_Ratio")
             if ratio is None:
                 continue
             data[sample_id]["y"].append(ratio)
@@ -118,7 +118,7 @@ def get_box_data_for_coverage_plot(samples):
     for chr in range(1, 23):
         data[chr] = []
         for sample in samples:
-            ratio = sample.get(f"chr{str(chr)}_Ratio")
+            ratio = sample.get(f"Chr{str(chr)}_Ratio")
             if ratio is None:
                 continue
             data[chr].append(ratio)
diff --git a/NIPTool/server/views.py b/NIPTool/server/views.py
index 6a822301..7a462d33 100644
--- a/NIPTool/server/views.py
+++ b/NIPTool/server/views.py
@@ -238,9 +238,9 @@ def statistics():
     nr_batches = 3
     scatter_plots = ["Stdev_13", "Stdev_18", "Stdev_21"]
     box_plots = [
-        "chr13_Ratio",
-        "chr18_Ratio",
-        "chr21_Ratio",
+        "Chr13_Ratio",
+        "Chr18_Ratio",
+        "Chr21_Ratio",
         "FF_Formatted",
         "DuplicationRate",
         "MappedReads",

From 4401b23386cf07d4c7b565d467e9d674d05df653 Mon Sep 17 00:00:00 2001
From: mayabrandi <maya.brandi@scilifelab.se>
Date: Mon, 16 Nov 2020 08:52:47 +0100
Subject: [PATCH 3/3] finally

---
 tests/build/test_build_batch.py    | 74 ------------------------
 tests/build/test_build_document.py | 31 ++++++++++
 tests/build/test_build_sample.py   | 91 ------------------------------
 3 files changed, 31 insertions(+), 165 deletions(-)
 delete mode 100644 tests/build/test_build_batch.py
 create mode 100644 tests/build/test_build_document.py
 delete mode 100644 tests/build/test_build_sample.py

diff --git a/tests/build/test_build_batch.py b/tests/build/test_build_batch.py
deleted file mode 100644
index 3ac41a06..00000000
--- a/tests/build/test_build_batch.py
+++ /dev/null
@@ -1,74 +0,0 @@
-from NIPTool.build.document import build_batch
-from NIPTool.models.constants import BATCH_KEYS
-import pytest
-
-
-def test_build_batch():
-    # GIVEN a batch_data with requiered key 'SampleProject'
-    batch_data = {
-        "Median_18": 1.01950547134618,
-        "SampleProject": 201862,
-        "Stdev_13": 0.009517510060085,
-    }
-
-    # WHEN building a mongo batch
-    mongo_batch = build_batch(batch_data=batch_data)
-
-    # THEN the mongo_batch has a key "_id" with the value of "SampleProject"
-    assert mongo_batch == {
-        "_id": "201862",
-        "Median_18": 1.01950547134618,
-        "Stdev_13": 0.009517510060085,
-    }
-
-
-def test_build_batch_wrong_keys():
-    # GIVEN a batch_data with not accepted keys: key1 key2 key3
-    batch_data = {
-        "SampleProject": 201862,
-        "key1": " ",
-        "key2": 201862,
-        "key3": -10.1836097044367,
-    }
-
-    # WHEN building a mongo batch
-    mongo_batch = build_batch(batch_data=batch_data)
-
-    # THEN the unaccepted keys will not be part of the mongo_batch"
-    assert mongo_batch == {"_id": "201862"}
-
-
-@pytest.mark.parametrize("batch_key", BATCH_KEYS)
-def test_build_batch_str_values(batch_key):
-    # GIVEN a batch_data dict with requiered key 'SampleProject' and a batch_key with some str value
-    batch_data = {"SampleProject": 201862, batch_key: "Value"}
-
-    # WHEN building a mongo batch
-    mongo_batch = build_batch(batch_data=batch_data)
-
-    # THEN the the batch_key will be loaded into the mongo_batch dict
-    assert mongo_batch == {"_id": "201862", batch_key: "Value"}
-
-
-@pytest.mark.parametrize("batch_key", BATCH_KEYS)
-def test_build_batch_zero_values(batch_key):
-    # GIVEN a batch_data dict with requiered key 'SampleProject' and a batch_key with value 0
-    batch_data = {"SampleProject": 201862, batch_key: 0}
-
-    # WHEN building a mongo batch
-    mongo_batch = build_batch(batch_data=batch_data)
-
-    # THEN the the batch_key will be loaded into the mongo_batch dict
-    assert mongo_batch == {"_id": "201862", batch_key: 0}
-
-
-@pytest.mark.parametrize("batch_key", BATCH_KEYS)
-def test_build_batch_empty_strings(batch_key):
-    # GIVEN a batch_data dict with requiered key 'SampleProject' and a batch_key with empty string as value
-    batch_data = {"SampleProject": 201862, batch_key: " "}
-
-    # WHEN building a mongo batch
-    mongo_batch = build_batch(batch_data=batch_data)
-
-    # THEN the the batch_key will not be loaded into the mongo_batch dict
-    assert mongo_batch == {"_id": "201862"}
\ No newline at end of file
diff --git a/tests/build/test_build_document.py b/tests/build/test_build_document.py
new file mode 100644
index 00000000..b8d0d17d
--- /dev/null
+++ b/tests/build/test_build_document.py
@@ -0,0 +1,31 @@
+from NIPTool.build.document import build_batch, build_sample
+from NIPTool.models.constants import BATCH_KEYS,  SAMPLE_KEYS
+import pytest
+
+
+@pytest.mark.parametrize("sample_key", SAMPLE_KEYS)
+@pytest.mark.parametrize("value", [124, 2.08, "randomstring"])
+def test_build_sample(sample_key, value):
+    # GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with some value and a non sample_key
+
+    sample_data = {"SampleID": "someid", sample_key: value, "other_key": 8983}
+
+    # WHEN building a mongo sample
+    mongo_sample = build_sample(sample_data=sample_data)
+
+    # THEN the SampleID will be _id and the non sample key will be removed
+    assert mongo_sample == {"_id": "someid", sample_key: value}
+
+
+@pytest.mark.parametrize("batch_key", BATCH_KEYS)
+@pytest.mark.parametrize("value", [124, 2.08, "randomstring"])
+def test_build_batch(batch_key, value):
+    # GIVEN a batch_data dict a batch_key with some value and a non batch_key
+
+    batch_data = {batch_key: value, "other_key": 8983}
+
+    # WHEN building a mongo batch
+    mongo_batch = build_batch(batch_data=batch_data)
+
+    # THEN the non batch_key will be removed
+    assert mongo_batch == {batch_key: value}
\ No newline at end of file
diff --git a/tests/build/test_build_sample.py b/tests/build/test_build_sample.py
deleted file mode 100644
index 4eda2bc0..00000000
--- a/tests/build/test_build_sample.py
+++ /dev/null
@@ -1,91 +0,0 @@
-from NIPTool.build.document import build_sample
-from NIPTool.models.constants import SAMPLE_KEYS
-import pytest
-
-
-def test_build_sample():
-    # GIVEN a sample_data with requiered key 'SampleID'
-    sample_data = {
-        "SampleID": "2020-07452-02",
-        "Description": " ",
-        "Zscore_13": -10.1836097044367,
-    }
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the mongo_sample has a key "_id" with the value of "SampleID"
-    assert mongo_sample == {
-        "_id": "2020-07452-02",
-        "Zscore_13": -10.1836097044367,
-    }
-
-
-def test_build_sample_SampleProject_key():
-    # GIVEN a sample_data with requiered key 'SampleID' and 'SampleProject' in int format
-    sample_data = {
-        "SampleID": "2020-07452-02",
-        "SampleProject": 201862,
-    }
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the value of "SampleProject" is in str format
-    assert mongo_sample == {
-        "_id": "2020-07452-02",
-        "SampleProject": "201862",
-    }
-
-
-def test_build_sample_wrong_keys():
-    # GIVEN a sample_data with not accepted keys: key1 key2 key3
-    sample_data = {
-        "SampleID": "2020-07452-02",
-        "key1": " ",
-        "key2": 201862,
-        "key3": -10.1836097044367,
-    }
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the unaccepted keys will not be part of the mongo_sample"
-    assert mongo_sample == {"_id": "2020-07452-02"}
-
-
-@pytest.mark.parametrize("sample_key", SAMPLE_KEYS)
-def test_build_sample_str_values(sample_key):
-    # GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with some str value
-    sample_data = {"SampleID": "2020-07452-02", sample_key: "Value"}
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the the sample_key will be loaded into the mongo_sample dict
-    if sample_key == "SampleID":
-        assert mongo_sample == {"_id": "2020-07452-02", sample_key: "Value"}
-
-
-@pytest.mark.parametrize("sample_key", SAMPLE_KEYS)
-def test_build_sample_empty_strings(sample_key):
-    # GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with empty string as value
-    sample_data = {"SampleID": "2020-07452-02", sample_key: " "}
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the the sample_key will not be loaded into the mongo_sample dict
-    assert mongo_sample == {"_id": "2020-07452-02"}
-
-
-@pytest.mark.parametrize("sample_key", SAMPLE_KEYS)
-def test_build_sample_zero_values(sample_key):
-    # GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with value 0
-    sample_data = {"SampleID": "2020-07452-02", sample_key: 0}
-
-    # WHEN building a mongo sample
-    mongo_sample = build_sample(sample_data=sample_data)
-
-    # THEN the the sample_key will be loaded into the mongo_sample dict
-    assert mongo_sample == {"_id": "2020-07452-02", sample_key: 0}