From 3c341b425dad8adf532c848f81e2c867bc647b5c Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 24 Mar 2022 19:09:58 +0300
Subject: rename template to gn3_wgcna_results

---
 wqflask/wqflask/templates/gn3_wgcna_results.html  | 165 ++++++++++++++++++++++
 wqflask/wqflask/templates/test_wgcna_results.html | 165 ----------------------
 wqflask/wqflask/views.py                          |   2 +-
 3 files changed, 166 insertions(+), 166 deletions(-)
 create mode 100644 wqflask/wqflask/templates/gn3_wgcna_results.html
 delete mode 100644 wqflask/wqflask/templates/test_wgcna_results.html

diff --git a/wqflask/wqflask/templates/gn3_wgcna_results.html b/wqflask/wqflask/templates/gn3_wgcna_results.html
new file mode 100644
index 00000000..952f479e
--- /dev/null
+++ b/wqflask/wqflask/templates/gn3_wgcna_results.html
@@ -0,0 +1,165 @@
+{% extends "base.html" %}
+{% block title %}WCGNA results{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.css" integrity="sha512-iLYuqv+v/P4u9erpk+KM83Ioe/l7SEmr7wB6g+Kg1qmEit8EShDKnKtLHlv2QXUp7GGJhmqDI+1PhJYLTsfb8w==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+
+<link rel="stylesheet" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css">
+
+
+<style type="text/css">
+
+
+.container {
+    min-height: 100vh;
+    width: 100vw;
+    padding: 20px;
+
+}
+
+.grid_container {
+
+
+    width: 80vw;
+    margin: auto;
+    padding: 20px;
+
+
+    display: grid;
+    grid-template-columns: repeat(7, 1fr);
+    /*grid-gap: 5px;*/
+    border: 1px solid black;
+    grid-column-gap: 20px;
+
+}
+
+.control_sft_column {
+    text-align: center;
+}
+
+.grid_container div:not(:last-child) {
+    border-right: 1px solid #000;
+}
+
+.grid_container .control_sft_column h3 {
+    font-weight: bold;
+    font-size: 18px;
+}
+
+.control_net_colors {
+
+    display: flex;
+    flex-wrap: wrap;
+    justify-content: space-between;
+    align-items: center;
+    text-align: center;
+}
+
+
+.control_mod_eigens {
+    display: grid;
+    grid-template-columns: repeat(2, 200px);
+}
+
+.control-image{
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+  width: 80vw;
+}
+</style>
+<div class="container">
+    {% if  error!='null' %}
+     <h4 style="text-align: center;">{{error}}</h4>
+
+    {% else %}
+    <div>
+        <div >
+            <h2 style="text-align:center">Soft Thresholds </h2>
+            <div class="grid_container">
+
+            {% for key, value in results["data"]["output"]["soft_threshold"].items()%}
+            <div class="control_sft_column">
+                <h3>{{key}}</h3>
+                {% for val in value %}
+                <p>{{val|round(3)}}</p>
+                {% endfor %}
+            </div>
+            {% endfor %}
+            </div>
+        </div>
+
+        <div>
+        
+            {% if image["image_generated"] %}
+            <div >
+                <img class="control-image" src="data:image/jpeg;base64,{{ image['image_data']| safe }}">
+            </div>
+
+            {% endif %}
+<!--                 <div >
+                <img class="control-image" src="data:image/jpeg;base64,{{ results['data']['output']['image_data2']| safe }}">
+            </div> -->
+        </div>
+
+        <div>
+            <h2 style="text-align:center;"> Module eigen genes </h2>
+            <table id="eigens" class="display" width="80vw"></table>
+        </div>
+
+        <div>
+            <h2 style="text-align:center;">Phenotype modules </h2>
+
+             <table id="phenos" class="display"  width="40vw" ></table>
+        </div>
+    </div>
+
+{% endif %}
+
+</div>
+
+{% endblock %}
+
+{% block js %}
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.js"></script>
+
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+
+
+<script type="text/javascript">
+
+
+let results = {{results|safe}}
+
+let phenoModules = results["data"]["output"]["net_colors"]
+let phenotypes = Object.keys(phenoModules)
+let phenoMods = Object.values(phenoModules)
+
+let {col_names,mod_dataset} = {{data|safe}}
+    $('#eigens').DataTable( {
+        data: mod_dataset,
+        columns: col_names.map((name)=>{
+            return {
+                title:name
+            }
+        })
+    } );
+    $('#phenos').DataTable( {
+        data:phenotypes.map((phenoName,idx)=>{
+            return [phenoName,phenoMods[idx]]
+        }),
+        columns: [{
+            title:"Phenotypes"
+        },
+        {
+        title: "Modules"
+        }]
+    } );
+
+
+</script>
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/test_wgcna_results.html b/wqflask/wqflask/templates/test_wgcna_results.html
deleted file mode 100644
index 952f479e..00000000
--- a/wqflask/wqflask/templates/test_wgcna_results.html
+++ /dev/null
@@ -1,165 +0,0 @@
-{% extends "base.html" %}
-{% block title %}WCGNA results{% endblock %}
-{% block content %}
-<!-- Start of body -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.css" integrity="sha512-iLYuqv+v/P4u9erpk+KM83Ioe/l7SEmr7wB6g+Kg1qmEit8EShDKnKtLHlv2QXUp7GGJhmqDI+1PhJYLTsfb8w==" crossorigin="anonymous" referrerpolicy="no-referrer" />
-
-<link rel="stylesheet" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css">
-
-
-<style type="text/css">
-
-
-.container {
-    min-height: 100vh;
-    width: 100vw;
-    padding: 20px;
-
-}
-
-.grid_container {
-
-
-    width: 80vw;
-    margin: auto;
-    padding: 20px;
-
-
-    display: grid;
-    grid-template-columns: repeat(7, 1fr);
-    /*grid-gap: 5px;*/
-    border: 1px solid black;
-    grid-column-gap: 20px;
-
-}
-
-.control_sft_column {
-    text-align: center;
-}
-
-.grid_container div:not(:last-child) {
-    border-right: 1px solid #000;
-}
-
-.grid_container .control_sft_column h3 {
-    font-weight: bold;
-    font-size: 18px;
-}
-
-.control_net_colors {
-
-    display: flex;
-    flex-wrap: wrap;
-    justify-content: space-between;
-    align-items: center;
-    text-align: center;
-}
-
-
-.control_mod_eigens {
-    display: grid;
-    grid-template-columns: repeat(2, 200px);
-}
-
-.control-image{
-  display: block;
-  margin-left: auto;
-  margin-right: auto;
-  width: 80vw;
-}
-</style>
-<div class="container">
-    {% if  error!='null' %}
-     <h4 style="text-align: center;">{{error}}</h4>
-
-    {% else %}
-    <div>
-        <div >
-            <h2 style="text-align:center">Soft Thresholds </h2>
-            <div class="grid_container">
-
-            {% for key, value in results["data"]["output"]["soft_threshold"].items()%}
-            <div class="control_sft_column">
-                <h3>{{key}}</h3>
-                {% for val in value %}
-                <p>{{val|round(3)}}</p>
-                {% endfor %}
-            </div>
-            {% endfor %}
-            </div>
-        </div>
-
-        <div>
-        
-            {% if image["image_generated"] %}
-            <div >
-                <img class="control-image" src="data:image/jpeg;base64,{{ image['image_data']| safe }}">
-            </div>
-
-            {% endif %}
-<!--                 <div >
-                <img class="control-image" src="data:image/jpeg;base64,{{ results['data']['output']['image_data2']| safe }}">
-            </div> -->
-        </div>
-
-        <div>
-            <h2 style="text-align:center;"> Module eigen genes </h2>
-            <table id="eigens" class="display" width="80vw"></table>
-        </div>
-
-        <div>
-            <h2 style="text-align:center;">Phenotype modules </h2>
-
-             <table id="phenos" class="display"  width="40vw" ></table>
-        </div>
-    </div>
-
-{% endif %}
-
-</div>
-
-{% endblock %}
-
-{% block js %}
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/xterm/3.14.5/xterm.min.js"></script>
-
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
-
-
-<script type="text/javascript">
-
-
-let results = {{results|safe}}
-
-let phenoModules = results["data"]["output"]["net_colors"]
-let phenotypes = Object.keys(phenoModules)
-let phenoMods = Object.values(phenoModules)
-
-let {col_names,mod_dataset} = {{data|safe}}
-    $('#eigens').DataTable( {
-        data: mod_dataset,
-        columns: col_names.map((name)=>{
-            return {
-                title:name
-            }
-        })
-    } );
-    $('#phenos').DataTable( {
-        data:phenotypes.map((phenoName,idx)=>{
-            return [phenoName,phenoMods[idx]]
-        }),
-        columns: [{
-            title:"Phenotypes"
-        },
-        {
-        title: "Modules"
-        }]
-    } );
-
-
-</script>
-{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b2cf95fb..31e31875 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -345,7 +345,7 @@ def wcgna_setup():
 def wcgna_results():
     """call the gn3 api to get wgcna response data"""
     results = run_wgcna(dict(request.form))
-    return render_template("test_wgcna_results.html", **results)
+    return render_template("gn3_wgcna_results.html", **results)
 
 @app.route("/ctl_setup", methods=('POST',))
 def ctl_setup():
-- 
cgit v1.2.3


From 12598c7a6be757efcc040e8e160190cae0af4596 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 24 Mar 2022 20:32:49 +0300
Subject: display parametric values used

---
 wqflask/wqflask/templates/gn3_wgcna_results.html | 44 +++++++++++++++++++++++-
 1 file changed, 43 insertions(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/gn3_wgcna_results.html b/wqflask/wqflask/templates/gn3_wgcna_results.html
index 952f479e..3a517954 100644
--- a/wqflask/wqflask/templates/gn3_wgcna_results.html
+++ b/wqflask/wqflask/templates/gn3_wgcna_results.html
@@ -75,6 +75,12 @@
 
     {% else %}
     <div>
+        <div>
+            <h2 style="text-align:center;">Parameters used</h2>
+
+            <table id="summary" class="display"  width="40vw" ></table>
+
+        </div>
         <div >
             <h2 style="text-align:center">Soft Thresholds </h2>
             <div class="grid_container">
@@ -135,11 +141,47 @@
 
 let results = {{results|safe}}
 
+let parameters = {{parameters|safe}}
+
 let phenoModules = results["data"]["output"]["net_colors"]
 let phenotypes = Object.keys(phenoModules)
 let phenoMods = Object.values(phenoModules)
 
 let {col_names,mod_dataset} = {{data|safe}}
+
+let {MinModuleSize,TOMtype,corType,mergeCutHeight} = parameters
+
+const summary = {
+
+  strain_numbers:6,
+
+  nphe:12,
+
+  modules_found:phenoMods.length,
+  MinModuleSize,
+  TOMtype,
+  corType,
+  mergeCutHeight
+
+}
+
+    $("#summary").DataTable( {
+
+        data: Object.keys(summary).map((key)=>{
+            return [key,summary[key]]
+        }),
+        columns: [ {
+            title: "parameter",
+
+        },
+
+        {
+            title:" param_values"
+        }
+        ]
+    })
+
+
     $('#eigens').DataTable( {
         data: mod_dataset,
         columns: col_names.map((name)=>{
@@ -162,4 +204,4 @@ let {col_names,mod_dataset} = {{data|safe}}
 
 
 </script>
-{% endblock %}
\ No newline at end of file
+{% endblock %}
-- 
cgit v1.2.3


From 0ee7de23de1a29c909fb0a461d980f8474ecadb9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 24 Mar 2022 22:04:53 +0300
Subject: code refactoring

---
 wqflask/wqflask/templates/gn3_wgcna_results.html | 21 +++------------------
 wqflask/wqflask/wgcna/gn3_wgcna.py               | 13 ++++++++++---
 2 files changed, 13 insertions(+), 21 deletions(-)

diff --git a/wqflask/wqflask/templates/gn3_wgcna_results.html b/wqflask/wqflask/templates/gn3_wgcna_results.html
index 3a517954..8a31bf28 100644
--- a/wqflask/wqflask/templates/gn3_wgcna_results.html
+++ b/wqflask/wqflask/templates/gn3_wgcna_results.html
@@ -139,30 +139,15 @@
 <script type="text/javascript">
 
 
-let results = {{results|safe}}
-
-let parameters = {{parameters|safe}}
-
-let phenoModules = results["data"]["output"]["net_colors"]
+let phenoModules = {{results|safe}}["data"]["output"]["net_colors"]
 let phenotypes = Object.keys(phenoModules)
 let phenoMods = Object.values(phenoModules)
 
 let {col_names,mod_dataset} = {{data|safe}}
-
-let {MinModuleSize,TOMtype,corType,mergeCutHeight} = parameters
-
 const summary = {
-
-  strain_numbers:6,
-
-  nphe:12,
-
   modules_found:phenoMods.length,
-  MinModuleSize,
-  TOMtype,
-  corType,
-  mergeCutHeight
-
+  ...{{parameters|safe}}
+  
 }
 
     $("#summary").DataTable( {
diff --git a/wqflask/wqflask/wgcna/gn3_wgcna.py b/wqflask/wqflask/wgcna/gn3_wgcna.py
index 7bf5c62b..ab7fe46c 100644
--- a/wqflask/wqflask/wgcna/gn3_wgcna.py
+++ b/wqflask/wqflask/wgcna/gn3_wgcna.py
@@ -76,8 +76,6 @@ def run_wgcna(form_data):
 
     wgcna_api = f"{GN3_LOCAL_URL}/api/wgcna/run_wgcna"
 
-    # parse form data
-
     trait_dataset = fetch_trait_data(form_data)
     form_data["minModuleSize"] = int(form_data["MinModuleSize"])
 
@@ -86,8 +84,10 @@ def run_wgcna(form_data):
 
     try:
 
+        unique_strains = list(set(trait_dataset["sample_names"]))
+
         response = requests.post(wgcna_api, json={
-            "sample_names": list(set(trait_dataset["sample_names"])),
+            "sample_names": unique_strains,
             "trait_names": trait_dataset["trait_names"],
             "trait_sample_data": list(trait_dataset["input"].values()),
             **form_data
@@ -98,8 +98,15 @@ def run_wgcna(form_data):
         status_code = response.status_code
         response = response.json()
 
+        parameters = {
+            "nstrains": len(unique_strains),
+            "nphe": len(trait_dataset["trait_names"]),
+            **{key: val for key, val in form_data.items() if key not in ["trait_list"]}
+        }
+
         return {"error": response} if status_code != 200 else {
             "error": 'null',
+            "parameters": parameters,
             "results": response,
             "data": process_wgcna_data(response["data"]),
             "image": process_image(response["data"])
-- 
cgit v1.2.3