From 93dcba89f7e424a759e3177a74b1ce322cdd7c57 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Mar 2015 16:11:56 +0000
Subject: Pair scan image now loads properly

---
 wqflask/base/webqtlConfig.py                       |  2 +-
 .../wqflask/marker_regression/marker_regression.py |  6 +--
 wqflask/wqflask/templates/pair_scan_results.html   | 55 ++++------------------
 wqflask/wqflask/templates/show_image.html          |  5 ++
 wqflask/wqflask/views.py                           | 23 ++++++++-
 5 files changed, 38 insertions(+), 53 deletions(-)
 create mode 100644 wqflask/wqflask/templates/show_image.html

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e74b9ce5..49a596aa 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -58,7 +58,7 @@ SNP_PATH = '/home/zas1024/snps/'
 IMGDIR = GNROOT + '/wqflask/wqflask/images/'
 IMAGESPATH = HTMLPATH + 'images/'
 UPLOADPATH = IMAGESPATH + 'upload/'
-TMPDIR = '/tmp/'
+TMPDIR = '/home/zas1024/tmp/' # Will remove this and dependent items later
 GENODIR = HTMLPATH + 'genotypes/'
 NEWGENODIR = HTMLPATH + 'new_genotypes/'
 GENO_ARCHIVE_DIR = GENODIR + 'archive/'
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index af441489..3fb9915b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -321,9 +321,9 @@ class MarkerRegression(object):
                 print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=self.model, method=self.method, n_cluster = 16)
  
             print("Pair scan results:", result_data_frame)
-            
-            self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_")
-            png(file=webqtlConfig.IMGDIR+self.pair_scan_filename+".png")
+
+            self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
+            png(file=webqtlConfig.TMPDIR+self.pair_scan_filename)
             plot(result_data_frame)
             dev_off()
             
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index a0041e11..869dabed 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -1,13 +1,13 @@
 {% extends "base.html" %}
-{% block title %}Interval Mapping{% endblock %}
+{% block title %}Pair Scan{% endblock %}
 {% block css %}
-<!--    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
+
 {% block content %} <!-- Start of body -->
 
     {{ header("Mapping",
@@ -21,7 +21,12 @@
         </div>
         <div id="chart_container">
             <div class="pair_scan_figure" id="pair_scan_figure">
-                <img src="/images/{{ pair_scan_filename }}.png">
+                <a href="/tmp/{{ pair_scan_filename }}">
+                    <img alt="Embedded Image" src="data:image/png;base64,
+                    {% for elem in pair_scan_array -%}
+                    {% print("%c"|format(elem)) %}
+                    {%- endfor %}
+                    " /></a>
             </div>
         </div>
         <div>
@@ -31,30 +36,12 @@
         </div>
     </div>
 
-    <!-- End of body -->
-
 {% endblock %}
 
 {% block js %}  
-    <script>
-        js_data = {{ js_data | safe }}
-    </script>
 
-    <!--[if lt IE 9]>
-<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
-    <![endif]-->
     <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
-<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
-<!--    <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.js"></script>-->
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
@@ -62,30 +49,4 @@
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
-    <script type="text/javascript" charset="utf-8">
-        $(document).ready( function () {
-            console.time("Creating table");
-            $('#qtl_results').dataTable( {
-                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
-                "sDom": "lTftipr",
-                "oTableTools": {
-                    "aButtons": [
-                        "copy",
-                        "print",
-                        {
-                            "sExtends":    "collection",
-                            "sButtonText": 'Save <span class="caret" />',
-                            "aButtons":    [ "csv", "xls", "pdf" ]
-                        }
-                    ],
-                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
-                },
-                "iDisplayLength": 50,
-                "bLengthChange": true,
-                "bDeferRender": true,
-                "bSortClasses": false
-            } );
-            console.timeEnd("Creating table");
-        });
-    </script>
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_image.html b/wqflask/wqflask/templates/show_image.html
new file mode 100644
index 00000000..521f5414
--- /dev/null
+++ b/wqflask/wqflask/templates/show_image.html
@@ -0,0 +1,5 @@
+<img alt="Embedded Image" src="data:image/png;base64,
+{% for elem in img_base64 -%}
+    {% print("%c"|format(elem)) %}
+{%- endfor %}
+" />
\ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 4b7bd639..7fec0456 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import, division, print_function
 
 import sys
@@ -20,6 +21,8 @@ import redis
 Redis = redis.StrictRedis()
 
 import flask
+import base64
+import array
 import sqlalchemy
 #import config
 
@@ -83,11 +86,18 @@ def index_page():
     return render_template("index_page.html")
 
 
-@app.route("/tmp")
-def tmp_page():
+@app.route("/tmp/<img_path>")
+def tmp_page(img_path):
     print("In tmp_page")
+    print("img_path:", img_path)
     initial_start_vars = request.form
     print("initial_start_vars:", initial_start_vars)
+    imgfile = open('/home/zas1024/tmp/' + img_path, 'rb')
+    imgdata = imgfile.read()
+    imgB64 = imgdata.encode("base64")
+    bytesarray = array.array('B', imgB64)
+    return render_template("show_image.html",
+                            img_base64 = bytesarray )
 
 
 @app.route("/data_sharing")
@@ -344,6 +354,15 @@ def marker_regression_page():
 
     with Bench("Rendering template"):
         if result['pair_scan'] == True:
+            img_path = result['pair_scan_filename']
+            print("img_path:", img_path)
+            initial_start_vars = request.form
+            print("initial_start_vars:", initial_start_vars)
+            imgfile = open('/home/zas1024/tmp/' + img_path, 'rb')
+            imgdata = imgfile.read()
+            imgB64 = imgdata.encode("base64")
+            bytesarray = array.array('B', imgB64)
+            result['pair_scan_array'] = bytesarray
             rendered_template = render_template("pair_scan_results.html", **result)
         else:
             rendered_template = render_template("marker_regression.html", **result)
-- 
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