Resolved conflict from putting tool buttons in a separate template

14 files changed, 89 insertions, 27 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 36aeea83..a22c2b54 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -117,6 +117,8 @@ def check_packaged_js_files(args_obj, parser):
         "/js/nvd3/nv.d3.min.css",
         "/js/qtip2/jquery.qtip.min.js",
         "/js/js_alt/md5.min.js",
+        "/js/typeahead/typeahead.bundle.js",
+        "/js/underscore-string/underscore.string.min.js",
         "/js/js_alt/jstat.min.js",
         "/js/js_alt/parsley.min.js",
         "/js/js_alt/timeago.min.js",
@@ -136,6 +138,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
         "/js/cytoscape-qtip/cytoscape-qtip.js",
         "/css/d3-tip/d3-tip.css",
+        "/js/javascript-twitter-post-fetcher/js/twitterFetcher_min.js",
         "/js/DataTables/images/sort_asc_disabled.png",
         "/js/DataTables/images/sort_desc_disabled.png",
     ]
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 6ab8c3d8..c87776bb 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -29,6 +29,8 @@ class CorrScatterPlot(object):
         self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
         #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3)
 
+        self.method = params['method']
+
         primary_samples = self.dataset_1.group.samplelist
         if self.dataset_1.group.parlist != None:
             primary_samples += self.dataset_1.group.parlist
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0269ce68..a77877d2 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -20,24 +20,23 @@
 
 import datetime
 import math
+import random
+import string
+
 import numpy as np
 import scipy
 import rpy2.robjects as robjects
-import utility.webqtlUtil  # this is for parallel computing only.
-import utility.logger
+from rpy2.robjects.packages import importr
 
 from base import data_set
+from base.webqtlConfig import GENERATED_TEXT_DIR
 from functools import reduce
 from functools import cmp_to_key
-from rpy2.robjects.packages import importr
-
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import corr_result_helpers
 from utility.redis_tools import get_redis_conn
 
-logger = utility.logger.getLogger(__name__)
-
 Redis = get_redis_conn()
 THIRTY_DAYS = 60 * 60 * 24 * 30
 
@@ -135,6 +134,8 @@ class CorrelationMatrix(object):
             self.corr_results.append(corr_result_row)
             self.pca_corr_results.append(pca_corr_result_row)
 
+        self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results)
+
         self.trait_data_array = []
         for trait_db in self.trait_list:
             this_trait = trait_db[0]
@@ -232,6 +233,36 @@ class CorrelationMatrix(object):
             loadings_array.append(loadings_row)
         return loadings_array
 
+def export_corr_matrix(corr_results):
+    corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+    matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
+    with open(matrix_export_path, "w+") as output_file:
+        output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
+        output_file.write("\n")
+        output_file.write("Correlation ")
+        for i, item in enumerate(corr_results[0]):
+            output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+        output_file.write("\n")
+        for i, row in enumerate(corr_results):
+            output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+            for item in row:
+                output_file.write(str(item[1]) + "\t")
+            output_file.write("\n")
+
+        output_file.write("\n")
+        output_file.write("\n")
+        output_file.write("N ")
+        for i, item in enumerate(corr_results[0]):
+            output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+        output_file.write("\n")
+        for i, row in enumerate(corr_results):
+            output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+            for item in row:
+                output_file.write(str(item[2]) + "\t")
+            output_file.write("\n")
+
+    return corr_matrix_filename, matrix_export_path
+
 def zScore(trait_data_array):
     NN = len(trait_data_array[0])
     if NN < 10:
diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 38ae834c..21ef5653 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -82,7 +82,7 @@
 {% block js %}
      <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
 
     <script type="text/javascript" charset="utf-8">
     </script>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index e3dd03d5..d77e0515 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -31,7 +31,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
 
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index a0436ade..f44350ab 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -118,17 +118,17 @@
   {% endif %}
 
   <ul class="nav nav-tabs">
-    <li class="active">
+    <li {% if method == 'pearson' %}class="active"{% endif %}>
       <a href="#tp1" data-toggle="tab">Pearson</a>
     </li>
-    <li>
+    <li {% if method == 'spearman' %}class="active"{% endif %}>
       <a href="#tp2" data-toggle="tab">Spearman Rank</a>
     </li>
   </ul>
 
   <div class="tab-content" style="min-width: 800px;">
 
-    <div class="tab-pane active" id="tp1">
+    <div class="tab-pane {% if method == 'pearson' %}active{% endif %}" id="tp1">
       <br>
       <div id="scatterplot2"></div>
       <br>
@@ -243,7 +243,7 @@
       </div>
     </div>
 
-    <div class="tab-pane" id="tp2">
+    <div class="tab-pane {% if method == 'spearman' %}active{% endif %}" id="tp2">
       <br>
       <div id="srscatterplot2"></div>
       <br>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 96ad9c35..8275f1dd 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,10 +1,11 @@
 {% extends "base.html" %}
+{% block title %}Correlation Matrix{% endblock %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
 {% endblock %}
 {% block content %}
 
@@ -32,6 +33,7 @@
       {% endfor %}
     </tr>
     {% for trait in traits %}
+    {% set outer_loop = loop.index %}
     <tr>
       <td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td>
       <td align="right" style="padding-right: 4px;" >
@@ -54,7 +56,7 @@
       {% if result[1] == 0 %}
       <td nowrap="ON" align="middle" bgcolor="#eeeeee" style="padding: 3px; line-height: 1.1;">N/A</td>
       {% else %}
-      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?method={% if loop.index > outer_loop %}spearman{% else %}pearson{% endif %}&dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
       {% endif %}
       {% endif %}
       {% endfor %}
@@ -63,6 +65,12 @@
   </tbody>
 </table>
 <br>
+<form method="post" target="_blank" action="/export_corr_matrix" id="matrix_export_form">
+  <input type="hidden" name="export_filepath" value="{{ export_filepath }}">
+  <input type="hidden" name="export_filename" value="{{ export_filename }}">
+  <button class="btn btn-default" id="export">Download <span class="glyphicon glyphicon-download"></span></button>
+</form>
+<br>
 {% if pca_works == "True" %}
 <h2>PCA Traits</h2>
 <div style="margin-bottom: 20px; overflow:hidden;">
@@ -133,7 +141,7 @@
 
     <script type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='chroma/chroma.min.js') }}"></script>
@@ -172,6 +180,14 @@
         "paging": false,
         "orderClasses": true
       } );
+
+      export_corr_matrix = function() {
+            $('#matrix_export_form').attr('action', '/export_corr_matrix');
+            return $('#matrix_export_form').submit();
+      }
+
+      $('#export').click(export_corr_matrix);
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index a9a3a2ca..8e2a23fd 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -32,9 +32,7 @@
             {% for this_trait in trait_list %}
                 {{ this_trait.name }}:{{ this_trait.dataset }},
             {% endfor %}" >
-
             {% include 'tool_buttons.html' %}
-
           </form>
         </div>
         <br />
@@ -135,9 +133,10 @@
     <script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.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/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
@@ -313,7 +312,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
@@ -434,7 +433,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
@@ -488,7 +487,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index b16de42e..92754266 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -39,6 +39,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
 
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 13ca52df..7efbdccf 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -326,7 +326,7 @@
         }
     </script>
 
-    <script type="text/javascript" src="/twitter/js/twitterFetcher_min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script>
 
     <script type="text/javascript">
       var configProfile = {
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 38dca514..b31e3b7a 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -69,6 +69,6 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <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 language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
 
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c95a0522..32cf3c0a 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -130,7 +130,7 @@
 
     <script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index fb564b28..a96b8e3b 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -217,7 +217,7 @@
 {% block js %}
   <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
   <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
-  <script language="javascript" type="text/javascript" src="/static/new/js_external/typeahead.bundle.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='typeahead/typeahead.bundle.js') }}"></script>
 
   <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3557a62a..25563e86 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -799,6 +799,17 @@ def export_mapping_results():
 
     return response
 
+@app.route("/export_corr_matrix", methods = ('POST',))
+def export_corr_matrix():
+    file_path = request.form.get("export_filepath")
+    file_name = request.form.get("export_filename")
+    results_csv = open(file_path, "r").read()
+    response = Response(results_csv,
+                        mimetype='text/csv',
+                        headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
+
+    return response
+
 @app.route("/export", methods = ('POST',))
 def export():
     logger.info("request.form:", request.form)