Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

22 files changed, 31 insertions, 44 deletions

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 5c8edab8..3b6adde2 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -165,7 +165,7 @@
 
 {% block js %}
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.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/search_results.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/plugins/sorting/natural.js') }}"></script>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index dc74ddb2..f791457f 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -28,8 +28,8 @@
         js_data = {{ js_data | safe }}
     </script>
 
-    <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="{{ 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 type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 4739b467..1fd5cd15 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -3,8 +3,8 @@
 {% 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/panelutil.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
-    <link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.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='nvd3/nv.d3.min.css') }}">
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot.css" />
 {% endblock %}
 
@@ -346,9 +346,9 @@
     <script>
        js_data = {{ js_data | safe }};
     </script>
-    <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-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="{{ url_for('js', filename='d3js/d3.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='d3-tip/d3-tip.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 5659dca7..d9fd8540 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -127,10 +127,10 @@
         loadings = {{ loadings_array | safe }}
     </script>
 
-    <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+    <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="/static/new/js_external/md5.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>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index afa19c4a..362fb1c5 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -200,7 +200,7 @@
 {% endblock %}
 
 {% block js %}
-    <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
+    <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>
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 0108d93a..e374eb4e 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -2,7 +2,7 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
     <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
-    <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.css">
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
     <style>
         /* The Cytoscape Web container must have its dimensions set. */
         html, body { height: 100%; width: 100%; padding: 0; margin: 0; }
@@ -65,8 +65,8 @@
     </script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.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='qtip2/jquery.qtip.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="/js/cytoscape/cytoscape.min.js"></script>
     <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
     <!-- should be using cytoscape-popper for tips, see docs -->
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 617bdc0f..acb3ee75 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -46,7 +46,7 @@
 {% endblock %}
 
 {% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.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="/static/new/js_external/jszip.min.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 66995346..0a58952c 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -46,7 +46,7 @@
 {% endblock %}
 
 {% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.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="/static/new/js_external/jszip.min.js"></script>
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 275ff1ba..497838dd 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -32,8 +32,8 @@
         js_data = {{ js_data | safe }}
     </script>
 
-    <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="{{ 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/new/javascript/lodheatmap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 961c3b21..224ba905 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -332,11 +332,11 @@
 
 {% block js %}  
 
-    <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/md5.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="/static/new/js_external/d3-tip.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.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="/static/new/js_external/plotly-latest.min.js"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 25af7bb1..be3d0402 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -2,7 +2,7 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
     <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
-    <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.css">
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
     <style>
         /* The Cytoscape Web container must have its dimensions set. */
         html, body { height: 100%; width: 100%; padding: 0; margin: 0; }
@@ -141,8 +141,8 @@
     </script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.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='qtip2/jquery.qtip.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="/js/cytoscape/cytoscape.min.js"></script>
     <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html
index a981b6bd..e5c42a45 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password.html
@@ -48,8 +48,6 @@
   {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
-
     {% include "new_security/_scripts.html" %}
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
index e32ef753..473fa377 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
@@ -20,8 +20,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
-
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 80fed82a..095036f0 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -114,8 +114,6 @@ label.error,div.error{
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
-
     <!-- Disable plugin, see https://github.com/genenetwork/genenetwork2/issues/310
 
     <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html
index cda1e477..7110dc79 100644
--- a/wqflask/wqflask/templates/new_security/password_reset.html
+++ b/wqflask/wqflask/templates/new_security/password_reset.html
@@ -72,7 +72,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
 
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html
index da74090c..325d8aa5 100644
--- a/wqflask/wqflask/templates/new_security/register_user.html
+++ b/wqflask/wqflask/templates/new_security/register_user.html
@@ -99,7 +99,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
 
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html
index 349cbdd4..e71d5598 100644
--- a/wqflask/wqflask/templates/new_security/registered.html
+++ b/wqflask/wqflask/templates/new_security/registered.html
@@ -18,7 +18,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
 
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html
index 290961e6..459bd66a 100644
--- a/wqflask/wqflask/templates/new_security/thank_you.html
+++ b/wqflask/wqflask/templates/new_security/thank_you.html
@@ -18,8 +18,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
-
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html
index 817fa963..3aa24e37 100644
--- a/wqflask/wqflask/templates/new_security/verification_still_needed.html
+++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html
@@ -21,8 +21,6 @@
 {% endblock %}
 
 {% block js %}
-    <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
-
     {% include "new_security/_scripts.html" %}
     <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 5c776fc1..f1646af7 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -62,8 +62,8 @@
 
 {% block js %}  
 
-    <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="{{ 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/packages/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/plugins/sorting/scientific.js') }}"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index dbdca9f8..94e8de46 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -154,7 +154,7 @@
 {% endblock %}
 
 {% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 15442ca7..56df2049 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -132,7 +132,7 @@
     <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="/static/new/js_external/d3-tip.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
     <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>