From 78c472aeb77fb76c54ac93f5811425e05888983f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 29 Apr 2016 16:52:36 +0000
Subject: Fixed links in correlation descriptions on trait page and removed
 target=_blank (so will not open in new window unless user specifies)

Fixed javascript so description changes when user changes the method and "Type" option is removed for literature correlation
---
 wqflask/wqflask/static/new/javascript/show_trait.js      |  9 ++++-----
 .../templates/show_trait_calculate_correlations.html     | 16 ++++++++--------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 9e249c28..2fa77ae0 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -296,18 +296,17 @@
     };
     on_corr_method_change = function() {
       var corr_method;
-      console.log("in beginning of on_corr_method_change");
-      corr_method = $('select[name=corr_method]').val();
+      corr_method = $('select[name=corr_type]').val();
       console.log("corr_method is:", corr_method);
       $('.correlation_desc').hide();
       $('#' + corr_method + "_r_desc").show().effect("highlight");
       if (corr_method === "lit") {
-        return $("#corr_sample_method_options").hide();
+        return $("#corr_sample_method").hide();
       } else {
-        return $("#corr_sample_method_options").show();
+        return $("#corr_sample_method").show();
       }
     };
-    $('select[name=corr_method]').change(on_corr_method_change);
+    $('select[name=corr_type]').change(on_corr_method_change);
 
     submit_special = function(url) {
       $("#trait_data_form").attr("action", url);
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index ed58b32c..80fafa5e 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -63,7 +63,7 @@
             </div>
         </div>
             
-        <div class="form-group">
+        <div id="corr_sample_method" class="form-group">
             <label for="corr_sample_method" class="col-xs-1 control-label">Type</label>
             <div class="col-xs-2 controls">
                 <select name="corr_sample_method" class="form-control">
@@ -112,30 +112,30 @@
             <label for="descriptions" class="col-xs-1 control-label"></label>
             <div class="col-xs-6 controls">
             <span id="sample_r_desc" class="correlation_desc fs12">
-                The <a href="/correlationAnnotation.html#sample_r" target="_blank">Sample Correlation</a>
+                The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
                 is computed
                 between trait data and any
                 other traits in the sample database selected above. Use
-                <a href="/glossary.html#Correlations" target="_blank">Spearman
+                <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
                 Rank</a>
                 when the sample size is small (&lt;20) or when there are influential outliers.
             </span>
             <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
-                The <a href="/correlationAnnotation.html" target="_blank">Literature Correlation</a>
+                The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
                 (Lit r) between
                 this gene and all other genes is computed<br>
-                using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html" target="_blank">
+                using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
                 Semantic Gene Organizer</a>
                 and human, rat, and mouse data from PubMed.
                 Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
-                <a href="/glossary.html#Literature" target="_blank">More on using Lit r</a>
+                <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
             </span>
             <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
-                The <a href="/webqtl/main.py?FormID=tissueCorrelation" target="_blank">Tissue Correlation</a>
+                The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
                 (Tissue r)
                 estimates the similarity of expression of two genes
                 or transcripts across different cells, tissues, or organs
-                (<a href="/correlationAnnotation.html#tissue_r" target="_blank">glossary</a>).
+                (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
                 Tissue correlations
                 are generated by analyzing expression in multiple samples usually taken from single cases.<br>
                 <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
-- 
cgit v1.2.3


From 53fc74097ba82d3903d844e12bde61e53b4b9b2c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 29 Apr 2016 16:57:29 +0000
Subject: Also fixed links in statistics section (for normal probability plot)
 and removed 'target=_blank's

---
 wqflask/wqflask/templates/show_trait_statistics.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 242f1c26..3ee8bdea 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -108,8 +108,8 @@
                         </div>
 
                         <div>
-                            More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
-                            about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a>
+                            More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot">Normal Probability Plots</a> and more
+                            about interpreting these plots from the <a href="http://genenetwork.org/glossary.html#normal_probability">glossary</a>
                             </div>
 
                     </div>
-- 
cgit v1.2.3


From b7cabb198f7d3c47074da3e6d0d523281aad7e13 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 29 Apr 2016 17:06:34 +0000
Subject: Fixed database link in trait page details

---
 wqflask/wqflask/templates/show_trait_details.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index ccb3b51b..95a3b967 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -26,7 +26,7 @@
     <tr>
         <td>Database</td>
         <td>
-            <a href="{{ url_for('static', filename='dbdoc/' + dataset.fullname + '.html') }}" target="_blank">
+            <a href="http://genenetwork.org/dbdoc/{{ dataset.name }}.html">
                 {{ dataset.fullname }}
             </a>
         </td>
-- 
cgit v1.2.3