From 5c71ead0411b834b51bf084c147543208390c310 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Tue, 17 Sep 2024 15:13:57 +0300
Subject: Refactor: remove hardcoded links and fix bug for path.

---
 gn2/wqflask/static/new/javascript/show_trait.js              |  2 +-
 gn2/wqflask/templates/mapping_results.html                   | 10 +++++-----
 gn2/wqflask/templates/show_trait_calculate_correlations.html |  2 +-
 gn2/wqflask/templates/show_trait_statistics.html             |  2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/gn2/wqflask/static/new/javascript/show_trait.js b/gn2/wqflask/static/new/javascript/show_trait.js
index edb2cfab..6d77e130 100644
--- a/gn2/wqflask/static/new/javascript/show_trait.js
+++ b/gn2/wqflask/static/new/javascript/show_trait.js
@@ -68,7 +68,7 @@ statTableRows.push(
   }, {
     vn: "interquartile",
     pretty: "<font color='black'>Interquartile Range</font>",
-    url: "http://www.genenetwork.org/glossary.html#Interquartile",
+    url: "{{ url_for('gn_docs_blueprint.glossary') }}#Interquartile",
     digits: 3
   }, {
     vn: "skewness",
diff --git a/gn2/wqflask/templates/mapping_results.html b/gn2/wqflask/templates/mapping_results.html
index 2fed79c1..2b1660fd 100644
--- a/gn2/wqflask/templates/mapping_results.html
+++ b/gn2/wqflask/templates/mapping_results.html
@@ -116,7 +116,7 @@
                     <label class="radio-inline">
                       <input type="radio" name="LRSCheck" value="{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %}" {% if LRS_LOD == "LOD" or LRS_LOD == "-logP" %}checked{% endif %}>{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %}
                     </label>
-                    <a href="https://genenetwork.org/glossary.html#LOD" target="_blank">
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#LOD" target="_blank">
                       <sup style="color:#f00"> ?</sup>
                     </a>
                   </td>
@@ -158,27 +158,27 @@
             <div class="col-xs-4" style="padding: 0px;">
                   {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
                   <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test 
-                    <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank">
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#Permutation" target="_blank">
                       <sup style="color:#f00"> ?</sup>
                     </a>
                   <br>
                   {% endif %}
                   {% if mapping_method == "reaper" and nboot > 0 %}
                   <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test 
-                    <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank">
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#bootstrap" target="_blank">
                       <sup style="color:#f00"> ?</sup>
                     </a>
                   <br>
                   {% endif %}
                   {% if mapping_method == "reaper" %}
                   <input type="checkbox" name="additiveCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if additiveChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Allele Effects
-                    <a href="http://genenetwork.org/glossary.html#additive" target="_blank">
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#additive" target="_blank">
                       <sup style="color:#f00"> ?</sup>
                     </a>
                   <br>
                   {% endif %}
                   <input type="checkbox" name="showSNP" class="checkbox" style="display: inline; margin-top: 0px;" {% if SNPChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">SNP Track </span>
-                    <a href="http://genenetwork.org/glossary.html#snpSeismograph" target="_blank">
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#snpSeismograph" target="_blank">
                       <sup style="color:#f00"> ?</sup>
                     </a>
                     <span style="color:red;">*</span>
diff --git a/gn2/wqflask/templates/show_trait_calculate_correlations.html b/gn2/wqflask/templates/show_trait_calculate_correlations.html
index d2e6624e..2f78a095 100644
--- a/gn2/wqflask/templates/show_trait_calculate_correlations.html
+++ b/gn2/wqflask/templates/show_trait_calculate_correlations.html
@@ -148,7 +148,7 @@
                     Semantic Gene Organizer</span>
                     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="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a></dd>
+                    <a href="{{ url_for('gn_docs_blueprint.glossary') }}#Literature">More on using Lit r</a></dd>
                 <dt class="map-method-text">Tissue Correlation</dt>
                 <dd>The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
                     (Tissue r)
diff --git a/gn2/wqflask/templates/show_trait_statistics.html b/gn2/wqflask/templates/show_trait_statistics.html
index 9ee0de5c..d16835e7 100644
--- a/gn2/wqflask/templates/show_trait_statistics.html
+++ b/gn2/wqflask/templates/show_trait_statistics.html
@@ -87,7 +87,7 @@
                     <br>
                     <div>
                         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>
+                        about interpreting these plots from the <a href="{{ url_for('gn_docs_blueprint.glossary') }}#normal_probability">glossary</a>
                     </div>
                 </div>
             </div>
-- 
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