Fixed bug for creating one of the third party links on the trait page

Changed text in several pages (submit trait, mapping error)

Changed header menu structure some

8 files changed, 42 insertions, 36 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index a08acb0a..b9e6abd8 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -53,7 +53,7 @@ ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%
 EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
 WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
 ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
-DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
+DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 5178ece8..5c349bf3 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -291,7 +291,12 @@ class ShowTrait(object):
                         FROM GeneList_rn33
                         WHERE geneSymbol = '{}'""".format(self.this_trait.symbol)
 
-                kgId, chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None
+                results = g.db.execute(query).fetchone()
+		if results:
+                    kgId, chr, transcript_start, transcript_end = results
+                else:
+                    kgId = chr = transcript_start = transcript_end = None
+
                 if chr and transcript_start and transcript_end and kgId:
                     transcript_start = int(transcript_start*1000000) # Convert to bases from megabases
                     transcript_end = int(transcript_end*1000000)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 3fd9faf5..b1977b7f 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -44,10 +44,19 @@
                             <a href="/intro">Intro</a>
                         </li>
                         <li class="">
-                            <a href="/">Search</a>
+                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Info <span class="caret"></a>
+                            <ul class="dropdown-menu">
+                              <li><a href="/news">News</a></li>
+                              <li><a href="http://genenetwork.org/faq.html">FAQ</a></li>
+                              <li><a href="http://genenetwork.org/glossary.html">Glossary of Term</a></li>
+                              <li><a href="/references">References</a></li>
+                              <li><a href="/policies">Policies</a></li>
+                              <li><a href="/links">Links</a></li>
+                              <li><a href="/environments">Environments</a></li>
+                            </ul>
                         </li>
                         <li class="">
-                            <a href="/submit_trait">Submit Trait</a>
+                            <a href="/submit_trait">Submit Data</a>
                         </li>
                         <li class="">
                             <a href="/collections/list">Collections
@@ -62,29 +71,19 @@
                             <a href="/snp_browser">SNP Browser</a>
                         </li>
                         <li class="">
-                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a>
-                            <ul class="dropdown-menu">
-                              <li><a href="/news">News</a></li>
-                              <li><a href="http://genenetwork.org/faq.html">FAQ</a></li>
-                              <li><a href="http://genenetwork.org/glossary.html">Glossary of Term</a></li>
-                              <li><a href="/references">References</a></li>
-                              <li><a href="/policies">Policies</a></li>
-                              <li><a href="/links">Links</a></li>
-                              <li><a href="/environments">Environments</a></li>
-                            </ul>
-                        </li>
-                        <li class="">
                             {% if g.user_session.logged_in %}
                             <a id="login_out" title="Signed in as {{ g.user_session.user_name }}" href="/n/logout">Sign out</a>
                             {% else %}
                             <a id="login_in" href="/n/login">Sign in</a>
                             {% endif %}
                         </li>
+                        <!--
                         <li style="margin-left: 20px;">
                             <a href="http://gn2-staging.genenetwork.org" style="font-weight: bold;" >Use Staging Branch</a>
                         </li>
+                        -->
                         <li style="margin-left: 20px;">
-                            <a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GeneNetwork 1</a>
+                            <a href="http://www.genenetwork.org" style="font-weight: bold;" >Use GN1</a>
                         </li>
                     </ul>
                 </div>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 70390830..9b584ea5 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -9,7 +9,7 @@
 
     <div class="container" style="width: 2000px;">
 
-        <h3>GN searched 754 datasets and 39765944 traits across 10 species, and found {{ trait_count }} results that match your query.
+        <h3>GN searched 754 datasets and 39,765,944 traits across 10 species, and found {{ trait_count }} results that match your query.
         You can filter these results by adding key words in the fields below and you can also sort results on most columns.</h3>
         <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p>
 
@@ -21,14 +21,13 @@
             <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
             <input type="text" id="searchbox" class="form-control" style="width: 180px; display: inline;" placeholder="Search This Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 120px; display: inline;" placeholder="Select Top ...">
-            <br />
-            <br />
-            <form id="export_form" method="POST" action="/export_traits_csv">
+            <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;">
               <input type="hidden" name="database_name" id="database_name" value="None">
               <input type="hidden" name="export_data" id="export_data" value="">
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+              <button class="btn btn-default" id="export_traits">Download</button>
             </form>
             <br />
+            <br />
             <div style="width: 100%;">
               <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
                 <tbody>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 42bf1b64..609c1852 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -21,14 +21,13 @@
             <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
-            <br />
-            <br />
-            <form id="export_form" method="POST" action="/export_traits_csv">
+            <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;">
               <input type="hidden" name="database_name" id="database_name" value="None">
               <input type="hidden" name="export_data" id="export_data" value="">
               <button class="btn btn-default" id="export_traits">Download CSV</button>
             </form>
             <br />
+            <br />
             <div style="width: 100%;">
               <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
                 <tbody>
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 30e3f2f6..251a816f 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -181,7 +181,6 @@
                         <h1>Affiliates</h1>
                         <ul>
                           <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</a> at UTHSC</li>
-                          <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at UTHSC</li>
                           <li><a href="https://systems-genetics.org/">Systems Genetics</a> @ EPFL</li>
                           <li>UTHSC <a href="http://bnw.genenetwork.org/">Bayesian Network Web Server</a></li>
                         </ul>
diff --git a/wqflask/wqflask/templates/mapping_error.html b/wqflask/wqflask/templates/mapping_error.html
index b73a2c31..884d4df8 100644
--- a/wqflask/wqflask/templates/mapping_error.html
+++ b/wqflask/wqflask/templates/mapping_error.html
@@ -5,7 +5,13 @@
     {{ header("An error occurred during mapping") }}
 
     <div class="container">
+    <h3>
         <p>There is likely an issue with the genotype file associated with this group/RISet. Please contact Zach Sloan (zachary.a.sloan@gmail.com) or Arthur Centeno (acenteno@gmail.com) about the data set in question.</p>
+    </h3>
+    <br>
+    <h3>
+        <p>Try mapping using interval mapping instead; some genotype files with many columns of NAs have issues with GEMMA or R/qtl.</p>
+    </h3>
     </div>
 
 
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index c9f716bf..0dd38fe5 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -8,7 +8,7 @@
         {{ flash_me() }}
 
         <div class="row" style="width: 1400px !important;">
-            <div class="col-xs-5">
+            <div class="col-xs-3">
                 <section id="description">
                     <div>
                         <h2 style="color: #5a5a5a;">Introduction</h2>
@@ -33,7 +33,7 @@
                         <h2 style="color: #5a5a5a;">Trait Submission Form</h2>
                         <hr>
                         <div style="padding-bottom: 50px;" class="form-horizontal">
-                          <h3>1. Choose cross or RI set:</h3>
+                          <h3>1. Choose Species and Group:</h3>
                           <br>
                           <div class="col-xs-2" style="min-height: 15vh; display: flex; align-items: center;">
                             <img src="/static/new/images/step1.gif">
@@ -52,7 +52,6 @@
                               </div>
                             </div>
                           </div>
-                          <div class="form-horizontal"><img src="/static/new/images/arrowdown.gif" style="display:block; margin-left: 50%; margin-right: 50%;"></div>
                         </div>
                         <div style="padding-bottom: 50px;" class="form-horizontal">
                           <h3>2. Enter Trait Data:</h3>
@@ -66,9 +65,9 @@
                             <div class="form-group" style="padding-left: 15px;">
                               <p>
                                  <b>From a File:</b> You can enter data by entering a file name here. The file should contain a series of numbers representing trait values. 
-                                 The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual 
-	                         or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set,  
-                                 when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that 
+                                 The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual
+	                         or recombinant inbred line. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set,
+                                 when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name here, any data that
                                  you paste into the next section will be ignored.
                               </p>
                               <input type="file" name="trait_file" style="border-width: 1px; border-style: solid; border-color: #999999;">
@@ -77,10 +76,10 @@
                             <div class="form-group" style="padding-left: 15px;">
                               <p>
                                  <b>Paste or Type Multiple Values:</b> You can enter data by pasting a series of numbers representing trait values into this area. 
-                                 The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each progeny individual 
-                                 or recombinant inbredline. Represent missing values with a non-numeric character such as "x". If you have chosen a recombinant inbred set, 
-                                 when you submit your data will be displayed in a form where you can confirm and/or edit them. If you enter a file name in the previous section, 
-                                 any data that you paste here will be ignored. Check sample data for the correct format. 
+                                 The values can be on one line separated by spaces or tabs, or they can be on separate lines. Include one value for each individual 
+                                 or line. Use an "x" for missing values. If you have chosen a set of inbred strains, then your data will be displayed in a form in 
+                                 which you can confirm and/or edit. If you enter a file name in the previous section, 
+                                 any data that you paste here will be ignored. Check <a href="http://genenetwork.org/RIsample.html">sample data</a> for the correct format. 
                               </p>
                               <textarea name="trait_paste" rows="6" cols="70"></textarea>
                             </div>