Changed header drop-down menu layout

Added a couple new third party links

Added link to GN1 trait page in trait pages

Fixed gene global search table appearance

6 files changed, 38 insertions, 23 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index b9e6abd8..0b884815 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -54,6 +54,8 @@ 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://ensembl.org/Mus_musculus/Variation/Population?v=%s'
+PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
+OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%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 02c65d47..880a291f 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -255,7 +255,6 @@ class ShowTrait(object):
         self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.this_trait.pubmed_id if check_if_attr_exists(self.this_trait, 'pubmed_id') else None
         self.ncbi_gene_link = webqtlConfig.NCBI_LOCUSID % self.this_trait.geneid if check_if_attr_exists(self.this_trait, 'geneid') else None
         self.omim_link = webqtlConfig.OMIM_ID % self.this_trait.omim if check_if_attr_exists(self.this_trait, 'omim') else None
-        self.unigene_link = webqtlConfig.UNIGEN_ID % tuple(string.split(self.this_trait.unigeneid, '.')[:2]) if check_if_attr_exists(self.this_trait, 'unigeneid') else None
         self.homologene_link = webqtlConfig.HOMOLOGENE_ID % self.this_trait.homologeneid if check_if_attr_exists(self.this_trait, 'homologeneid') else None
 
         self.genbank_link = None
@@ -265,14 +264,16 @@ class ShowTrait(object):
                 genbank_id = genbank_id[0:-1]
             self.genbank_link = webqtlConfig.GENBANK_ID % genbank_id
 
-        self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = None
-        self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = None
+        self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None
+        self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_link = None
         if self.this_trait.symbol:
             self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol
             self.gtex_link = webqtlConfig.GTEX_URL % self.this_trait.symbol
             self.string_link = webqtlConfig.STRING_URL % self.this_trait.symbol
             self.panther_link = webqtlConfig.PANTHER_URL % self.this_trait.symbol
             self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol
+            self.protein_atlas_link = webqtlConfig.PROTEIN_ATLAS_URL % self.this_trait.symbol
+            self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol
 
             if self.dataset.group.species == "mouse" or self.dataset.group.species == "human":
                 if self.dataset.group.species == "mouse":
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 2366bdec..f9bc1055 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -41,7 +41,12 @@
                             <a href="/" style="font-weight: bold;">GeneNetwork</a>
                         </li>
                         <li class="">
-                            <a href="/intro">Intro</a>
+                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Intro <span class="caret"></a>
+                            <ul class="dropdown-menu">
+                                <li><a href="/intro">Intro</a></li>
+                                <li><a href="/submit_trait">Submit Trait</a></li>
+                                <li><a href="http://genenetwork.org/webqtl/main.py?FormID=batSubmit">Batch Submission</a></li>
+                            </ul>
                         </li>
                         <li class="">
                             <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Info <span class="caret"></a>
@@ -56,7 +61,13 @@
                             </ul>
                         </li>
                         <li class="">
-                            <a href="/submit_trait">Submit Data</a>
+                                <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Tools <span class="caret"></a>
+                                <ul class="dropdown-menu">
+                                  <li><a href="/snp_browser">Variant Browser</a></li>
+                                  <li><a href="http://bnw.genenetwork.org/BNW/sourcecodes/home.php">Bayesian Network Webserver</a></li>
+                                  <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
+                                  <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
+                                </ul>
                         </li>
                         <li class="">
                             <a href="/collections/list">Collections
@@ -68,9 +79,6 @@
                             </a>
                         </li>
                         <li class="">
-                            <a href="/snp_browser">SNP Browser</a>
-                        </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 %}
@@ -82,9 +90,6 @@
                             <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 GN1</a>
-                        </li>
                     </ul>
                 </div>
             </div>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 0ee98972..1a4ff752 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -202,7 +202,8 @@
                     },
                     { 
                       'title': "Location",
-                      'type': "natural", 
+                      'type': "natural",
+                      'width': "100px",
                       'data': "location_repr"
                     },
                     {
@@ -212,19 +213,21 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     { 
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max<br>LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
                       'type': "natural", 
                       'data': "LRS_score_repr",
                       'orderSequence': [ "desc", "asc"]
                     },
                     { 
-                      'title': "Max LRS Location",
-                      'type': "natural", 
+                      'title': "Max LRS<br>Location",
+                      'type': "natural",
+                      'width': "100px",
                       'data': "max_lrs_text"
                     },
                     { 
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
-                      'type': "natural", 
+                      'title': "Additive<br>Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'type': "natural",
+                      'width': "50px",
                       'data': "additive",
                       'orderSequence': [ "desc", "asc"]
                     }
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index bdf51bf8..5706c870 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -191,6 +191,7 @@
                           <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</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>
+                          <li><a href="http://genenetwork.org">GeneNetwork 1</a></li>
                         </ul>
                     </div>
                 </section>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index bb0b62fe..63a87825 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -100,15 +100,15 @@
             </a>
             &nbsp;&nbsp;
             {% endif %}
-            {% if unigene_link %}
-            <a href="{{ unigene_link }}" target="_blank" title="NCBI UniGene">
-                UniGene
+            {% if protein_atlas_link %}
+            <a href="{{ protein_atlas_link }}" target="_blank" title="Human Protein Atlas">
+                    Protein Atlas
             </a>
             &nbsp;&nbsp;
             {% endif %}
-            {% if genbank_link %}
-            <a href="{{ genbank_link }}" target="_blank" title="Find the original GenBank sequence used to design the probes">
-                GenBank
+            {% if open_targets_link %}
+            <a href="{{ open_targets_link }}" target="_blank" title="Open Targets">
+                Open Targets
             </a>
             &nbsp;&nbsp;
             {% endif %}
@@ -219,6 +219,9 @@
         </a>
         {% endif %}
         {% endif %}
+        <a target="_blank" href="http://www.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
+        </a>
     </div>
 </div>