From 0f3f194726ced9f41641c9041c6a0416dcb58975 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Dec 2019 13:55:42 -0600
Subject: Added RGD link to trait page and removed Genotation link since it
 isn't working

---
 wqflask/base/webqtlConfig.py                      | 1 +
 wqflask/wqflask/show_trait/show_trait.py          | 4 +++-
 wqflask/wqflask/templates/show_trait_details.html | 8 ++++++++
 3 files changed, 12 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 9dddc63e..018d5d54 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -57,6 +57,7 @@ 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"
 UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
+RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%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 09004396..5d2f52cb 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -271,7 +271,7 @@ class ShowTrait(object):
         if check_if_attr_exists(self.this_trait, 'uniprotid'):
             self.uniprot_link = webqtlConfig.UNIPROT_URL % self.this_trait.uniprotid
 
-        self.genotation_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None
+        self.genotation_link = self.rgd_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
@@ -283,6 +283,7 @@ class ShowTrait(object):
             #self.open_targets_link = webqtlConfig.OPEN_TARGETS_URL % self.this_trait.symbol
 
             if self.dataset.group.species == "mouse" or self.dataset.group.species == "human":
+                self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize())
                 if self.dataset.group.species == "mouse":
                     self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol)
                 else:
@@ -307,6 +308,7 @@ class ShowTrait(object):
                         self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % ('mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end)
 
             if self.dataset.group.species == "rat":
+                self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize())
                 self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol)
 
                 query = """SELECT kgID, chromosome, txStart, txEnd
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 7c2da752..b64b34d7 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -119,10 +119,18 @@
               
             {% endif %}
             {% if this_trait.symbol %}
+            <!--
             <a href="{{ genotation_link }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
                 Genotation
             </a>
             &nbsp;&nbsp;
+            -->
+            {% if rgd_link %}
+            <a href="{{ rgd_link }}" target="_blank">
+                Rat Genome DB
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
             <a href="{{ gtex_link }}" target="_blank" title="GTEx Portal">
                 GTEx Portal
             </a>
-- 
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