Added GeneMANIA link

Fixed issue that caused error when creating UCSC RefSeq link

Fixed issue that sometimes caused an error for phenotype searches

Changed some text on collections page

5 files changed, 22 insertions, 7 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index b14cc4b0..a08acb0a 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -43,6 +43,7 @@ HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s"
 GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s"
 GTEX_URL = "https://www.gtexportal.org/home/gene/%s"
 GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s"
+GENEMANIA_URL = "https://genemania.org/search/%s/%s"
 UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
 BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s"
 STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s"
@@ -87,4 +88,3 @@ if not valid_path(JSON_GENODIR):
 PORTADDR = "http://50.16.251.170"
 INFOPAGEHREF = '/dbdoc/%s.html'
 CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
-SCRIPTFILE = 'main.py'
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 66d3a448..e10b31c0 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -257,7 +257,7 @@ class ShowTrait(object):
             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 = None
+        self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_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
@@ -266,7 +266,10 @@ class ShowTrait(object):
             self.ebi_gwas_link = webqtlConfig.EBIGWAS_URL % self.this_trait.symbol
 
             if self.dataset.group.species == "mouse" or self.dataset.group.species == "human":
-                self.genebridge_link = webqtlConfig.GENEBRIDGE_URL % (self.this_trait.symbol, self.dataset.group.species)
+                if self.dataset.group.species == "mouse":
+                    self.genemania_link = webqtlConfig.GENEMANIA_URL % ("mus-musculus", self.this_trait.symbol)
+                else:
+                    self.genemania_link = webqtlConfig.GENEMANIA_URL % ("homo-sapiens", self.this_trait.symbol)
 
                 if self.dataset.group.species == "mouse":
                     self.aba_link = webqtlConfig.ABA_URL % self.this_trait.symbol
@@ -282,8 +285,10 @@ 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.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol)
+
                 query = """SELECT kgID, chromosome, txStart, txEnd
-                        FROM GeneLink_rn33
+                        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
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 8d22b2a8..7e1001fc 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -84,8 +84,8 @@
             <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-            <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete From Collection</button>
-            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy Record to Other Collection</button>
+            <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete Rows</button>
+            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy to Other Collection</button>
             <br />
             <br />
             <form id="export_form" method="POST" action="/export_traits_csv">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index e20ea2d3..bf434452 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -324,7 +324,11 @@
                       'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
-                        return decodeURIComponent(escape(data.description))
+                        try {
+                          return decodeURIComponent(escape(data.description))
+                        } catch {
+                          return escape(data.description)
+                        }
                       }
                     },
                     {
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 09f36021..43efa314 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -88,6 +88,12 @@
             </a>
             &nbsp;&nbsp;
             {% endif %}
+            {% if genemania_link %}
+            <a href="{{ genemania_link }}" title="GeneMANIA">
+                GeneMANIA
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
             {% if unigene_link %}
             <a href="{{ unigene_link }}" title="NCBI UniGene">
                 UniGene