From dc002daace320135b4d32ac08de2ee568e68ba51 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 20 May 2020 14:17:17 -0500
Subject: Fixed issue when some case attribute values don't exist + added
 phenogen link to trait page

---
 wqflask/wqflask/show_trait/show_trait.py          | 9 ++++++---
 wqflask/wqflask/templates/show_trait_details.html | 6 ++++++
 2 files changed, 12 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 072d7f8c..29b2f77e 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -294,7 +294,7 @@ 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.rgd_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.phenogen_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
@@ -332,6 +332,7 @@ class ShowTrait(object):
 
             if self.dataset.group.species == "rat":
                 self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize())
+                self.phenogen_link = webqtlConfig.PHENOGEN_URL % (self.this_trait.symbol)
                 self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol)
 
                 query = """SELECT kgID, chromosome, txStart, txEnd
@@ -603,8 +604,10 @@ def get_categorical_variables(this_trait, sample_list):
         for attribute in sample_list.attributes:
             attribute_vals = []
             for sample_name in this_trait.data.keys():
-                attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
-
+                if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes:
+                    attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
+                else:
+                    attribute_vals.append("N/A")
             num_distinct = len(set(attribute_vals))
 
             if num_distinct < 10:
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 62268a54..878b6ced 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -141,6 +141,12 @@
                 GTEx Portal
             </a>
             &nbsp;&nbsp;
+            {% if phenogen_link %}
+            <a href="{{ phenogen_link }}" target="_blank">
+                PhenoGen
+            </a>
+            &nbsp;&nbsp;
+            {% endif %}
             {% if genebridge_link %}
             <a href="{{ genebridge_link }}" target="_blank">
                 GeneBridge
-- 
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