From de77a333a7bcc7260e5cf91bf786f84c9c68bc06 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 Feb 2020 15:47:32 -0600
Subject: Added NCBI summary to trait page when applicable

---
 wqflask/wqflask/show_trait/show_trait.py          | 18 +++++++++++++++++-
 wqflask/wqflask/templates/show_trait_details.html |  6 ++++++
 2 files changed, 23 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 4efaa968..10ce38a7 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -5,6 +5,7 @@ import os
 import datetime
 import cPickle
 import uuid
+import requests
 import json as json
 
 from collections import OrderedDict
@@ -129,6 +130,8 @@ class ShowTrait(object):
         self.get_external_links()
         self.build_correlation_tools()
 
+        self.ncbi_summary = get_ncbi_summary(self.this_trait)
+
         #Get nearest marker for composite mapping
         if not self.temp_trait:
             if check_if_attr_exists(self.this_trait, 'locus_chr') and self.dataset.type != "Geno" and self.dataset.type != "Publish":
@@ -560,4 +563,17 @@ def check_if_attr_exists(the_trait, id_type):
         else:
             return True
     else:
-        return False
\ No newline at end of file
+        return False
+
+def get_ncbi_summary(this_trait):
+    if check_if_attr_exists(this_trait, 'geneid'):
+        #ZS: Need to switch this try/except to something that checks the output later
+        try:
+            response = requests.get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=%s&retmode=json" % this_trait.geneid)
+            logger.debug("NCBI:", json.loads(response.content)['result'][this_trait.geneid])
+            summary = json.loads(response.content)['result'][this_trait.geneid]['summary']
+            return summary
+        except:
+            return None
+    else:
+        return None
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 3584be22..20dee54e 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -50,6 +50,12 @@
         <td>{{ this_trait.location_fmt }}</td>
     </tr>
     {% endif %}
+    {% if ncbi_summary != None and ncbi_summary != "" %}
+    <tr>
+        <td><b>Summary</b></td>
+        <td>{{ ncbi_summary }}</td>
+    </tr>
+    {% endif %}
     <tr>
         <td><b>Database</b></td>
         <td>
-- 
cgit v1.2.3