From 0563c40825b648f76cd7eb25831f86f03339c615 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 27 Aug 2019 11:30:53 -0500
Subject: Fixed issue that caused Variant Browser to stop working (related to
 change to return query results as unicode)

Fixed issue that was causing Indel results in the Variant Browser to not work
---
 wqflask/wqflask/snp_browser/snp_browser.py | 56 +++++++++++++++---------------
 wqflask/wqflask/templates/snp_browser.html |  8 +++--
 2 files changed, 33 insertions(+), 31 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 9a980cb1..7f0a0a31 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -477,8 +477,8 @@ class SnpBrowser(object):
 
                 the_bases = []
                 for j, item in enumerate(allele_value_list):
-                    if item and isinstance(item, str):
-                        this_base = [item, base_color_dict[item]]
+                    if item and isinstance(item, basestring):
+                        this_base = [str(item), base_color_dict[item]]
                     else:
                         this_base = ""
 
@@ -486,24 +486,24 @@ class SnpBrowser(object):
 
                 this_row = {
                     "index": i + 1,
-                    "rs": rs,
-                    "snp_url": snp_url,
-                    "snp_name": snp_name,
-                    "chr": chr,
+                    "rs": str(rs),
+                    "snp_url": str(snp_url),
+                    "snp_name": str(snp_name),
+                    "chr": str(chr),
                     "mb_formatted": mb_formatted,
-                    "alleles": alleles,
-                    "snp_source": snp_source,
+                    "alleles": str(alleles),
+                    "snp_source": str(snp_source),
                     "source_urls": source_urls,
-                    "conservation_score": conservation_score,
-                    "gene_name": gene_name,
-                    "gene_link": gene_link,
-                    "transcript": transcript,
-                    "transcript_link": transcript_link,
-                    "exon": exon,
-                    "domain_1": domain_1,
-                    "domain_2": domain_2,
-                    "function": function, 
-                    "function_details": function_details,
+                    "conservation_score": str(conservation_score),
+                    "gene_name": str(gene_name),
+                    "gene_link": str(gene_link),
+                    "transcript": str(transcript),
+                    "transcript_link": str(transcript_link),
+                    "exon": str(exon),
+                    "domain_1": str(domain_1),
+                    "domain_2": str(domain_2),
+                    "function": str(function),
+                    "function_details": str(function_details),
                     "allele_value_list": the_bases
                 }
 
@@ -511,15 +511,15 @@ class SnpBrowser(object):
                 indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name = result
                 this_row = {
                     "index": i,
-                    "indel_name": indel_name,
-                    "indel_chr": indel_chr,
-                    "indel_mb_s": indel_mb_s,
-                    "indel_mb_e": indel_mb_e,
-                    "indel_strand": indel_strand,
-                    "indel_type": indel_type,
-                    "indel_size": indel_size,
-                    "indel_sequence": indel_sequence,
-                    "source_name": source_name
+                    "indel_name": str(indel_name),
+                    "indel_chr": str(indel_chr),
+                    "indel_mb_s": str(indel_mb_s),
+                    "indel_mb_e": str(indel_mb_e),
+                    "indel_strand": str(indel_strand),
+                    "indel_type": str(indel_type),
+                    "indel_size": str(indel_size),
+                    "indel_sequence": str(indel_sequence),
+                    "source_name": str(source_name)
                 }
                 #this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
             else:
@@ -612,7 +612,7 @@ class SnpBrowser(object):
             this_allele_list = []
 
             for item in self.allele_list:
-                if item and isinstance(item, str) and (item.lower() not in this_allele_list) and (item != "-"):
+                if item and isinstance(item, basestring) and (item.lower() not in this_allele_list) and (item != "-"):
                     this_allele_list.append(item.lower())
 
             total_allele_count = len(this_allele_list)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 9d85f767..4422ba73 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -382,6 +382,8 @@
           'render': function(data, type, row, meta) {
             return '<input type="checkbox" name="trait_check">'
           }
+        }, {
+          'data': 'index'
         }, {
           'data': 'indel_name'
         }, {
@@ -393,11 +395,11 @@
         }, {
           'data': 'indel_mb_e'
         }, {
-          'data': 'strand'
+          'data': 'indel_strand'
         }, {
-          'data': 'size'
+          'data': 'indel_size'
         }, {
-          'data': 'sequence'
+          'data': 'indel_sequence'
         }, {
           'data': 'source_name'
         }
-- 
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