From 991f3901cdd25b56bad447b0b1bb6d4131e43e36 Mon Sep 17 00:00:00 2001
From: kvnjng <kvvnjng@gmail.com>
Date: Thu, 17 Sep 2020 13:42:54 -0600
Subject: [PATCH] fix svg export

---
 LDlink/LDlink-4.2.0.js     |  4 ++--
 LDlink/LDproxy.py          |  2 +-
 LDlink/LDproxy_plot_sub.py | 12 +++++++-----
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/LDlink/LDlink-4.2.0.js b/LDlink/LDlink-4.2.0.js
index a62bb00c..f85475e3 100755
--- a/LDlink/LDlink-4.2.0.js
+++ b/LDlink/LDlink-4.2.0.js
@@ -2828,7 +2828,7 @@ function updateLDproxy() {
     var $btn = $('#' + id).button('loading');
     var population = getPopulationCodes(id+'-population-codes');
     var r2_d;
-    var window = $("#" + id + "-bp-window").val().replace(/\,/g, '');
+    var windowSize = $("#" + id + "-bp-window").val().replace(/\,/g, '');
 
     if($('#proxy_color_r2').hasClass('active')) {
         r2_d='r2'; // i.e. R2
@@ -2845,7 +2845,7 @@ function updateLDproxy() {
         pop : population.join("+"),
         reference : Math.floor(Math.random() * (99999 - 10000 + 1)),
         r2_d : r2_d,
-        window: window
+        window: windowSize
     };
 
     updateHistoryURL(id, ldproxyInputs);
diff --git a/LDlink/LDproxy.py b/LDlink/LDproxy.py
index d19bc03f..21c459e1 100755
--- a/LDlink/LDproxy.py
+++ b/LDlink/LDproxy.py
@@ -832,7 +832,7 @@ def get_output(process):
     # Generate high quality images only if accessed via web instance
     if web:
         # Open thread for high quality image exports
-        command = "python3 LDproxy_plot_sub.py " + snp + " " + pop + " " + request + " " + r2_d
+        command = "python3 LDproxy_plot_sub.py " + snp + " " + pop + " " + request + " " + r2_d + " " + str(window)
         subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
 
     ###########################
diff --git a/LDlink/LDproxy_plot_sub.py b/LDlink/LDproxy_plot_sub.py
index 724884a3..8c3b934b 100644
--- a/LDlink/LDproxy_plot_sub.py
+++ b/LDlink/LDproxy_plot_sub.py
@@ -15,7 +15,7 @@
 # LDproxy subprocess to export bokeh to high quality images in the background
 
 
-def calculate_proxy_svg(snp, pop, request, r2_d="r2"):
+def calculate_proxy_svg(snp, pop, request, r2_d="r2", window=500000):
 
     # Set data directories using config.yml
     with open('config.yml', 'r') as f:
@@ -172,7 +172,7 @@ def replace_coord_rsid(db, snp):
         return None
 
     # Define window of interest around query SNP
-    window = 500000
+    # window = 500000
     coord1 = int(snp_coord['position']) - window
     if coord1 < 0:
         coord1 = 0
@@ -607,21 +607,23 @@ def get_output(process):
 def main():
 
     # Import LDproxy options
-    if len(sys.argv) == 4:
+    if len(sys.argv) == 5:
         snp = sys.argv[1]
         pop = sys.argv[2]
         request = False
         r2_d = "r2"
-    elif len(sys.argv) == 5:
+        window = sys.argv[5]
+    elif len(sys.argv) == 6:
         snp = sys.argv[1]
         pop = sys.argv[2]
         request = sys.argv[3]
         r2_d = sys.argv[4]
+        window = sys.argv[5]
     else:
         sys.exit()
 
     # Run function
-    calculate_proxy_svg(snp, pop, request, r2_d)
+    calculate_proxy_svg(snp, pop, request, r2_d, int(window))
 
 
 if __name__ == "__main__":