From 848a24fef9e69e46be1001e2ee602af594ecbb25 Mon Sep 17 00:00:00 2001
From: ecwood <wooderi@stanford.edu>
Date: Mon, 2 Sep 2024 14:14:38 -0700
Subject: [PATCH] #408 issue with DisGeNET download

---
 extract/extract-disgenet.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/extract/extract-disgenet.sh b/extract/extract-disgenet.sh
index c4c6c74e..5e6ddd73 100755
--- a/extract/extract-disgenet.sh
+++ b/extract/extract-disgenet.sh
@@ -22,9 +22,12 @@ disgenet_output_file=${1:-"${BUILD_DIR}/all_gene_disease_pmid_associations.tsv"}
 
 disgenet_download_link="https://www.disgenet.org/static/disgenet_ap1/files/downloads/all_gene_disease_pmid_associations.tsv.gz"
 
-${curl_get} ${disgenet_download_link} > ${disgenet_output_file}.gz
+# ${curl_get} ${disgenet_download_link} > ${disgenet_output_file}.gz
 
-gzip -d ${disgenet_output_file}.gz
+# gzip -d ${disgenet_output_file}.gz
+
+# Temporary patch due to link failing to resolve
+${s3_cp_cmd} s3://${s3_bucket}/all_gene_disease_pmid_associations.tsv ${disgenet_output_file}
 
 
 date