From bd93687f8d20224edbeb95c31520b293d7a52b96 Mon Sep 17 00:00:00 2001
From: ecwood <wooderi@stanford.edu>
Date: Mon, 2 Sep 2024 14:07:28 -0700
Subject: [PATCH] #405 umls cleanup issue

---
 build/snakemake-config-var.yaml | 2 --
 extract/extract-umls.sh         | 2 ++
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/build/snakemake-config-var.yaml b/build/snakemake-config-var.yaml
index 2c5e1863..2943089f 100644
--- a/build/snakemake-config-var.yaml
+++ b/build/snakemake-config-var.yaml
@@ -13,8 +13,6 @@ umls_output_base: kg2-umls
 umls_extraction_script: ${EXTRACT_CODE_DIR}/${umls_extraction_base}.sh
 umls_extraction_log: ${BUILD_DIR}/${umls_extraction_base}${version_suffix}${test_suffix}.log
 umls_extract_file: ${BUILD_DIR}/umls.jsonl
-umls_dir: ${BUILD_DIR}/umls
-umls_dest_dir: ${umls_dir}/META
 umls_conversion_script: ${CONVERT_CODE_DIR}/${umls_conversion_base}.py
 umls_conversion_log: ${BUILD_DIR}/${umls_conversion_base}${version_suffix}${test_suffix}.log
 umls_name_heirarchy: ${MAPS_CODE_DIR}/umls-name-heirarchy.yaml
diff --git a/extract/extract-umls.sh b/extract/extract-umls.sh
index dcaae277..d25e2028 100755
--- a/extract/extract-umls.sh
+++ b/extract/extract-umls.sh
@@ -19,6 +19,8 @@ source ${config_dir}/master-config.shinc
 
 output_file=${2:-${BUILD_DIR}/umls.jsonl}
 
+umls_dir=${BUILD_DIR}/umls
+umls_dest_dir=${umls_dir}/META
 umls_ver=2023AA
 umls_file_base=umls-${umls_ver}-metathesaurus-full
 config_file=${umls_dir}/config.prop