#405 umls cleanup issue

RTXteam · Sep 2, 2024 · bd93687 · bd93687
1 parent e104912
commit bd93687
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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