#140 made sure its only defined once

RTXteam · Jul 17, 2024 · 184fa6e · 184fa6e
1 parent 07c8549
commit 184fa6e
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Showing 6 changed files with 12 additions and 16 deletions.
diff --git a/build/Snakefile-post-etl b/build/Snakefile-post-etl
@@ -126,7 +126,7 @@ rule Simplify:
     log:
         config['SIMPLIFY_LOG']
     shell:
-        "bash -x {input.code} {input.nodes} {input.edges} {output.nodes} {output.edges} " + config['VERSION_FILE'] + " " + config['TEST_FLAG'] + " > {log} 2>&1" 
+        "bash -x {input.code} {input.nodes} {input.edges} {output.nodes} {output.edges} " + config['TEST_FLAG'] + " > {log} 2>&1" 
 
 rule Slim:
     input:

diff --git a/build/build-kg2-snakemake.sh b/build/build-kg2-snakemake.sh
@@ -64,8 +64,6 @@ then
     run_flag="-F"
 fi
 
-kg2_version_file="kg2-version.txt"
-local_kg2_version_file="${BUILD_DIR}/${kg2_version_file}"
 trigger_file_is_major_release=${BUILD_DIR}/major-release
 trigger_file_is_minor_release=${BUILD_DIR}/minor-release
 
@@ -89,14 +87,14 @@ if [[ "${ci_flag}" == "ci" ]]
 then
     sed -i "\@^kg2_version=@ckg2_version=KG2.CI" ${CODE_DIR}/master-config.shinc
 else
-    ${s3_cp_cmd} s3://${s3_bucket_public}/${kg2_version_file} ${local_kg2_version_file}
+    ${s3_cp_cmd} s3://${s3_bucket_public}/${kg2_version_file} ${kg2_version_file_local}
     if [[ "${increment_flag}" != '' ]]
     then
-        ${VENV_DIR}/bin/python3 ${PROCESS_CODE_DIR}/update_version.py ${increment_flag} ${local_kg2_version_file}
+        ${VENV_DIR}/bin/python3 ${PROCESS_CODE_DIR}/update_version.py ${increment_flag} ${kg2_version_file_local}
     else
         echo "*** TEST MODE -- NO INCREMENT ***"
     fi
-    curr_kg2_version=`cat ${local_kg2_version_file}`
+    curr_kg2_version=`cat ${kg2_version_file_local}`
     sed -i "\@^kg2_version=@ckg2_version=${curr_kg2_version}" ${CODE_DIR}/master-config.shinc
 fi
 
@@ -156,7 +154,7 @@ cd ~ && ${VENV_DIR}/bin/snakemake --snakefile ${snakefile} ${run_flag} -R Finish
 
 if [[ "${ci_flag}" != "ci" ]]
 then
-    ${s3_cp_cmd} ${local_kg2_version_file} s3://${s3_bucket_public}/${kg2_version_file}
+    ${s3_cp_cmd} ${kg2_version_file_local} s3://${s3_bucket_public}/${kg2_version_file}
 fi
 
 if [[ -f ${trigger_file_is_major_release} ]]

diff --git a/build/snakemake-config-var.yaml b/build/snakemake-config-var.yaml
@@ -291,5 +291,3 @@ kg2_tsv_tarball: ${BUILD_DIR}/kg2-tsv-for-neo4j${version_suffix}${test_suffix}.t
 tsv_placeholder: ${BUILD_DIR}/tsv_placeholder.empty
 
 finish_script: ${BUILD_CODE_DIR}/finish-snakemake.sh
-
-version_file: ${BUILD_DIR}/kg2-version.txt
diff --git a/master-config.shinc b/master-config.shinc
@@ -30,4 +30,6 @@ ont_load_inventory_file=${MAPS_CODE_DIR}/ont-load-inventory${test_suffix}.yaml
 rtx_config_file=RTXConfiguration-config.json
 biolink_model_version=4.2.0
 infores_registry_version=0.2.8
+kg2_version_file=version.txt
+kg2_version_file_local=${BUILD_DIR}/${kg2_version_file}
 kg2_version=
diff --git a/neo4j/tsv-to-neo4j.sh b/neo4j/tsv-to-neo4j.sh
@@ -54,9 +54,8 @@ rm -r -f ${tsv_dir}
 mkdir -p ${tsv_dir}
 
 # get the latest KG2 version
-kg2_version_file="kg2-version.txt"
-${s3_cp_cmd} s3://${s3_bucket}/${kg2_version_file} ${BUILD_DIR}/${kg2_version_file}
-kg2_version=`cat ${BUILD_DIR}/${kg2_version_file}`
+${s3_cp_cmd} s3://${s3_bucket}/${kg2_version_file} ${kg2_version_file_local}
+kg2_version=`cat ${kg2_version_file_local}`
 
 # download the latest TSV files from the S3 Bucket
 ${s3_cp_cmd} s3://${s3_bucket}/kg2-tsv-for-neo4j-${kg2_version}${test_arg}.tar.gz ${tsv_tarball}

diff --git a/process/run-simplify.sh b/process/run-simplify.sh
@@ -10,7 +10,7 @@ if [[ "${1:-}" == "--help" || "${1:-}" == "-h" ]]; then
     exit 2
 fi
 
-# Usage: run-simplify.sh <input_nodes_json> <input_edges_json> <output_nodes_json> <output_edges_json> [version_filename] [test]
+# Usage: run-simplify.sh <input_nodes_json> <input_edges_json> <output_nodes_json> <output_edges_json> [test]
 
 echo "================= starting run-simplify.sh =================="
 date
@@ -22,15 +22,14 @@ input_nodes_json=${1:-}
 input_edges_json=${2:-}
 output_nodes_json=${3:-}
 output_edges_json=${4:-}
-local_version_filename=${5:-"${BUILD_DIR}/kg2-version.txt"}
-build_flag=${6:-""}
+build_flag=${5:-""}
 
 # TODO: Inhibits and increase are not in biolink model anymore - Find out what that should be now
 ${VENV_DIR}/bin/python3 -u ${PROCESS_CODE_DIR}/filter_kg_and_remap_predicates.py ${test_flag} --dropNegated \
                         --dropSelfEdgesExcept interacts_with,regulates,inhibits,increase \
                         ${predicate_mapping_file} ${infores_mapping_file} ${curies_to_urls_file} \
                         ${knowledge_level_agent_type_mapping_file} ${input_nodes_json} ${input_edges_json} \
-                        ${output_nodes_json} ${output_edges_json} ${local_version_filename}
+                        ${output_nodes_json} ${output_edges_json} ${kg2_version_file_local}
 
 date
 echo "================= finishing run-simplify.sh =================="
Original file line number	Diff line number	Diff line change
Expand Up		@@ -291,5 +291,3 @@ kg2_tsv_tarball: ${BUILD_DIR}/kg2-tsv-for-neo4j${version_suffix}${test_suffix}.t
		tsv_placeholder: ${BUILD_DIR}/tsv_placeholder.empty

		finish_script: ${BUILD_CODE_DIR}/finish-snakemake.sh

		version_file: ${BUILD_DIR}/kg2-version.txt