From ea06cf8b890ac9e762c8a2cc2a773b1cb7f4882b Mon Sep 17 00:00:00 2001 From: sshugsc Date: Thu, 4 Apr 2024 14:45:21 -0700 Subject: [PATCH 1/2] update running command for clinicaltrialsgov --- Snakefile | 13 ++----------- package.json | 2 +- 2 files changed, 3 insertions(+), 12 deletions(-) diff --git a/Snakefile b/Snakefile index cf8d7e07..d3e8a363 100644 --- a/Snakefile +++ b/Snakefile @@ -167,14 +167,6 @@ rule download_cancerhotspots: ''') -rule download_clinicaltrialsgov: - output: directory(f'{DATA_DIR}/clinicaltrialsgov') - shell: dedent(f'''\ - mkdir -p {DATA_DIR}/clinicaltrialsgov - cd {DATA_DIR}/clinicaltrialsgov - wget https://clinicaltrials.gov/AllPublicXML.zip - unzip AllPublicXML.zip''') - rule download_cosmic_resistance: output: f'{DATA_DIR}/cosmic/CosmicResistanceMutations.tsv' @@ -413,12 +405,11 @@ rule load_approvals: rule load_clinicaltrialsgov: input: expand(rules.load_local.output, local=['vocab']), rules.all_diseases.output, - rules.all_drugs.output, - data=rules.download_clinicaltrialsgov.output + rules.all_drugs.output container: CONTAINER log: f'{LOGS_DIR}/clinicaltrialsgov.logs.txt' output: f'{DATA_DIR}/clinicaltrialsgov.COMPLETE' - shell: LOADER_COMMAND + ' api clinicaltrialsgov &> {log}; cp {log} {output}' + shell: LOADER_COMMAND + ' clinicaltrialsgov &> {log}; cp {log} {output}' rule load_cosmic_resistance: diff --git a/package.json b/package.json index 72866258..3bae7b31 100644 --- a/package.json +++ b/package.json @@ -57,7 +57,7 @@ "lint": "eslint -c .eslintrc.json src test", "version": "echo $npm_package_version", "start": "node bin/load.js", - "start:recent-trials": "node bin/load.js api clinicaltrialsgov", + "start:recent-trials": "node bin/load.js clinicaltrialsgov --days 7", "start:fda-approvals": "node bin/load.js api fdaApprovals", "start:oncotree": "node bin/load.js api oncotree", "start:civic": "node bin/load.js civic", From 5d2ec04ff551894a5d9e2e5d62007decdf5607a6 Mon Sep 17 00:00:00 2001 From: sshugsc Date: Tue, 9 Apr 2024 10:28:19 -0700 Subject: [PATCH 2/2] use 14 days for recent-trials --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 3bae7b31..34c90448 100644 --- a/package.json +++ b/package.json @@ -57,7 +57,7 @@ "lint": "eslint -c .eslintrc.json src test", "version": "echo $npm_package_version", "start": "node bin/load.js", - "start:recent-trials": "node bin/load.js clinicaltrialsgov --days 7", + "start:recent-trials": "node bin/load.js clinicaltrialsgov --days 14", "start:fda-approvals": "node bin/load.js api fdaApprovals", "start:oncotree": "node bin/load.js api oncotree", "start:civic": "node bin/load.js civic",