From 5256e4bec5030f0c8488926d3237700dc36a969f Mon Sep 17 00:00:00 2001 From: aeg Date: Thu, 27 Sep 2018 21:25:14 +1000 Subject: [PATCH] Add more logging --- aws_batch/README.md | 5 ++++- source/pipeline/main_pipeline_abstractprep.py | 4 ++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/aws_batch/README.md b/aws_batch/README.md index cb8af10..d2c9b52 100644 --- a/aws_batch/README.md +++ b/aws_batch/README.md @@ -16,5 +16,8 @@ export PYTHONPATH=./aws_batch export tag='latest' -python aws_batch/register_job_download_raw_files.py lanax/kegg-pathway-extractor:$tag +python aws_batch/register_job_download_raw_files.py lanax/kegg-pathway-extractor:$tag + + +python aws_batch/register_job_simple_pipeline.py lanax/kegg-pathway-extractor:$tag ``` \ No newline at end of file diff --git a/source/pipeline/main_pipeline_abstractprep.py b/source/pipeline/main_pipeline_abstractprep.py index 1b7f271..227d182 100644 --- a/source/pipeline/main_pipeline_abstractprep.py +++ b/source/pipeline/main_pipeline_abstractprep.py @@ -100,5 +100,9 @@ def run(input_dir, out_file): logging.basicConfig(level=logging.getLevelName(args.log_level), handlers=[logging.StreamHandler(sys.stdout)], format='%(asctime)s - %(name)s - %(levelname)s - %(message)s') + logger = logging.getLogger(__name__) + logger.info("Starting run with arguments...\n{}".format(args.__dict__)) run(args.input_dir, args.out_file) + logger.info("Completed run...") +