This is probably not very interesting unless you work in the pathogen informatics team at the Wellcome Trust Sanger Institute and almost certainly not it you don't use the vr-pipe pipeline.
Given a config directory, this script finds all of the *_pipeline.conf files in the directory and its immediate children. It parses these files and outputs their contents in json. This is either saved to a file or stdout.
This is used in collaboration with jsontoemail and a cron job to send updates / reminders to the pathogen informatics team.
$ list-pathogen-pipeline-jobs -h
usage: list-pathogen-pipeline-jobs [-h] [--output_file OUTPUT_FILE] config_dir
Outputs details of all of the pathogen jobs in the pipeline
positional arguments:
config_dir Config directory to be searched for job trackers (also
searches child dircectories)
optional arguments:
-h, --help show this help message and exit
--output_file OUTPUT_FILE, -o OUTPUT_FILE
File to output results to (defaults to stdout){
"created_at": "2015-03-24T15:26:17.246253",
"jobs": [
{
"approval_required": true,
"config_file": "/parent_dir/assembly_jobs/job_1.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": true,
"config_file": "/parent_dir/assembly_jobs/job_2.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/assembly_jobs/job_3.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": true,
"config_file": "/parent_dir/annotation_jobs/job_1.conf",
"job_type": "__Annotation__",
"pipeline_tracker": "/parent_dir/annotation_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/mapping_jobs/job_1.conf",
"job_type": "__Mapping__",
"pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/mapping_jobs/job_2.conf",
"job_type": "__Mapping__",
"pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
}
]
}./run_tests.shTests require:
- mock
path_pipe_conf_tools has been tested on Ubuntu 12.04 with python 2.7.3