Pathogen Pipeline Configuration Tools (path_pipe_conf_tools)

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.

Usage

$ 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)

Example output

{
  "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"
    }
  ]
}

Testing

./run_tests.sh

Dependencies

Tests require:

mock

path_pipe_conf_tools has been tested on Ubuntu 12.04 with python 2.7.3

Metadata

Release files for path_pipe_conf_tools 0.0.2

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Source distribution for path_pipe_conf_tools 0.0.2
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0.0.2 This release

Mar 26, 2015 1 release file

path_pipe_conf_tools 0.0.2