Metadata-Version: 2.0
Name: biomaj-process
Version: 3.0.9
Summary: BioMAJ process service
Home-page: http://biomaj.genouest.org
Author: Olivier Sallou
Author-email: olivier.sallou@irisa.fr
License: UNKNOWN
Download-URL: http://biomaj.genouest.org
Description-Content-Type: UNKNOWN
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Requires-Dist: biomaj-core
Requires-Dist: biomaj-zipkin
Requires-Dist: pika
Requires-Dist: redis
Requires-Dist: PyYAML
Requires-Dist: flask
Requires-Dist: python-consul
Requires-Dist: prometheus-client (>=0.0.18)
Requires-Dist: protobuf
Requires-Dist: requests

# About

Microservice to manage the process execution of biomaj.

A protobuf interface is available in biomaj_process/message/message_pb2.py to exchange messages between BioMAJ and the download service.
Messages go through RabbitMQ (to be installed).

# Protobuf

To compile protobuf, in biomaj_process/message:

    protoc --python_out=. message.proto

# Development

    flake8  biomaj_process

# Run

## Message consumer:
export BIOMAJ_CONFIG=path_to_config.yml
python bin/biomaj_process_consumer.py

## Web server

If package is installed via pip, you need a file named *gunicorn_conf.py* containing somehwhere on local server:

    def worker_exit(server, worker):
        from prometheus_client import multiprocess
        multiprocess.mark_process_dead(worker.pid)

If you cloned the repository and installed it via python setup.py install, just refer to the *gunicorn_conf.py* in the cloned repository.


    export BIOMAJ_CONFIG=path_to_config.yml
    rm -rf ..path_to/prometheus-multiproc
    mkdir -p ..path_to/prometheus-multiproc
    export prometheus_multiproc_dir=..path_to/prometheus-multiproc
    gunicorn -c ..path_to/gunicorn_conf.py biomaj_download.biomaj_process_web:app

Web processes should be behind a proxy/load balancer, API base url /api/download


3.0.9:
  Allow local_endpoint definition per service
  Fix volumes for docker with dependency banks
3.0.8:
  Fix #1, DRMAA needs colon in front of output and error path (mandatory depending on versions)
3.0.7:
  fix case if process desc or type is missing in bank properties
3.0.6:
  disable web thread logging
3.0.5:
  retry in case of contact failure with proxy
3.0.4:
  for docker, restrict directory to bank directory and dependencies
  add host in prometheus stats
3.0.3:
  fix prometheus + gunicorn multi process
  add consul supervision
3.0.2:
  add logging info
  execute docker processes in biomaj micro service
3.0.1:
  bug fixes
3.0.0:
  move process management out of biomaj main package


