Metadata-Version: 2.0
Name: biomaj-daemon
Version: 3.0.17
Summary: BioMAJ daemon service
Home-page: http://biomaj.genouest.org
Author: Olivier Sallou
Author-email: olivier.sallou@irisa.fr
License: UNKNOWN
Download-URL: http://biomaj.genouest.org
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: PyYAML
Requires-Dist: biomaj
Requires-Dist: biomaj-core
Requires-Dist: biomaj-user
Requires-Dist: biomaj-zipkin
Requires-Dist: flask
Requires-Dist: prometheus-client (>=0.0.18)
Requires-Dist: python-consul
Requires-Dist: redis
Requires-Dist: requests

# About

Microservice to manage biomaj, acts as a frontend to receive biomaj-cli commands and execute operations

Needs mongo and redis



# Development

    flake8 --ignore E501 biomaj_daemon


# Run

## Message consumer:

    export BIOMAJ_CONFIG=path_to_config.yml
    python bin/biomaj_daemon_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_daemon.daemon.biomaj_daemon_web:app

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

## API

For authentication, add api key to HTTP header X-API-KEY

For admin only, operations, add to config.yml

    general:
      admin:
        - admin_user_id



TO use API, some operations are limited to 


3.0.17:
  Allow use of env variables to override micro.x and rabbitmq variables in global.properties
    like for config.yml.
    Ex: WEB_LOCAL_ENDPOINT_DOWNLOAD defines proxy address for download web service,
        WEB_LOCAL_ENDPOINT defines global proxy address for all web services, etc.
    If not defined, will use values from global.properties
3.0.16:
  After migration checks, update db_schema to current version
3.0.15:
  Add --history option
  Catch SIGTERM to cancel bank update for SIGKILL
3.0.14:
  Fake version for Pypi re-upload
3.0.13:
  Allow per service local_endpoint definition
  Add --stats option
  Modify --version option to get all module details
  Add REST API to daemon (/api/daemon/...)

3.0.12:
  Add biomaj_daemon_consumer.py to python scripts for install with package
3.0.11:
  Disable daemon web service logging
3.0.10:
  Fix tail endpoint syntax
3.0.9:
  Fix #1 remove debug log
  Fix #2 log dir not removed with --remove-all if proxy option not set
3.0.8:
  Fix #78, for multiple banks update in monolithic config, if one fails, next banks are not updated
  Add /api/daemon/bank/x/log[/y] endpoint to get last bank session log file
3.0.7:
  Add whatsup support for non proxy config
  Skip bank config with errors
3.0.6:
  Fix logging for monolithic setup
  Add whatsup option
  Fix prometheus stats
3.0.5:
  Fix for python 2.x
3.0.4:
  Fix status page with other services
  Add missing README in package
3.0.3:
  Fix missing parameters
3.0.2:
  Move options to management to utils for reuse
  Fix --about-me
3.0.1:
  Micro service to manage biomaj updates


