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BioMAJ daemon service

Project description

# 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


3.0.20:
Add some checks on options
Add data-list and data-import options
3.0.19:
Fix traefix prefix
3.0.18:
Fix some bank status info checks
Add new endpoint /api/daemon/bank/<bank>/owns
Add queued bank names in whatsup
Update pika dependency release
Add tags for traefik support
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


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