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

3.0.24: Fix pyaml setup

3.0.23: Expose endpoint, return 404 if bank does not exists

3.0.22: Add /api/daemon/expose endpoint for traefik auth requests to allow/deny access to /db web access

3.0.21: Add support for repair option Add cors support Fix /status/ko

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//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