New upstream version 3.0.17 (cf36d55f) · Commits · Debian Med / biomaj3-daemon

CHANGES.txt

+11 −0

Original line number	Diff line number	Diff line
		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:

biomaj_daemon/daemon/biomaj_daemon_web.py

+24 −1

Original line number	Diff line number	Diff line
		@@ -72,6 +72,7 @@ redis_client = redis.StrictRedis(

		logging.info("Check database schema and upgrade if necessary")
		SchemaVersion.migrate_pendings()
		SchemaVersion.set_version()

		app = Flask(__name__)

		@@ -136,7 +137,9 @@ OPTIONS_PARAMS = {
		'userlogin': None,
		'userpassword': None,
		'proxy': None,
		'schedule': False
		'schedule': False,
		'history': False,
		'historyLimit': 20
		}


		@@ -543,6 +546,26 @@ def biomaj_daemon_version():
		except Exception as e:
		abort(500, str(e))


		@app.route('/api/daemon/history', methods=['GET'])
		def biomaj_daemon_history():
		(http_code, options, error) = daemon_api_auth(request)
		if error:
		abort(http_code, error)

		options.history = True
		options.historyLimit = request.args.get('limit', 100)
		try:
		(res, msg) = biomaj_client_action(options, config)
		if res:
		if isinstance(msg, dict):
		return jsonify(msg)
		else:
		return jsonify({'msg': msg})
		except Exception as e:
		abort(500, str(e))


		@app.route('/api/daemon/bank', methods=['GET'])
		def biomaj_daemon_banks_status():
		(http_code, options, error) = daemon_api_auth(request)

biomaj_daemon/daemon/daemon_service.py

+33 −0

Original line number	Diff line number	Diff line
		@@ -6,6 +6,8 @@ import datetime
		import time
		import json
		import threading
		import signal
		import sys

		import redis
		import consul
		@@ -82,6 +84,7 @@ class DaemonService(object):

		def __init__(self, config_file):
		self.logger = logging
		self.curBank = None
		self.session = None
		self.executed_callback = None
		with open(config_file, 'r') as ymlfile:
		@@ -91,6 +94,24 @@ class DaemonService(object):
		Zipkin.set_config(self.config)

		BiomajConfig.load_config(self.config['biomaj']['config'])
		for svc in Utils.services:
		service = svc.lower()
		if self.config['web'].get('local_endpoint_' + service, None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.service.' + service , '1')
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.proxy.' + service , self.config['web']['local_endpoint_' + service])
		if self.config['web'].get('local_endpoint', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.proxy' , self.config['web']['local_endpoint'])
		if self.config.get('rabbitmq', None):
		if self.config['rabbitmq'].get('host', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.rabbit_mq' , self.config['rabbitmq']['host'])
		if self.config['rabbitmq'].get('port', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.rabbit_mq_port' , str(self.config['rabbitmq']['port']))
		if self.config['rabbitmq'].get('user', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.rabbit_mq_user' , self.config['rabbitmq']['user'])
		if self.config['rabbitmq'].get('password', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.rabbit_mq_password' , self.config['rabbitmq']['password'])
		if self.config['rabbitmq'].get('virtual_host', None):
		BiomajConfig.global_config.set('GENERAL', 'micro.biomaj.rabbit_mq_virtual_host' , self.config['rabbitmq']['virtual_host'])

		if 'log_config' in self.config:
		for handler in list(self.config['log_config']['handlers'].keys()):
		@@ -106,6 +127,16 @@ class DaemonService(object):
		)

		self.logger.info('Daemon service started')
		signal.signal(signal.SIGTERM, self.catch)
		signal.siginterrupt(signal.SIGTERM, False)

		def catch(self, signum, frame):
		self.logger.warn('SIGTERM signal received')
		if self.curBank:
		self.redis_client.set(self.config['redis']['prefix'] + ':' + self.curBank + ':action:cancel', 1)
		self.logger.warn('SIGTERM signal received, cancelling update for ' + self.curBank)
		else:
		sys.exit(1)

		def close(self):
		if self.channel:
		@@ -115,6 +146,7 @@ class DaemonService(object):
		self.executed_callback = func

		def __start_action(self, bank, action):
		self.curBank = bank
		whatsup = bank + ':' + str(action)
		self.redis_client.hset(
		self.config['redis']['prefix'] + ':daemons:status',
		@@ -133,6 +165,7 @@ class DaemonService(object):
		self.config['consul']['id'],
		'pending'
		)
		self.curBank = None

		def execute(self, options):
		'''

biomaj_daemon/daemon/utils.py

+25 −0

Original line number	Diff line number	Diff line
		@@ -810,11 +810,36 @@ def biomaj_stats(options, config):
		msg += tabulate(results, headers="firstrow", tablefmt="grid")
		return (True, msg)

		def biomaj_history(options, config):
		history = Bank.get_history(options.historyLimit)
		results = []
		headers = ["Bank", "Action", "Start", "End", "Updated", "Error"]
		if not options.json:
		results.append(headers)
		msg = 'BioMAJ history\n'
		for h in history:
		results.append([h['bank'],
		h['action'],
		datetime.datetime.utcfromtimestamp(h['start']),
		datetime.datetime.utcfromtimestamp(h['end']),
		str(h['updated']),
		str(h['error'])
		])
		if options.json:
		msg = {'headers': headers, 'history': results}
		else:
		msg += tabulate(results, headers="firstrow", tablefmt="grid")
		return (True, msg)


		def biomaj_client_action(options, config=None):
		check_options(options, config)
		if options.version:
		return biomaj_version(options, config)

		if options.history:
		return biomaj_history(options, config)

		if options.stats:
		return biomaj_stats(options, config)

requirements.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -8,3 +8,4 @@ python-consul
		prometheus_client>=0.0.18
		requests
		biomaj-core>=3.0.10
		biomaj>=3.1.6