[med-svn] [Git][med-team/biomaj3-daemon][master] 3 commits: New upstream version 3.0.17
Olivier Sallou
gitlab at salsa.debian.org
Thu Oct 25 10:31:44 BST 2018
Olivier Sallou pushed to branch master at Debian Med / biomaj3-daemon
Commits:
cf36d55f by Olivier Sallou at 2018-10-25T09:23:33Z
New upstream version 3.0.17
- - - - -
b7f5ec3b by Olivier Sallou at 2018-10-25T09:23:37Z
Updated version 3.0.17 from 'upstream/3.0.17'
with Debian dir 33795086981658cb16eaf6d1da2b248d83943c44
- - - - -
fb7b94d7 by Olivier Sallou at 2018-10-25T09:24:48Z
new upstream release 3.0.17
- - - - -
8 changed files:
- CHANGES.txt
- biomaj_daemon/daemon/biomaj_daemon_web.py
- biomaj_daemon/daemon/daemon_service.py
- biomaj_daemon/daemon/utils.py
- debian/changelog
- debian/control
- requirements.txt
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,14 @@
+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
=====================================
@@ -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))
+
+ at 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
=====================================
@@ -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
=====================================
@@ -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)
=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
-biomaj3-daemon (3.0.14-2) UNRELEASED; urgency=medium
+biomaj3-daemon (3.0.17-1) unstable; urgency=medium
+ [ Jelmer Vernooij ]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
- -- Jelmer Vernooij <jelmer at debian.org> Sat, 20 Oct 2018 13:15:27 +0000
+ [ Olivier Sallou ]
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 25 Oct 2018 09:23:42 +0000
biomaj3-daemon (3.0.14-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -23,8 +23,8 @@ Build-Depends: debhelper (>= 9), dh-python,
python3-biomaj3
Standards-Version: 4.1.3
Homepage: https://github.com/genouest/biomaj-daemon
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/biomaj3-daemon.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/biomaj3-daemon.git
+Vcs-Browser: https://salsa.debian.org/med-team/biomaj3-daemon
+Vcs-Git: https://salsa.debian.org/med-team/biomaj3-daemon.git
Package: python3-biomaj3-daemon
Architecture: all
=====================================
requirements.txt
=====================================
@@ -8,3 +8,4 @@ python-consul
prometheus_client>=0.0.18
requests
biomaj-core>=3.0.10
+biomaj>=3.1.6
=====================================
setup.py
=====================================
@@ -21,7 +21,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.14',
+ 'version': '3.0.17',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-daemon/compare/433773ba49ed787282e460d862da1515ea964e5a...fb7b94d764d121f120704485858fddba95d11aa7
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-daemon/compare/433773ba49ed787282e460d862da1515ea964e5a...fb7b94d764d121f120704485858fddba95d11aa7
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