[med-svn] [Git][med-team/biomaj3-daemon][upstream] New upstream version 3.0.24
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Jun 29 10:57:28 BST 2022
Andreas Tille pushed to branch upstream at Debian Med / biomaj3-daemon
Commits:
2e4adef6 by Andreas Tille at 2022-06-29T11:55:29+02:00
New upstream version 3.0.24
- - - - -
5 changed files:
- CHANGES.txt
- bin/biomaj_daemon_consumer.py
- biomaj_daemon/daemon/biomaj_daemon_web.py
- biomaj_daemon/daemon/daemon_service.py
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,34 +1,49 @@
+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/<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
@@ -37,32 +52,43 @@
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
=====================================
bin/biomaj_daemon_consumer.py
=====================================
@@ -3,6 +3,10 @@ import logging
import requests
import yaml
+try:
+ from yaml import CLoader as Loader
+except ImportError:
+ from yaml import Loader
from biomaj_daemon.daemon.daemon_service import DaemonService
from biomaj_core.utils import Utils
@@ -13,7 +17,7 @@ if 'BIOMAJ_CONFIG' in os.environ:
config = None
with open(config_file, 'r') as ymlfile:
- config = yaml.load(ymlfile)
+ config = yaml.load(ymlfile, Loader=Loader)
Utils.service_config_override(config)
=====================================
biomaj_daemon/daemon/biomaj_daemon_web.py
=====================================
@@ -1,6 +1,10 @@
import ssl
import os
import yaml
+try:
+ from yaml import CLoader as Loader
+except ImportError:
+ from yaml import Loader
import logging
from collections import deque
import copy
@@ -41,7 +45,7 @@ if 'BIOMAJ_CONFIG' in os.environ:
config = None
with open(config_file, 'r') as ymlfile:
- config = yaml.load(ymlfile)
+ config = yaml.load(ymlfile, Loader=Loader)
Utils.service_config_override(config)
BiomajConfig.load_config(config['biomaj']['config'])
@@ -1127,7 +1131,13 @@ def expose():
requested_bank = elts[2]
user = None
options = Options({})
- bank = Bank(requested_bank, options=Options({}), no_log=True)
+ bank = None
+ try:
+ # if bank is not defined and requesting a local/temp dir
+ bank = Bank(requested_bank, options=Options({}), no_log=True)
+ except Exception:
+ abort(404)
+
if bank.bank['properties']['visibility'] == 'public':
return jsonify({'msg': 'access allowed'})
=====================================
biomaj_daemon/daemon/daemon_service.py
=====================================
@@ -1,6 +1,10 @@
import logging
import logging.config
import yaml
+try:
+ from yaml import CLoader as Loader
+except ImportError:
+ from yaml import Loader
import traceback
import datetime
import time
@@ -88,7 +92,7 @@ class DaemonService(object):
self.session = None
self.executed_callback = None
with open(config_file, 'r') as ymlfile:
- self.config = yaml.load(ymlfile)
+ self.config = yaml.load(ymlfile, Loader=Loader)
Utils.service_config_override(self.config)
Zipkin.set_config(self.config)
=====================================
setup.py
=====================================
@@ -17,11 +17,12 @@ with open(os.path.join(here, 'CHANGES.txt')) as f:
config = {
'description': 'BioMAJ daemon service',
'long_description': README + '\n\n' + CHANGES,
+ 'long_description_content_type': 'text/markdown',
'author': 'Olivier Sallou',
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.22',
+ 'version': '3.0.24',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
@@ -39,7 +40,6 @@ config = {
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
'Programming Language :: Python :: 3',
- 'Programming Language :: Python :: 3.4'
],
'install_requires': [
'biomaj-core',
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-daemon/-/commit/2e4adef65ccd6c6c09af17680e9798cdfffe25a2
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-daemon/-/commit/2e4adef65ccd6c6c09af17680e9798cdfffe25a2
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