[med-svn] [Git][med-team/biomaj3-process][master] 5 commits: New upstream version 3.0.18
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Jun 29 13:36:46 BST 2022
Andreas Tille pushed to branch master at Debian Med / biomaj3-process
Commits:
fabbb676 by Andreas Tille at 2022-06-29T14:34:05+02:00
New upstream version 3.0.18
- - - - -
e429c954 by Andreas Tille at 2022-06-29T14:34:05+02:00
routine-update: New upstream version
- - - - -
4776dfca by Andreas Tille at 2022-06-29T14:34:05+02:00
Update upstream source from tag 'upstream/3.0.18'
Update to upstream version '3.0.18'
with Debian dir eb599ca18f8296c5754c48e983091ab4da39587c
- - - - -
4805acdc by Andreas Tille at 2022-06-29T14:34:05+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
e6af82e7 by Andreas Tille at 2022-06-29T14:34:46+02:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- .travis.yml
- CHANGES.txt
- bin/biomaj_process_consumer.py
- biomaj_process/biomaj_process_web.py
- biomaj_process/process.py
- biomaj_process/process_service.py
- debian/changelog
- debian/control
- setup.py
Changes:
=====================================
.travis.yml
=====================================
@@ -2,7 +2,6 @@ language: python
sudo: false
python:
- '2.7'
- - '3.4'
- '3.5'
- '3.6'
services:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,7 @@
+3.0.18:
+ Normalize yaml setup with other biomaj components
+3.0.17:
+ Fix yaml load warnings
3.0.16:
In case of proxy comm failure, sleep a few seconds before retry
3.0.15:
=====================================
bin/biomaj_process_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
import consul
from biomaj_process.process_service import ProcessService
@@ -14,7 +18,7 @@ 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_process/biomaj_process_web.py
=====================================
@@ -7,6 +7,10 @@ import ssl
import os
import yaml
+try:
+ from yaml import CLoader as Loader
+except ImportError:
+ from yaml import Loader
from flask import Flask
from flask import jsonify
from flask import request
@@ -33,7 +37,7 @@ 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_process/process.py
=====================================
@@ -262,14 +262,10 @@ class DockerProcess(Process):
{sudo} docker {docker_url} run --rm -w {bank_dir} {depends_vol} -v {host_data_dir}:{container_data_dir} {env} {container_id} \
{exe} {args} \
'''.format(
- uid=os.getuid(),
- gid=os.getgid(),
host_data_dir=host_data_dir,
container_data_dir=container_data_dir,
env=env,
container_id=self.docker,
- group_biomaj='biomaj',
- user_biomaj='biomaj',
exe=self.exe,
args=' '.join(self.args),
bank_dir=release_dir,
=====================================
biomaj_process/process_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 redis
import uuid
import traceback
@@ -73,7 +77,7 @@ class ProcessService(object):
self.bank = 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)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+biomaj3-process (3.0.18-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.1 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 29 Jun 2022 14:34:14 +0200
+
biomaj3-process (3.0.16-2) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -1,10 +1,11 @@
Source: biomaj3-process
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends: debhelper-compat (= 13), dh-python,
+Build-Depends: debhelper-compat (= 13),
+ dh-python,
protobuf-compiler,
python3-all,
python3-bcrypt,
@@ -21,18 +22,20 @@ Build-Depends: debhelper-compat (= 13), dh-python,
python3-yaml,
python3-biomaj3-core,
python3-biomaj3-zipkin
-Standards-Version: 4.5.1
-Homepage: https://github.com/genouest/biomaj-process
-Rules-Requires-Root: no
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/biomaj3-process
Vcs-Git: https://salsa.debian.org/med-team/biomaj3-process.git
+Homepage: https://github.com/genouest/biomaj-process
+Rules-Requires-Root: no
Package: python3-biomaj3-process
Architecture: all
-Depends: ${misc:Depends}, ${python3:Depends}
+Depends: ${misc:Depends},
+ ${python3:Depends}
Recommends: ${python3:Recommends}
-Suggests: ${python3:Suggests}, python3-gunicorn, mongodb, redis-server
-XB-Python-Egg-Name: biomaj-process
+Suggests: ${python3:Suggests},
+ python3-gunicorn,
+ redis-server
Description: BioMAJ process management library
BioMAJ downloads remote data banks, checks their status and applies
transformation workflows, with consistent state, to provide ready-to-use
@@ -44,3 +47,4 @@ Description: BioMAJ process management library
.
This package contains the library and microservice to manage processes
in BioMAJ3
+XB-Python-Egg-Name: biomaj-process
=====================================
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': '3.0.16',
+ 'version': '3.0.18',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-process/-/compare/3321f59623d16cf4fcd9e828dbccbd1b0c2dad65...e6af82e771ed7a0bf44d2b3df0abe9300f11db0e
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-process/-/compare/3321f59623d16cf4fcd9e828dbccbd1b0c2dad65...e6af82e771ed7a0bf44d2b3df0abe9300f11db0e
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