[med-svn] [Git][med-team/biomaj3-process][upstream] New upstream version 3.0.18

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / biomaj3-process


Commits:
fabbb676 by Andreas Tille at 2022-06-29T14:34:05+02:00
New upstream version 3.0.18
- - - - -


7 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
- 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)


=====================================
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/-/commit/fabbb676a5896ac7e2fcb7ade7352bda4a71a102

-- 
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-process/-/commit/fabbb676a5896ac7e2fcb7ade7352bda4a71a102
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220629/ede131a3/attachment-0001.htm>