[med-svn] [Git][med-team/biomaj3-core][master] 5 commits: New upstream version 3.0.27
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Jun 29 10:56:41 BST 2022
Andreas Tille pushed to branch master at Debian Med / biomaj3-core
Commits:
7e1c9a4d by Andreas Tille at 2022-06-29T11:55:09+02:00
New upstream version 3.0.27
- - - - -
a1d5a993 by Andreas Tille at 2022-06-29T11:55:09+02:00
routine-update: New upstream version
- - - - -
c9267728 by Andreas Tille at 2022-06-29T11:55:10+02:00
Update upstream source from tag 'upstream/3.0.27'
Update to upstream version '3.0.27'
with Debian dir 4f45e4adad30affd54d4c2b569e2b49e190d7bb3
- - - - -
d4db1ee7 by Andreas Tille at 2022-06-29T11:55:10+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
d77425c2 by Andreas Tille at 2022-06-29T11:55:47+02:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- CHANGES.txt
- biomaj_core/utils.py
- debian/changelog
- debian/control
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,63 +1,91 @@
+3.0.27:
+ add .tgz extension support
+
3.0.26:
check use_ldap and use_elastic as bool (true/false or 0/1)
+
3.0.25:
utils/get_folder_size: if file not found, catch error and continue
+
3.0.24:
get_more_recent_file, return also file info
+
3.0.23:
PR #9 Add missing ssh defaults for download
+
3.0.21 [3.0.22 ,tag issue]:
Pin elasticsearch dependency, v7 breaks some API calls
+
3.0.20:
PR #7 from institut-de-genomique/retry_method, rename default values of retryer.
Rename wait_condition to wait_policy in default values
PR #6 from institut-de-genomique/retry_method, add default values for retryer
Add default values for retryer (see the corresponding branch biomaj-download).
+
3.0.19:
Add ftps and directftps protocols
#4 Harden hardlinks
copy_files_with_regexp: remove duplicates
Add utils fonctions
Code cleanup
+
3.0.18:
Allow to use hardlinks in copy_files and copy_files_with_regexp
+
3.0.17:
Fix --log option
+
3.0.16:
Add some warnings if some file is missing
+
3.0.15:
Fix check on bank properties config file when args is empty vs not defined
+
3.0.14:
Fix checks on local_endpoint_XXX in config.yml
In rabbitmq not defined on config.yml add an empty dict
+
3.0.13:
Add archive integrity checks
+
3.0.12:
Add irods support
+
3.0.11:
Add get_module_version static method, checks module version and latest version on pypi
Allow .args fo process to be empty
+
3.0.10:
Add env variables WEB_LOCAL_ENDPOINT_XX with XX as a service (defined in utils.py Utils.services) to define an endpoint per service
+
3.0.9:
#1 Add checks on bank properties
+
3.0.8:
Add DOCKER_URL, MONGO_URL, MONGO_DB env variable in override
Do not fail on elasticsearch index creation, just log
Add rsync check
+
3.0.7:
set logging only if necessary
+
3.0.6:
Fix configparser import for python 2 vs 3
+
3.0.5:
Add config override with env variables
+
3.0.4:
Code cleanup
+
3.0.3:
Put index management in core
+
3.0.2:
Add missing deps
+
3.0.1:
Add README etc..
+
3.0.0:
separation of biomaj and biomaj_core
=====================================
biomaj_core/utils.py
=====================================
@@ -414,7 +414,7 @@ class Utils(object):
"""
logger = logging.getLogger('biomaj')
try:
- if archivefile.endswith('.tar.gz'):
+ if archivefile.endswith(('.tar.gz', '.tgz')):
subprocess.check_call("tar tfz " + archivefile, shell=True)
elif archivefile.endswith('.tar'):
subprocess.check_call("tar tf " + archivefile, shell=True)
@@ -424,6 +424,8 @@ class Utils(object):
subprocess.check_call("gunzip -t " + archivefile, shell=True)
elif archivefile.endswith('.zip'):
subprocess.check_call("unzip -t " + archivefile, shell=True)
+ else:
+ logger.warn("archive_check: unable to process check call for '" + str(archivefile) + "'")
except CalledProcessError as uncompresserror:
logger.error("Archive integrity error of %s: %s" % (archivefile, str(uncompresserror)))
return False
@@ -445,7 +447,7 @@ class Utils(object):
is_archive = False
logger = logging.getLogger('biomaj')
try:
- if archivefile.endswith('.tar.gz'):
+ if archivefile.endswith(('.tar.gz', '.tgz')):
subprocess.check_call("tar xfz " + archivefile + " --overwrite -C " + os.path.dirname(archivefile), shell=True)
is_archive = True
elif archivefile.endswith('.tar'):
@@ -460,9 +462,14 @@ class Utils(object):
elif archivefile.endswith('.zip'):
subprocess.check_call("unzip -o " + archivefile + " -d " + os.path.dirname(archivefile), shell=True)
is_archive = True
+ else:
+ raise Exception("uncompress: Unknown file extension in '" + str(archivefile) + "'")
except CalledProcessError as uncompresserror:
logger.error("Uncompress error of %s: %s" % (archivefile, str(uncompresserror)))
return False
+ except Exception as e:
+ logger.error(e)
+ return False
if is_archive:
logger.debug('Uncompress:uncompress:' + archivefile)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+biomaj3-core (3.0.27-1) 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 11:55:16 +0200
+
biomaj3-core (3.0.26-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-nose,
python3-requests,
python3-setuptools
-Standards-Version: 4.5.1
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/biomaj3-core
Vcs-Git: https://salsa.debian.org/med-team/biomaj3-core.git
Homepage: https://github.com/genouest/biomaj-core
=====================================
setup.py
=====================================
@@ -22,7 +22,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.26',
+ 'version': '3.0.27',
'classifiers': [
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/78cccfb24e553f21cd2b5fb1ee53651e40e874b6...d77425c2314e5222fd12f72d230d20883e84b981
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/78cccfb24e553f21cd2b5fb1ee53651e40e874b6...d77425c2314e5222fd12f72d230d20883e84b981
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