[med-svn] [Git][med-team/biomaj3-core][upstream] New upstream version 3.0.27

[Andreas Tille (@tille)]

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


Commits:
7e1c9a4d by Andreas Tille at 2022-06-29T11:55:09+02:00
New upstream version 3.0.27
- - - - -


3 changed files:

- CHANGES.txt
- biomaj_core/utils.py
- 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)


=====================================
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/-/commit/7e1c9a4df474ebf6609378600994a56c3c5d78b0

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View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/commit/7e1c9a4df474ebf6609378600994a56c3c5d78b0
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