[med-svn] [Git][med-team/biomaj3-core][upstream] New upstream version 3.0.26

[Andreas Tille]

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


Commits:
921d3c65 by Andreas Tille at 2021-01-17T09:28:52+01:00
New upstream version 3.0.26
- - - - -


6 changed files:

- .travis.yml
- CHANGES.txt
- biomaj_core/config.py
- biomaj_core/utils.py
- requirements.txt
- setup.py


Changes:

=====================================
.travis.yml
=====================================
@@ -1,10 +1,14 @@
 language: python
+arch: 
+  - ppc64le
+  - amd64
 sudo: false
 python:
   - '2.7'
-  - '3.4'
   - '3.5'
   - '3.6'
+  - '3.7'
+  - '3.8'
 branches:
   except:
   - "/^feature.*$/"


=====================================
CHANGES.txt
=====================================
@@ -1,7 +1,24 @@
-3.0.19 [unreleased]:
+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:


=====================================
biomaj_core/config.py
=====================================
@@ -44,7 +44,11 @@ class BiomajConfig(object):
         'keep.old.sessions': 0,
         'docker.sudo': '1',
         'auto_publish': 0,
-        'use_hardlinks': 0
+        'use_hardlinks': 0,
+        'wait_policy': 'wait_fixed(3)',
+        'stop_condition': 'stop_after_attempt(3)',
+        'ssh_hosts_file': os.path.expanduser('~/.ssh/known_hosts'),
+        'ssh_new_host': 'reject',
     }
 
     # Old biomaj level compatibility
@@ -361,12 +365,12 @@ class BiomajConfig(object):
             logging.warn('db.fullname is not set')
         if not self.get('db.formats'):
             logging.warn('db.formats is not set')
-        if self.get('use_ldap'):
+        if self.get_bool('use_ldap'):
             if not self.get('ldap.host') or not self.get('ldap.port') or \
                     not self.get('ldap.dn'):
                 logging.error('use_ldap set to 1 but missing configuration')
                 status = False
-        if self.get('use_elastic'):
+        if self.get_bool('use_elastic'):
             if not self.get('elastic_nodes') or not self.get('elastic_index'):
                 logging.error('use_elastic set to 1 but missing configuration')
                 status = False


=====================================
biomaj_core/utils.py
=====================================
@@ -126,13 +126,17 @@ class Utils(object):
         :param folder: directory path
         :type folder: str
         """
+        logger = logging.getLogger('biomaj')
         if not os.path.exists(folder):
             return -1
         folder_size = 0
         for (path, dirs, files) in os.walk(folder):
             for ffile in files:
                 filename = os.path.join(path, ffile)
-                folder_size += os.path.getsize(filename)
+                try:
+                    folder_size += os.path.getsize(filename)
+                except Exception:
+                    logger.error('[stat][size] file not found %s' % filename)
         return folder_size
 
     @staticmethod
@@ -157,7 +161,7 @@ class Utils(object):
             return None
         # release = None
         rfile = files[0]
-        release = {'year': rfile['year'], 'month': rfile['month'], 'day': rfile['day']}
+        release = {'year': rfile['year'], 'month': rfile['month'], 'day': rfile['day'], 'file': rfile}
         for rfile in files:
             rel_date = datetime.date(int(release['year']), int(release['month']), int(release['day']))
             file_date = datetime.date(int(rfile['year']), int(rfile['month']), int(rfile['day']))
@@ -165,6 +169,7 @@ class Utils(object):
                 release['year'] = rfile['year']
                 release['month'] = rfile['month']
                 release['day'] = rfile['day']
+                release['file'] = rfile
         return release
 
     @staticmethod


=====================================
requirements.txt
=====================================
@@ -1,5 +1,5 @@
 nose
 mock
 future
-elasticsearch
+elasticsearch==5.5.3
 requests


=====================================
setup.py
=====================================
@@ -17,11 +17,12 @@ with open(os.path.join(here, 'CHANGES.txt')) as f:
 config = {
     'description': 'BioMAJ core library',
     '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': '3.0.19',
+    'version': '3.0.26',
      'classifiers': [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -36,8 +37,7 @@ config = {
         # that you indicate whether you support Python 2, Python 3 or both.
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4'
+        'Programming Language :: Python :: 3'
     ],
     'install_requires': [
                          'future',



View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0

-- 
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/commit/921d3c655f33f9c11e486abcae8bdced9e502ed0
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