[med-svn] [Git][med-team/biomaj3][upstream] New upstream version 3.1.8
Olivier Sallou
gitlab at salsa.debian.org
Sat Mar 9 10:22:12 GMT 2019
Olivier Sallou pushed to branch upstream at Debian Med / biomaj3
Commits:
2fd6682f by Olivier Sallou at 2019-03-09T10:18:43Z
New upstream version 3.1.8
- - - - -
6 changed files:
- .travis.yml
- CHANGES.txt
- biomaj/process/metaprocess.py
- biomaj/workflow.py
- requirements.txt
- setup.py
Changes:
=====================================
.travis.yml
=====================================
@@ -1,36 +1,33 @@
language: python
sudo: false
python:
- - "2.7"
- - "3.4"
- - "3.5"
- - "3.6"
+- '2.7'
+- '3.4'
+- '3.5'
+- '3.6'
services:
- - mongodb
- - elasticsearch
-# Apply only on main branches
+- mongodb
+- elasticsearch
branches:
except:
- - /^feature.*$/
-# command to install dependencies
-#before_install:
-# - "sudo apt-get update -qq"
-# - "sudo apt-get install -qq libldap2-dev libsasl2-dev"
+ - "/^feature.*$/"
install:
- - "pip install flake8"
- - "pip install -r requirements.txt"
- - "pip install coverage"
- - "pip install python-coveralls"
- - "python setup.py -q install"
-# - "echo data_file=$TRAVIS_BUILD_DIR/.coverage >> .coveragerc"
-# command to run tests
+- pip install flake8
+- pip install -r requirements.txt
+- pip install coverage
+- pip install python-coveralls
+- python setup.py -q install
before_script:
- - sleep 10
-#script: nosetests --with-coverage --cover-package=biomaj -a '!network'
-#script: nosetests --with-coverage --cover-package=biomaj
+- sleep 10
script:
- - python setup.py test
- - flake8 --ignore E501,E123 biomaj
-#after_success:
-# - coveralls
-
+- nosetests -a '!network'
+- flake8 --ignore E501,E123 biomaj
+deploy:
+ provider: pypi
+ skip_existing: true
+ user: osallou
+ password:
+ secure: UrZI37Ab+Zz4XtpcTIwuWorV+7iY26Mbfga7Rw5TK0OTJsiI3oZiy0CBFkSO0IGsh8nea6mPZ8KYqzHhLN1EK+mCT0uej09jMIVlI23wGQSigwinO+2nA664bbikcKhsAy5NNlqB73VGyw4eBUf2XXV+dPMXj8aaVM0LZ148Qag=
+ distributions: sdist bdist_wheel
+ on:
+ tags: true
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,8 @@
+3.1.8:
+ Fix uncompress when saved files contains subdirectory
+3.1.7:
+ Fix utf/ascii encoding issue with python3
+ In case of uncompress failure, put back all compressed files to avoid redownload
3.1.6:
Fix #100 Catch error and log error if biomaj fails to connect to InfluxDB
Add history to update/remove operations
=====================================
biomaj/process/metaprocess.py
=====================================
@@ -139,7 +139,7 @@ class MetaProcess(threading.Thread):
def set_progress(self, name, status=None):
'''
- Update progress on download
+ Update progress on execution
:param name: name of process
:type name: str
=====================================
biomaj/workflow.py
=====================================
@@ -11,6 +11,7 @@ import re
import traceback
import json
import hashlib
+import sys
from biomaj_core.utils import Utils
from biomaj_download.downloadclient import DownloadClient
@@ -682,7 +683,11 @@ class UpdateWorkflow(Workflow):
# Download and extract
tmp_dir = tempfile.mkdtemp('biomaj')
rel_files = release_downloader.download(tmp_dir)
- rel_file = open(tmp_dir + '/' + rel_files[0]['name'])
+ rel_file = None
+ if (sys.version_info > (3, 0)):
+ rel_file = open(tmp_dir + '/' + rel_files[0]['name'], encoding='utf-8')
+ else:
+ rel_file = open(tmp_dir + '/' + rel_files[0]['name'])
rel_content = rel_file.read()
rel_file.close()
shutil.rmtree(tmp_dir)
@@ -1480,13 +1485,43 @@ class UpdateWorkflow(Workflow):
return True
no_extract = self.session.config.get('no.extract')
if no_extract is None or no_extract == 'false':
+ archives = []
for file in self.downloaded_files:
if 'save_as' not in file:
file['save_as'] = file['name']
nb_try = 1
+ origFile = self.session.get_offline_directory() + '/' + file['save_as']
+ is_archive = False
+ if origFile.endswith('.tar.gz'):
+ is_archive = True
+ elif origFile.endswith('.tar'):
+ is_archive = True
+ elif origFile.endswith('.bz2'):
+ is_archive = True
+ elif origFile.endswith('.gz'):
+ is_archive = True
+ elif origFile.endswith('.zip'):
+ is_archive = True
+
+ logging.info('Workflow:wf_uncompress:Uncompress:' + origFile)
+ if not os.path.exists(origFile):
+ logging.warn('Workflow:wf_uncompress:NotExists:' + origFile)
+ continue
+
+ tmpCompressedFile = origFile
+ if is_archive:
+ tmpFileNameElts = file['save_as'].split('/')
+ tmpFileNameElts[len(tmpFileNameElts) - 1] = 'tmp_' + tmpFileNameElts[len(tmpFileNameElts) - 1]
+ tmpCompressedFile = self.session.get_offline_directory() + '/' + '/'.join(tmpFileNameElts)
+ archives.append({'from': origFile, 'to': tmpCompressedFile})
+ else:
+ continue
+
+ shutil.copy(origFile, tmpCompressedFile)
+
not_ok = True
while nb_try < 3 and not_ok:
- status = Utils.uncompress(self.session.get_offline_directory() + '/' + file['save_as'])
+ status = Utils.uncompress(origFile)
if status:
not_ok = False
else:
@@ -1494,7 +1529,17 @@ class UpdateWorkflow(Workflow):
nb_try += 1
if not_ok:
logging.error('Workflow:wf_uncompress:Failure:' + file['name'])
+ # Revert archive files
+ for archive in archives:
+ if os.path.exists(archive['to']):
+ logging.info("Workflow:wf_uncompress:RevertArchive:" + archive['from'])
+ shutil.move(archive['to'], archive['from'])
return False
+ for archive in archives:
+ if os.path.exists(archive['to']):
+ logging.info("Workflow:wf_uncompress:RemoveAfterExtract:" + archive['to'])
+ os.remove(archive['to'])
+
else:
logging.info("Workflow:wf_uncompress:NoExtract")
return True
=====================================
requirements.txt
=====================================
@@ -1,7 +1,7 @@
biomaj_core
biomaj_user
-biomaj_download>=3.0.18
-biomaj_process
+biomaj_download>=3.0.20
+biomaj_process>=3.0.12
biomaj_cli
mock
nose
=====================================
setup.py
=====================================
@@ -35,7 +35,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.1.6',
+ 'version': '3.1.8',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/commit/2fd6682f7717986c2a50c12ea76953d1ddd838e8
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/commit/2fd6682f7717986c2a50c12ea76953d1ddd838e8
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