New upstream version 3.1.8

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

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

script:

  - python setup.py test

- nosetests -a '!network'

- flake8 --ignore E501,E123 biomaj

#after_success:

#  - coveralls

deploy:

  provider: pypi

  skip_existing: true

  user: osallou

  password:

    secure: UrZI37Ab+Zz4XtpcTIwuWorV+7iY26Mbfga7Rw5TK0OTJsiI3oZiy0CBFkSO0IGsh8nea6mPZ8KYqzHhLN1EK+mCT0uej09jMIVlI23wGQSigwinO+2nA664bbikcKhsAy5NNlqB73VGyw4eBUf2XXV+dPMXj8aaVM0LZ148Qag=

  distributions: sdist bdist_wheel

  on:

    tags: true

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

    def set_progress(self, name, status=None):

        '''

        Update progress on download

        Update progress on execution

        :param name: name of process

        :type name: str

import traceback

import json

import hashlib

import sys

from biomaj_core.utils import Utils

from biomaj_download.downloadclient import DownloadClient

                # Download and extract

                tmp_dir = tempfile.mkdtemp('biomaj')

                rel_files = release_downloader.download(tmp_dir)

                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()

            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:

                        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

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