Python get_logger Examples

Example #1

File: test_merger.py Project: faircloth-lab/sate-core

#! /usr/bin/env python

import unittest
import datetime
import logging
import os

from sate.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled

from sate import get_logger
from sate.alignment import Alignment
from sate.scheduler import jobq, start_worker
from sate.filemgr import TempFS

_LOG = get_logger(__name__)

config = get_testing_configuration()

start_worker(1)

class MergerTest(unittest.TestCase):
    def setUp(self):
        self.ts = TempFS()
        self.ts.create_top_level_temp(prefix='mergerTesting', parent=os.curdir)

    def tearDown(self):
        dir_list = self.ts.get_remaining_directories()
        for dir in dir_list:
            self.ts.remove_dir(dir)

    def get_merger(self, name):

Example #2

File: __init__.py Project: faircloth-lab/sate-core

# You should have received a copy of the GNU General Public License
# along with this program.      If not, see <http://www.gnu.org/licenses/>.

# Jiaye Yu, Mark Holder, and Jeet Sukumaran, University of Kansas

"""
SATe testing suite.
"""

import unittest
import re
import os

from sate import get_logger
from sate.configure import get_configuration
_LOG = get_logger("sate.tests")

try:
    import pkg_resources
    TESTS_DIR = pkg_resources.resource_filename("sate", "test")
    #SCRIPTS_DIR = pkg_resources.resource_filename("sate", os.path.join(os.pardir, "scripts"))
    _LOG.info("using pkg_resources path mapping")
except:
    LOCAL_DIR = os.path.dirname(__file__)
    TESTS_DIR = os.path.join(LOCAL_DIR, os.path.pardir)
    PACKAGE_DIR = os.path.join(TESTS_DIR, os.path.pardir)
    #SCRIPTS_DIR = os.path.join(PACKAGE_DIR, os.path.pardir, "scripts")
    _LOG.info("using local filesystem path mapping")

TESTS_DATA_DIR = os.path.join(TESTS_DIR, "data")
TESTS_OUTPUT_DIR = os.path.join(TESTS_DIR, "output")

Example #3

File: test_aligners.py Project: kibet-gilbert/sate-core

#! /usr/bin/env python

import unittest
import datetime
import logging
import sys
import os

from sate.test import get_testing_configuration, data_source_path, TestLevel, is_test_enabled

from sate import get_logger
from sate.alignment import Alignment
from sate.scheduler import jobq, start_worker
from sate.filemgr import TempFS

_LOG = get_logger(__name__)

config = get_testing_configuration()

start_worker(1)

class AlignerTest(unittest.TestCase):
    def setUp(self):
        self.ts = TempFS()
        self.ts.create_top_level_temp(prefix='alignerTesting', parent=os.curdir)

    def tearDown(self):
        dir_list = self.ts.get_remaining_directories()
        for dir in dir_list:
            self.ts.remove_dir(dir)
    def get_aligner(self, name):

Example #4

# You should have received a copy of the GNU General Public License
# along with this program.      If not, see <http://www.gnu.org/licenses/>.

# Jiaye Yu, Mark Holder, and Jeet Sukumaran, University of Kansas
"""
SATe testing suite.
"""

import unittest
import re
import os

from sate import get_logger
from sate.configure import get_configuration

_LOG = get_logger("sate.tests")

try:
    import pkg_resources
    TESTS_DIR = pkg_resources.resource_filename("sate", "test")
    #SCRIPTS_DIR = pkg_resources.resource_filename("sate", os.path.join(os.pardir, "scripts"))
    _LOG.info("using pkg_resources path mapping")
except:
    LOCAL_DIR = os.path.dirname(__file__)
    TESTS_DIR = os.path.join(LOCAL_DIR, os.path.pardir)
    PACKAGE_DIR = os.path.join(TESTS_DIR, os.path.pardir)
    #SCRIPTS_DIR = os.path.join(PACKAGE_DIR, os.path.pardir, "scripts")
    _LOG.info("using local filesystem path mapping")

TESTS_DATA_DIR = os.path.join(TESTS_DIR, "data")
TESTS_OUTPUT_DIR = os.path.join(TESTS_DIR, "output")