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"""Pytest fixtures and test helper functions"""
import collections
import contextlib
from datetime import datetime
import io
import os
import shutil
import subprocess
import tarfile
import tempfile
import pytest
import requests
import yaml
from bcbio.pipeline.config_utils import load_system_config
if os.environ.get("BCBIO_TEST_DIR"):
BCBIO_TEST_DIR = os.environ.get("BCBIO_TEST_DIR")
else:
BCBIO_TEST_DIR = tempfile.TemporaryDirectory(prefix="bcbio_").name # /tmp/bcbio
def pytest_addoption(parser):
parser.addoption('--keep-test-dir', action='store_true', default=False,
help='Preserve test output directory after each test')
@pytest.fixture(scope='session')
def test_dir(pytestconfig):
os.makedirs(BCBIO_TEST_DIR, exist_ok=True)
yield
if not pytestconfig.getoption('--keep-test-dir'):
shutil.rmtree(BCBIO_TEST_DIR)
@pytest.fixture(scope='session')
def data_dir(test_dir):
# workaround for hardcoded data file paths in test run config files
test_data_dir = os.path.join(BCBIO_TEST_DIR, 'data') # /tmp/bcbio/data
with contextlib.suppress(FileExistsError):
os.symlink(os.path.join(os.path.dirname(__file__), 'data'), test_data_dir)
return os.path.join(test_data_dir, 'automated') # /tmp/bcbio/data/automated
@pytest.fixture
def work_dir(pytestconfig):
"""Provide and manage output directory for tests"""
test_output_dir = os.path.join(BCBIO_TEST_DIR, 'test_automated_output')
os.makedirs(test_output_dir, exist_ok=True)
original_dir = os.getcwd()
os.chdir(test_output_dir)
yield test_output_dir
os.chdir(original_dir)
if not pytestconfig.getoption('--keep-test-dir'):
shutil.rmtree(test_output_dir)
@pytest.fixture
def global_config(data_dir, work_dir):
"""Prepare a bcbio_system YAML file pointing to test data"""
system = _get_bcbio_system(work_dir, data_dir)
# create local config pointing to reduced genomes
test_system = os.path.join(work_dir, 'bcbio_system.yaml')
with open(system) as in_handle:
config = yaml.safe_load(in_handle)
config["galaxy_config"] = os.path.join(data_dir, "universe_wsgi.ini")
with open(test_system, "w") as out_handle:
yaml.dump(config, out_handle)
return test_system
@contextlib.contextmanager
def install_cwl_test_files():
orig_dir = os.getcwd()
url = "https://github.com/bcbio/test_bcbio_cwl/archive/master.tar.gz"
dirname = os.path.join(BCBIO_TEST_DIR, 'test_bcbio_cwl-master')
if os.path.exists(dirname):
# check for updated commits if the directory exists
ctime = os.path.getctime(os.path.join(dirname, "README.md"))
dtime = datetime.fromtimestamp(ctime).isoformat()
r = requests.get("https://api.github.com/repos/bcbio/test_bcbio_cwl/commits?since=%s" % dtime).json()
if len(r) > 0:
shutil.rmtree(dirname)
try:
if not os.path.exists(dirname):
print("Downloading CWL test directory: %s" % url)
os.makedirs(dirname)
os.chdir(os.path.dirname(dirname))
r = requests.get(url)
tf = tarfile.open(fileobj=io.BytesIO(r.content), mode='r|gz')
tf.extractall()
os.chdir(dirname)
yield dirname
finally:
os.chdir(orig_dir)
def _get_bcbio_system(workdir, data_dir):
system = _get_bcbiovm_config(data_dir)
if _config_is_invalid(system):
system = _get_system_config(workdir, system)
if _config_is_invalid(system):
system = os.path.join(data_dir, "post_process-sample.yaml")
return system
def _get_bcbiovm_config(data_dir):
try:
from bcbiovm.docker.defaults import get_datadir
datadir = data_dir or get_datadir()
sys_conf_file = os.path.join(datadir, "galaxy", "bcbio_system.yaml")
system = sys_conf_file if datadir else None
except ImportError:
system = None
return system
def _config_is_invalid(config_fname):
return config_fname is None or not os.path.exists(config_fname)
def _get_system_config(work_dir, system):
try:
_, system = load_system_config(
config_file="bcbio_system.yaml",
work_dir=work_dir
)
except ValueError:
system = None
return system
@pytest.fixture
def install_test_files(data_dir):
"""Download required sequence and reference files."""
DlInfo = collections.namedtuple("DlInfo", "fname dirname version")
download_data = [
DlInfo("110106_FC70BUKAAXX.tar.gz", None, None),
DlInfo("genomes_automated_test.tar.gz", "genomes", 34),
DlInfo("110907_ERP000591.tar.gz", None, None),
DlInfo("100326_FC6107FAAXX.tar.gz", None, 12),
DlInfo("tcga_benchmark.tar.gz", None, 3),
DlInfo("singlecell-rnaseq-test-data.tar.gz", "Harvard-inDrop", 1)
]
for dl in download_data:
url = f"https://bcbio-nextgen.s3.amazonaws.com/test_data/{dl.fname}"
dirname = os.path.join(
data_dir, os.pardir,
dl.fname.replace(".tar.gz", "") if dl.dirname is None
else dl.dirname
)
if os.path.exists(dirname) and dl.version is not None:
version_file = os.path.join(dirname, "VERSION")
is_old = True
if os.path.exists(version_file):
with open(version_file) as in_handle:
version = int(in_handle.read())
is_old = version < dl.version
if is_old:
shutil.rmtree(dirname)
if not os.path.exists(dirname):
_download_to_dir(url, dirname)
def _download_to_dir(url, dirname):
subprocess.check_call(['wget', '--progress=dot:giga', url])
subprocess.check_call(['tar', '-xzvpf', os.path.basename(url)])
shutil.move(os.path.basename(dirname), dirname)
os.remove(os.path.basename(url))
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