def setUpClass(cls):
cmd = '{} -m pip install . -q --upgrade --use-feature=in-tree-build'.format(
sys.executable)
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args, cwd=PathManager.get_project_path())
cls.package_path = os.path.join(PathManager.get_package_path())
cls.test_path = os.path.join(PathManager.get_test_path())
cls.outdir_path = os.path.join(cls.test_path, 'outdir')
cls.outdir_data_path = os.path.join(cls.outdir_path, 'data')
shutil.rmtree(cls.outdir_path, ignore_errors=True)
pathlib.Path(cls.outdir_data_path).mkdir(parents=True, exist_ok=True)
############################################################################################
#
# Download sorted reads dataset
#
############################################################################################
sorted_tar_path = os.path.join(cls.outdir_data_path, "sorted.tar.gz")
pathlib.Path(os.path.dirname(sorted_tar_path)).mkdir(parents=True,
exist_ok=True)
# Test first in local dir, otherwise in the remote URLs
if not os.path.isfile(sorted_tar_path) or pathlib.Path(
sorted_tar_path).stat().st_size < 1000000:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url1, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url1,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url2, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url2,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
# urllib.request.urlretrieve(sorted_tar_gz_url3, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url3,
sorted_tar_path,
reporthook=tqdm_hook(t))
tar = tarfile.open(sorted_tar_path, "r:gz")
tar.extractall(path=cls.outdir_data_path)
tar.close()
def setUp(self):
# vtam needs to be in the tsv_path
cmd = '{} -m pip install . -q --upgrade --use-feature=in-tree-build'.format(
sys.executable)
if sys.platform.startswith("win"):
args = cmd
else:
args = shlex.split(cmd)
subprocess.run(args=args, cwd=PathManager.get_project_path())
self.package_path = os.path.join(PathManager.get_package_path())
self.test_path = os.path.join(PathManager.get_test_path())
self.outdir_path = os.path.join(self.test_path, 'outdir')
self.outdir_data_path = os.path.join(self.outdir_path, 'data')
# during development of the test, this prevents errors
shutil.rmtree(self.outdir_path, ignore_errors=True)
pathlib.Path(self.outdir_data_path).mkdir(parents=True, exist_ok=True)
os.environ['VTAM_LOG_VERBOSITY'] = str(10)
############################################################################################
#
# Download sorted fasta test dataset
#
############################################################################################
sorted_tar_path = os.path.join(self.outdir_data_path, "sorted.tar.gz")
# Test first in local dir, otherwise in the remote URLs
if not os.path.isfile(sorted_tar_path) or pathlib.Path(
sorted_tar_path).stat().st_size < 1000000:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url1, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url1,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
try:
# urllib.request.urlretrieve(sorted_tar_gz_url2, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url2,
sorted_tar_path,
reporthook=tqdm_hook(t))
except Exception:
# urllib.request.urlretrieve(sorted_tar_gz_url3, sorted_tar_path, MyProgressBar())
with tqdm(...) as t:
t.set_description(os.path.basename(sorted_tar_path))
urllib.request.urlretrieve(sorted_tar_gz_url3,
sorted_tar_path,
reporthook=tqdm_hook(t))
tar = tarfile.open(sorted_tar_path, "r:gz")
tar.extractall(path=self.outdir_path)
tar.close()
############################################################################################
#
# Paths
#
############################################################################################
self.asvtable_path = os.path.join(self.outdir_path,
"asvtable_default.tsv")
self.args = {}
self.args['sortedinfo'] = os.path.join(os.path.dirname(__file__),
"sortedinfo.tsv")
self.args['params'] = os.path.join(os.path.dirname(__file__),
"params_min_replicate_number1.yml")
self.args['params_lfn_variant'] = os.path.join(
os.path.dirname(__file__), "params_lfn_variant.yml")
self.args['params_lfn_variant_replicate'] = os.path.join(
os.path.dirname(__file__), "params_lfn_variant_replicate.yml")