def setUp(self):
self.filesystem = fake_filesystem.FakeFilesystem(path_separator='/')
self.filesystem.is_windows_fs = False
pathlib = fake_pathlib.FakePathlibModule(self.filesystem)
self.path = pathlib.Path
self.filesystem.CreateFile('/home/jane/test.py',
st_size=100,
st_mode=stat.S_IFREG | 0o666)
self.filesystem.CreateDirectory('/home/john')
self.filesystem.CreateLink('/john', '/home/john')
self.filesystem.CreateLink('/test.py', '/home/jane/test.py')
self.filesystem.CreateLink('/broken_dir_link', '/home/none')
self.filesystem.CreateLink('/broken_file_link', '/home/none/test.py')
def gamedb() -> Path:
"""Mock supported game database file."""
file_path = '/gamedb.yaml'
file_contents = {
'minecraft': dict(id=432, version='DEFAULT'),
}
fs = fake_filesystem.FakeFilesystem(path_separator='/')
pathlib = fake_pathlib.FakePathlibModule(fs)
fs.CreateFile(file_path,
contents=yaml.dump(file_contents),
encoding='utf-8')
return pathlib.Path(file_path)
def _refresh(self):
"""Renew the fake file system and set the _isStale flag to `False`."""
if self._stubs is not None:
self._stubs.SmartUnsetAll()
self._stubs = mox3.stubout.StubOutForTesting()
self.fs = fake_filesystem.FakeFilesystem()
self.fake_os = fake_filesystem.FakeOsModule(self.fs)
self.fake_path = self.fake_os.path
if self.HAS_PATHLIB:
self.fake_pathlib = fake_pathlib.FakePathlibModule(self.fs)
self.fake_shutil = fake_filesystem_shutil.FakeShutilModule(self.fs)
self.fake_tempfile_ = fake_tempfile.FakeTempfileModule(self.fs)
self.fake_open = fake_filesystem.FakeFileOpen(self.fs)
self.fake_io = fake_filesystem.FakeIoModule(self.fs)
self._isStale = False
def setUp(self):
super().setUp()
if not self.use_real_fs():
self.pathlib = fake_pathlib.FakePathlibModule(self.filesystem)
self.path = self.pathlib.Path
def setUp(self):
self.filesystem = fake_filesystem.FakeFilesystem(path_separator='/')
self.pathlib = fake_pathlib.FakePathlibModule(self.filesystem)
self.os = fake_filesystem.FakeOsModule(self.filesystem)
def test_run_sodar_ingest_fastq_smoke_test(mocker, requests_mock):
# --- setup arguments
irods_path = "/irods/dest"
landing_zone_uuid = "landing_zone_uuid"
dest_path = "target/folder/generic_file.fq.gz"
fake_base_path = "/base/path"
argv = [
"--verbose",
"sodar",
"ingest-fastq",
"--num-parallel-transfers",
"0",
"--sodar-api-token",
"XXXX",
"--yes",
"--remote-dir-pattern",
dest_path,
fake_base_path,
landing_zone_uuid,
]
parser, _subparsers = setup_argparse()
args = parser.parse_args(argv)
# Setup fake file system but only patch selected modules. We cannot use the Patcher approach here as this would
# break biomedsheets.
fs = fake_filesystem.FakeFilesystem()
fake_os = fake_filesystem.FakeOsModule(fs)
fake_pl = fake_pathlib.FakePathlibModule(fs)
# --- add test files
fake_file_paths = []
for member in ("sample1", "sample2", "sample3"):
for ext in ("", ".md5"):
fake_file_paths.append("%s/%s/%s-N1-RNA1-RNA_seq1.fastq.gz%s" %
(fake_base_path, member, member, ext))
fs.create_file(fake_file_paths[-1])
fake_file_paths.append("%s/%s/%s-N1-DNA1-WES1.fq.gz%s" %
(fake_base_path, member, member, ext))
fs.create_file(fake_file_paths[-1])
# Remove index's log MD5 file again so it is recreated.
fs.remove(fake_file_paths[3])
# --- mock modules
mocker.patch("glob.os", fake_os)
mocker.patch("cubi_tk.sea_snap.itransfer_results.pathlib", fake_pl)
mocker.patch("cubi_tk.sea_snap.itransfer_results.os", fake_os)
mocker.patch("cubi_tk.snappy.itransfer_common.os", fake_os)
mock_check_output = mock.MagicMock(return_value=0)
mocker.patch("cubi_tk.snappy.itransfer_common.check_output",
mock_check_output)
mock_check_call = mock.MagicMock(return_value=0)
mocker.patch("cubi_tk.snappy.itransfer_common.check_call", mock_check_call)
mocker.patch("cubi_tk.sodar.ingest_fastq.pathlib", fake_pl)
mocker.patch("cubi_tk.sodar.ingest_fastq.os", fake_os)
fake_open = fake_filesystem.FakeFileOpen(fs)
mocker.patch("cubi_tk.snappy.itransfer_common.open", fake_open)
# necessary because independent test fail
mock_value = mock.MagicMock()
mocker.patch("cubi_tk.sodar.ingest_fastq.Value", mock_value)
mocker.patch("cubi_tk.snappy.itransfer_common.Value", mock_value)
# requests mock
return_value = dict(
assay="",
config_data="",
configuration="",
date_modified="",
description="",
irods_path=irods_path,
project="",
sodar_uuid="",
status="",
status_info="",
title="",
user=dict(sodar_uuid="", username="", name="", email=""),
)
url = os.path.join(args.sodar_url, "landingzones", "api", "retrieve",
args.destination)
requests_mock.register_uri("GET", url, text=json.dumps(return_value))
# --- run tests
res = main(argv)
assert not res
# TODO: make mock check_output actually create the file?
# assert fs.exists(fake_file_paths[3])
assert mock_check_call.call_count == 1
assert mock_check_call.call_args[0] == ([
"md5sum", "sample1-N1-DNA1-WES1.fq.gz"
], )
assert mock_check_output.call_count == len(fake_file_paths) * 3
remote_path = os.path.join(irods_path, dest_path)
for path in fake_file_paths:
expected_mkdir_argv = ["imkdir", "-p", os.path.dirname(remote_path)]
ext = ".md5" if path.split(".")[-1] == "md5" else ""
expected_irsync_argv = [
"irsync", "-a", "-K", path, ("i:%s" + ext) % remote_path
]
expected_ils_argv = ["ils", os.path.dirname(remote_path)]
assert ((expected_mkdir_argv, ), ) in mock_check_output.call_args_list
assert ((expected_irsync_argv, ), ) in mock_check_output.call_args_list
assert ((expected_ils_argv, ), {
"stderr": -2
}) in mock_check_output.call_args_list
def setUp(self):
filesystem = fake_filesystem.FakeFilesystem(path_separator='/')
filesystem.is_windows_fs = True
pathlib = fake_pathlib.FakePathlibModule(filesystem)
self.path = pathlib.Path
def setUp(self):
self.filesystem = fake_filesystem.FakeFilesystem(path_separator='!')
# self.filesystem.is_windows_fs = False
self.filesystem.is_case_sensitive = True
pathlib = fake_pathlib.FakePathlibModule(self.filesystem)
self.path = pathlib.Path
def test_run_seasnap_itransfer_results_smoke_test(mocker):
# --- setup arguments
dest_path = "/irods/dest"
fake_base_path = "/base/path"
blueprint_path = os.path.join(os.path.dirname(__file__), "data",
"test_blueprint.txt")
argv = [
"--verbose",
"sea-snap",
"itransfer-results",
blueprint_path,
dest_path,
"--num-parallel-transfers",
"0",
]
parser, subparsers = setup_argparse()
# Setup fake file system but only patch selected modules. We cannot use the Patcher approach here as this would
# break biomedsheets.
fs = fake_filesystem.FakeFilesystem()
fake_os = fake_filesystem.FakeOsModule(fs)
fake_pl = fake_pathlib.FakePathlibModule(fs)
# --- add test files
fake_file_paths = []
for member in ("sample1", "sample2", "sample3"):
for ext in ("", ".md5"):
fake_file_paths.append(
"%s/mapping/star/%s/out/star.%s-N1-RNA1-RNA-Seq1.bam%s" %
(fake_base_path, member, member, ext))
fs.create_file(fake_file_paths[-1])
fake_file_paths.append(
"%s/mapping/star/%s/report/star.%s-N1-RNA1-RNA-Seq1.log%s" %
(fake_base_path, member, member, ext))
fs.create_file(fake_file_paths[-1])
fs.add_real_file(blueprint_path)
fake_pl.Path(blueprint_path).touch()
# Remove index's log MD5 file again so it is recreated.
fs.remove(fake_file_paths[3])
# --- mock modules
mocker.patch("glob.os", fake_os)
mocker.patch("cubi_tk.sea_snap.itransfer_results.pathlib", fake_pl)
mocker.patch("cubi_tk.sea_snap.itransfer_results.os", fake_os)
mocker.patch("cubi_tk.snappy.itransfer_common.os", fake_os)
mock_check_output = mock.mock_open()
mocker.patch("cubi_tk.sea_snap.itransfer_results.check_output",
mock_check_output)
mocker.patch("cubi_tk.snappy.itransfer_common.check_output",
mock_check_output)
mock_check_call = mock.mock_open()
mocker.patch("cubi_tk.snappy.itransfer_common.check_call", mock_check_call)
fake_open = fake_filesystem.FakeFileOpen(fs)
mocker.patch("cubi_tk.snappy.itransfer_common.open", fake_open)
# necessary because independent test fail
mock_value = mock.MagicMock()
mocker.patch("cubi_tk.sea_snap.itransfer_results.Value", mock_value)
mocker.patch("cubi_tk.snappy.itransfer_common.Value", mock_value)
# --- run tests
res = main(argv)
print(mock_check_output.call_args_list)
assert not res
assert fs.exists(fake_file_paths[3])
assert mock_check_call.call_count == 1
assert mock_check_call.call_args[0] == ([
"md5sum", "star.sample1-N1-RNA1-RNA-Seq1.log"
], )
assert mock_check_output.call_count == len(fake_file_paths) * 2
remote_path = os.path.join(dest_path, "fakedest")
for path in fake_file_paths:
expected_mkdir_argv = f"imkdir -p $(dirname {remote_path} )"
ext = ".md5" if path.split(".")[-1] == "md5" else ""
expected_irsync_argv = f"irsync -a -K {path} {('i:%s' + ext) % remote_path}"
assert ((expected_mkdir_argv, ), {
"shell": True
}) in mock_check_output.call_args_list
assert ((expected_irsync_argv, ), {
"shell": True
}) in mock_check_output.call_args_list
