def test_create_volume_string_set_with_two_files_in_same_dir():
dir_ = tempfile.mkdtemp()
files = [
hlp.create_tmp_file("file_0", dir_),
hlp.create_tmp_file("file_1", dir_)
]
assert len(list(vol.create_volume_string_set(files))) == 1
def test_get_biobox_paths_with_two_files():
path_0 = hlp.create_tmp_file("file_0")
path_1 = hlp.create_tmp_file("file_1")
biobox = [{"fastq": [
{"id": 0, "type": "paired", "value": path_0},
{"id": 0, "type": "paired", "value": path_1}
]
}]
assert cnf.get_all_biobox_paths(biobox) == [path_0, path_1]
def test_create_volume_string_set_with_single_file():
dir_ = tempfile.mkdtemp()
path = hlp.create_tmp_file("file_0", dir_)
expected = "{}:{}:ro".format(
dir_,
vol.get_container_mount(path)['container_dir'])
assert vol.create_volume_string_set([path]) == [expected]
def test_get_biobox_paths_with_single_file():
path = hlp.create_tmp_file("file_0")
biobox = [{"fastq": [
{"id": 0, "type": "paired", "value": path}
]
}]
assert cnf.get_all_biobox_paths(biobox) == [path]
def test_create_volume_string_set_with_two_files_in_different_dir():
files = [hlp.create_tmp_file("file_0"), hlp.create_tmp_file("file_1")]
assert len(list(vol.create_volume_string_set(files))) == 2
def test_get_container_mount_with_single_file():
path = hlp.create_tmp_file("file_0")
volume = vol.get_container_mount(path)
assert volume['host_dir'] == vol.host_directory(path)
assert DIR_RE.search(volume['container_dir']) != None
assert TARGET_RE.search(volume['biobox_target']) != None
def test_create_volume_string_set_with_two_files_in_different_dir():
files = [hlp.create_tmp_file("file_0"), hlp.create_tmp_file("file_1")]
assert len(list(vol.create_volume_string_set(files))) == 2
def test_create_volume_string_set_with_two_files_in_same_dir():
dir_ = tempfile.mkdtemp()
files = [hlp.create_tmp_file("file_0", dir_), hlp.create_tmp_file("file_1", dir_)]
assert len(list(vol.create_volume_string_set(files))) == 1
def test_create_volume_string_set_with_single_file():
dir_ = tempfile.mkdtemp()
path = hlp.create_tmp_file("file_0", dir_)
expected = "{}:{}:ro".format(dir_, vol.get_container_mount(path)['container_dir'])
assert vol.create_volume_string_set([path]) == [expected]
def test_get_container_mount_with_single_file():
path = hlp.create_tmp_file("file_0")
volume = vol.get_container_mount(path)
assert volume['host_dir'] == vol.host_directory(path)
assert DIR_RE.search(volume['container_dir']) != None
assert TARGET_RE.search(volume['biobox_target']) != None
def test_remap_args_with_single_file_entry():
host_file = hlp.create_tmp_file("file_0")
container_file = vol.get_container_mount(host_file)['biobox_target']
assert cnf.remap_biobox_input_paths(wrap("fastq", [fastq(host_file)])) == \
wrap("fastq", [fastq(container_file)])