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_prepare_biobox_file():
config = biobox_cfg(hlp.short_read_fastq())
biobox_file = os.path.join(
vol.get_host_path(exe.prepare_biobox_file(config)), "biobox.yaml")
assert os.path.isfile(biobox_file)
with open(biobox_file, 'r') as f:
biobox_args = yaml.load(f.read())['arguments']
assert biobox_args == biobox_cfg(
vol.get_container_mount(hlp.short_read_fastq())['biobox_target'])
def test_prepare_biobox_file():
config = biobox_cfg(hlp.short_read_fastq())
biobox_file = os.path.join(
vol.get_host_path(exe.prepare_biobox_file(config)),
"biobox.yaml")
assert os.path.isfile(biobox_file)
with open(biobox_file, 'r') as f:
biobox_args = yaml.load(f.read())['arguments']
assert biobox_args == biobox_cfg(vol.get_container_mount(hlp.short_read_fastq())['biobox_target'])
def remap(x):
f = lambda i: vol.get_container_mount(i)['biobox_target']
return funcy.update_in(x, ['value'], f)
def test_get_container_mount_with_single_dir():
path = hlp.create_tmp_dir("dir_1")
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_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_dir():
path = hlp.create_tmp_dir("dir_1")
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 remap(x):
f = lambda i: vol.get_container_mount(i)['biobox_target']
return funcy.update_in(x, ['value'], f)
def test_remap_args_with_single_directory_entry():
host_dir = hlp.create_tmp_dir("dir_0")
container_dir = vol.get_container_mount(host_dir)['biobox_target']
assert cnf.remap_biobox_input_paths(wrap("fasta_dir", [reference(host_dir)])) == \
wrap("fasta_dir", [reference(container_dir)])
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)])