def _teardown(self, config, temp):
# Picard creates a folder named after the user in the temp-root
try_rmtree(os.path.join(temp, getpass.getuser()))
# Some JREs may create a folder for temporary performance counters
try_rmtree(os.path.join(temp, "hsperfdata_" + getpass.getuser()))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
# Picard creates a folder named after the user in the temp-root
try_rmtree(os.path.join(temp, getpass.getuser()))
# Some JREs may create a folder for temporary performance counters
try_rmtree(os.path.join(temp, "hsperfdata_" + getpass.getuser()))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
os.remove(os.path.join(temp, self.PIPE_FILE))
if self._index_format:
os.remove(os.path.join(temp, swap_ext(self.PIPE_FILE,
self._index_format)))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
# Validate output from MAFFT
output_file = reroot_path(temp, self._output_file)
try:
MSA.from_file(output_file)
except MSAError as error:
raise NodeError("Invalid MSA produced by MAFFT:\n%s" % (error, ))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
os.remove(os.path.join(temp, "RAxML_info.output"))
source = os.path.join(temp, "RAxML_parsimonyTree.output.0")
destination = fileutils.reroot_path(temp, self._output_tree)
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
os.remove(os.path.join(temp, self.PIPE_FILE))
if self._index_format:
os.remove(
os.path.join(temp, swap_ext(self.PIPE_FILE,
self._index_format)))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
for ext in ("log", "nosex"):
os.rename(
os.path.join(temp, self._basename + "." + ext),
os.path.join(temp, self._basename + ".frq.strat." + ext),
)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
basename = os.path.basename(self._output_tree)
os.rename(
os.path.join(temp, "RAxML_parsimonyTree.Pypeline"),
os.path.join(temp, basename),
)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
os.remove(os.path.join(temp, "RAxML_info.output"))
source = os.path.join(temp, "RAxML_parsimonyTree.output.0")
destination = fileutils.reroot_path(temp, self._output_tree)
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
with open(fileutils.reroot_path(temp, self._params_file), "w") as out:
out.write("k: %i\n" % (self._param_k, ))
out.write("m: %i\n" % (self._param_m, ))
out.write("outgroup: %r\n" % (list(self._param_outgroup), ))
open(fileutils.reroot_path(temp, self._parameters_hash), "w").close()
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
template = self._output_template
bootstraps = self._bootstrap_num
start = self._bootstrap_start
for (src_file, dst_file) in self._bootstraps(template, bootstraps, start):
src_file = os.path.join(temp, src_file)
dst_file = fileutils.reroot_path(temp, dst_file)
fileutils.move_file(src_file, dst_file)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
with open(fileutils.reroot_path(temp, self._params_file), "w") as out:
out.write("k: %i\n" % (self._param_k,))
out.write("m: %i\n" % (self._param_m,))
out.write("outgroup: %r\n" % (list(self._param_outgroup),))
open(fileutils.reroot_path(temp, self._parameters_hash), "w").close()
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
for filename in os.listdir(temp):
match = re.match("RAxML_(.*).PALEOMIX", filename)
if match:
source = os.path.join(temp, filename)
destination = os.path.join(temp, self._template % match.groups())
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
for filename in os.listdir(temp):
match = re.match("RAxML_(.*).PALEOMIX", filename)
if match:
source = os.path.join(temp, filename)
destination = os.path.join(temp, self._template % match.groups())
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
# No Length_plot.pdf file is written if there are no SE reads in the
# input_file. In that case, we write a dummy PDF to ensure that all
# expected files exist.
err_message = "No length distributions are available"
with open(os.path.join(temp, "pipe_mapDamage.stderr")) as in_handle:
if any(line.startswith(err_message) for line in in_handle):
fpath = os.path.join(temp, "Length_plot.pdf")
with open(fpath, "w") as out_handle:
out_handle.write(_DUMMY_LENGTH_PLOT_PDF)
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
for filename in os.listdir(temp):
match = re.match("ExaML_(.*).Pypeline", filename)
if match:
if "binaryCheckpoint" in match.groups():
os.remove(os.path.join(temp, filename))
else:
source = os.path.join(temp, filename)
destination = os.path.join(temp, self._template % match.groups())
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def test_commandnode_teardown__missing_optional_files(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
TEMP_OUT_BAR="bar.txt",
OUT_STDOUT=os.path.join(destination, "foo.txt"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
node = CommandNode(cmd)
node._teardown(None, temp_folder)
assert_equal(os.listdir(temp_folder), [])
assert_equal(os.listdir(destination), ["foo.txt"])
def test_commandnode_teardown(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
OUT_STDOUT=os.path.join(destination, "foo.txt"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
node = CommandNode(cmd)
assert os.path.exists(os.path.join(temp_folder, "foo.txt"))
assert not os.path.exists(os.path.join(destination, "foo.txt"))
node._teardown(None, temp_folder)
assert not os.path.exists(os.path.join(temp_folder, "foo.txt"))
assert os.path.exists(os.path.join(destination, "foo.txt"))
def _teardown(self, config, temp):
for filename in os.listdir(temp):
match = re.match("ExaML_(.*).Pypeline", filename)
if match:
if "binaryCheckpoint" in match.groups():
os.remove(os.path.join(temp, filename))
else:
source = os.path.join(temp, filename)
destination = os.path.join(temp,
self._template % match.groups())
fileutils.move_file(source, destination)
CommandNode._teardown(self, config, temp)
def test_commandnode_teardown__missing_optional_files(tmp_path):
destination, tmp_path = _setup_temp_folders(tmp_path)
cmd = AtomicCmd(
("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
TEMP_OUT_BAR="bar.txt",
OUT_STDOUT=os.path.join(destination, "foo.txt"),
)
cmd.run(tmp_path)
assert cmd.join() == [0]
node = CommandNode(cmd)
node._teardown(None, tmp_path)
assert os.listdir(tmp_path) == []
assert os.listdir(destination) == ["foo.txt"]
def _teardown(self, config, temp):
for postfix in ("ALIGNMENT", "PARTITION"):
filenames = [self._kwargs["TEMP_IN_" + postfix],
self._kwargs["TEMP_IN_" + postfix] + ".reduced",
self._kwargs["OUT_" + postfix]]
for (source, destination) in zip(filenames, filenames[1:]):
source = fileutils.reroot_path(temp, source)
destination = fileutils.reroot_path(temp, destination)
if not os.path.exists(destination):
fileutils.copy_file(source, destination)
os.remove(source)
CommandNode._teardown(self, config, temp)
class MAFFTNode(CommandNode):
@create_customizable_cli_parameters
def customize(cls, input_file, output_file, algorithm = "auto", dependencies = ()):
command = AtomicCmdBuilder(_PRESETS[algorithm.lower()])
command.add_value("%(IN_FASTA)s")
command.set_kwargs(IN_FASTA = input_file,
OUT_STDOUT = output_file,
CHECK_VERSION = MAFFT_VERSION)
return {"command" : command,
"dependencies" : dependencies}
@use_customizable_cli_parameters
def __init__(self, parameters):
self._output_file = parameters.output_file
description = "<MAFFTNode (%s): '%s' -> '%s'>" \
% (parameters.algorithm,
parameters.input_file,
parameters.output_file)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = description,
dependencies = parameters.dependencies)
def _teardown(self, config, temp):
# Validate output from MAFFT
output_file = reroot_path(temp, self._output_file)
try:
MSA.from_file(output_file)
except MSAError, error:
raise NodeError("Invalid MSA produced by MAFFT:\n%s" % (error,))
CommandNode._teardown(self, config, temp)
def test_commandnode_teardown(tmp_path):
destination, tmp_path = _setup_temp_folders(tmp_path)
cmd = AtomicCmd(
("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
OUT_STDOUT=os.path.join(destination, "foo.txt"),
)
cmd.run(tmp_path)
assert cmd.join() == [0]
node = CommandNode(cmd)
assert os.path.exists(os.path.join(tmp_path, "foo.txt"))
assert not os.path.exists(os.path.join(destination, "foo.txt"))
node._teardown(None, tmp_path)
assert not os.path.exists(os.path.join(tmp_path, "foo.txt"))
assert os.path.exists(os.path.join(destination, "foo.txt"))
def test_commandnode_teardown__missing_files_in_dest(tmp_path):
destination, tmp_path = _setup_temp_folders(tmp_path)
class _CmdMock(AtomicCmd):
def commit(self, temp):
AtomicCmd.commit(self, temp)
os.remove(os.path.join(destination, "foo.txt"))
cmd = _CmdMock(
("touch", "%(OUT_FOO)s", "%(OUT_BAR)s"),
IN_DUMMY=_EMPTY_FILE,
OUT_FOO=os.path.join(destination, "foo.txt"),
OUT_BAR=os.path.join(destination, "bar.txt"),
)
cmd.run(tmp_path)
assert cmd.join() == [0]
node = CommandNode(cmd)
with pytest.raises(NodeError):
node._teardown(None, tmp_path)
def test_commandnode_teardown__extra_files_in_temp(tmp_path):
destination, tmp_path = _setup_temp_folders(tmp_path)
cmd = AtomicCmd(
("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
OUT_STDOUT=os.path.join(destination, "foo.txt"),
)
cmd.run(tmp_path)
assert cmd.join() == [0]
node = CommandNode(cmd)
(tmp_path / "bar.txt").write_text("1 2 3")
temp_files_before = set(os.listdir(tmp_path))
dest_files_before = set(os.listdir(destination))
with pytest.raises(CmdNodeError):
node._teardown(None, tmp_path)
assert temp_files_before == set(os.listdir(tmp_path))
assert dest_files_before == set(os.listdir(destination))
def test_command_node__run():
cfg_mock = Mock(temp_root=_DUMMY_TEMP_ROOT)
mock = _build_cmd_mock()
node_mock = CommandNode(mock)
node_mock._create_temp_dir = mock._test_node_._create_temp_dir
node_mock._create_temp_dir.return_value = _DUMMY_TEMP
node_mock._setup = mock._test_node_._setup
node_mock._teardown = mock._test_node_._teardown
node_mock._remove_temp_dir = mock._test_node_._remove_temp_dir
node_mock.run(cfg_mock)
assert mock.mock_calls == [
call._test_node_._create_temp_dir(cfg_mock),
call._test_node_._setup(cfg_mock, _DUMMY_TEMP),
call.run(_DUMMY_TEMP),
call.join(),
call._test_node_._teardown(cfg_mock, _DUMMY_TEMP),
call._test_node_._remove_temp_dir(_DUMMY_TEMP),
]
def _teardown(self, config, temp):
os.rename(os.path.join(temp, self._basename) + ".calmd",
os.path.join(temp, self._basename))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
# Ensure that this file exists even when no filtered SNPs
deleted_snps = os.path.basename(self._output_prefix) + ".deleted_snps"
open(os.path.join(temp, deleted_snps), "a").close()
CommandNode._teardown(self, config, temp)
def test_commandnode_teardown__commit(temp_folder):
cmd_mock = _build_cmd_mock()
cmd_mock.should_receive("commit").with_args(temp_folder).once
node = CommandNode(cmd_mock)
node._teardown(None, temp_folder)
def _teardown(self, config, temp):
for ext in ("log", "nosex"):
os.rename(os.path.join(temp, self._basename + "." + ext),
os.path.join(temp, self._basename + ".frq.strat." + ext))
CommandNode._teardown(self, config, temp)
def test_commandnode_teardown__commit(tmp_path):
cmd_mock = _build_cmd_mock()
node = CommandNode(cmd_mock)
node._teardown(None, tmp_path)
assert cmd_mock.mock_calls == [call.commit(tmp_path)]
def _teardown(self, config, temp):
"""See CommandNode._teardown."""
os.remove(reroot_path(temp, self._infile))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
"""See CommandNode._teardown."""
os.remove(reroot_path(temp, self._infile))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
basename = os.path.basename(self._output_tree)
os.rename(os.path.join(temp, "RAxML_parsimonyTree.Pypeline"),
os.path.join(temp, basename))
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp):
# Ensure that this file exists even when no filtered SNPs
deleted_snps = os.path.basename(self._output_prefix) + ".deleted_snps"
open(os.path.join(temp, deleted_snps), "a").close()
CommandNode._teardown(self, config, temp)
def _teardown(self, config, temp_root):
pipe_fname = os.path.join(temp_root, self._bam_input.pipe)
os.remove(pipe_fname)
try_remove(pipe_fname + ".bai")
CommandNode._teardown(self, config, temp_root)
