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):
for filename in os.listdir(temp):
if filename.endswith(".txt") or filename.endswith(
".pdf") or filename.endswith(".csv"):
if not filename.startswith("pipe_"):
os.remove(os.path.join(temp, filename))
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, "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):
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):
for filename in os.listdir(temp):
match = re.match("RAxML_(.*).Pypeline", 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):
fileutils.move_file(os.path.join(temp, "RAxML_info.Pypeline"),
os.path.join(temp, fileutils.swap_ext(self._output_alignment, ".info")))
fileutils.move_file(os.path.join(temp, "input.alignment.BS0"),
os.path.join(temp, self._output_alignment))
os.remove(os.path.join(temp, "input.alignment"))
os.remove(os.path.join(temp, "input.partition"))
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):
for filename in os.listdir(temp):
match = re.match("RAxML_(.*).Pypeline", 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 test_commandnode_teardown__missing_optional_files(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
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 _teardown(self, config, temp):
fileutils.move_file(
os.path.join(temp, "RAxML_info.Pypeline"),
os.path.join(temp,
fileutils.swap_ext(self._output_alignment, ".info")))
fileutils.move_file(os.path.join(temp, "input.alignment.BS0"),
os.path.join(temp, self._output_alignment))
os.remove(os.path.join(temp, "input.alignment"))
os.remove(os.path.join(temp, "input.partition"))
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(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
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 _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 _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)
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_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)
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):
for filename in os.listdir(temp):
if filename.endswith(".txt") or filename.endswith(".pdf") or filename.endswith(".csv"):
if not filename.startswith("pipe_"):
os.remove(os.path.join(temp, filename))
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):
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_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)
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 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):
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)