def test_commandnode_run__exception_on_error():
cmd_mock = _build_cmd_mock(return_codes=(1, ))
node = CommandNode(cmd_mock)
with pytest.raises(CmdNodeError):
node._run(None, "xTMPx")
assert cmd_mock.mock_calls == [call.run("xTMPx"), call.join()]
def _run(self, config, temp):
try:
CommandNode._run(self, config, temp)
except NodeError, error:
if self._command.join() == [1, None]:
with open(fileutils.reroot_path(temp, "template.stdout")) as handle:
lines = handle.readlines()
if lines and ("Giving up." in lines[-1]):
error = NodeError("%s\n\n%s" % (error, lines[-1]))
raise error
def _run(self, config, temp):
try:
CommandNode._run(self, config, temp)
except NodeError, error:
if self._command.join() == [1, None]:
with open(fileutils.reroot_path(temp,
"template.stdout")) as handle:
lines = handle.readlines()
if lines and ("Giving up." in lines[-1]):
error = NodeError("%s\n\n%s" % (error, lines[-1]))
raise error
def _run(self, config, temp):
with gzip.open(self._in_vcf) as handle:
with open(os.path.join(temp, "heterozygous_snps.bed"), "w") as bed:
for line in handle:
if line.startswith("#"):
continue
fields = line.split("\t", 5)
if "," in fields[4]:
pos = int(fields[1])
bed.write("%s\t%i\t%i\n" % (fields[0], pos - 1, pos))
CommandNode._run(self, config, temp)
def _run(self, config, temp):
try:
CommandNode._run(self, config, temp)
except NodeError, error:
err_message = "DNA damage levels are too low"
if self._command.join() == [1]:
fpath = os.path.join(temp, "pipe_mapDamage.stdout")
with open(fpath) as handle:
for line in handle:
if err_message in line:
line = line.strip().replace("Warning:", "ERROR:")
error = NodeError("%s\n\n%s" % (error, line))
break
raise error
def _run(self, config, temp):
try:
CommandNode._run(self, config, temp)
except NodeError, error:
err_message = "DNA damage levels are too low"
if self._command.join() == [1]:
fpath = os.path.join(temp, "pipe_mapDamage.stdout")
with open(fpath) as handle:
for line in handle:
if err_message in line:
line = line.strip().replace("Warning:", "ERROR:")
error = NodeError("%s\n\n%s" % (error, line))
break
raise error
def test_commandnode_run__call_order():
cmd_mock = _build_cmd_mock()
node = CommandNode(cmd_mock)
node._run(None, "xTMPx")
assert cmd_mock.mock_calls == [call.run("xTMPx"), call.join()]
def test_commandnode_run__call_order():
cmd_mock = _build_cmd_mock()
cmd_mock.should_receive("run").with_args("xTMPx").ordered.once
cmd_mock.should_receive("join").with_args().and_return((0,)).ordered.once
node = CommandNode(cmd_mock)
node._run(None, "xTMPx")