def test_sequential_commands__abort_on_error_3(temp_folder):
cmd_1 = AtomicCmd("true")
cmd_2 = AtomicCmd("true")
cmd_3 = AtomicCmd("false")
cmds = SequentialCmds([cmd_1, cmd_2, cmd_3])
cmds.run(temp_folder)
assert_equal(cmds.join(), [0, 0, 1])
def test_sequential_commands__abort_on_error_3(temp_folder):
cmd_1 = AtomicCmd("true")
cmd_2 = AtomicCmd("true")
cmd_3 = AtomicCmd("false")
cmds = SequentialCmds([cmd_1, cmd_2, cmd_3])
cmds.run(temp_folder)
assert_equal(cmds.join(), [0, 0, 1])
def test_sequential_commands__abort_on_error_1(temp_folder):
cmd_1 = AtomicCmd("false")
cmd_2 = AtomicCmd(("sleep", 10))
cmd_3 = AtomicCmd(("sleep", 10))
cmds = SequentialCmds([cmd_1, cmd_2, cmd_3])
cmds.run(temp_folder)
assert_equal(cmds.join(), [1, None, None])
def test_sequential_commands__abort_on_error_1(temp_folder):
cmd_1 = AtomicCmd("false")
cmd_2 = AtomicCmd(("sleep", 10))
cmd_3 = AtomicCmd(("sleep", 10))
cmds = SequentialCmds([cmd_1, cmd_2, cmd_3])
cmds.run(temp_folder)
assert_equal(cmds.join(), [1, None, None])
def __init__(self, config, reference, input_files, output_file,
dependencies):
cat_cmds, cat_obj = concatenate_input_bams(config, input_files)
cmd_map = AtomicCmd([
"mapDamage", "-n", _MAPDAMAGE_MAX_READS, "-i", "-", "-d",
"%(TEMP_DIR)s", "-r", reference
],
IN_STDIN=cat_obj,
CHECK_VERSION=MAPDAMAGE_VERSION)
train_cmds = ParallelCmds(cat_cmds + [cmd_map])
cat_cmds, cat_obj = concatenate_input_bams(config, input_files)
cmd_scale = AtomicCmd([
"mapDamage", "--rescale-only", "-n", _MAPDAMAGE_MAX_READS, "-i",
"-", "-d", "%(TEMP_DIR)s", "-r", reference, "--rescale-out",
"%(OUT_BAM)s"
],
IN_STDIN=cat_obj,
OUT_BAM=output_file,
CHECK_VERSION=MAPDAMAGE_VERSION)
rescale_cmds = ParallelCmds(cat_cmds + [cmd_scale])
description = "<mapDamageRescale: %i file(s) -> '%s'>" % (
len(input_files), output_file)
CommandNode.__init__(self,
command=SequentialCmds([train_cmds,
rescale_cmds]),
description=description,
dependencies=dependencies)
def test_sequential_commands__atomiccmds():
mocks = []
for _ in range(3):
cmd_mock = flexmock(AtomicCmd(["ls"]))
cmd_mock.should_receive('run').with_args("xTMPx").once
cmd_mock.should_receive('join').with_args().and_return([0]).twice
mocks.append(cmd_mock)
cmds = SequentialCmds(mocks)
assert not cmds.ready()
cmds.run("xTMPx")
assert cmds.ready()
assert_equal(cmds.join(), [0, 0, 0])
def test_sequential_commands__atomiccmds():
mocks = []
for _ in range(3):
cmd_mock = flexmock(AtomicCmd(["ls"]))
cmd_mock.should_receive('run').with_args("xTMPx").once
cmd_mock.should_receive('join').with_args().and_return([0]).twice
mocks.append(cmd_mock)
cmds = SequentialCmds(mocks)
assert not cmds.ready()
cmds.run("xTMPx")
assert cmds.ready()
assert_equal(cmds.join(), [0, 0, 0])
def test_pformat__sets__nested():
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd_3 = AtomicCmd("sha1sum")
set_1 = ParallelCmds((cmd_1, cmd_2))
set_2 = SequentialCmds((set_1, cmd_3))
assert_equal(pformat(set_2), ("<Sequential commands:\n"
" - Parallel commands:\n"
" - <00> Command = ['echo', 'foo']\n"
" STDOUT = <01>\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1_id}.stderr'\n"
" - <01> Command = ['gzip']\n"
" STDIN = <00>\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stderr'\n"
" - <02> Command = ['sha1sum']\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3_id}.stderr'>") \
.format(cmd_1_id = id(cmd_1),
cmd_2_id = id(cmd_2),
cmd_3_id = id(cmd_3)))
def test_sequential_commands__reject_empty_commandset():
SequentialCmds([])
def test_sequential_commands__reject_noncommand():
SequentialCmds([object()])
def test_sequential_commands__accept_sequential():
command = AtomicCmd(["ls"])
seqcmd = SequentialCmds([command])
SequentialCmds([seqcmd])
def test_sequential_commands__accept_parallel():
command = AtomicCmd(["ls"])
parcmd = ParallelCmds([command])
SequentialCmds([parcmd])
def test_parallel_commands__reject_sequential():
command = AtomicCmd(["ls"])
seqcmd = SequentialCmds([command])
assert_raises(CmdError, ParallelCmds, [seqcmd])
