本文整理汇总了Python中paleomix.atomiccmd.command.AtomicCmd类的典型用法代码示例。如果您正苦于以下问题：Python AtomicCmd类的具体用法？Python AtomicCmd怎么用？Python AtomicCmd使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了AtomicCmd类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_atomiccmd__commit_before_join
def test_atomiccmd__commit_before_join(temp_folder):
cmd = AtomicCmd(("sleep", "0.1"))
cmd.run(temp_folder)
while cmd._proc.poll() is None:
pass
assert_raises(CmdError, cmd.commit, temp_folder)
cmd.join()示例2: test_atomiccmd__paths_non_str
def test_atomiccmd__paths_non_str(temp_folder):
cmd = AtomicCmd(("touch", 1234),
OUT_FOO="1234",
set_cwd=True)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert os.path.exists(os.path.join(temp_folder, "1234"))示例3: test_atomiccmd__paths__key
def test_atomiccmd__paths__key(temp_folder):
cmd = AtomicCmd(("echo", "-n", "%(TEMP_DIR)s"),
OUT_STDOUT=AtomicCmd.PIPE)
cmd.run(temp_folder)
path = cmd._proc.stdout.read()
assert os.path.samefile(temp_folder, path), (temp_folder, path)
assert_equal(cmd.join(), [0])示例4: _do_test_atomiccmd__pipes_out
def _do_test_atomiccmd__pipes_out(temp_folder, stdout, stderr, kwargs):
cmd = AtomicCmd(("bash", "-c", "echo -n 'STDERR!' > /dev/stderr; echo -n 'STDOUT!';"), **kwargs)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
result_out = get_file_contents(os.path.join(temp_folder, stdout.format(id(cmd))))
result_err = get_file_contents(os.path.join(temp_folder, stderr.format(id(cmd))))
assert_equal(result_out, "STDOUT!")
assert_equal(result_err, "STDERR!")示例5: test_atomiccmd__pipes_stdin__temp_file
def test_atomiccmd__pipes_stdin__temp_file(temp_folder):
cmd = AtomicCmd("cat",
TEMP_IN_STDIN="infile.fasta",
OUT_STDOUT="result.txt")
assert_equal(cmd.input_files, frozenset())
set_file_contents(os.path.join(temp_folder, "infile.fasta"), "a\nbc\nd")
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
result = get_file_contents(os.path.join(temp_folder, "result.txt"))
assert_equal(result, "a\nbc\nd")示例6: test_atomiccmd__commit_missing_files
def test_atomiccmd__commit_missing_files(temp_folder):
destination, temp_folder = _setup_for_commit(temp_folder, False)
cmd = AtomicCmd(("touch", "%(OUT_FOO)s"),
OUT_FOO=os.path.join(destination, "1234"),
OUT_BAR=os.path.join(destination, "4567"))
cmd.run(temp_folder)
cmd.join()
before = set(os.listdir(temp_folder))
assert_raises(CmdError, cmd.commit, temp_folder)
assert_equal(before, set(os.listdir(temp_folder)))示例7: test_pformat__simple__done__set_cwd
def test_pformat__simple__done__set_cwd(temp_folder):
cmd = AtomicCmd("true", set_cwd=True)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd), ("<Command = ['true']\n"
" Status = Exited with return-code 0\n"
" STDOUT* = 'pipe_true_{id}.stdout'\n"
" STDERR* = 'pipe_true_{id}.stderr'\n"
" CWD = '{temp_dir}'>").format(id=id(cmd),
temp_dir=temp_folder))示例8: test_atomiccmd__pipes_stdin
def test_atomiccmd__pipes_stdin(temp_folder):
fname = test_file("fasta_file.fasta")
cmd = AtomicCmd("cat",
IN_STDIN=fname,
OUT_STDOUT="result.txt")
assert_equal(cmd.input_files, frozenset([fname]))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
result = get_file_contents(os.path.join(temp_folder, "result.txt"))
assert_equal(result, ">This_is_FASTA!\nACGTN\n>This_is_ALSO_FASTA!\nCGTNA\n")示例9: _test_atomiccmd__paths_temp_in
def _test_atomiccmd__paths_temp_in(temp_folder, set_cwd, kwargs):
cmd = AtomicCmd(("echo", "-n", "%%(%s)s" % tuple(kwargs.keys())),
TEMP_OUT_STDOUT="result.txt",
set_cwd=set_cwd,
**kwargs)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
expected = os.path.join("" if set_cwd else temp_folder, "test_file")
result = get_file_contents(os.path.join(temp_folder, "result.txt"))
assert_equal(os.path.abspath(expected), os.path.abspath(result))示例10: _do_test_atomiccmd__cleanup_proc
def _do_test_atomiccmd__cleanup_proc(temp_folder, func):
assert_equal(paleomix.atomiccmd.command._PROCS, set())
cmd = AtomicCmd("ls")
cmd.run(temp_folder)
ref = iter(paleomix.atomiccmd.command._PROCS).next()
assert ref
assert_equal(ref(), cmd._proc)
assert_equal(cmd.join(), [0])
cmd = func(cmd, temp_folder)
assert ref not in paleomix.atomiccmd.command._PROCS示例11: test_pformat__simple__done
def test_pformat__simple__done(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd),
("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))示例12: _do_test_atomiccmd__set_cwd
def _do_test_atomiccmd__set_cwd(temp_folder, set_cwd):
cwd = os.getcwd()
cmd = AtomicCmd(("bash", "-c", "echo -n ${PWD}"),
TEMP_OUT_STDOUT="result.txt",
set_cwd=set_cwd)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(cwd, os.getcwd())
expected = temp_folder if set_cwd else cwd
result = get_file_contents(os.path.join(temp_folder, "result.txt"))
assert os.path.samefile(expected, result), "%r != %r" % (expected, result)示例13: test_commandnode_teardown__missing_optional_files
def test_commandnode_teardown__missing_optional_files(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
IN_DUMMY=_EMPTY_FILE,
TEMP_OUT_BAR="bar.txt",
OUT_STDOUT=os.path.join(destination, "foo.txt"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
node = CommandNode(cmd)
node._teardown(None, temp_folder)
assert_equal(os.listdir(temp_folder), [])
assert_equal(os.listdir(destination), ["foo.txt"])示例14: test_atomiccmd__piping_is_only_allowed_once
def test_atomiccmd__piping_is_only_allowed_once(temp_folder):
cmd_1 = AtomicCmd(["echo", "-n", "foo\nbar"],
OUT_STDOUT=AtomicCmd.PIPE)
cmd_2a = AtomicCmd(["grep", "foo"],
IN_STDIN=cmd_1)
cmd_2b = AtomicCmd(["grep", "bar"],
IN_STDIN=cmd_1)
cmd_1.run(temp_folder)
cmd_2a.run(temp_folder)
assert_raises(CmdError, cmd_2b.run, temp_folder)
assert_equal(cmd_1.join(), [0])
assert_equal(cmd_2a.join(), [0])
assert_equal(cmd_2b.join(), [None])示例15: test_pformat__simple__temp_root_in_arguments
def test_pformat__simple__temp_root_in_arguments(temp_folder):
cmd = AtomicCmd(("echo", "${TEMP_DIR}"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd),
("Command = echo '{temp_dir}'\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_echo_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_echo_{id}.stderr'\n"
"CWD = '{cwd}'")
.format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))