本文整理汇总了Python中pypeline.atomiccmd.command.AtomicCmd.join方法的典型用法代码示例。如果您正苦于以下问题：Python AtomicCmd.join方法的具体用法？Python AtomicCmd.join怎么用？Python AtomicCmd.join使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pypeline.atomiccmd.command.AtomicCmd的用法示例。
在下文中一共展示了AtomicCmd.join方法的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
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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__ready
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_atomiccmd__ready(temp_folder):
cmd = AtomicCmd("ls")
assert_equal(cmd.join(), [None])
assert not cmd.ready()
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert cmd.ready()示例3: _do_test_atomiccmd__stdout
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def _do_test_atomiccmd__stdout(temp_folder, kwargs):
cmd = AtomicCmd(("echo", "-n", "foo"), **kwargs)
assert cmd.stdout is None
cmd.run(temp_folder)
assert isinstance(cmd.stdout, types.FileType), cmd.stdout
assert_equal(cmd.stdout.read(), "foo")
cmd.join()
cmd.commit(temp_folder)
assert cmd.stdout is None示例4: test_atomiccmd__commit_missing_files
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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5: test_pformat__simple__running__set_cwd
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_pformat__simple__running__set_cwd(temp_folder):
cmd = AtomicCmd(("sleep", "10"), set_cwd = True)
cmd.run(temp_folder)
assert_equal(pformat(cmd), ("<Command = ['sleep', '10']\n"
" Status = Running ...\n"
" STDOUT* = 'pipe_sleep_{id}.stdout'\n"
" STDERR* = 'pipe_sleep_{id}.stderr'\n"
" CWD = '{temp_dir}'>").format(id = id(cmd),
temp_dir = temp_folder))
cmd.terminate()
cmd.join()示例6: test_atomiccmd__piping_is_only_allowed_once
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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7: test_atomiccmd__piping_temp
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_atomiccmd__piping_temp(temp_folder):
cmd_1 = AtomicCmd(["echo", "-n", "#@!$^"],
TEMP_OUT_STDOUT = AtomicCmd.PIPE)
assert_equal(cmd_1.output_files, frozenset())
cmd_2 = AtomicCmd(["cat"],
TEMP_IN_STDIN = cmd_1,
OUT_STDOUT = "piped.txt")
assert_equal(cmd_2.input_files, frozenset())
cmd_1.run(temp_folder)
cmd_2.run(temp_folder)
assert_equal(cmd_1.join(), [0])
assert_equal(cmd_2.join(), [0])
result = get_file_contents(os.path.join(temp_folder, "piped.txt"))
assert_equal(result, "#@!$^")示例8: test_atomiccmd__terminate_race_condition
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_atomiccmd__terminate_race_condition(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
while cmd._proc.poll() is None:
pass
cmd.terminate()
assert_equal(cmd.join(), [0])示例9: test_atomiccmd__paths__key
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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10: test_atomiccmd__paths_non_str
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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11: test_atomiccmd__commit_temp_only
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_atomiccmd__commit_temp_only(temp_folder):
cmd = AtomicCmd(("echo", "foo"),
TEMP_OUT_STDOUT = "bar.txt")
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert os.path.exists(os.path.join(temp_folder, "bar.txt"))
cmd.commit(temp_folder)
assert_equal(os.listdir(temp_folder), [])示例12: _do_test_atomiccmd__pipes_out
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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13: test_atomiccmd__pipes_stdin__temp_file
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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, "infile.fasta"))
assert_equal(result, "a\nbc\nd")示例14: test_pformat__simple__done__set_cwd
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
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15: test_atomiccmd__pipes_stdin
# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import join [as 别名]
def test_atomiccmd__pipes_stdin(temp_folder):
fname = os.path.join("tests", "data", "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")