Python AtomicCmd.run方法代码示例

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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])

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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()

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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"))

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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])

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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()

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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!")

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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), [])

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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")

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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")

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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))

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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)))

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [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()

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [as 别名]
def test_atomiccmd__commit_temp_out(temp_folder):
    dest, temp = _setup_for_commit(temp_folder, create_cmd = False)
    cmd = AtomicCmd(("echo", "foo"),
                    OUT_STDOUT   = os.path.join(dest, "foo.txt"),
                    TEMP_OUT_FOO = "bar.txt")
    cmd.run(temp)
    assert_equal(cmd.join(), [0])
    set_file_contents(os.path.join(temp, "bar.txt"), "1 2 3")
    cmd.commit(temp)
    assert_equal(os.listdir(temp), [])
    assert_equal(os.listdir(dest), ["foo.txt"])

# 需要导入模块: from pypeline.atomiccmd.command import AtomicCmd [as 别名]
# 或者: from pypeline.atomiccmd.command.AtomicCmd import run [as 别名]
    def _do_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))