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!")
def test_copy_file__copy_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
copy_file("file_1", "dst/file_1")
assert_equal(set(os.listdir(".")), set(["file_1", "dst"]))
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("file_1"), "3")
assert_equal(get_file_contents("dst/file_1"), "3")
def test_copy_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "4")
assert_equal(get_file_contents("file_2"), "4")
def test_copy_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "4")
assert_equal(get_file_contents("file_2"), "4")
def test_copy_file__copy_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
copy_file("file_1", "dst/file_1")
assert_equal(set(os.listdir(".")), set(["file_1", "dst"]))
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("file_1"), "3")
assert_equal(get_file_contents("dst/file_1"), "3")
def test_copy_file__simple_copy_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "1")
assert_equal(get_file_contents("file_2"), "1")
def test_copy_file__simple_copy_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "1")
assert_equal(get_file_contents("file_2"), "1")
def test_copy_file__simple_copy(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
copy_file(file_1, file_2)
assert_equal(set(os.listdir(temp_folder)), set(["file_1", "file_2"]))
assert_equal(get_file_contents(file_1), "1")
assert_equal(get_file_contents(file_2), "1")
def test_copy_file__simple_copy(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
copy_file(file_1, file_2)
assert_equal(set(os.listdir(temp_folder)), set(["file_1", "file_2"]))
assert_equal(get_file_contents(file_1), "1")
assert_equal(get_file_contents(file_2), "1")
def test_copy_file__copy_to_new_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
copy_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), ["file_1"])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_1), "2")
assert_equal(get_file_contents(file_2), "2")
def test_copy_file__copy_to_new_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
copy_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), ["file_1"])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_1), "2")
assert_equal(get_file_contents(file_2), "2")
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")
def test_move_file__simple_move(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
move_file(file_1, file_2)
assert_equal(os.listdir(temp_folder), ["file_2"])
assert_equal(get_file_contents(file_2), "1")
def test_move_file__simple_move(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
move_file(file_1, file_2)
assert_equal(os.listdir(temp_folder), ["file_2"])
assert_equal(get_file_contents(file_2), "1")
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")
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")
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")
def test_move_file__move_to_existing_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
assert make_dirs(os.path.join(temp_folder, "dst"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
move_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), [])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_2), "2")
def test_move_file__move_to_existing_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
assert make_dirs(os.path.join(temp_folder, "dst"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
move_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), [])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_2), "2")
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))
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))
def test_atomiccmd__piping_temp(temp_folder):
cmd_1 = AtomicCmd(["echo", "-n", "#@!$^"], TEMP_OUT_STDOUT=AtomicCmd.PIPE)
assert_equal(cmd_1.output_files, frozenset())
cmd_2 = AtomicCmd(["cat"], TEMP_IN_STDIN=cmd_1, OUT_STDOUT="piped.txt")
assert_equal(cmd_2.input_files, frozenset())
cmd_1.run(temp_folder)
cmd_2.run(temp_folder)
assert_equal(cmd_1.join(), [0])
assert_equal(cmd_2.join(), [0])
result = get_file_contents(os.path.join(temp_folder, "piped.txt"))
assert_equal(result, "#@!$^")
def _do_test_atomiccmd__set_cwd(temp_folder, set_cwd):
cwd = os.getcwd()
cmd = AtomicCmd(("bash", "-c", "echo -n ${PWD}"),
TEMP_OUT_STDOUT = "result.txt",
set_cwd = set_cwd)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(cwd, os.getcwd())
expected = temp_folder if set_cwd else cwd
result = get_file_contents(os.path.join(temp_folder, "result.txt"))
assert os.path.samefile(expected, result), "%r != %r" % (expected, result)
def _do_test_run__error_log__node_error(temp_folder, exception):
temp = os.path.join(temp_folder, "xTMPx")
cfg_mock = flexmock(temp_root = temp_folder)
node_mock = flexmock(Node())
node_mock.should_receive("_create_temp_dir").with_args(cfg_mock) \
.and_return(temp).ordered.once
node_mock.should_receive("_run").and_raise(exception).ordered.once
os.mkdir(temp)
assert_raises(NodeError, node_mock.run, cfg_mock) # pylint: disable=E1103
log_file = os.path.join(temp_folder, "xTMPx", "pipe.errors")
assert os.path.exists(log_file)
assert_in("Errors =", get_file_contents(log_file))
def _do_test_run__error_log__node_error(temp_folder, exception):
temp = os.path.join(temp_folder, "xTMPx")
cfg_mock = flexmock(temp_root=temp_folder)
node_mock = flexmock(Node())
node_mock.should_receive("_create_temp_dir").with_args(cfg_mock) \
.and_return(temp).ordered.once
node_mock.should_receive("_run").and_raise(exception).ordered.once
os.mkdir(temp)
assert_raises(NodeError, node_mock.run, cfg_mock) # pylint: disable=E1103
log_file = os.path.join(temp_folder, "xTMPx", "pipe.errors")
assert os.path.exists(log_file)
assert_in("Errors =", get_file_contents(log_file))
def test_atomiccmd__piping_temp(temp_folder):
cmd_1 = AtomicCmd(["echo", "-n", "#@!$^"],
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, "#@!$^")
def _do_test_run__error_log__node_error(temp_folder, exception):
cfg_mock = flexmock(temp_root = temp_folder)
node_mock = flexmock(Node())
node_mock.should_receive("_run").and_raise(exception).once
try:
os.mkdir(os.path.join(temp_folder, "xTMPx"))
with MonkeypatchCreateTempDir(root = temp_folder, subfolder = "xTMPx"):
# pylint: disable=E1103
node_mock.run(cfg_mock) # pragma: no coverage
except NodeError:
log_file = os.path.join(temp_folder, "xTMPx", "pipe.errors")
assert os.path.exists(log_file)
assert_in("Errors =", get_file_contents(log_file))
return
assert False # pragma: no coverage
