def test_is_done__subnode_output_changes(temp_folder):
temp_file = os.path.join(temp_folder, "file.txt")
subnode = Node(output_files = temp_file)
my_node = Node(subnodes = subnode)
assert not my_node.is_done
set_file_contents(temp_file, "foo")
assert my_node.is_done
def test_move_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
move_file("file_1", "file_2")
assert_equal(os.listdir("."), ["file_2"])
assert_equal(get_file_contents("file_2"), "4")
def test_move_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
move_file("file_1", "file_2")
assert_equal(os.listdir("."), ["file_2"])
assert_equal(get_file_contents("file_2"), "4")
def test_move_file__move_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
move_file("file_1", "dst/file_1")
assert_equal(os.listdir("."), ["dst"])
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("dst/file_1"), "3")
def test_move_file__move_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
move_file("file_1", "dst/file_1")
assert_equal(os.listdir("."), ["dst"])
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("dst/file_1"), "3")
def test_move_file__simple_move_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
move_file("file_1", "file_2")
assert_equal(os.listdir("."), ["file_2"])
assert_equal(get_file_contents("file_2"), "1")
def test_move_file__simple_move_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
move_file("file_1", "file_2")
assert_equal(os.listdir("."), ["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_is_done__output_changes(temp_folder):
temp_file_1 = os.path.join(temp_folder, "file_1.txt")
temp_file_2 = os.path.join(temp_folder, "file_2.txt")
my_node = Node(output_files = (temp_file_1, temp_file_2))
assert not my_node.is_done
set_file_contents(temp_file_1, "foo")
assert not my_node.is_done
set_file_contents(temp_file_2, "bar")
assert my_node.is_done
def test_move_file__move_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")
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_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")
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__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_nodegraph_is_done__output_changes(temp_folder):
temp_file_1 = os.path.join(temp_folder, "file_1.txt")
temp_file_2 = os.path.join(temp_folder, "file_2.txt")
my_node = flexmock(output_files=(temp_file_1, temp_file_2))
assert not NodeGraph._is_done(my_node, FileStatusCache())
set_file_contents(temp_file_1, "foo")
assert not NodeGraph._is_done(my_node, FileStatusCache())
set_file_contents(temp_file_2, "bar")
assert NodeGraph._is_done(my_node, FileStatusCache())
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_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_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_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")
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__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"])
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"])
def test_copy_file__copy_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")
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_move_dirs__permission_denied(temp_folder):
dst_folder = os.path.join(temp_folder, "dst")
file_1 = os.path.join(temp_folder, "file")
file_2 = os.path.join(dst_folder, "file")
set_file_contents(file_1, "1")
# Make destination folder read-only
assert make_dirs(os.path.join(temp_folder, "dst"))
mode = os.stat(dst_folder).st_mode
ro_mode = mode & ~(stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH)
os.chmod(dst_folder, ro_mode)
# Non ENOENT errors should be re-raised:
assert_raises(IOError, move_file, file_1, file_2)
def test_commandnode_teardown__extra_files_in_temp(temp_folder):
destination, temp_folder = _setup_temp_folders(temp_folder)
cmd = AtomicCmd(("echo", "-n", "1 2 3"),
OUT_STDOUT = os.path.join(destination, "foo.txt"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
node = CommandNode(cmd)
set_file_contents(os.path.join(temp_folder, "bar.txt"), "1 2 3")
temp_files_before = set(os.listdir(temp_folder))
dest_files_before = set(os.listdir(destination))
assert_raises(CmdNodeError, node._teardown, None, temp_folder)
assert_equal(temp_files_before, set(os.listdir(temp_folder)))
assert_equal(dest_files_before, set(os.listdir(destination)))
def test_try_remove(temp_folder):
fpath = os.path.join(temp_folder, "test.txt")
set_file_contents(fpath, "1 2 3")
assert try_remove(fpath)
def test_try_rmtree(temp_folder):
fpath = os.path.join(temp_folder, "testdir")
os.mkdir(fpath)
set_file_contents(os.path.join(fpath, "file"), "1 2 3")
assert try_rmtree(fpath)
assert not os.path.exists(fpath)
def test_try_rmdir__non_file(temp_folder):
fpath = os.path.join(temp_folder, "test.txt")
set_file_contents(fpath, "1 2 3")
assert_raises(OSError, try_rmdir, fpath)
def test_try_remove(temp_folder):
fpath = os.path.join(temp_folder, "test.txt")
set_file_contents(fpath, "1 2 3")
assert try_remove(fpath)
