def test_inputs_context_manager():
op = boyleworkflow.core.Op()
CMD = "command"
a = shell("command a").out("a")
b = shell("command b").out("a")
ta1 = shell(CMD, [a])
with a:
ta2 = shell(CMD)
assert ta1 == ta2
t1 = shell(CMD)
assert t1 != ta1
assert t1 != ta2
with b:
tb1 = shell(CMD)
with a:
tab1 = shell(CMD)
t2 = shell(CMD)
assert t1 == t2
tb2 = shell(CMD, b)
assert tb1 == tb2
tab2 = shell(CMD, [a, b])
assert tab1 == tab2
def test_stdout_chain(log, storage):
a = shell("echo 'like piping a chain'").stdout
b = shell("cat", stdin=a).stdout
c = shell("cat", stdin=b).stdout
make_and_check_expected_contents({c: "like piping a chain\n"}, log,
storage)
def test_rename(log, storage):
# redirect stdout to stderr
# not sure if this is the way to do it...
a = shell("echo 'hello world' > a").out("a")
b = rename(a, "b")
c = shell("cp b c", [b]).out("c")
make_and_check_expected_contents({c: "hello world\n"}, log, storage)
def test_special_files_access():
stdout_1 = shell("command").out(SpecialFilePath.STDOUT.value)
stdout_2 = shell("command").stdout
assert stdout_1 == stdout_2
stderr_1 = shell("command").out(SpecialFilePath.STDERR.value)
stderr_2 = shell("command").stderr
assert stderr_1 == stderr_2
def test_single_or_multiple_inputs():
op = boyleworkflow.core.Op()
a = shell("command").out("a")
t1 = shell("command", [a])
t2 = shell("command", a)
assert t1 == t2
def test_simple_shell(log, storage):
a = shell("echo hello > a").out("a")
b = shell("echo world > b").out("b")
c = shell("cat a b > c && echo test", inputs=(a, b)).out("c")
make_and_check_expected_contents(
{
a: "hello\n",
b: "world\n",
c: "hello\nworld\n"
}, log, storage)
def test_specal_files_disallowed():
op = boyleworkflow.core.Op()
# stdin cannot be an output
with pytest.raises(ValueError):
Task(op).out(SpecialFilePath.STDIN.value)
# stdout can be output but not input
stdout = shell("command").stdout
with pytest.raises(ValueError):
Task(op, [stdout])
# stderr can be output but not input
stderr = shell("command").stderr
with pytest.raises(ValueError):
Task(op, [stderr])
def test_stderr(log, storage):
# redirect stdout to stderr
# not sure if this is the way to do it...
task = shell("echo 'testing stderr' 1>&2")
make_and_check_expected_contents(
{
task.stderr: "testing stderr\n",
task.stdout: ""
}, log, storage)
def test_stdout_output(log, storage):
task = shell("echo something > a && echo 'testing stdout'")
make_and_check_expected_contents(
{
task.out("a"): "something\n",
task.stdout: "testing stdout\n"
},
log,
storage,
)
def test_stdin(log, storage):
a = shell("echo 'testing stdin' > a").out("a")
b = shell("cat > b", stdin=a).out("b")
make_and_check_expected_contents({b: "testing stdin\n"}, log, storage)
def test_stdout_input(log, storage):
a = shell("echo 'like piping'").stdout
b = shell("cat > b", stdin=a).out("b")
make_and_check_expected_contents({b: "like piping\n"}, log, storage)
