def test_redefined_args(self):
runtime_context = RuntimeContext()
runtime_context.use_container = False
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
assert f.runtime_context.use_container is False
assert f.runtime_context.on_error == "continue"
def test_redefined_args(self):
runtime_context = RuntimeContext()
runtime_context.use_container = False
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
assert f.runtime_context.use_container is False
assert f.runtime_context.on_error == "continue"
def test_factory_redefined_args() -> None:
runtime_context = RuntimeContext()
runtime_context.use_container = False
runtime_context.on_error = "continue"
factory = cwltool.factory.Factory(runtime_context=runtime_context)
assert factory.runtime_context.use_container is False
assert factory.runtime_context.on_error == "continue"
def test_factory_partial_output():
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
factory = cwltool.factory.Factory(runtime_context=runtime_context)
with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
factory.make(get_data("tests/wf/wffail.cwl"))()
err = err_info.value
assert err.out["out1"]["checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
assert err.out["out2"] is None
def test_factory_partial_output():
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
factory = cwltool.factory.Factory(runtime_context=runtime_context)
with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
factory.make(get_data("tests/wf/wffail.cwl"))()
err = err_info.value
assert err.out["out1"][
"checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
assert err.out["out2"] is None
def test_factory_partial_scatter():
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
factory = cwltool.factory.Factory(runtime_context=runtime_context)
with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
factory.make(get_data("tests/wf/scatterfail.cwl"))()
err = err_info.value
assert err.out["out"][0]["checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
assert err.out["out"][1] is None
assert err.out["out"][2]["checksum"] == 'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436'
def test_partial_output(self):
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
fail = f.make(get_data("tests/wf/wffail.cwl"))
try:
fail()
except cwltool.factory.WorkflowStatus as e:
self.assertEquals('sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e', e.out["out1"]["checksum"])
self.assertIsNone(e.out["out2"])
else:
self.fail("Should have raised WorkflowStatus")
def test_partial_output(self):
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
fail = f.make(get_data("tests/wf/wffail.cwl"))
try:
fail()
except cwltool.factory.WorkflowStatus as e:
self.assertEquals('sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e', e.out["out1"]["checksum"])
self.assertIsNone(e.out["out2"])
else:
self.fail("Should have raised WorkflowStatus")
def test_partial_scatter(self):
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
fail = f.make(get_data("tests/wf/scatterfail.cwl"))
try:
fail()
except cwltool.factory.WorkflowStatus as e:
self.assertEquals('sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e', e.out["out"][0]["checksum"])
self.assertIsNone(e.out["out"][1])
self.assertEquals('sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436', e.out["out"][2]["checksum"])
else:
self.fail("Should have raised WorkflowStatus")
def test_partial_scatter(self):
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
f = cwltool.factory.Factory(runtime_context=runtime_context)
fail = f.make(get_data("tests/wf/scatterfail.cwl"))
try:
fail()
except cwltool.factory.WorkflowStatus as e:
self.assertEquals('sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e', e.out["out"][0]["checksum"])
self.assertIsNone(e.out["out"][1])
self.assertEquals('sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436', e.out["out"][2]["checksum"])
else:
self.fail("Should have raised WorkflowStatus")
def test_factory_partial_scatter():
runtime_context = RuntimeContext()
runtime_context.on_error = "continue"
factory = cwltool.factory.Factory(runtime_context=runtime_context)
with pytest.raises(cwltool.factory.WorkflowStatus) as err_info:
factory.make(get_data("tests/wf/scatterfail.cwl"))()
err = err_info.value
assert err.out["out"][0][
"checksum"] == 'sha1$e5fa44f2b31c1fb553b6021e7360d07d5d91ff5e'
assert err.out["out"][1] is None
assert err.out["out"][2][
"checksum"] == 'sha1$a3db5c13ff90a36963278c6a39e4ee3c22e2a436'