def test_including_workflow_path_dispatches_to_include_path(self):
workflow = Workflow()
with patch.object(workflow, 'include_path', autospec=True) as mock_include_path:
workflow.include('/path/to/other_workflow.py')
mock_include_path.assert_called_once_with(
'/path/to/other_workflow.py', namespace=None)
def test_including_workflow_with_same_name_as_this_workflow_raises_an_exception(
self
):
workflow = Workflow(name="foo")
other_workflow = Workflow(name="foo")
with self.assertRaises(WorkflowError):
workflow.include(other_workflow)
def test_including_workflow_instance_dispatches_to_include_workflow(self):
workflow = Workflow()
other_workflow = Workflow()
with patch.object(workflow, 'include_workflow', autospec=True) as mock_include_workflow:
workflow.include(other_workflow)
mock_include_workflow.assert_called_once_with(
other_workflow, namespace=None)
def test_including_workflow_path_dispatches_to_include_path(self):
workflow = Workflow()
with patch.object(workflow, "include_path", autospec=True) as mock_include_path:
workflow.include("/path/to/other_workflow.py")
mock_include_path.assert_called_once_with(
"/path/to/other_workflow.py", namespace=None
)
def test_including_workflow_path_dispatches_to_include_path():
workflow = Workflow()
with patch.object(workflow, "include_path",
autospec=True) as mock_include_path:
workflow.include("/path/to/other_workflow.py")
mock_include_path.assert_called_once_with("/path/to/other_workflow.py",
namespace=None)
def test_raise_error_if_two_targets_in_different_namespaces_produce_the_same_file(self):
w1 = Workflow(name='foo')
w1.target('SayHello', inputs=[], outputs=['greeting.txt'])
w2 = Workflow(name='bar')
w2.target('SayHi', inputs=[], outputs=['greeting.txt'])
w2.include(w1)
with self.assertRaises(FileProvidedByMultipleTargetsError):
g = Graph(targets=w2.targets)
def test_including_workflow_instance_dispatches_to_include_workflow(self):
workflow = Workflow()
other_workflow = Workflow()
with patch.object(
workflow, "include_workflow", autospec=True
) as mock_include_workflow:
workflow.include(other_workflow)
mock_include_workflow.assert_called_once_with(
other_workflow, namespace=None
)
def test_including_workflow_module_gets_workflow_attribute_and_dispatches_to_include_workflow(self, mock_ismodule):
workflow = Workflow(working_dir='/some/dir')
other_workflow = Workflow(working_dir='/some/other/dir')
mock_module = Mock()
mock_module.gwf = other_workflow
with patch.object(workflow, 'include_workflow', autospec=True) as mock_include_workflow:
workflow.include(mock_module)
mock_ismodule.assert_called_once_with(mock_module)
mock_include_workflow.assert_called_once_with(
other_workflow, namespace=None)
def test_dependencies_correctly_resolved_for_named_workflow(self):
workflow = Workflow(name='foo')
target1 = workflow.target('TestTarget1', inputs=[], outputs=['test.txt'])
target2 = workflow.target('TestTarget2', inputs=['test.txt'], outputs=[])
other_workflow = Workflow(name='bar')
other_workflow.include(workflow)
other_target1 = other_workflow.target('TestTarget1', inputs=['test.txt'], outputs=[])
graph = Graph(targets=other_workflow.targets)
assert 'TestTarget1' in graph.targets
assert 'foo.TestTarget2' in graph.targets
assert 'foo.TestTarget2' in graph.targets
def test_include_target_from_workflow_in_two_different_workflows_():
w1 = Workflow()
target = w1.target("MyTarget", inputs=[], outputs=[])
w3 = Workflow()
w3.include(w1, namespace="bar")
w2 = Workflow()
w2.include(w1, namespace="foo")
assert target.name == "MyTarget"
assert "bar.MyTarget" in w3.targets
assert w3.targets["bar.MyTarget"].name == "bar.MyTarget"
assert "foo.MyTarget" in w2.targets
assert w2.targets["foo.MyTarget"].name == "foo.MyTarget"
def test_include_target_from_workflow_in_two_different_workflows_(self):
w1 = Workflow()
target = w1.target('MyTarget', inputs=[], outputs=[])
w3 = Workflow()
w3.include(w1, namespace='bar')
w2 = Workflow()
w2.include(w1, namespace='foo')
self.assertEqual(target.name, 'MyTarget')
self.assertIn('bar.MyTarget', w3.targets)
self.assertEqual(w3.targets['bar.MyTarget'].name, 'bar.MyTarget')
self.assertIn('foo.MyTarget', w2.targets)
self.assertEqual(w2.targets['foo.MyTarget'].name, 'foo.MyTarget')
def test_include_target_from_workflow_in_two_different_workflows_(self):
w1 = Workflow()
target = w1.target("MyTarget", inputs=[], outputs=[])
w3 = Workflow()
w3.include(w1, namespace="bar")
w2 = Workflow()
w2.include(w1, namespace="foo")
self.assertEqual(target.name, "MyTarget")
self.assertIn("bar.MyTarget", w3.targets)
self.assertEqual(w3.targets["bar.MyTarget"].name, "bar.MyTarget")
self.assertIn("foo.MyTarget", w2.targets)
self.assertEqual(w2.targets["foo.MyTarget"].name, "foo.MyTarget")
def test_including_workflow_module_gets_workflow_attribute_and_dispatches_to_include_workflow(
self, mock_ismodule
):
workflow = Workflow(working_dir="/some/dir")
other_workflow = Workflow(working_dir="/some/other/dir")
mock_module = Mock()
mock_module.gwf = other_workflow
with patch.object(
workflow, "include_workflow", autospec=True
) as mock_include_workflow:
workflow.include(mock_module)
mock_ismodule.assert_called_once_with(mock_module)
mock_include_workflow.assert_called_once_with(
other_workflow, namespace=None
)
def test_including_non_module_str_and_object_value_raises_type_error(self):
workflow = Workflow(working_dir="/some/dir")
with self.assertRaises(TypeError):
workflow.include(42)
def test_including_non_module_str_and_object_value_raises_type_error():
workflow = Workflow(working_dir="/some/dir")
with pytest.raises(TypeError):
workflow.include(42)
def test_including_workflow_with_no_name_raises_an_exception():
workflow = Workflow()
other_workflow = Workflow()
with pytest.raises(WorkflowError):
workflow.include(other_workflow)
from gwf import Workflow
gwf = Workflow()
gwf.include('other_workflow/workflow.py', namespace='other')
gwf.target('World', inputs=['other_workflow/a.txt'], outputs=['b.txt']) << """
cat other_workflow/a.txt > b.txt
echo world >> b.txt
"""
def test_including_workflow_with_no_name_raises_an_exception(self):
workflow = Workflow()
other_workflow = Workflow()
with self.assertRaises(WorkflowError):
workflow.include(other_workflow)
def test_including_workflow_with_same_name_as_this_workflow_raises_an_exception(self):
workflow = Workflow(name='foo')
other_workflow = Workflow(name='foo')
with self.assertRaises(IncludeWorkflowError):
workflow.include(other_workflow)
def test_including_workflow_with_no_name_raises_an_exception(self):
workflow = Workflow()
other_workflow = Workflow()
with self.assertRaises(IncludeWorkflowError):
workflow.include(other_workflow)
def test_including_workflow_with_same_name_as_this_workflow_raises_an_exception(
):
workflow = Workflow(name="foo")
other_workflow = Workflow(name="foo")
with pytest.raises(WorkflowError):
workflow.include(other_workflow)
def test_including_non_module_str_and_object_value_raises_type_error(self):
workflow = Workflow(working_dir='/some/dir')
with self.assertRaises(TypeError):
workflow.include(42)