def test_from_function(self):
def dummy_function(input1, input2, param1, param2):
return input1 + input2 + [param1] + [param2]
workflow = Workflow.from_function(dummy_function,
inputs={
'input1': DummyType,
'input2': DummyType,
'param1': Int,
'param2': Int
},
outputs=collections.OrderedDict([
('concatenated_inputs',
DummyType)
]),
name='Concatenate things',
doc="Let's concatenate some things!")
expected = Workflow(signature=Signature(
name='Concatenate things',
inputs={
'input1': DummyType,
'input2': DummyType,
'param1': Int,
'param2': Int,
},
outputs=collections.OrderedDict([('concatenated_inputs', DummyType)
])),
template=expected_template,
id_='dummy_function')
self.assertEqual(workflow, expected)
def _test_to_script_or_to_markdown(self, to_method, template_lines):
# These methods are so similar that it makes sense to have a helper
# that can test either one instead of duplicating a bunch of code.
workflow = Workflow.from_markdown(self.markdown_fp)
artifact_fp1 = os.path.join(self.test_dir.name, 'artifact1.qtf')
artifact_fp2 = os.path.join(self.test_dir.name, 'artifact2.qtf')
Artifact.save([-1, 42, 0, 43, 43], DummyType, None, artifact_fp1)
Artifact.save([1, 2, 100], DummyType, None, artifact_fp2)
artifact_fp3 = os.path.join(self.test_dir.name, 'artifact3.qtf')
job = to_method(
workflow,
input_artifact_filepaths={
'input1': artifact_fp1,
'input2': artifact_fp2
},
parameter_references={
'param1': 99,
'param2': -999,
},
output_artifact_filepaths={'concatenated_inputs': artifact_fp3})
provenance_lines = [
"provenance = Provenance(", "parameters={", "'param2': -999"
]
setup_lines = [
"input1 = Artifact(%r).data" % artifact_fp1,
"input2 = Artifact(%r).data" % artifact_fp2, "param1 = 99",
"param2 = -999"
]
teardown_lines = [
"Artifact.save(concatenated_inputs, DummyType, provenance, "
"%r)" % artifact_fp3
]
for expected_lines in (provenance_lines, setup_lines, template_lines,
teardown_lines):
for expected_line in expected_lines:
self.assertIn(expected_line, job.code)
self.assertIsInstance(job.uuid, uuid.UUID)
self.assertEqual(job.uuid.version, 4)
self.assertEqual(job.input_artifact_filepaths, {
'input1': artifact_fp1,
'input2': artifact_fp2
})
self.assertEqual(job.parameter_references, {
'param1': 99,
'param2': -999
})
self.assertEqual(job.output_artifact_filepaths,
{'concatenated_inputs': artifact_fp3})
def test_from_markdown(self):
workflow = Workflow.from_markdown(self.markdown_fp)
expected = Workflow(signature=Signature(
name='Dummy markdown workflow',
inputs={
'input1': DummyType,
'input2': DummyType,
'param1': Int,
'param2': Int,
},
outputs=collections.OrderedDict([('concatenated_inputs', DummyType)
])),
template=frontmatter.parse(markdown_template)[1],
id_='dummy_markdown_workflow')
self.assertEqual(workflow, expected)
def test_register_function_and_workflow(self):
self.assertEqual(self.plugin.workflows, {})
self.plugin.register_function(
name='Dummy function',
function=dummy_function,
inputs={},
outputs=[('answer', Int)],
doc='Computes the answer to life, the universe, and everything')
with unittest.mock.patch.object(pkg_resources,
'resource_filename',
return_value=self.markdown_fp):
self.plugin.register_workflow(self.markdown_fp)
workflows = {
'dummy_function':
Workflow(signature=Signature(name='Dummy function',
inputs={},
outputs=collections.OrderedDict([
('answer', Int)
])),
template=expected_dummy_function_template,
id_='dummy_function'),
'dummy_markdown_workflow':
Workflow(signature=Signature(name='Dummy markdown workflow',
inputs={
'param1': Int,
'param2': Int
},
outputs=collections.OrderedDict([
('the_sum', Int)
])),
template=frontmatter.parse(markdown_template)[1],
id_='dummy_markdown_workflow')
}
self.assertEqual(self.plugin.workflows, workflows)
def test_register_function(self):
self.assertEqual(self.plugin.workflows, {})
self.plugin.register_function(
name='Dummy function',
function=dummy_function,
inputs={},
outputs=[('answer', Int)],
doc='Computes the answer to life, the universe, and everything')
self.plugin.register_function(
name='Dummy function',
function=other_dummy_function,
inputs={},
outputs=[('answer', Int)],
doc='Computes the answer to life, the universe, and everything')
workflows = {
'dummy_function':
Workflow(signature=Signature(name='Dummy function',
inputs={},
outputs=collections.OrderedDict([
('answer', Int)
])),
template=expected_dummy_function_template,
id_='dummy_function'),
'other_dummy_function':
Workflow(signature=Signature(name='Dummy function',
inputs={},
outputs=collections.OrderedDict([
('answer', Int)
])),
template=expected_other_dummy_function_template,
id_='other_dummy_function')
}
self.assertEqual(self.plugin.workflows, workflows)
def test_signature(self):
workflow = Workflow.from_markdown(self.markdown_fp)
signature = Signature(name='Dummy markdown workflow',
inputs={
'input1': DummyType,
'input2': DummyType,
'param1': Int,
'param2': Int,
},
outputs=collections.OrderedDict([
('concatenated_inputs', DummyType)
]))
self.assertEqual(workflow.signature, signature)
def test_register_workflow(self):
self.assertEqual(self.plugin.workflows, {})
with unittest.mock.patch.object(pkg_resources,
'resource_filename',
return_value=self.markdown_fp):
self.plugin.register_workflow(self.markdown_fp)
workflows = {
'dummy_markdown_workflow':
Workflow(signature=Signature(name='Dummy markdown workflow',
inputs={
'param1': Int,
'param2': Int
},
outputs=collections.OrderedDict([
('the_sum', Int)
])),
template=frontmatter.parse(markdown_template)[1],
id_='dummy_markdown_workflow')
}
self.assertEqual(self.plugin.workflows, workflows)
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-temp-')
self.workflow = Workflow.from_function(
dummy_function,
inputs={
'input1': DummyType,
'input2': DummyType,
'param1': Int,
'param2': Int
},
outputs=collections.OrderedDict([
('concatenated_inputs', DummyType)
]),
name='Concatenate things',
doc="Let's concatenate some things!"
)
self.artifact_fp1 = os.path.join(self.test_dir.name, 'artifact1.qtf')
self.artifact_fp2 = os.path.join(self.test_dir.name, 'artifact2.qtf')
Artifact.save([-1, 42, 0, 43, 43], DummyType, None, self.artifact_fp1)
Artifact.save([1, 2, 100], DummyType, None, self.artifact_fp2)
self.artifact_fp3 = os.path.join(self.test_dir.name, 'artifact3.qtf')
def test_reference(self):
workflow = Workflow.from_markdown(self.markdown_fp)
self.assertTrue(workflow.reference.startswith(workflow.id))
def test_name(self):
workflow = Workflow.from_markdown(self.markdown_fp)
self.assertEqual(workflow.name, 'Dummy markdown workflow')
def test_id(self):
workflow = Workflow.from_markdown(self.markdown_fp)
self.assertEqual(workflow.id, 'dummy_markdown_workflow')
def test_template(self):
workflow = Workflow.from_markdown(self.markdown_fp)
self.assertEqual(workflow.template,
frontmatter.parse(markdown_template)[1])
