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_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_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_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_signature(self):
workflow = Workflow.from_markdown(self.markdown_fp)
signature = Signature(
name='Dummy markdown workflow',
inputs={
'input1': (qiime.core.testing.TestType, list),
'input2': (qiime.core.testing.TestType, list)},
parameters={
'param1': (qiime.plugin.Int, int),
'param2': (qiime.plugin.Int, int)},
outputs=collections.OrderedDict([
('concatenated_inputs', (qiime.core.testing.TestType, list))
])
)
self.assertEqual(workflow.signature, signature)
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_from_markdown(self):
workflow = Workflow.from_markdown(self.markdown_fp)
expected = Workflow(
signature=Signature(
name='Dummy markdown workflow',
inputs={
'input1': (qiime.core.testing.TestType, list),
'input2': (qiime.core.testing.TestType, list),
},
parameters={
'param1': (qiime.plugin.Int, int),
'param2': (qiime.plugin.Int, int),
},
outputs=collections.OrderedDict([
('concatenated_inputs',
(qiime.core.testing.TestType, list))
])
),
template=frontmatter.parse(markdown_template)[1],
id_='dummy_markdown_workflow'
)
self.assertEqual(workflow, expected)
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])
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])
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})
