class TestPlugin(unittest.TestCase):
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-temp-')
self.markdown_fp = os.path.join(self.test_dir.name,
'dummy_markdown_workflow.md')
with open(self.markdown_fp, 'w') as markdown_fh:
markdown_fh.write(markdown_template)
self.plugin = Plugin(name='dummy-plugin',
version='0.4.2',
website='www.dummy-plugin-hub.com',
package='dummy_plugin')
def tearDown(self):
self.test_dir.cleanup()
def test_constructor(self):
self.assertEqual(self.plugin.name, 'dummy-plugin')
self.assertEqual(self.plugin.version, '0.4.2')
self.assertEqual(self.plugin.website, 'www.dummy-plugin-hub.com')
self.assertEqual(self.plugin.package, 'dummy_plugin')
self.assertEqual(self.plugin.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_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 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)
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin, Str
import q2_diversity
from q2_types import FeatureTable, Frequency, DistanceMatrix, Phylogeny
plugin = Plugin(
name='diversity',
version=q2_diversity.__version__,
website='https://github.com/qiime2-plugins/q2-diversity',
package='q2_diversity'
)
# TODO create decorator for promoting functions to workflows. This info would
# be moved to the decorator calls.
plugin.register_function(
function=q2_diversity.beta_diversity,
# TODO require a uniform sampling effort FeatureTable when predicates exist
inputs={'metric': Str,
'feature_table': FeatureTable[Frequency],
# TODO this is optional; how do we handle that here?
'phylogeny': Phylogeny},
outputs=[('distance_matrix', DistanceMatrix)],
name='Beta diversity',
doc="Let's compute some pairwise distances!"
)
plugin.register_workflow('workflows/feature_table_to_pcoa.md')
class TestPlugin(unittest.TestCase):
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-temp-')
self.markdown_fp = os.path.join(self.test_dir.name,
'dummy_markdown_workflow.md')
with open(self.markdown_fp, 'w') as markdown_fh:
markdown_fh.write(markdown_template)
self.plugin = Plugin(
name='dummy-plugin',
version='0.4.2',
website='www.dummy-plugin-hub.com',
package='dummy_plugin'
)
def tearDown(self):
self.test_dir.cleanup()
def test_constructor(self):
self.assertEqual(self.plugin.name, 'dummy-plugin')
self.assertEqual(self.plugin.version, '0.4.2')
self.assertEqual(self.plugin.website, 'www.dummy-plugin-hub.com')
self.assertEqual(self.plugin.package, 'dummy_plugin')
self.assertEqual(self.plugin.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_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 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)
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin, Str
import q2_diversity
from q2_types import FeatureTable, Frequency, DistanceMatrix, Phylogeny
plugin = Plugin(name='diversity',
version=q2_diversity.__version__,
website='https://github.com/qiime2-plugins/q2-diversity',
package='q2_diversity')
# TODO create decorator for promoting functions to workflows. This info would
# be moved to the decorator calls.
plugin.register_function(
function=q2_diversity.beta_diversity,
# TODO require a uniform sampling effort FeatureTable when predicates exist
inputs={
'metric': Str,
'feature_table': FeatureTable[Frequency],
# TODO this is optional; how do we handle that here?
'phylogeny': Phylogeny
},
outputs=[('distance_matrix', DistanceMatrix)],
name='Beta diversity',
doc="Let's compute some pairwise distances!")
plugin.register_workflow('workflows/feature_table_to_pcoa.md')
