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)
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')
# 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')
import q2_feature_table from q2_types import (FeatureTable, Frequency, RelativeFrequency, PresenceAbsence) plugin = Plugin(name='feature-table', version=q2_feature_table.__version__, website='https://github.com/qiime2-plugins/q2-feature-table', package='q2_feature_table') # TODO create decorator for promoting functions to workflows. This info would # be moved to the decorator calls. plugin.register_function( function=q2_feature_table.rarefy, # TODO use more restrictive primitive type for `depth` inputs={ 'table': FeatureTable[Frequency], 'depth': Int }, outputs=[('rarefied_table', FeatureTable[Frequency])], name='Rarefaction', doc="Let's rarefy!") plugin.register_function(function=q2_feature_table.presence_absence, inputs={'table': FeatureTable[~PresenceAbsence]}, outputs=[('presence_absence_table', FeatureTable[PresenceAbsence])], name='Convert to presence/absence', doc="Let's convert to presence/absence!") plugin.register_function(function=q2_feature_table.relative_frequency, inputs={'table': FeatureTable[Frequency]}, outputs=[('relative_frequency_table',