def test_constructor(self):
class MockEntryPoint(pkg_resources.EntryPoint):
def __init__(self, plugin):
self.plugin = plugin
def load(self):
return self.plugin
plugin1 = Plugin(name='dummy-plugin',
version='0.4.2',
website='www.dummy-plugin-hub.com',
package='dummy_plugin')
plugin2 = Plugin(name='other-dummy-plugin',
version='0.4.2',
website='www.dummy-plugin-hub.com',
package='dummy_plugin')
def mock_iter_entry_points(group):
return [MockEntryPoint(plugin1), MockEntryPoint(plugin2)]
with unittest.mock.patch.object(pkg_resources, 'iter_entry_points',
mock_iter_entry_points):
plugin_manager = PluginManager()
self.assertEqual(plugin_manager.plugins, {
'dummy-plugin': plugin1,
'other-dummy-plugin': plugin2
})
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')
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, Jorden Kreps.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin, Int, Bool
import test_plugin
from q2_types import FeatureTable, Frequency, RelativeFrequency
plugin = Plugin(name='test-plugin',
version=test_plugin.__version__,
website='http://github.com/jakereps/q2-test-plugin',
package='test_plugin')
plugin.methods.register_function(
function=test_plugin.blocking_test,
inputs={'table': FeatureTable[Frequency]},
parameters={'timeout': Int},
outputs=[('rarefied_table', FeatureTable[Frequency])],
name='Blocking test',
description='Set a timeout for this script to run, '
'then try to run more things!')
plugin.methods.register_function(
function=test_plugin.stdio_test,
inputs={'table': FeatureTable[Frequency]},
parameters={'number': Int},
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, QIIME development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin
import q2_alignment
plugin = Plugin(name='alignment',
version=q2_alignment.__version__,
website='https://github.com/qiime2/q2-alignment',
package='q2_alignment')
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, QIIME development team.
#
# Distributed under the terms of the Modified BSD License.
#
# 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',
# Copyright (c) 2016--, QIIME development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin
from q2_types.tree import Phylogeny, Unrooted, Rooted
from q2_types.feature_data import FeatureData, AlignedSequence
from q2_types.feature_table import FeatureTable, Frequency
import q2_phylogeny
plugin = Plugin(name='phylogeny',
version=q2_phylogeny.__version__,
website='https://github.com/qiime2/q2-phylogeny',
package='q2_phylogeny')
plugin.methods.register_function(
function=q2_phylogeny.midpoint_root,
inputs={'tree': Phylogeny[Unrooted]},
parameters={},
outputs=[('rooted_tree', Phylogeny[Rooted])],
name='Midpoint root an unrooted phylogenetic tree.',
description=("Midpoint root an unrooted phylogenetic tree."))
plugin.methods.register_function(
function=q2_phylogeny.fasttree,
inputs={'alignment': FeatureData[AlignedSequence]},
parameters={},
outputs=[('tree', Phylogeny[Unrooted])],
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, QIIME development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime.plugin import Plugin, Int
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!")
