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')
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'
)
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import io
import os
import base64
import shutil
from qiime.plugin import Plugin, Int, Properties, SemanticType, FileFormat, DataLayout
plugin = Plugin(
name='gba',
version='0.0.1dev',
website='https://github.com/ebolyen/q2-gba',
package='q2_gba'
)
Game = SemanticType('Game', field_names='type')
GBA = SemanticType('GBA', variant_of=Game.field['type'])
plugin.register_semantic_type(Game)
plugin.register_semantic_type(GBA)
class GBAFormat(FileFormat):
name = 'GBA'
@classmethod
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)
Bio.Phylo.write(tree, tree_out, 'newick')
if isinstance(mapping_df, pd.DataFrame):
mapping_out = os.path.join(dat_dir, 'mapping.txt')
mapping_df.to_csv(mapping_out, sep='\t')
# FEEDBACK
print("All your files have been written to the directory", output_dir)
print("Simply open the file index.html in a browser that has")
print("an internet connection to view the interactive phylogram.")
plugin = Plugin(
name='phylogram',
version=__version__,
website='https://github.com/ConstantinoSchillebeeckx/q2-phylogram',
package='q2_phylogram'
)
plugin.visualizers.register_function(
function=make_d3_phylogram,
inputs={'tree': Phylogeny},
parameters={'otu_metadata': qiime.plugin.Metadata},
name='Visualize phylogram',
description='Generate interactive visualization of your phylogenetic tree.'
)
def tree_to_biopython_tree(data_dir):
with open(os.path.join(data_dir, 'tree.nwk'), 'r') as fh:
return Bio.Phylo.read(fh, 'newick')
# ----------------------------------------------------------------------------
# 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},
# index.html, tree.tre, mapping.txt (optional)
dat_dir = os.path.join(output_dir,'dat')
if not os.path.exists(dat_dir):
os.makedirs(dat_dir)
with open(os.path.join(output_dir,'index.html'), 'w') as fout:
fout.write(index)
tree_out = os.path.join(dat_dir,'tree.tre')
with open(tree_out, 'w') as fout:
fout.write("d3.jsonp.readNewick('%s');" %str(tree).strip()) # add callback around Newick string for use in cross-origin setting
plugin = Plugin(
name='phylogram',
version=__version__,
website='https://github.com/ConstantinoSchillebeeckx/q2-phylogram',
package='q2_phylogram'
)
plugin.visualizers.register_function(
function=make_d3_phylogram,
inputs={'tree': Phylogeny},
parameters={'otu_metadata': qiime.plugin.Metadata},
name='Visualize phylogram',
description='Generate interactive visualization of your phylogenetic tree.'
)
def tree_to_skbio_tree(data_dir):
with open(os.path.join(data_dir, 'tree.nwk'), 'r') as fh:
return read(fh, format="newick", into=TreeNode)
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)
# ----------------------------------------------------------------------------
# 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',
doc="Let's compute some pairwise distances!"
# ----------------------------------------------------------------------------
# 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!")
