def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.data_dir = os.path.join(self.test_dir.name, 'viz-output')
os.mkdir(self.data_dir)
mapping_viz(self.data_dir, {
'abc': 'foo',
'def': 'bar'
}, {
'ghi': 'baz',
'jkl': 'bazz'
},
key_label='Key',
value_label='Value')
self.provenance = Provenance(
execution_uuid=uuid.UUID('7e909a23-21e2-44c2-be17-0723fae91dc8'),
executor_reference=(
'dummy_action_id. Details on plugin, version, website, etc. '
'will also be included, see '
'https://github.com/biocore/qiime2/issues/26'),
artifact_uuids={
'input1': uuid.UUID('f16ca3d0-fe83-4b1e-8eea-7e35db3f6b0f'),
'input2': uuid.UUID('908dece5-db23-4562-ad03-876bb5750145')
},
parameter_references={
'param1': 'abc',
'param2': '100'
})
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.provenance_capture = archive.ImportProvenanceCapture()
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.data_dir = os.path.join(self.test_dir.name, 'viz-output')
os.mkdir(self.data_dir)
mapping_viz(self.data_dir,
{'abc': 'foo', 'def': 'bar'},
{'ghi': 'baz', 'jkl': 'bazz'},
key_label='Key', value_label='Value')
def setUp(self):
self.plugin = get_dummy_plugin()
self.concatenate_ints_sig = MethodSignature(
inputs={
'ints1': (IntSequence1 | IntSequence2, list),
'ints2': (IntSequence1, list),
'ints3': (IntSequence2, list)
},
parameters={
'int1': (qiime.plugin.Int, int),
'int2': (qiime.plugin.Int, int)
},
outputs=collections.OrderedDict([
('concatenated_ints', (IntSequence1, list))
])
)
self.split_ints_sig = MethodSignature(
inputs={
'ints': (IntSequence1, list)
},
parameters={},
outputs=collections.OrderedDict([
('left', (IntSequence1, list)),
('right', (IntSequence1, list))
])
)
def setUp(self):
self.plugin = get_dummy_plugin()
self.concatenate_ints_sig = Signature(
inputs={
'ints1': (IntSequence1 | IntSequence2, list),
'ints2': (IntSequence1, list),
'ints3': (IntSequence2, list)
},
parameters={
'int1': (qiime.plugin.Int, int),
'int2': (qiime.plugin.Int, int)
},
outputs=collections.OrderedDict([
('concatenated_ints', (IntSequence1, list))
])
)
self.split_ints_sig = Signature(
inputs={
'ints': (IntSequence1, list)
},
parameters={},
outputs=collections.OrderedDict([
('left', (IntSequence1, list)),
('right', (IntSequence1, list))
])
)
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.provenance = Provenance(
execution_uuid=uuid.UUID('7e909a23-21e2-44c2-be17-0723fae91dc8'),
executor_reference=(
'dummy_method_id. Details on plugin, version, website, etc. '
'will also be included, see '
'https://github.com/biocore/qiime2/issues/26'
),
artifact_uuids={
'input1': uuid.UUID('f16ca3d0-fe83-4b1e-8eea-7e35db3f6b0f'),
'input2': uuid.UUID('908dece5-db23-4562-ad03-876bb5750145')
},
parameter_references={
'param1': 'abc',
'param2': '100'
}
)
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.plugin = get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
def setUp(self):
self._sys_modules = sys.modules.copy()
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
# PluginManager is a singleton so there's no issue creating it again.
self.pm = qiime.sdk.PluginManager()
def setUp(self):
self._sys_modules = sys.modules.copy()
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.plugin = get_dummy_plugin()
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded. PluginManager is
# a singleton so there's no issue creating it again.
get_dummy_plugin()
self.pm = qiime.sdk.PluginManager()
def setUp(self):
self.plugin = get_dummy_plugin()
# PluginManager is a singleton so there's no issue creating it again.
self.pm = qiime.sdk.PluginManager()