def typical_pipeline_complex(use):
ints1 = use.init_data('ints1', ints1_factory)
mapper1 = use.init_data('mapper1', mapping1_factory)
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='typical_pipeline'),
UsageInputs(int_sequence=ints1, mapping=mapper1, do_extra_thing=True),
UsageOutputNames(out_map='out_map1',
left='left1',
right='right1',
left_viz='left_viz1',
right_viz='right_viz1'))
ints2 = use.get_result('left1')
mapper2 = use.get_result('out_map1')
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='typical_pipeline'),
UsageInputs(int_sequence=ints2, mapping=mapper2, do_extra_thing=False),
UsageOutputNames(out_map='out_map2',
left='left2',
right='right2',
left_viz='left_viz2',
right_viz='right_viz2'))
right2 = use.get_result('right2')
right2.assert_has_line_matching(
label='a nice label about this assertion',
path='ints.txt',
expression='1',
)
def optional_inputs(use):
ints_a = use.init_data('ints', ints1_factory)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='optional_artifacts_method'),
UsageInputs(ints=ints_a, num1=1),
UsageOutputNames(output='output'),
)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='optional_artifacts_method'),
UsageInputs(ints=ints_a, num1=1, num2=2),
UsageOutputNames(output='output'),
)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='optional_artifacts_method'),
UsageInputs(ints=ints_a, num1=1, num2=None),
UsageOutputNames(output='ints_b'),
)
ints_b = use.get_result('ints_b')
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='optional_artifacts_method'),
UsageInputs(ints=ints_a, optional1=ints_b, num1=3, num2=4),
UsageOutputNames(output='output'),
)
def __call__(self, use):
inputs = {}
transformed_inputs = {}
for name, argument in self.inputs.items():
template = self.param_templates[name]
if argument is None or not is_semantic_type(template.qiime_type):
inputs[name] = transformed_inputs[name] = argument
else:
inputs[name] = use.init_data(argument.__name__, argument)
artifact = argument()
view = artifact.view(template.view_type)
view.__hide_from_garbage_collector = artifact
transformed_inputs[name] = view
use.action(
UsageAction(plugin_id='mystery_stew', action_id=self.name),
UsageInputs(**inputs),
UsageOutputNames(**self.output_names),
)
for idx, (output_name, expected_type) in enumerate(self.outputs):
self._assert_output(use, transformed_inputs, self.defaults,
output_name, expected_type, idx)
def concatenate_ints_complex(use):
ints_a = use.init_data('ints_a', ints1_factory)
ints_b = use.init_data('ints_b', ints2_factory)
ints_c = use.init_data('ints_c', ints3_factory)
use.comment('This example demonstrates chained usage (pt 1).')
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='concatenate_ints'),
UsageInputs(ints1=ints_a, ints2=ints_b, ints3=ints_c, int1=4, int2=2),
UsageOutputNames(concatenated_ints='ints_d'),
)
ints_d = use.get_result('ints_d')
use.comment('This example demonstrates chained usage (pt 2).')
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='concatenate_ints'),
UsageInputs(ints1=ints_d, ints2=ints_b, ints3=ints_c, int1=41, int2=0),
UsageOutputNames(concatenated_ints='concatenated_ints'),
)
def identity_with_metadata_simple(use):
ints = use.init_data('ints', ints1_factory)
md = use.init_metadata('md', md1_factory)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='identity_with_metadata'),
UsageInputs(ints=ints, metadata=md),
UsageOutputNames(out='out'),
)
def variadic_input_simple(use):
ints = use.init_data('int', int_sequence_list_factory)
int_set = use.init_data('int_set', single_int_set_factory)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='variadic_input_method'),
UsageInputs(ints=ints, int_set=int_set, nums={7, 8, 9}),
UsageOutputNames(output='out'),
)
def identity_with_metadata_column_from_factory(use):
ints = use.init_data('ints', ints1_factory)
mdc = use.init_data('mdc', mdc1_factory)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='identity_with_metadata_column'),
UsageInputs(ints=ints, metadata=mdc),
UsageOutputNames(out='out'),
)
def typical_pipeline_simple(use):
ints = use.init_data('ints', ints1_factory)
mapper = use.init_data('mapper', mapping1_factory)
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='typical_pipeline'),
UsageInputs(int_sequence=ints, mapping=mapper, do_extra_thing=True),
UsageOutputNames(out_map='out_map', left='left', right='right',
left_viz='left_viz', right_viz='right_viz')
)
def concatenate_ints_simple(use):
ints_a = use.init_data('ints_a', ints1_factory)
ints_b = use.init_data('ints_b', ints2_factory)
ints_c = use.init_data('ints_c', ints3_factory)
use.comment('This example demonstrates basic usage.')
use.action(
UsageAction(plugin_id='dummy_plugin', action_id='concatenate_ints'),
UsageInputs(ints1=ints_a, ints2=ints_b, ints3=ints_c, int1=4, int2=2),
UsageOutputNames(concatenated_ints='ints_d'),
)
def identity_with_metadata_merging(use):
ints = use.init_data('ints', ints1_factory)
md1 = use.init_metadata('md1', md1_factory)
md2 = use.init_metadata('md2', md2_factory)
md3 = use.merge_metadata('md3', md1, md2)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='identity_with_metadata'),
UsageInputs(ints=ints, metadata=md3),
UsageOutputNames(out='out'),
)
def variadic_input_simple(use):
ints_a = use.init_data('ints_a', ints1_factory)
ints_b = use.init_data('ints_b', ints2_factory)
ints = use.init_data_collection('ints', list, ints_a, ints_b)
single_int1 = use.init_data('single_int1', single_int1_factory)
single_int2 = use.init_data('single_int2', single_int2_factory)
int_set = use.init_data_collection('int_set', set, single_int1,
single_int2)
use.action(
UsageAction(plugin_id='dummy_plugin',
action_id='variadic_input_method'),
UsageInputs(ints=ints, int_set=int_set, nums={7, 8, 9}),
UsageOutputNames(output='out'),
)
