# ---------------------------------------------------------------------------- # Copyright (c) 2016-2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- import os import collections import tempfile import unittest import warnings import qiime2.core.archive as archive from qiime2.core.testing.util import get_dummy_plugin from qiime2.plugin.testing import TestPluginBase from qiime2.sdk import Artifact, Visualization from qiime2.core.testing.type import IntSequence1, IntSequence2, SingleInt from qiime2.core.testing.visualizer import most_common_viz from qiime2 import Metadata from qiime2.metadata.tests.test_io import get_data_path # NOTE: This test suite exists for tests not easily split into # test_method, test_visualizer, test_pipeline # TestBadInputs tests type mismatches between Action signatures and passed args class TestBadInputs(TestPluginBase): def make_provenance_capture(self): # importing visualizations is not supported, but we do that here to # simplify testing machinery return archive.ImportProvenanceCapture() def setUp(self): self.plugin = get_dummy_plugin() # TODO standardize temporary directories created by QIIME 2 # create a temporary data_dir for sample Visualizations 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) most_common_viz(self.data_dir, collections.Counter(range(42))) def tearDown(self): self.test_dir.cleanup() def test_viz_passed_as_input(self): saved_viz = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) method = self.plugin.methods['optional_artifacts_method'] ints1 = Artifact.import_data(IntSequence1, [0, 42, 43]) # tests Viz passed as primitive parameter with self.assertRaisesRegex( TypeError, 'Visualizations may not be used as inputs.'): method(saved_viz, 42) # tests Viz passed as Artifact input with self.assertRaisesRegex( TypeError, 'Visualizations may not be used as inputs.'): method(ints1, 42, optional1=saved_viz) # tests Viz passed as metadata method = self.plugin.methods['identity_with_optional_metadata'] with self.assertRaisesRegex( TypeError, 'Visualizations may not be used as inputs.'): method(ints1, metadata=saved_viz) def test_artifact_passed_incorrectly(self): concatenate_ints = self.plugin.methods['concatenate_ints'] identity_with_metadata = self.plugin.methods['identity_with_metadata'] ints1 = Artifact.import_data(IntSequence1, [0, 42, 43]) ints2 = Artifact.import_data(IntSequence1, [99, -22]) ints3 = Artifact.import_data(IntSequence2, [12, 111]) inappropriate_Artifact = Artifact.import_data(IntSequence1, [-9999999]) int1 = 4 int2 = 5 # tests Artifact passed as integer with self.assertRaisesRegex( TypeError, 'int1.*type Int.*IntSequence1'): concatenate_ints(ints1, ints2, ints3, inappropriate_Artifact, int2) # tests Artifact passed as metadata with self.assertRaisesRegex( TypeError, '\'metadata\'.*type Metadata.*IntSequence1'): identity_with_metadata(ints1, inappropriate_Artifact) # tests wrong type of Artifact passed with self.assertRaisesRegex( TypeError, 'ints3.*IntSequence2.*IntSequence1'): concatenate_ints(ints1, ints2, inappropriate_Artifact, int1, int2) def test_primitive_passed_incorrectly(self): concatenate_ints = self.plugin.methods['concatenate_ints'] identity_with_metadata = self.plugin.methods['identity_with_metadata'] params_only_method = self.plugin.methods['params_only_method'] md_fp = get_data_path('valid/simple.tsv') inappropriate_metadata = Metadata.load(md_fp) ints1 = Artifact.import_data(IntSequence1, [0, 42, 43]) ints3 = Artifact.import_data(IntSequence1, [12, 111]) int1 = 4 int2 = 5 arbitrary_int = 43 # tests primitive int passed as IntSequence artifact with self.assertRaisesRegex(TypeError, 'ints2.*43.*incompatible.*IntSequence1'): concatenate_ints(ints1, arbitrary_int, ints3, int1, int2) # tests primitive passed as metadata with self.assertRaisesRegex(TypeError, 'metadata.*43.*incompatible.*Metadata'): identity_with_metadata(ints1, arbitrary_int) # tests wrong type of primitive passed with self.assertRaisesRegex(TypeError, 'age.*arbitraryString.*incompatible.*Int'): params_only_method('key string', 'arbitraryString') # tests metadata passed as artifact with self.assertRaisesRegex(TypeError, '\'ints2\'.*Metadata.*IntSequence1'): concatenate_ints(ints1, inappropriate_metadata, ints3, int1, int2) def test_primitive_param_out_of_range(self): range_nested_in_list = self.plugin.methods['variadic_input_method'] range_not_nested_in_list = self.plugin.visualizers['params_only_viz'] ints_list = [Artifact.import_data(IntSequence1, [0, 42, 43]), Artifact.import_data(IntSequence2, [4, 5, 6])] int_set = {Artifact.import_data(SingleInt, 7), Artifact.import_data(SingleInt, 8)} nums = {9, 10} bad_range_val = [11, 12, -9999] invalid_age = -99999 # Tests primitives of correct type but outside of Range... # ... in a list with self.assertRaisesRegex( TypeError, 'opt_nums.*-9999.*incompatible.*List'): range_nested_in_list(ints_list, int_set, nums, bad_range_val) # ... not in a list with self.assertRaisesRegex( TypeError, r'\'age\'.*-99999.*incompatible.*Int % Range\(0, None\)'): range_not_nested_in_list('John Doe', invalid_age) def test_primitive_param_not_valid_choice(self): pipeline = self.plugin.pipelines['failing_pipeline'] int_sequence = Artifact.import_data(IntSequence1, [0, 42, 43]) break_from = "invalid choice" # test String not a valid choice with self.assertRaisesRegex( TypeError, 'break_from.*\'invalid choice\''): pipeline(int_sequence, break_from) class TestDeprecation(unittest.TestCase): def setUp(self): self.plugin = get_dummy_plugin() self.method = self.plugin.methods['deprecated_method'] def test_successful_registration(self): self.assertTrue(self.method.deprecated) def test_deprecation_warning(self): with warnings.catch_warnings(record=True) as w: self.method() self.assertEqual(1, len(w)) warning = w[0] self.assertEqual(warning.category, FutureWarning) self.assertTrue('Method is deprecated' in str(warning.message)) def test_docstring(self): self.assertIn('Method is deprecated', self.method.__call__.__doc__)