def setUp(self): # TODO standardize temporary directories created by QIIME 2 self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-') # Using `mapping_viz` because it produces multiple files, including a # nested directory. 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): # 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 2 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): # 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 2 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 test_call_with_artifacts_and_parameters(self): mapping_viz = self.plugin.visualizers['mapping_viz'] artifact1 = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'}) artifact2 = Artifact.import_data( Mapping, {'baz': 'abc', 'bazz': 'ghi'}) result = mapping_viz(artifact1, artifact2, 'Key', 'Value') # Test properties of the `Results` object. self.assertIsInstance(result, tuple) self.assertIsInstance(result, Results) self.assertEqual(len(result), 1) self.assertEqual(result.visualization, result[0]) result = result[0] self.assertIsInstance(result, Visualization) self.assertEqual(result.type, qiime2.core.type.Visualization) self.assertIsInstance(result.uuid, uuid.UUID) # TODO qiime2.sdk.Visualization doesn't have an API to access its # contents yet. For now, save and assert the correct files are present. filepath = os.path.join(self.test_dir.name, 'visualization.qzv') result.save(filepath) root_dir = str(result.uuid) expected = { 'VERSION', 'checksums.md5', 'metadata.yaml', 'data/index.html', 'data/css/style.css', 'provenance/metadata.yaml', 'provenance/VERSION', 'provenance/citations.bib', 'provenance/action/action.yaml', 'provenance/artifacts/%s/metadata.yaml' % artifact1.uuid, 'provenance/artifacts/%s/VERSION' % artifact1.uuid, 'provenance/artifacts/%s/citations.bib' % artifact1.uuid, 'provenance/artifacts/%s/action/action.yaml' % artifact1.uuid, 'provenance/artifacts/%s/metadata.yaml' % artifact2.uuid, 'provenance/artifacts/%s/VERSION' % artifact2.uuid, 'provenance/artifacts/%s/citations.bib' % artifact2.uuid, 'provenance/artifacts/%s/action/action.yaml' % artifact2.uuid } self.assertArchiveMembers(filepath, root_dir, expected)