def test_load_with_archive_filepath_modified(self): # Save a visualization for use in the following test case. fp = os.path.join(self.test_dir.name, 'visualization.qzv') Visualization._from_data_dir(self.data_dir, self.make_provenance_capture()).save(fp) # Load the visualization from a filepath then save a different # visualization to the same filepath. Assert that both visualizations # access the correct data. # # `load` used to be lazy, only extracting data when it needed to (e.g. # when `save` or `get_index_paths` was called). This was buggy as the # filepath could have been deleted, or worse, modified to contain a # different .qzv file. Thus, the wrong archive could be extracted on # demand, or the archive could be missing altogether. There isn't an # easy cross-platform compatible way to solve this problem, so # Visualization.load is no longer lazy and always extracts its data # immediately. The real motivation for lazy loading was for quick # inspection of archives without extracting/copying data, so that API # is now provided through Visualization.peek. visualization1 = Visualization.load(fp) new_data_dir = os.path.join(self.test_dir.name, 'viz-output2') os.mkdir(new_data_dir) most_common_viz(new_data_dir, collections.Counter(range(42))) Visualization._from_data_dir(new_data_dir, self.make_provenance_capture()).save(fp) visualization2 = Visualization.load(fp) self.assertEqual(visualization1.get_index_paths(), {'html': 'data/index.html'}) self.assertEqual(visualization2.get_index_paths(), {'html': 'data/index.html', 'tsv': 'data/index.tsv'})
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 test_get_index_paths_multiple_from_data_dir(self): data_dir = os.path.join(self.test_dir.name, 'mc-viz-output2') os.mkdir(data_dir) most_common_viz(data_dir, collections.Counter(range(42))) visualization = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) actual = visualization.get_index_paths() expected = {'html': 'data/index.html', 'tsv': 'data/index.tsv'} self.assertEqual(actual, expected)
def test_ne_different_data_different_uuid(self): visualization1 = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1') os.mkdir(data_dir) most_common_viz(data_dir, collections.Counter(range(42))) visualization2 = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) self.assertNotEqual(visualization1, visualization2)
def test_get_index_paths_relative_false(self): data_dir = os.path.join(self.test_dir.name, 'mc-viz-output2') os.mkdir(data_dir) most_common_viz(data_dir, collections.Counter(range(42))) visualization = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) def get_abs_path(rel): return str(visualization._archiver.root_dir / rel) actual = visualization.get_index_paths(relative=False) expected = {'html': get_abs_path('data/index.html'), 'tsv': get_abs_path('data/index.tsv')} self.assertEqual(actual, expected)
def test_call_with_no_parameters(self): most_common_viz = self.plugin.visualizers['most_common_viz'] artifact = Artifact.import_data( IntSequence1, [42, 42, 10, 0, 42, 5, 0]) result = most_common_viz(artifact) # 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/index.tsv', 'provenance/metadata.yaml', 'provenance/VERSION', 'provenance/citations.bib', 'provenance/action/action.yaml', 'provenance/artifacts/%s/metadata.yaml' % artifact.uuid, 'provenance/artifacts/%s/VERSION' % artifact.uuid, 'provenance/artifacts/%s/citations.bib' % artifact.uuid, 'provenance/artifacts/%s/action/action.yaml' % artifact.uuid } self.assertArchiveMembers(filepath, root_dir, expected)