# ---------------------------------------------------------------------------- # 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 tempfile import unittest import uuid import collections import pathlib import qiime2.core.type from qiime2.sdk import Visualization from qiime2.sdk.result import ResultMetadata import qiime2.core.archive as archive from qiime2.core.testing.visualizer import ( mapping_viz, most_common_viz, multi_html_viz) from qiime2.core.testing.util import ArchiveTestingMixin class TestVisualization(unittest.TestCase, ArchiveTestingMixin): def make_provenance_capture(self): # You can't actually import a visualization, but I won't tell # visualization if you don't... return archive.ImportProvenanceCapture() 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 tearDown(self): self.test_dir.cleanup() def test_private_constructor(self): with self.assertRaisesRegex( NotImplementedError, 'Visualization constructor.*private.*Visualization.load'): Visualization() # Note on testing strategy below: many of the tests for `_from_data_dir` # and `load` are similar, with the exception that when `load`ing, the # visualization's UUID is known so more specific assertions can be # performed. While these tests appear somewhat redundant, they are # important because they exercise the same operations on Visualization # objects constructed from different sources, whose codepaths have very # different internal behavior. This internal behavior could be tested # explicitly but it is safer to test the public API behavior (e.g. as a # user would interact with the object) in case the internals change. def test_from_data_dir(self): visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) self.assertEqual(visualization.type, qiime2.core.type.Visualization) self.assertIsInstance(visualization.uuid, uuid.UUID) def test_from_data_dir_and_save(self): fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization.save(fp) root_dir = str(visualization.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' } self.assertArchiveMembers(fp, root_dir, expected) def test_load(self): saved_visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) fp = os.path.join(self.test_dir.name, 'visualization.qzv') saved_visualization.save(fp) visualization = Visualization.load(fp) self.assertEqual(visualization.type, qiime2.core.type.Visualization) self.assertEqual(visualization.uuid, saved_visualization.uuid) def test_load_and_save(self): fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv') fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv') visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization.save(fp1) visualization = Visualization.load(fp1) # Overwriting its source file works. visualization.save(fp1) # Saving to a new file works. visualization.save(fp2) root_dir = str(visualization.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' } self.assertArchiveMembers(fp1, root_dir, expected) root_dir = str(visualization.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' } self.assertArchiveMembers(fp2, root_dir, expected) def test_roundtrip(self): fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv') fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv') visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization.save(fp1) visualization1 = Visualization.load(fp1) visualization1.save(fp2) visualization2 = Visualization.load(fp2) self.assertEqual(visualization1.type, visualization2.type) self.assertEqual(visualization1.uuid, visualization2.uuid) 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 test_extract(self): fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization.save(fp) root_dir = str(visualization.uuid) # pathlib normalizes away the `.`, it doesn't matter, but this is the # implementation we're using, so let's test against that assumption. output_dir = pathlib.Path(self.test_dir.name) / 'viz-extract-test' result_dir = Visualization.extract(fp, output_dir=output_dir) self.assertEqual(result_dir, str(output_dir / root_dir)) 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' } self.assertExtractedArchiveMembers(output_dir, root_dir, expected) def test_get_index_paths_single_load(self): fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization.save(fp) visualization = Visualization.load(fp) actual = visualization.get_index_paths() expected = {'html': 'data/index.html'} self.assertEqual(actual, expected) def test_get_index_paths_single_from_data_dir(self): visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) actual = visualization.get_index_paths() expected = {'html': 'data/index.html'} self.assertEqual(actual, expected) def test_get_index_paths_multiple_load(self): 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))) fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) visualization.save(fp) visualization = Visualization.load(fp) actual = visualization.get_index_paths() expected = {'html': 'data/index.html', 'tsv': 'data/index.tsv'} self.assertEqual(actual, expected) 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_get_index_paths_multiple_html_load(self): data_dir = os.path.join(self.test_dir.name, 'multi-html-viz1') os.mkdir(data_dir) multi_html_viz(data_dir, [1, 42]) fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) visualization.save(fp) visualization = Visualization.load(fp) with self.assertRaises(ValueError): visualization.get_index_paths() def test_get_index_paths_multiple_html_from_data_dir(self): data_dir = os.path.join(self.test_dir.name, 'multi-html-viz2') os.mkdir(data_dir) multi_html_viz(data_dir, [1, 42]) visualization = Visualization._from_data_dir( data_dir, self.make_provenance_capture()) with self.assertRaises(ValueError): visualization.get_index_paths() 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_peek(self): visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization.save(fp) metadata = Visualization.peek(fp) self.assertIsInstance(metadata, ResultMetadata) self.assertEqual(metadata.type, 'Visualization') self.assertEqual(metadata.uuid, str(visualization.uuid)) self.assertIsNone(metadata.format) def test_eq_identity(self): visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) self.assertEqual(visualization, visualization) def test_eq_same_uuid(self): fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization1 = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization1.save(fp) visualization2 = Visualization.load(fp) self.assertEqual(visualization1, visualization2) def test_ne_same_data_different_uuid(self): visualization1 = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization2 = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) self.assertNotEqual(visualization1, visualization2) 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_ne_subclass_same_uuid(self): class VisualizationSubclass(Visualization): pass fp = os.path.join(self.test_dir.name, 'visualization.qzv') visualization1 = VisualizationSubclass._from_data_dir( self.data_dir, self.make_provenance_capture()) visualization1.save(fp) visualization2 = Visualization.load(fp) self.assertNotEqual(visualization1, visualization2) self.assertNotEqual(visualization2, visualization1) def test_ne_different_type_same_uuid(self): visualization = Visualization._from_data_dir( self.data_dir, self.make_provenance_capture()) class Faker: @property def uuid(self): return visualization.uuid faker = Faker() self.assertNotEqual(visualization, faker) if __name__ == '__main__': unittest.main()