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_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_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_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)
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)
