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):
# 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)
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)
