def test_load_visualization(self):
saved_visualization = Visualization._from_data_dir(self.data_dir)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
saved_visualization.save(fp)
visualization = Result.load(fp)
self.assertIsInstance(visualization, Visualization)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
def test_load_visualization(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 = Result.load(fp)
self.assertIsInstance(visualization, Visualization)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
def test_load_artifact(self):
saved_artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
saved_artifact.save(fp)
artifact = Result.load(fp)
self.assertIsInstance(artifact, Artifact)
self.assertEqual(artifact.type, FourInts)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
def test_peek_artifact(self):
artifact = Artifact.import_data(FourInts, [0, 0, 42, 1000])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'FourInts')
self.assertEqual(metadata.uuid, str(artifact.uuid))
self.assertEqual(metadata.format, 'FourIntsDirectoryFormat')
def test_peek_visualization(self):
visualization = Visualization._from_data_dir(self.data_dir)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'Visualization')
self.assertEqual(metadata.uuid, str(visualization.uuid))
self.assertIsNone(metadata.format)
def test_peek_visualization(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 = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'Visualization')
self.assertEqual(metadata.uuid, str(visualization.uuid))
self.assertIsNone(metadata.format)
def test_peek_visualization(self):
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, qiime.core.type.Visualization)
self.assertEqual(metadata.provenance, self.provenance)
self.assertEqual(metadata.uuid, visualization.uuid)
def test_peek_artifact(self):
artifact = Artifact._from_view(FourInts, [0, 0, 42, 1000], list,
self.provenance)
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, FourInts)
self.assertEqual(metadata.provenance, self.provenance)
self.assertEqual(metadata.uuid, artifact.uuid)
def test_extract_visualization(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp)
root_dir = str(visualization.uuid)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/css/style.css'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_extract_artifact(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list)
artifact.save(fp)
root_dir = str(artifact.uuid)
output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION', 'metadata.yaml', 'data/file1.txt', 'data/file2.txt',
'data/nested/file3.txt', 'data/nested/file4.txt'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_extract_visualization(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, output_dir)
contents = [
'visualization/VERSION', 'visualization/metadata.yaml',
'visualization/README.md', 'visualization/data/index.html',
'visualization/data/css/style.css'
]
for fp in contents:
expected_fp = os.path.join(output_dir, fp)
self.assertTrue(os.path.exists(expected_fp),
'File %s was not extracted.' % fp)
def test_extract_artifact(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
self.provenance)
artifact.save(fp)
output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, output_dir)
contents = [
'artifact/VERSION', 'artifact/metadata.yaml', 'artifact/README.md',
'artifact/data/file1.txt', 'artifact/data/file2.txt',
'artifact/data/nested/file3.txt', 'artifact/data/nested/file4.txt'
]
for fp in contents:
expected_fp = os.path.join(output_dir, fp)
self.assertTrue(os.path.exists(expected_fp),
'File %s was not extracted.' % fp)
def test_extract_visualization(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)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_extract_artifact(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp)
root_dir = str(artifact.uuid)
output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_private_constructor(self):
with self.assertRaisesRegex(
NotImplementedError,
'Result constructor.*private.*Result.load'):
Result()