本文整理匯總了Python中qiime.sdk.Artifact類的典型用法代碼示例。如果您正苦於以下問題：Python Artifact類的具體用法？Python Artifact怎麽用？Python Artifact使用的例子？那麽, 這裏精選的類代碼示例或許可以為您提供幫助。
在下文中一共展示了Artifact類的15個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: test_call_with_no_parameters
def test_call_with_no_parameters(self):
merge_mappings = self.plugin.methods['merge_mappings']
artifact1 = Artifact._from_view({'foo': 'abc', 'bar': 'def'}, Mapping,
None)
artifact2 = Artifact._from_view({'bazz': 'abc'}, Mapping, None)
result = merge_mappings(artifact1, artifact2)
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, Mapping)
provenance = result.provenance
self.assertIsInstance(provenance, Provenance)
self.assertIsInstance(provenance.execution_uuid, uuid.UUID)
self.assertTrue(
provenance.executor_reference.startswith(merge_mappings.id))
self.assertEqual(provenance.artifact_uuids, {
'mapping1': artifact1.uuid,
'mapping2': artifact2.uuid
})
self.assertEqual(provenance.parameter_references, {})
self.assertIsInstance(result.uuid, uuid.UUID)
self.assertEqual(result.view(dict),
{'foo': 'abc', 'bar': 'def', 'bazz': 'abc'})示例2: get_artifacts
def get_artifacts(named=False):
context_manager = Q2D3Context(os.getcwd())
return sorted(
[(context_manager.names[Artifact.load(fp).uuid], Artifact.load(fp))
if named else Artifact.load(fp)
for fp in context_manager.data.values()],
key=lambda art: repr(art[1].type) if named else repr(art.type))示例3: setUp
def setUp(self):
# TODO standardize temporary directories created by QIIME
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-temp-')
self.dummy_provenance = Provenance(
job_uuid='7e909a23-21e2-44c2-be17-0723fae91dc8',
artifact_uuids={
'input1': 'f16ca3d0-fe83-4b1e-8eea-7e35db3f6b0f',
'input2': '908dece5-db23-4562-ad03-876bb5750145',
},
parameters={
'param1': 'abc',
'param2': 100,
},
workflow_reference=(
'dummy workflow reference, see '
'https://github.com/biocore/qiime2/issues/26'
)
)
self.artifact_with_provenance = Artifact._from_view(
[-1, 42, 0, 43, 43], qiime.core.testing.TestType,
self.dummy_provenance)
self.artifact_without_provenance = Artifact._from_view(
[-1, 42, 0, 43, 43], qiime.core.testing.TestType, None)示例4: test_import_data_with_unreachable_path
def test_import_data_with_unreachable_path(self):
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(IntSequence1,
os.path.join(self.test_dir.name, 'foo.txt'))
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(FourInts,
os.path.join(self.test_dir.name, 'bar', ''))示例5: test_import_data_with_filepath_multi_file_data_layout
def test_import_data_with_filepath_multi_file_data_layout(self):
fp = os.path.join(self.test_dir.name, 'test.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
with self.assertRaisesRegex(ValueError,
"FourIntsDirectoryFormat.*directory"):
Artifact.import_data(FourInts, fp)示例6: test_import_data_invalid_type
def test_import_data_invalid_type(self):
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data(qiime.core.type.Visualization, self.test_dir)
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data('Visualization', self.test_dir)示例7: test_eq_same_uuid
def test_eq_same_uuid(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact1 = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact1.save(fp)
artifact2 = Artifact.load(fp)
self.assertEqual(artifact1, artifact2)示例8: test_constructor_no_provenance
def test_constructor_no_provenance(self):
fp = os.path.join(self.test_dir.name, 'artifact.qtf')
Artifact.save([-1, 42, 0, 43, 43], DummyType, None, fp)
artifact = Artifact(fp)
self.assertEqual(artifact.data, [-1, 42, 0, 43, 43])
self.assertEqual(artifact.type, DummyType)
self.assertEqual(artifact.provenance, None)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.uuid.version, 4)示例9: test_async
def test_async(self):
concatenate_ints = self.plugin.methods['concatenate_ints']
concatenate_ints_markdown = \
self.plugin.methods['concatenate_ints_markdown']
artifact1 = Artifact._from_view([0, 42, 43], IntSequence1, None)
artifact2 = Artifact._from_view([99, -22], IntSequence2, None)
for method in concatenate_ints, concatenate_ints_markdown:
future = method.async(artifact1, artifact1, artifact2, 55, 1)
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, IntSequence1)
provenance = result.provenance
self.assertIsInstance(provenance, Provenance)
self.assertIsInstance(provenance.execution_uuid, uuid.UUID)
self.assertTrue(
provenance.executor_reference.startswith(method.id))
self.assertEqual(provenance.artifact_uuids, {
'ints1': artifact1.uuid,
'ints2': artifact1.uuid,
'ints3': artifact2.uuid
})
self.assertEqual(provenance.parameter_references, {
'int1': '55',
'int2': '1'
})
self.assertIsInstance(result.uuid, uuid.UUID)
# Can retrieve multiple views of different type.
exp_list_view = [0, 42, 43, 0, 42, 43, 99, -22, 55, 1]
self.assertEqual(result.view(list), exp_list_view)
self.assertEqual(result.view(list), exp_list_view)
exp_counter_view = collections.Counter(
{0: 2, 42: 2, 43: 2, 99: 1, -22: 1, 55: 1, 1: 1})
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
# Accepts IntSequence1 | IntSequence2
artifact3 = Artifact._from_view([10, 20], IntSequence2, None)
future = method.async(artifact3, artifact1, artifact2, 55, 1)
result = future.result()
self.assertEqual(result.type, IntSequence1)
self.assertEqual(result.view(list),
[10, 20, 0, 42, 43, 99, -22, 55, 1])示例10: test_import_data_with_invalid_format_single_file
def test_import_data_with_invalid_format_single_file(self):
fp = os.path.join(self.test_dir.name, 'foo.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
fh.write('43\n')
fh.write('abc\n')
fh.write('123\n')
error_regex = "foo.txt.*IntSequenceFormat"
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(IntSequence1, fp)示例11: test_save
def test_save(self):
fp = os.path.join(self.test_dir.name, 'artifact.qtf')
Artifact.save([-1, 42, 0, 43, 43], DummyType, self.dummy_provenance,
fp)
with tarfile.open(fp, mode='r') as tar:
fps = set(tar.getnames())
expected = {'artifact', 'artifact/metadata.yaml',
'artifact/README.md', 'artifact/data',
'artifact/data/data.txt'}
self.assertEqual(fps, expected)示例12: test_peek
def test_peek(self):
artifact = Artifact._from_view([0, 0, 42, 1000], FourInts, None)
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Artifact.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, FourInts)
self.assertIsNone(metadata.provenance)
self.assertEqual(metadata.uuid, artifact.uuid)示例13: test_load
def test_load(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 = Artifact.load(fp)
self.assertEqual(artifact.type, FourInts)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])示例14: test_peek
def test_peek(self):
artifact = Artifact.import_data(FourInts, [0, 0, 42, 1000])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Artifact.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'FourInts')
self.assertEqual(metadata.uuid, str(artifact.uuid))
self.assertEqual(metadata.format, 'FourIntsDirectoryFormat')示例15: retrieve_artifact_info
def retrieve_artifact_info(qclient, artifact_id, artifact_type):
fps_info = qclient.get("/qiita_db/artifacts/%s/filepaths/" % artifact_id)
filepaths = fps_info['filepaths']
translator_lookup = get_artifact_translators_lookup()
input_translator, _, _ = translator_lookup[str(artifact_type)]
artifact_data = input_translator(filepaths)
fd, temp_file_name = mkstemp(suffix='.qtf')
close(fd)
# TODO: None is the provenance
Artifact.save(artifact_data, artifact_type, None, temp_file_name)
return temp_file_name