Python Artifact._from_view方法代碼示例

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    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'})

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_load_with_archive_filepath_modified(self):
        # Save an artifact for use in the following test case.
        fp = os.path.join(self.test_dir.name, 'artifact.qza')
        Artifact._from_view([-1, 42, 0, 43], FourInts, None).save(fp)

        # Load the artifact from a filepath then save a different artifact to
        # the same filepath. Assert that both artifacts produce the correct
        # views of their data.
        #
        # `load` used to be lazy, only extracting data when it needed to (e.g.
        # when `save` or `view` was called). This was buggy as the filepath
        # could have been deleted, or worse, modified to contain a different
        # .qza 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 Artifact.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
        # Artifact.peek.
        artifact1 = Artifact.load(fp)
        Artifact._from_view([10, 11, 12, 13], FourInts, None).save(fp)
        artifact2 = Artifact.load(fp)

        self.assertEqual(artifact1.view(list), [-1, 42, 0, 43])
        self.assertEqual(artifact2.view(list), [10, 11, 12, 13])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    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)

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    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])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_call_with_multiple_outputs(self):
        split_ints = self.plugin.methods['split_ints']
        split_ints_markdown = self.plugin.methods['split_ints_markdown']

        artifact = Artifact._from_view([0, 42, -2, 43, 6], IntSequence1, None)

        for method in split_ints, split_ints_markdown:
            result = method(artifact)

            self.assertIsInstance(result, tuple)
            self.assertEqual(len(result), 2)

            for output_artifact in result:
                self.assertEqual(output_artifact.type, IntSequence1)

                provenance = output_artifact.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, {
                    'ints': artifact.uuid
                })
                self.assertEqual(provenance.parameter_references, {})

                self.assertIsInstance(output_artifact.uuid, uuid.UUID)

            # Output artifacts have the same provenance.
            self.assertEqual(result[0].provenance, result[1].provenance)

            # Output artifacts have different UUIDs.
            self.assertNotEqual(result[0].uuid, result[1].uuid)

            self.assertEqual(result[0].view(list), [0, 42])
            self.assertEqual(result[1].view(list), [-2, 43, 6])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_from_view_with_provenance(self):
        artifact = Artifact._from_view([-1, 42, 0, 43], FourInts,
                                       self.provenance)

        self.assertEqual(artifact.type, FourInts)
        self.assertEqual(artifact.provenance, self.provenance)
        self.assertIsInstance(artifact.uuid, uuid.UUID)
        self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
        self.assertEqual(artifact.view(list), [-1, 42, 0, 43])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_from_view(self):
        artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
                                       self.provenance_capture)

        self.assertEqual(artifact.type, FourInts)
        # We don't know what the UUID is because it's generated within
        # Artifact._from_view.
        self.assertIsInstance(artifact.uuid, uuid.UUID)
        self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
        # Can produce same view if called again.
        self.assertEqual(artifact.view(list), [-1, 42, 0, 43])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    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)

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_peek_with_provenance(self):
        artifact = Artifact._from_view({'foo': 'bar', 'baz': 'bazz'}, Mapping,
                                       self.provenance)
        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, Mapping)
        self.assertEqual(metadata.provenance, self.provenance)
        self.assertEqual(metadata.uuid, artifact.uuid)

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_load(self):
        saved_artifact = Artifact._from_view([-1, 42, 0, 43], FourInts, None)
        fp = os.path.join(self.test_dir.name, 'artifact.qza')
        saved_artifact.save(fp)

        artifact = Artifact.load(fp)

        self.assertEqual(artifact.type, FourInts)
        self.assertIsNone(artifact.provenance)
        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])

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_from_view_different_type_with_multiple_view_types(self):
        artifact = Artifact._from_view([42, 42, 43, -999, 42], IntSequence1,
                                       None)

        self.assertEqual(artifact.type, IntSequence1)
        self.assertIsNone(artifact.provenance)
        self.assertIsInstance(artifact.uuid, uuid.UUID)

        self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])
        self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])

        self.assertEqual(artifact.view(collections.Counter),
                         collections.Counter({42: 3, 43: 1, -999: 1}))
        self.assertEqual(artifact.view(collections.Counter),
                         collections.Counter({42: 3, 43: 1, -999: 1}))

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_roundtrip(self):
        fp1 = os.path.join(self.test_dir.name, 'artifact1.qza')
        fp2 = os.path.join(self.test_dir.name, 'artifact2.qza')
        artifact = Artifact._from_view([-1, 42, 0, 43], FourInts,
                                       self.provenance)
        artifact.save(fp1)

        artifact1 = Artifact.load(fp1)
        artifact1.save(fp2)
        artifact2 = Artifact.load(fp2)

        self.assertEqual(artifact1.type, artifact2.type)
        self.assertEqual(artifact1.provenance, artifact2.provenance)
        self.assertEqual(artifact1.uuid, artifact2.uuid)
        self.assertEqual(artifact1.view(list), artifact2.view(list))
        self.assertEqual(artifact1.view(list), artifact2.view(list))

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_load_different_type_with_multiple_view_types(self):
        saved_artifact = Artifact._from_view([42, 42, 43, -999, 42],
                                             IntSequence1, None)
        fp = os.path.join(self.test_dir.name, 'artifact.qza')
        saved_artifact.save(fp)

        artifact = Artifact.load(fp)

        self.assertEqual(artifact.type, IntSequence1)
        self.assertIsNone(artifact.provenance)
        self.assertEqual(artifact.uuid, saved_artifact.uuid)

        self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])
        self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])

        self.assertEqual(artifact.view(collections.Counter),
                         collections.Counter({42: 3, 43: 1, -999: 1}))
        self.assertEqual(artifact.view(collections.Counter),
                         collections.Counter({42: 3, 43: 1, -999: 1}))

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_from_view_and_save(self):
        fp = os.path.join(self.test_dir.name, 'artifact.qza')
        # Using four-ints data layout because it has multiple files, some of
        # which are in a nested directory.
        artifact = Artifact._from_view([-1, 42, 0, 43], FourInts,
                                       self.provenance)

        artifact.save(fp)

        with zipfile.ZipFile(fp, mode='r') as zf:
            fps = set(zf.namelist())
            expected = {
                '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'
            }
            self.assertEqual(fps, expected)

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import _from_view [as 別名]
    def test_extract(self):
        fp = os.path.join(self.test_dir.name, 'artifact.qza')
        artifact = Artifact._from_view([-1, 42, 0, 43], FourInts,
                                       self.provenance)
        artifact.save(fp)

        output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
        result_dir = Artifact.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)