Python Artifact.save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 save [as 別名]
    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)

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

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

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import save [as 別名]
    def setUp(self):
        # TODO standardize temporary directories created by QIIME
        self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-temp-')

        self.workflow = Workflow.from_function(
            dummy_function,
            inputs={
                'input1': DummyType,
                'input2': DummyType,
                'param1': Int,
                'param2': Int
            },
            outputs=collections.OrderedDict([
                ('concatenated_inputs', DummyType)
            ]),
            name='Concatenate things',
            doc="Let's concatenate some things!"
        )

        self.artifact_fp1 = os.path.join(self.test_dir.name, 'artifact1.qtf')
        self.artifact_fp2 = os.path.join(self.test_dir.name, 'artifact2.qtf')
        Artifact.save([-1, 42, 0, 43, 43], DummyType, None, self.artifact_fp1)
        Artifact.save([1, 2, 100], DummyType, None, self.artifact_fp2)
        self.artifact_fp3 = os.path.join(self.test_dir.name, 'artifact3.qtf')

# 需要導入模塊: from qiime.sdk import Artifact [as 別名]
# 或者: from qiime.sdk.Artifact import save [as 別名]
    def _test_to_script_or_to_markdown(self, to_method, template_lines):
        # These methods are so similar that it makes sense to have a helper
        # that can test either one instead of duplicating a bunch of code.
        workflow = Workflow.from_markdown(self.markdown_fp)

        artifact_fp1 = os.path.join(self.test_dir.name, 'artifact1.qtf')
        artifact_fp2 = os.path.join(self.test_dir.name, 'artifact2.qtf')
        Artifact.save([-1, 42, 0, 43, 43], DummyType, None, artifact_fp1)
        Artifact.save([1, 2, 100], DummyType, None, artifact_fp2)

        artifact_fp3 = os.path.join(self.test_dir.name, 'artifact3.qtf')

        job = to_method(
            workflow,
            input_artifact_filepaths={
                'input1': artifact_fp1,
                'input2': artifact_fp2
            },
            parameter_references={
                'param1': 99,
                'param2': -999,
            },
            output_artifact_filepaths={
                'concatenated_inputs': artifact_fp3
            }
        )

        provenance_lines = [
            "provenance = Provenance(",
            "parameters={",
            "'param2': -999"
        ]

        setup_lines = [
            "input1 = Artifact(%r).data" % artifact_fp1,
            "input2 = Artifact(%r).data" % artifact_fp2,
            "param1 = 99",
            "param2 = -999"
        ]

        teardown_lines = [
            "Artifact.save(concatenated_inputs, DummyType, provenance, "
            "%r)" % artifact_fp3
        ]

        for expected_lines in (provenance_lines, setup_lines, template_lines,
                               teardown_lines):
            for expected_line in expected_lines:
                self.assertIn(expected_line, job.code)

        self.assertIsInstance(job.uuid, uuid.UUID)
        self.assertEqual(job.uuid.version, 4)

        self.assertEqual(
            job.input_artifact_filepaths,
            {'input1': artifact_fp1, 'input2': artifact_fp2})

        self.assertEqual(
            job.parameter_references,
            {'param1': 99, 'param2': -999})

        self.assertEqual(
            job.output_artifact_filepaths,
            {'concatenated_inputs': artifact_fp3})