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How to use _run_transformers method in lisa

Best Python code snippet using lisa_python

__init__.py

Source:__init__.py

...124    try:125        transformer.transform_bundle(bundle_path, bundle_manifest_path)126    except Exception as ex:127        _log_error(f"{bundle_uuid}.{bundle_version}", ex, traceback.format_exc(), extractor)128def _run_transformers(extractor: DSSExtractor, transformers: list):129    """130    Executes a provided list of transformers.131    :param extractor: DSSExtractor132    :param transformers: List of MetadataToPsvTransformers to execute133    """134    logger.info(f"ETL: All bundles downloaded. Performing final PSV transformations.")135    for transformer in transformers:136        try:137            transformer.transform(os.path.join(extractor.sd, 'bundles'))138        except Exception as ex:139            _log_error(transformer.__class__.__name__, ex, traceback.format_exc(), extractor)140    logger.info(f"ETL: All transformations complete.")141def finalizer_reload(extractor: DSSExtractor):142    """143    Final callback during ETL for loading an empty database. Invokes Loader.144    """145    _run_transformers(extractor, [146        FeatureTransformer(extractor.sd),147        AnalysisTransformer(extractor.sd),148        SpecimenLibraryTransformer(extractor.sd),149        ProjectPublicationContributorTransformer(extractor.sd)150    ])151    upload_and_load(extractor.sd, is_update=False)152def finalizer_update(extractor: DSSExtractor):153    """154    Final callback during ETL to perform database updates. Invokes Loader with update flag.155    :return:156    """157    _run_transformers(extractor, [158        FeatureTransformer(extractor.sd),159        AnalysisTransformer(extractor.sd),160        SpecimenLibraryTransformer(extractor.sd),161        ProjectPublicationContributorTransformer(extractor.sd)162    ])163    upload_and_load(extractor.sd, is_update=True)164def finalizer_notification(extractor: DSSExtractor):165    """166    Final callback during ETL to handle DSS notifications. Invokes Loader with update flag.167    :return:168    """169    _run_transformers(extractor, [170        AnalysisTransformer(extractor.sd),171        SpecimenLibraryTransformer(extractor.sd),172        ProjectPublicationContributorTransformer(extractor.sd)173    ])174    upload_and_load(extractor.sd, is_update=True)175def _log_error(entity: str, exception: Exception, trace: str, extractor: DSSExtractor):176    """177    Logs an ETL error and exception stack trace to a file.178    Error messages and exceptions are written to 'errors.txt'179    A list of failed entities are written to 'failed_transforms.txt'180    :param entity: A MetadataToPsvTransformer, or a bundle FQID for CellExpressionTransformer errors181    :param exception: Thrown exception string182    :param trace: Exception stack trace183    :param extractor: DSSExtractor...

test_transformer.py

Source:test_transformer.py

...57    def test_transformer_keep_all_values(self) -> None:58        # no value is overridden, all values are kept59        transformers = self._generate_transformers_runbook(2)60        runbook_builder = self._generate_runbook_builder(transformers)61        result = transformer._run_transformers(runbook_builder)62        self._validate_variables(63            {64                "v0": "original",65                "va": "original",66                "t0_v0": "0_0 processed",67                "t1_v0": "1_0 processed",68                "t1_v1": "1_1 processed",69            },70            result,71        )72    def test_transformer_overridden_values(self) -> None:73        # value is overridden74        transformers = self._generate_transformers_runbook(2)75        transformers[0].rename = {"t0_v0": "v0"}76        transformers[1].rename = {"t1_v0": "v0", "t1_v1": "v1"}77        runbook_builder = self._generate_runbook_builder(transformers)78        result = transformer._run_transformers(runbook_builder)79        self._validate_variables(80            {81                "va": "original",82                "v0": "1_0 processed",83                "v1": "1_1 processed",84            },85            result,86        )87    def test_transformer_rename_not_exist(self) -> None:88        # not exist name raise exception89        transformers = self._generate_transformers_runbook(1)90        transformers[0].rename = {"v0": "v0_1"}91        runbook_builder = self._generate_runbook_builder(transformers)92        with self.assertRaises(LisaException) as cm:93            transformer._run_transformers(runbook_builder)94        self.assertEqual("unmatched rename variable: {'v0': 'v0_1'}", str(cm.exception))95    def test_transformer_customized_prefix(self) -> None:96        # modified prefix97        transformers = self._generate_transformers_runbook(1)98        transformers[0].prefix = "v0_1"99        runbook_builder = self._generate_runbook_builder(transformers)100        result = transformer._run_transformers(runbook_builder)101        self._validate_variables(102            {103                "v0": "original",104                "va": "original",105                "v0_1_v0": "0_0 processed",106            },107            result,108        )109    def test_transformer_no_name(self) -> None:110        # no name, the type will be used. in name111        transformers_data: List[Any] = [{"type": MOCK, "items": {"v0": "v0_1"}}]112        transformers = schema.load_by_type_many(schema.Transformer, transformers_data)113        runbook_builder = self._generate_runbook_builder(transformers)114        result = transformer._run_transformers(runbook_builder)115        self._validate_variables(116            {117                "v0": "original",118                "va": "original",119                "mock_v0": "v0_1 processed",120            },121            result,122        )123    def test_transformer_skip_disabled(self) -> None:124        # the second transformer should be skipped, so the value is original.125        transformers = self._generate_transformers_runbook(2)126        transformers[0].rename = {"t0_v0": "v0"}127        transformers[0].enabled = False128        runbook_builder = self._generate_runbook_builder(transformers)129        result = transformer._run_transformers(runbook_builder)130        self._validate_variables(131            {132                "v0": "original",133                "va": "original",134                "t1_v0": "1_0 processed",135                "t1_v1": "1_1 processed",136            },137            result,138        )139    def _validate_variables(140        self, expected: Dict[str, str], actual: Dict[str, VariableEntry]141    ) -> None:142        actual_pairs = {name: value.data for name, value in actual.items()}143        self.assertDictEqual(expected, actual_pairs)...

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