Source code for enrichment_api.tests.test_enrichment_serializer

# pylint: disable=W0621,C0114,C0116,W0212,W0613
from dae.enrichment_tool.event_counters import EnrichmentSingleResult

from enrichment_api.enrichment_serializer import EnrichmentSerializer


[docs] def test_serialize(enrichment_serializer: EnrichmentSerializer) -> None: # pylint: disable=too-many-statements serialize = enrichment_serializer.serialize() assert len(serialize) == 2 assert serialize[0]["selector"] == "phenotype 1" assert serialize[0]["peopleGroupId"] == "phenotype" assert len(serialize[0]["childrenStats"]) == 3 assert serialize[0]["childrenStats"]["M"] == 1 assert serialize[0]["childrenStats"]["F"] == 1 assert serialize[0]["childrenStats"]["U"] == 0 all_serialized = serialize[0]["missense"]["all"] assert all_serialized["name"] == "all" assert all_serialized["count"] == 2 assert all_serialized["overlapped"] == 2 assert all_serialized["expected"] == 2 assert all_serialized["pvalue"] == 1 assert all_serialized["countFilter"]["datasetId"] == "f1_trio" assert all_serialized["countFilter"]["effectTypes"] == ["missense"] assert all_serialized["countFilter"]["gender"] == [ "male", "female", "unspecified", ] assert all_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert all_serialized["countFilter"]["peopleGroup"]["checkedValues"] == [ "phenotype1", ] assert all_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert all_serialized["countFilter"]["studyTypes"] == ["we"] assert all_serialized["countFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] assert all_serialized["overlapFilter"]["datasetId"] == "f1_trio" assert all_serialized["overlapFilter"]["effectTypes"] == ["missense"] assert all_serialized["overlapFilter"]["gender"] == [ "male", "female", "unspecified", ] assert all_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert all_serialized["overlapFilter"]["peopleGroup"]["checkedValues"] == [ "phenotype1", ] assert all_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert all_serialized["overlapFilter"]["studyTypes"] == ["we"] assert all_serialized["overlapFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] rec_serialized = serialize[0]["missense"]["rec"] assert rec_serialized["name"] == "rec" assert rec_serialized["count"] == 1 assert rec_serialized["overlapped"] == 1 assert rec_serialized["expected"] == 1 assert rec_serialized["pvalue"] == 1 assert rec_serialized["countFilter"]["datasetId"] == "f1_trio" assert rec_serialized["countFilter"]["effectTypes"] == ["missense"] assert rec_serialized["countFilter"]["gender"] == [ "male", "female", "unspecified"] assert rec_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert rec_serialized["countFilter"]["peopleGroup"]["checkedValues"] == [ "phenotype1", ] assert rec_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert rec_serialized["countFilter"]["studyTypes"] == ["we"] assert rec_serialized["countFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] assert rec_serialized["overlapFilter"]["datasetId"] == "f1_trio" assert rec_serialized["overlapFilter"]["effectTypes"] == ["missense"] assert rec_serialized["overlapFilter"]["gender"] == \ ["male", "female", "unspecified"] assert rec_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert rec_serialized["overlapFilter"]["peopleGroup"]["checkedValues"] == [ "phenotype1", ] assert rec_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert rec_serialized["overlapFilter"]["studyTypes"] == ["we"] assert rec_serialized["overlapFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] assert rec_serialized["overlapFilter"]["overlappedGenes"] == {"SAMD11"} male_serialized = serialize[0]["missense"]["male"] assert male_serialized["name"] == "male" assert male_serialized["count"] == 1 assert male_serialized["overlapped"] == 1 assert male_serialized["expected"] == 1 assert male_serialized["pvalue"] == 1 assert male_serialized["countFilter"]["datasetId"] == "f1_trio" assert male_serialized["countFilter"]["effectTypes"] == ["missense"] assert male_serialized["countFilter"]["gender"] == ["male"] assert male_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert male_serialized["countFilter"]["peopleGroup"]["checkedValues"] == [ "phenotype1", ] assert male_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert male_serialized["countFilter"]["studyTypes"] == ["we"] assert male_serialized["countFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] assert male_serialized["overlapFilter"]["datasetId"] == "f1_trio" assert male_serialized["overlapFilter"]["effectTypes"] == ["missense"] assert male_serialized["overlapFilter"]["gender"] == ["male"] assert male_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert male_serialized["overlapFilter"]["peopleGroup"][ "checkedValues" ] == ["phenotype1"] assert male_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" assert male_serialized["overlapFilter"]["studyTypes"] == ["we"] assert male_serialized["overlapFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] female_serialized = serialize[0]["missense"]["female"] assert female_serialized["name"] == "female" assert female_serialized["count"] == 1 assert female_serialized["overlapped"] == 1 assert female_serialized["expected"] == 1 assert female_serialized["pvalue"] == 1 assert female_serialized["countFilter"]["datasetId"] == "f1_trio" assert female_serialized["countFilter"]["effectTypes"] == ["missense"] assert female_serialized["countFilter"]["gender"] == ["female"] assert female_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert female_serialized["countFilter"]["peopleGroup"][ "checkedValues" ] == ["phenotype1"] assert female_serialized["countFilter"]["peopleGroup"]["id"] == "phenotype" assert female_serialized["countFilter"]["studyTypes"] == ["we"] assert female_serialized["countFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ] assert female_serialized["overlapFilter"]["datasetId"] == "f1_trio" assert female_serialized["overlapFilter"]["effectTypes"] == ["missense"] assert female_serialized["overlapFilter"]["gender"] == ["female"] assert ( female_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" ) assert female_serialized["overlapFilter"]["peopleGroup"][ "checkedValues" ] == ["phenotype1"] assert ( female_serialized["overlapFilter"]["peopleGroup"]["id"] == "phenotype" ) assert female_serialized["overlapFilter"]["studyTypes"] == ["we"] assert female_serialized["overlapFilter"]["variantTypes"] == [ "ins", "sub", "del", "complex", ]
[docs] def test_serialize_enrichment_result( enrichment_serializer: EnrichmentSerializer, ) -> None: enrichment_result = EnrichmentSingleResult( "all", 3, 1, 3, 0.5, ) res = enrichment_serializer.serialize_enrichment_result(enrichment_result) assert len(res) == 5 assert res["name"] == "all" assert res["count"] == 3 assert res["overlapped"] == 1 assert res["expected"] == 3 assert res["pvalue"] == 0.5