# 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