Models:
Philip Bordner
philipB/
femr
0
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[f54d94]: / tests / test_ontology.py

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# flake8: noqa: E501



import pathlib



import femr.ontology





def create_fake_athena(tmp_path: pathlib.Path) -> pathlib.Path:

    athena = tmp_path / "athena"

    athena.mkdir()



    concept = athena / "CONCEPT.csv"

    concept.write_text(

        """concept_id	concept_name	domain_id	vocabulary_id	concept_class_id	standard_concept	concept_code	valid_start_date	valid_end_date	invalid_reason

37200198\tType 2 diabetes mellitus with mild nonproliferative diabetic retinopathy with macular edema, right eye\tCondition\tICD10CM\t7-char billing code\t\tE11.3211\t19700101\t20991231\t

380097\tMacular edema due to diabetes mellitus\tCondition\tSNOMED\tClinical Finding\tS\t312912001\t20020131\t20991231

4334884	Disorder of macula due to diabetes mellitus	Condition	SNOMED	Clinical Finding	S	232020009	20020131	20991231

4174977	Retinopathy due to diabetes mellitus	Condition	SNOMED	Clinical Finding	S	4855003	20020131	20991231

4208223	Disorder of macula of retina	Condition	SNOMED	Clinical Finding	S	312999006	20020131	20991231

4290333	Macular retinal edema	Condition	SNOMED	Clinical Finding	S	37231002	20020131	20991231

35626904	Retinal edema due to diabetes mellitus	Condition	SNOMED	Clinical Finding	S	770323005	20180731	20991231

45757435	Mild nonproliferative retinopathy due to type 2 diabetes mellitus	Condition	SNOMED	Clinical Finding	S	138911000119106	20150131	20991231

"""

    )

    relationship = athena / "CONCEPT_RELATIONSHIP.csv"

    relationship.write_text(

        """concept_id_1	concept_id_2	relationship_id	valid_start_date	valid_end_date	invalid_reason

37200198	380097	Maps to	20171001	20991231

37200198	1567956	Is a	20170428	20991231

37200198	1567959	Is a	20170428	20991231

37200198	45757435	Maps to	20171001	20991231

37200198	1567961	Is a	20170428	20991231

37200198	45552385	Is a	20170428	20991231

35977781	35977781	Mapped from	20200913	20991231

46135811	40642538	Has status	20220128	20991231

46135811	35631990	Has Module	20220128	20991231"""

    )



    ancestor = athena / "CONCEPT_ANCESTOR.csv"

    ancestor.write_text(

        """ancestor_concept_id\tdescendant_concept_id\tmin_levels_of_separation\tmax_levels_of_separation

373499	4334884	4	6

442793	4334884	3	3

255919	4334884	6	9

433128	4334884	4	4

4180628	4334884	6	8

4209989	4334884	3	3

441840	4334884	6	10

4274025	4334884	5	9

4082284	4334884	2	2

4042836	4334884	5	7

443767	4334884	2	2

4038502	4334884	5	8

4174977	4334884	1	1

4334884	4334884	0	0

4134440	4334884	5	7

4247371	4334884	5	8

375252	4334884	3	5

4027883	4334884	4	4

4208223	4334884	1	1

378416	4334884	2	2

4080992	4334884	4	6

4162092	4334884	3	3

255919	380097	7	10

433128	380097	5	5

442793	380097	4	4

373499	380097	5	7

4180628	380097	7	9

4209989	380097	4	4

37018677	380097	3	3

441840	380097	5	11

380097	380097	0	0

4274025	380097	4	10

372903	380097	2	2

433595	380097	4	4

4042836	380097	6	8

4082284	380097	3	3

443767	380097	3	3

4038502	380097	6	9

4174977	380097	2	2

4334884	380097	1	1

4134440	380097	6	8

4247371	380097	6	9

4290333	380097	1	1

375252	380097	4	6

4027883	380097	5	5

4040388	380097	3	3

4208223	380097	2	2

35626904	380097	1	1

378416	380097	3	3

4080992	380097	5	7

4162092	380097	4	4

"""

    )



    return athena





def test_only_athena(tmp_path: pathlib.Path) -> None:

    fake_athena = create_fake_athena(tmp_path)



    ontology = femr.ontology.Ontology(str(fake_athena))



    assert (

        ontology.get_description("ICD10CM/E11.3211")

        == "Type 2 diabetes mellitus with mild nonproliferative diabetic retinopathy with macular edema, right eye"

    )



    assert ontology.get_parents("ICD10CM/E11.3211") == {"SNOMED/312912001", "SNOMED/138911000119106"}

    assert ontology.get_parents("SNOMED/312912001") == {"SNOMED/37231002", "SNOMED/232020009", "SNOMED/770323005"}



    assert ontology.get_all_parents("ICD10CM/E11.3211") == {

        "SNOMED/37231002",

        "SNOMED/138911000119106",

        "SNOMED/4855003",

        "SNOMED/312999006",

        "SNOMED/312912001",

        "ICD10CM/E11.3211",

        "SNOMED/770323005",

        "SNOMED/232020009",

    }



    assert ontology.get_children("SNOMED/312912001") == {"ICD10CM/E11.3211"}

    assert ontology.get_children("SNOMED/37231002") == {"SNOMED/312912001"}



    assert ontology.get_all_children("SNOMED/37231002") == {"ICD10CM/E11.3211", "SNOMED/312912001", "SNOMED/37231002"}





def test_athena_and_custom(tmp_path: pathlib.Path) -> None:

    fake_athena = create_fake_athena(tmp_path)



    code_metadata = {

        "CUSTOM/CustomDiabetes": {"description": "A nice diabetes code", "parent_codes": ["ICD10CM/E11.3211"]}

    }



    ontology = femr.ontology.Ontology(str(fake_athena), code_metadata)



    assert ontology.get_description("CUSTOM/CustomDiabetes") == "A nice diabetes code"

    assert ontology.get_all_parents("CUSTOM/CustomDiabetes") == {

        "CUSTOM/CustomDiabetes",

        "SNOMED/37231002",

        "SNOMED/138911000119106",

        "SNOMED/4855003",

        "SNOMED/312999006",

        "SNOMED/312912001",

        "ICD10CM/E11.3211",

        "SNOMED/770323005",

        "SNOMED/232020009",

    }



    assert ontology.get_all_children("SNOMED/37231002") == {

        "CUSTOM/CustomDiabetes",

        "ICD10CM/E11.3211",

        "SNOMED/312912001",

        "SNOMED/37231002",

    }