Python get_current_valuesetsの例

コード例 #1

ファイル: test_bunsen_stu3.py プロジェクト: datnoor/bunsen

def test_isa_custom(spark_session, bundles):
    observations = extract_entry(spark_session, bundles, 'observation')
    observations.registerTempTable('observations')

    blood_pressure = {'blood_pressure': [('http://loinc.org', '8462-4')]}

    push_valuesets(spark_session, blood_pressure)

    results = spark_session.sql("SELECT subject.reference, " +
                                "effectiveDateTime, " +
                                "valueQuantity.value " + "FROM observations " +
                                "WHERE in_valueset(code, 'blood_pressure')")

    assert get_current_valuesets(spark_session) == blood_pressure
    assert results.count() == 14

コード例 #2

ファイル: test_bunsen_stu3.py プロジェクト: sanumula/bunsen

def test_isa_custom(spark_session, bundles):
    observations = extract_entry(spark_session, bundles, 'Observation')
    observations.registerTempTable('observations')

    blood_pressure = {'blood_pressure': [('http://loinc.org', '8462-4')]}

    spark_session.sql('create database custom_ontologies')
    create_value_sets(spark_session).write_to_database('custom_ontologies')
    create_hierarchies(spark_session).write_to_database('custom_ontologies')

    push_valuesets(spark_session, blood_pressure, database='custom_ontologies')

    results = spark_session.sql("SELECT subject.reference, " +
                                "effective.dateTime, " +
                                "value.quantity.value " +
                                "FROM observations " +
                                "WHERE in_valueset(code, 'blood_pressure')")

    assert get_current_valuesets(spark_session) == blood_pressure
    assert results.count() == 14

コード例 #3

ファイル: test_bunsen_stu3.py プロジェクト: datnoor/bunsen

def test_isa_snomed(spark_session):

    spark_session.sql('create database isa_snomed_ontologies')

    with_relationships(
        spark_session,
        create_hierarchies(spark_session),
        'tests/resources/SNOMED_RELATIONSHIP_SAMPLE.TXT',
        '20160901') \
      .write_to_database('isa_snomed_ontologies')

    create_value_sets(spark_session).write_to_database('isa_snomed_ontologies')

    push_valuesets(spark_session, {'diabetes': isa_snomed('73211009')},
                   database='isa_snomed_ontologies')

    expected = {
        'diabetes': [('http://snomed.info/sct', '73211009'),
                     ('http://snomed.info/sct', '44054006')]
    }

    assert get_current_valuesets(spark_session) == expected

コード例 #4

ファイル: test_bunsen_stu3.py プロジェクト: datnoor/bunsen

def test_isa_loinc(spark_session):

    spark_session.sql('create database isa_loinc_ontologies')

    with_loinc_hierarchy(
        spark_session,
        create_hierarchies(spark_session),
        'tests/resources/LOINC_HIERARCHY_SAMPLE.CSV',
        '2.56') \
      .write_to_database('isa_loinc_ontologies')

    create_value_sets(spark_session).write_to_database('isa_loinc_ontologies')

    push_valuesets(spark_session, {'leukocytes': isa_loinc('LP14738-6')},
                   database='isa_loinc_ontologies')

    expected = {
        'leukocytes': [('http://loinc.org', '5821-4'),
                       ('http://loinc.org', 'LP14738-6'),
                       ('http://loinc.org', 'LP14419-3')]
    }
    assert get_current_valuesets(spark_session) == expected