Examples with Hierarchies com.cerner.bunsen.codes.Hierarchies used on opensource projects

Example 1 with Hierarchies

use of com.cerner.bunsen.codes.Hierarchies in project bunsen by cerner.

the class BroadcastableValueSetsTest method setUp.

/**
 * Sets up Spark and loads test value sets.
 */
@BeforeClass
public static void setUp() throws IOException {
    // Create a local spark session using an in-memory metastore.
    // We must also use Hive and set the partition mode to non-strict to
    // support dynamic partitions.
    spark = SparkSession.builder().master("local[2]").appName("UdfsTest").enableHiveSupport().config("javax.jdo.option.ConnectionURL", "jdbc:derby:memory:metastore_db;create=true").config("hive.exec.dynamic.partition.mode", "nonstrict").config("spark.sql.warehouse.dir", Files.createTempDirectory("spark_warehouse").toString()).getOrCreate();
    spark.sql("CREATE DATABASE ontologies");
    Hierarchies withLoinc = Loinc.withLoincHierarchy(spark, Hierarchies.getEmpty(spark), "src/test/resources/LOINC_HIERARCHY_SAMPLE.CSV", "2.56");
    Hierarchies withLoincAndSnomed = Snomed.withRelationships(spark, withLoinc, "src/test/resources/SNOMED_RELATIONSHIP_SAMPLE.TXT", "20160901");
    withLoincAndSnomed.writeToDatabase(Hierarchies.HIERARCHIES_DATABASE);
    ValueSets.getEmpty(spark).withValueSetsFromDirectory("src/test/resources/xml/valuesets").writeToDatabase(ValueSets.VALUE_SETS_DATABASE);
}

Example 2 with Hierarchies

use of com.cerner.bunsen.codes.Hierarchies in project bunsen by cerner.

the class ValueSetUdfsTest method setUp.

/**
 * Sets up Spark and loads test value sets.
 */
@BeforeClass
public static void setUp() throws IOException {
    // Create a local spark session using an in-memory metastore.
    // We must also use Hive and set the partition mode to non-strict to
    // support dynamic partitions.
    spark = SparkSession.builder().master("local[2]").appName("UdfsTest").enableHiveSupport().config("javax.jdo.option.ConnectionURL", "jdbc:derby:memory:metastore_db;create=true").config("hive.exec.dynamic.partition.mode", "nonstrict").config("spark.sql.warehouse.dir", Files.createTempDirectory("spark_warehouse").toString()).getOrCreate();
    spark.sql("create database " + ConceptMaps.MAPPING_DATABASE);
    Hierarchies withLoinc = Loinc.withLoincHierarchy(spark, Hierarchies.getEmpty(spark), "src/test/resources/LOINC_HIERARCHY_SAMPLE.CSV", "2.56");
    Hierarchies withLoincAndSnomed = Snomed.withRelationships(spark, withLoinc, "src/test/resources/SNOMED_RELATIONSHIP_SAMPLE.TXT", "20160901");
    ValueSets withGender = ValueSets.getEmpty(spark).withValueSetsFromDirectory("src/test/resources/xml/valuesets");
    BroadcastableValueSets valueSets = BroadcastableValueSets.newBuilder().addCode("bp", Loinc.LOINC_CODE_SYSTEM_URI, "8462-4").addCode("albumin", Loinc.LOINC_CODE_SYSTEM_URI, "14959-1").addReference("married", "urn:cerner:bunsen:valueset:married_maritalstatus").addDescendantsOf("leukocytes", Loinc.LOINC_CODE_SYSTEM_URI, "LP14419-3", Loinc.LOINC_HIERARCHY_URI).addDescendantsOf("diabetes", Snomed.SNOMED_CODE_SYSTEM_URI, "73211009", Snomed.SNOMED_HIERARCHY_URI).addDescendantsOf("blood_disorder", Snomed.SNOMED_CODE_SYSTEM_URI, "266992002", Snomed.SNOMED_HIERARCHY_URI).addDescendantsOf("disorder_history", Snomed.SNOMED_CODE_SYSTEM_URI, "312850006", Snomed.SNOMED_HIERARCHY_URI).build(spark, withGender, withLoincAndSnomed);
    ValueSetUdfs.pushUdf(spark, valueSets);
    Dataset<Observation> loincObservations = spark.createDataset(ImmutableList.of(// "is a" LP14419-3
    observation("leukocytes", "5821-4"), // Blood pressure
    observation("bp", "8462-4")), encoders.of(Observation.class));
    loincObservations.createOrReplaceTempView("test_loinc_obs");
    // Conditions include history of anemia, which includes a cycling ancestor
    // in our test data. This ensures that can be loaded correctly.
    Dataset<Condition> conditions = spark.createDataset(ImmutableList.of(// "is a" 73211009 (diabetes)
    condition("diabetes", "44054006"), // 312850006 (history of disorder)
    condition("history_of_anemia", "275538002")), encoders.of(Condition.class));
    conditions.createOrReplaceTempView("test_snomed_cond");
    Dataset<Patient> patients = spark.createDataset(ImmutableList.of(patient("married", "M"), patient("unmarried", "U")), encoders.of(Patient.class));
    patients.createOrReplaceTempView("test_valueset_patient");
}