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Support OID data type #45

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Support OID data type #45

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1 change: 1 addition & 0 deletions bunsen-stu3/src/main/scala/com/cerner/bunsen/stu3/Stu3DataTypeMappings.scala
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Expand Up @@ -39,6 +39,7 @@ class Stu3DataTypeMappings extends DataTypeMappings {
classOf[CodeType] -> DataTypes.StringType,
classOf[StringType] -> DataTypes.StringType,
classOf[UriType] -> DataTypes.StringType,
classOf[OidType] -> DataTypes.StringType,
classOf[IntegerType] -> DataTypes.IntegerType,
classOf[UnsignedIntType] -> DataTypes.IntegerType,
classOf[PositiveIntType] -> DataTypes.IntegerType,
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17 changes: 17 additions & 0 deletions bunsen-stu3/src/test/java/com/cerner/bunsen/stu3/FhirEncodersTest.java
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Expand Up @@ -18,6 +18,7 @@
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.ImagingStudy;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationRequest;
Expand Down Expand Up @@ -60,6 +61,10 @@ public class FhirEncodersTest {
private static Dataset<MedicationRequest> medDataset;
private static MedicationRequest decodedMedRequest;

private static ImagingStudy imagingStudy = TestData.newImagingStudy();
private static Dataset<ImagingStudy> imagingStudyDataset;
private static ImagingStudy decodedImagingStudy;

/**
* Set up Spark.
*/
Expand All @@ -85,6 +90,10 @@ public static void setUp() {
medDataset = spark.createDataset(ImmutableList.of(medRequest),
encoders.of(MedicationRequest.class, Medication.class, Provenance.class));
decodedMedRequest = medDataset.head();

imagingStudyDataset = spark
.createDataset(ImmutableList.of(imagingStudy), encoders.of(ImagingStudy.class));
decodedImagingStudy = imagingStudyDataset.head();
}

/**
Expand Down Expand Up @@ -333,4 +342,12 @@ public void testEncoderCached() throws IOException {
Assert.assertSame(encoders.of(Patient.class),
encoders.of(Patient.class));
}

@Test
public void testOid() {
Assert.assertEquals(imagingStudy.getUid(),
imagingStudyDataset.select("uid").head().get(0));
Assert.assertEquals(imagingStudy.getUid(),
decodedImagingStudy.getUid());
}
}
25 changes: 25 additions & 0 deletions bunsen-stu3/src/test/java/com/cerner/bunsen/stu3/TestData.java
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@@ -1,18 +1,24 @@
package com.cerner.bunsen.stu3;

import com.google.common.collect.ImmutableList;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.dstu3.model.Annotation;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.Identifier;
import org.hl7.fhir.dstu3.model.ImagingStudy;
import org.hl7.fhir.dstu3.model.ImagingStudy.ImagingStudySeriesComponent;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.Medication.MedicationIngredientComponent;
import org.hl7.fhir.dstu3.model.Medication.MedicationStatus;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.Narrative;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.OidType;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Procedure;
import org.hl7.fhir.dstu3.model.Provenance;
Expand Down Expand Up @@ -192,4 +198,23 @@ public static MedicationRequest newMedRequest() {

return medReq;
}

/**
* Returns a FHIR ImagingStudy resource for testing purposes.
*/
public static ImagingStudy newImagingStudy() {
ImagingStudy imagingStudy = new ImagingStudy();

imagingStudy.setId("test-imaging-study");
imagingStudy.setUid("1.3.12.2.1107.5.1.4.45533.30000008102706401187500000052");
imagingStudy.setPatient(new Reference("Patient/test-patient"));
List<ImagingStudySeriesComponent> series = new ArrayList<>();
ImagingStudySeriesComponent seriesComponent = new ImagingStudySeriesComponent(
new OidType("1.3.12.2.1107.5.1.4.45533.30000008102706401187500000053"),
new Coding("http://dicom.nema.org/resources/ontology/DCM", "HD", "Hemodynamic Waveform"));
series.add(seriesComponent);
imagingStudy.setSeries(series);

return imagingStudy;
}
}
1 change: 1 addition & 0 deletions python/tests/test_bunsen_r4.py
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Expand Up @@ -50,6 +50,7 @@ def spark_session(request):
spark = SparkSession.builder \
.appName('bunsen-test') \
.master('local[2]') \
.config('spark.driver.host', 'localhost') \
.config('spark.jars', shaded_jar) \
.config('hive.exec.dynamic.partition.mode', 'nonstrict') \
.config('spark.sql.warehouse.dir', mkdtemp()) \
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1 change: 1 addition & 0 deletions python/tests/test_bunsen_stu3.py
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Expand Up @@ -50,6 +50,7 @@ def spark_session(request):
spark = SparkSession.builder \
.appName('bunsen-test') \
.master('local[2]') \
.config('spark.driver.host', 'localhost') \
.config('spark.jars', shaded_jar) \
.config('hive.exec.dynamic.partition.mode', 'nonstrict') \
.config('spark.sql.warehouse.dir', mkdtemp()) \
Expand Down