Support OID data type

Author: johngrimes

bunsen-stu3/src/main/scala/com/cerner/bunsen/stu3/Stu3DataTypeMappings.scala

@@ -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,

bunsen-stu3/src/test/java/com/cerner/bunsen/stu3/FhirEncodersTest.java

@@ -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;
@@ -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.
    */
@@ -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();
   }
 
   /**
@@ -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());
+  }
 }

bunsen-stu3/src/test/java/com/cerner/bunsen/stu3/TestData.java

@@ -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;
@@ -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;
+  }
 }

python/tests/test_bunsen_r4.py

@@ -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()) \

python/tests/test_bunsen_stu3.py

@@ -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()) \