Adding Specimen

pom.xml

@@ -13,6 +13,7 @@
 		<jetty.version>10.0.7</jetty.version>
 		<maven.compiler.source>17</maven.compiler.source>
 		<maven.compiler.target>17</maven.compiler.target>
+		<hapi.version>5.6.0</hapi.version>
 
 		<!-- jetty plugin properties (used when starting server locally) -->
 		<dev>true</dev>
@@ -46,7 +47,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-structures-r4</artifactId>
-			<version>3.8.0</version>
+			<version>${hapi.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
@@ -56,7 +57,7 @@
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
-			<version>3.8.0</version>
+			<version>6.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>

src/main/java/com/sdc/parser/Bundle/BundleHelper.java

@@ -6,6 +6,7 @@
 import static com.sdc.parser.Resource.PractitionerHelper.createPractitioner;
 import static com.sdc.parser.Resource.PractitionerHelper.generatePractitionerDisplay;
 import static com.sdc.parser.Resource.PractitionerRoleHelper.createPractitionerRolePractitioner;
+import static com.sdc.parser.Resource.SpecimenHelper.createSpecimen;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -59,6 +60,7 @@ public static Bundle createBundle(String bundleType, List<Observation> observati
 		patientReference = new Reference(ParserHelper.createReferenceString(patientEntry.getResource().getResourceType(), patientConfig.getIdentifier()))
 				.setDisplay(patientConfig.getFullName());
 		practitionerEntry = createBundleEntry(getUUID(), createPractitioner(configValues.getPractitionerConfig()));
+		specimenEntry = createBundleEntry(getUUID(), createSpecimen)
 
 		hydrateEntries(observations, ctx, sdcForm, configValues);
 		hydrateObservations(observations, ctx, configValues);

src/main/java/com/sdc/parser/Resource/DiagnosticReportHelper.java

@@ -24,6 +24,9 @@ public static DiagnosticReport createDiagnosticReport(FhirContext ctx, String sd
 
         // meta 
         diagReport.getMeta().addProfile(PROFILE_URL);
+        // narrative
+        diagReport.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+        diagReport.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
         //category 
         diagReport.getCategoryFirstRep().addCoding().setCode("LP7839-6").setSystem("http://loinc.org").setDisplay("Pathology"); 
         //code

src/main/java/com/sdc/parser/Resource/MessageHeaderHelper.java

@@ -24,7 +24,9 @@ public class MessageHeaderHelper extends ResourceHelper<MessageHeader> {
 
 	public MessageHeader initializeResource(FhirContext ctx) {
 		MessageHeader messageHeader = new MessageHeader();
-		messageHeader.getText().setStatus(NarrativeStatus.GENERATED);
+		//messageHeader.getText().setStatus(NarrativeStatus.GENERATED);
+		messageHeader.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+		messageHeader.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
 		messageHeader.getEventCoding().setSystem(EVENT_CODING_SYSTEM_NAME).setCode("admin-notify");
 		messageHeader.setSource(
 			new MessageSourceComponent()

src/main/java/com/sdc/parser/Resource/ObservationHelper.java

@@ -159,6 +159,8 @@ private static void vccTextReplacement(ArrayList<Element> listItemElements, Obse
 	public static void addObservationMetadata(Observation observation, String elemId, String elemTitle, String systemName) {
 		observation.addIdentifier().setSystem(systemName)
 				.setValue(getUUID());
+		observation.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+		observation.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
 		observation.setStatus(ObservationStatus.FINAL);
 		observation.getCode().addCoding().setSystem(systemName)
 				.setCode(elemId)
@@ -194,4 +196,4 @@ private static void addObservationMetadata(ConfigValues configValues, Observatio
 		String systemName = configValues.getSystemName();
 		addObservationMetadata(observation, elemId, elemTitle, systemName);
 	}
-}
+}

src/main/java/com/sdc/parser/Resource/PatientHelper.java

@@ -10,13 +10,14 @@ public class PatientHelper {
 	public static Patient createPatient(PatientConfig patientConfig) {
 		Patient patient = new Patient();
 		patient.getMeta().addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
-
+		patient.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+		patient.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
 		for (Entry<String, String> entry : patientConfig.getSystem().entrySet()) {
 			patient.addIdentifier().setSystem(entry.getKey()).setValue(entry.getValue());
 		}
 
 		patient.addName().setFamily(patientConfig.getLastName()).addGiven(patientConfig.getFirstName());
-		patient.setGender(org.hl7.fhir.r4.model.Enumerations.AdministrativeGender.MALE);
+		patient.setGender(org.hl7.fhir.r4.model.Enumerations.AdministrativeGender.FEMALE);
 //		String encoded = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
 		return patient;
 	}

src/main/java/com/sdc/parser/Resource/PractitionerHelper.java

@@ -11,6 +11,8 @@ public class PractitionerHelper {
 	public static Practitioner createPractitioner(PractitionerConfig practitionerConfig) {
 		Practitioner pract = new Practitioner();
         pract.getMeta().addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner");
+		pract.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+		pract.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
 		pract.addName().setFamily(practitionerConfig.getLastName()).addGiven(practitionerConfig.getFirstName());
 
 		 for (Entry<String, String> entry : practitionerConfig.getSystem().entrySet()) {

src/main/java/com/sdc/parser/Resource/PractitionerRoleHelper.java

@@ -8,8 +8,10 @@ public class PractitionerRoleHelper {
 
 	public static PractitionerRole createPractitionerRolePractitioner(FhirContext ctx) {
 		PractitionerRole practRole = new PractitionerRole();
-        practRole.getMeta().addProfile("hhttp://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-related-practitioner-role");
-		practRole.addIdentifier().setSystem("http://someIdentifier.com").setValue("pathpract1");
+        practRole.getMeta().addProfile("http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-related-practitioner-role");
+        practRole.getText().setStatus(org.hl7.fhir.r4.model.Narrative.NarrativeStatus.GENERATED);
+        practRole.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">fake Observation</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>6547</td></tr></tbody></table></div>");
+        practRole.addIdentifier().setSystem("http://someIdentifier.com").setValue("pathpract1");
         practRole.addIdentifier().setSystem("http://hl7.org/fhir/sid/us-npi").setValue("193757595");
         practRole.addCode().addCoding().setSystem("http://hl7.org/fhir/us/cancer-reporting/ValueSet/us-pathology-provider-types").setDisplay("Pathologist principally interpreting results on pathology testing").setCode("principal-result-interpreter");
         //TODO: add reference Practitioner as config/autogenerated link 

src/main/java/com/sdc/parser/Resource/SpecimenHelper.java

@@ -0,0 +1,26 @@
+package com.sdc.parser.Resource;
+
+import org.hl7.fhir.r4.model.Specimen;
+import org.hl7.fhir.r4.model.Specimen.SpecimenStatus;
+import com.sdc.parser.Config.PatientConfig;
+
+import ca.uhn.fhir.context.FhirContext;
+
+public class SpecimenHelper {
+
+	public static Specimen createSpecimen(FhirContext ctx) {
+		Specimen specimen = new Specimen();
+		//TODO update the specimen ID to generate
+		//specimen.addIdentifier().setSystem("http://someIdentifier.com").setValue("specimen875758333");
+		specimen.addIdentifier().setSystem(entry.getKey()).setValue(entry.getValue())
+        specimen.setStatus(SpecimenStatus.AVAILABLE);
+		specimen.getType().addCoding().setCode("TUMOR").setDisplay("Tumor").setSystem("http://terminology.hl7.org/CodeSystem/v2-0487");
+// bodysite and method are not possible in the parser since they are derived from the form. These should be coded as SNOMED
+		//add collection.bodysite
+		//add collection.method
+		//TODO add an accessionIdentifier 
+		// having trouble setting receivedTime 
+//		String encoded = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(practRole);
+		return specimen;
+	}
+}

src/main/resources/config.properties

@@ -8,8 +8,8 @@ patient.identifier=1234567893
 patient.address=sdfg
 patient.telecom=sdfg
 patient.profile=http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
-patient.urn.key=urn:NPI
-patient.urn.value=1234567893
+patient.urn.key=urn:system
+patient.urn.value=6547
 
 #Practitioner
 practitioner.first.name=Riki