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Korkmatik/Main.java

Last active April 11, 2021 13:28
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FHIR Reference, Patient, Practioner, Organization, Observation and Search example implemented with Java HAPI FHIR library
Raw
Main.java
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import org.hl7.fhir.r4.model.*;
public class Main {
public static void main(String[] args) {
FhirContext ctx = FhirContext.forR4();
String serverBase = "http://hapi.fhir.org/baseR4/"; // TODO: Change if using another FHIR server
IGenericClient client = ctx.newRestfulGenericClient(serverBase);
/*
Part 1: Create an Organization
*/
System.out.println("***\nPart 1: Create an Organizstion\n***");
Organization organization = new Organization();
organization.setActive(true);
organization.setName("Labor Top&Schnell");
// Type of the organization
CodeableConcept codeableConcept = new CodeableConcept();
Coding coding = new Coding();
coding.setCode("prov");
coding.setDisplay("Einrichtung des Gesundheitswesens - Labor");
coding.setSystem("http://terminology.hl7.org/CodeSystem/organization-type");
codeableConcept.addCoding(coding);
codeableConcept.setText("Art der Einrichtung des Gesundheitswesens");
organization.addType(codeableConcept);
// Address of the organization
Address address = new Address();
address.setText("Hauptstrasse 1, 01234 Neustadt, Deutschland");
address.setPostalCode("01234");
address.setCity("Neustadt");
address.setCountry("Deutschland");
organization.addAddress(address);
System.out.println("The organization so far (LOCAL):");
PrettyPrint(organization, ctx);
// Creating the organization on the server
Organization createdOrganization =
(Organization) client.create().resource(organization).execute().getResource();
System.out.println("Result from the creation transaction (REMOTE):");
PrettyPrint(createdOrganization, ctx);
System.out.println("Organization ID: " + createdOrganization.getIdElement().getValue());
/*
Part 2: Create a practitioner locally and show it
*/
System.out.println("\n***\nPart 2: Create a new Practitioner\n***");
Practitioner practitioner = new Practitioner();
practitioner.setActive(true);
// Setting practitioner name
HumanName name = practitioner.addName();
name.addGiven("Holger");
name.setFamily("Alleswirdgut");
name.addPrefix("Dr. med.");
name.setUse(HumanName.NameUse.OFFICIAL);
// Setting practitioner address
practitioner.addAddress()
.setCity("Neustadt")
.setCountry("Deutschland")
.setText("Schlossallee 27, 01234 Neustadt, Deutschland")
.setPostalCode("01234");
// Adding phone number
practitioner.addTelecom()
.setSystem(ContactPoint.ContactPointSystem.PHONE)
.setValue("055512345589");
// Print the local practitioner
System.out.println("The practitioner so far (LOCAL):");
PrettyPrint(practitioner, ctx);
// Creating the practitioner on the remote server
Practitioner createdPractitioner =
(Practitioner) client.create().resource(practitioner).execute().getResource();
System.out.println("Result from the creation transaction (REMOTE): ");
PrettyPrint(createdPractitioner, ctx);
System.out.println("Practitioner ID: " + createdPractitioner.getIdElement().getValue());
/*
Part 3: Create a patient locally and show it
*/
Patient patient = new Patient();
patient.addName()
.addGiven("Max")
.setFamily("Mustermann")
.setUse(HumanName.NameUse.OFFICIAL);
patient.addAddress()
.setCity("Neustadt")
.setCountry("Deutschland")
.setText("Hintere Gasse 5, 01234 Neustadt, Deutschland")
.setPostalCode("01234");
// Adding reference from patient to his general practitioner
Reference generalPractitionerRef = new Reference(createdPractitioner.getIdElement().getValue());
generalPractitionerRef.setType("Practitioner");
patient.addGeneralPractitioner(generalPractitionerRef);
// Showing the patient so far
System.out.println("The patient so far (LOCAL):");
PrettyPrint(patient, ctx);
// Creating the patient on the server
Patient createdPatient =
(Patient) client.create().resource(patient).execute().getResource();
System.out.println("Result from the creation transaction (REMOTE): ");
PrettyPrint(createdPatient, ctx);
System.out.println("Patient ID on remote server: " + createdPatient.getIdElement().getValue());
/*
Part 4: Adding a Observation
*/
Observation creatinineClearance = new Observation();
// Setting codeable concept of creatinine clearence
CodeableConcept creatinineClearenceCC = new CodeableConcept();
creatinineClearenceCC.addCoding()
.setCode("33914-3")
.setDisplay("Glomerular filtration rate/1.73 sq M.predicted by Creatinine-based formula (MDRD)")
.setSystem("http://loinc.org");
creatinineClearance.setCode(creatinineClearenceCC);
// Setting reference to lab
Reference labRef = new Reference(createdOrganization.getIdElement().getValue());
labRef.setType("Organization");
creatinineClearance.addPerformer(labRef);
// Setting reference to patient
Reference patientRef = new Reference(createdPatient.getIdElement().getValue());
patientRef.setType("Patient");
creatinineClearance.setSubject(patientRef);
// Creating the observation on the remote server
Observation createdCreatinineClearence =
(Observation) client.create().resource(creatinineClearance).execute().getResource();
System.out.println("Creatinine Clearence created:");
PrettyPrint(createdCreatinineClearence, ctx);
/*
Part 5: Perform searches with references
*/
// Searching for patients that were treated by a specific practitioner
Bundle patients = client.search()
.forResource(Patient.class)
.where(Patient.GENERAL_PRACTITIONER.hasId(createdPractitioner.getIdElement().getValue()))
.returnBundle(Bundle.class)
.execute();
System.out.println("Number of patients: " + patients.getTotal());
// Search for all observations for a specific patient
Bundle observations = client.search()
.forResource(Observation.class)
.where(Observation.SUBJECT.hasId(createdPatient.getIdElement().getValue()))
.returnBundle(Bundle.class)
.execute();
System.out.println(
String.format(
"Number of observations for patient %s %s: %d",
createdPatient.getName().get(0).getGiven().get(0),
createdPatient.getName().get(0).getFamily(),
observations.getTotal()
)
);
/*
Part 6: Add different observations to a patient
*/
// Adding glucose observation
Observation glucoseObservation = new Observation();
glucoseObservation.setValue(new SampledData().setData("6.3"));
glucoseObservation.setStatus(Observation.ObservationStatus.FINAL);
CodeableConcept glucoseObservationCC = new CodeableConcept();
glucoseObservationCC.addCoding()
.setSystem("https://loinc.org")
.setCode("15074-8")
.setDisplay("'Glucose [Moles/volume] in Blood', given as 'Glucose [Moles/volume] in Blood'");
glucoseObservation.setCode(glucoseObservationCC);
glucoseObservation.addPerformer(labRef);
glucoseObservation.setSubject(patientRef);
boolean created = client.create()
.resource(glucoseObservation)
.execute()
.getCreated();
if (!created) {
System.out.println("Failed to create glucose observation");
}
// Adding hemoglobin observation
Observation hemoglobinObservation = new Observation();
hemoglobinObservation.setValue(new SampledData().setData("7.2"));
hemoglobinObservation.setStatus(Observation.ObservationStatus.FINAL);
CodeableConcept hemoglobinCC = new CodeableConcept();
hemoglobinCC.addCoding()
.setSystem("https://loinc.org")
.setCode("718-7")
.setDisplay("'Hemoglobin [Mass/volume] in Blood', given as 'Hemoglobin [Mass/volume] in Blood'");
hemoglobinObservation.setCode(hemoglobinCC);
hemoglobinObservation.addPerformer(labRef);
hemoglobinObservation.setSubject(patientRef);
created = client.create()
.resource(hemoglobinObservation)
.execute()
.getCreated();
if (!created) {
System.out.println("Failed to created hemoglobin observation");
}
// Temperatur observation
Observation temperatureObservation = new Observation();
temperatureObservation.setValue(new SampledData().setData("39"));
CodeableConcept tempCC = new CodeableConcept();
tempCC.addCoding()
.setSystem("https://loinc.org")
.setCode("8310-5")
.setDisplay("'Body temperature', given as 'Body temperature'");
temperatureObservation.setCode(tempCC);
CodeableConcept tempInterpretationCC = new CodeableConcept();
tempInterpretationCC.addCoding()
.setSystem("http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation")
.setCode("H")
.setDisplay("High");
temperatureObservation.addInterpretation(tempInterpretationCC);
created = client.create()
.resource(temperatureObservation)
.execute()
.getCreated();
if (!created) {
System.out.println("Failed to created temperature observation");
}
/*
Part 7: Create observations for several patients
*/
Patient patient1 = new Patient();
patient1.addName()
.setFamily("Heuvel")
.addGiven("Peter")
.setUse(HumanName.NameUse.OFFICIAL);
patient1.addAddress()
.setPostalCode("01234")
.setCity("Neustadt")
.setCountry("Deutschland")
.setText("Schlossstraße 12, 01234 Neustadt, Deutschland");
if (!client.create().resource(patient1).execute().getCreated()) {
System.out.println("Could not create patient Peter Heuvel");
}
Observation carbonDioxidInBloodObservation = new Observation();
CodeableConcept co2CC = new CodeableConcept();
co2CC.addCoding()
.setDisplay("'Carbon dioxide [Partial pressure] in Blood', given as 'Carbon dioxide in blood'")
.setCode("11557-6")
.setSystem("https://loinc.org");
carbonDioxidInBloodObservation.setCode(co2CC);
carbonDioxidInBloodObservation.addPerformer(labRef);
carbonDioxidInBloodObservation.setSubject(new Reference(patient1.getIdElement().getValue()).setType("Patient"));
if (!client.create().resource(carbonDioxidInBloodObservation).execute().getCreated()) {
System.out.println("Could not create carbon dioxid in blood observation for Peter Heuvel!");
}
// Adding patient for blood pressure cancel observation
Patient patient2 = new Patient();
patient2.addName()
.setFamily("Chalmers")
.addGiven("Peter")
.setUse(HumanName.NameUse.OFFICIAL);
patient2.addAddress()
.setCountry("Deutschland")
.setPostalCode("01234")
.setCity("Neustadt")
.setText("Flussstraße 32, 01234 Neustadt, Deutschland");
Observation bloodPressureCancel = new Observation();
bloodPressureCancel.setSubject(new Reference(patient2.getIdElement().getValue()).setType("Patient"));
bloodPressureCancel.addPerformer(generalPractitionerRef);
bloodPressureCancel.setStatus(Observation.ObservationStatus.CANCELLED);
CodeableConcept bloodPressureCC = new CodeableConcept();
bloodPressureCC.addCoding()
.setSystem("https://loinc.org")
.setCode("85354-9")
.setDisplay("'Blood pressure panel with all children optional', given as 'Blood pressure panel with all children optional'");
bloodPressureCancel.setCode(bloodPressureCC);
var bloodPressurePatientResult = client.create().resource(bloodPressureCancel).execute();
if (!bloodPressurePatientResult.getCreated()) {
System.out.println("Could not create blood pressure canceled");
}
/*
Part 8: for a specific patient, search for all observations that were performed by a specific performer
*/
Bundle response = client.search()
.forResource(Observation.class)
.where(Observation.SUBJECT.hasId(createdPatient.getIdElement().getValue()))
.and(Observation.PERFORMER.hasId(createdOrganization.getIdElement().getValue()))
.returnBundle(Bundle.class)
.execute();
System.out.println(
"Number observations for a specific patient that were performed by a specific practitioner: "
+ response.getTotal()
);
}
public static void PrettyPrint(Resource resource, FhirContext context) {
IParser parser = context.newJsonParser();
parser.setPrettyPrint(true);
System.out.println(parser.encodeResourceToString(resource));
}
}
Raw
pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.example</groupId>
<artifactId>lab3</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<maven.compiler.source>1.11</maven.compiler.source>
<maven.compiler.target>1.11</maven.compiler.target>
</properties>
<dependencies>
<!-- Maven compiler plugin -->
<dependency>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-base -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>5.3.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-structures-r4 -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>5.3.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-client -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>5.3.0</version>
</dependency>
</dependencies>
</project>
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