Dheeraj | Add Immunization and Immunization Recommendation

src/main/java/in/projecteka/utils/data/FHIRUtils.java

@@ -1,6 +1,7 @@
 package in.projecteka.utils.data;
 
 import in.projecteka.utils.data.model.Doctor;
+import in.projecteka.utils.data.model.TargetDisease;
 import in.projecteka.utils.data.model.Vaccine;
 import in.projecteka.utils.data.model.Medicine;
 import in.projecteka.utils.data.model.SimpleCondition;
@@ -15,12 +16,14 @@
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.DateTimeType;
+import org.hl7.fhir.r4.model.DiagnosticReport;
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Immunization;
+import org.hl7.fhir.r4.model.ImmunizationRecommendation;
 import org.hl7.fhir.r4.model.Medication;
 import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.Meta;
@@ -32,12 +35,14 @@
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceType;
 import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.utilities.DateTimeUtil;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Date;
+import java.util.List;
 import java.util.Properties;
 import java.util.UUID;
 import java.util.stream.Collectors;
@@ -189,6 +194,7 @@ static CodeableConcept getChiefComplaintSectionType() {
         coding.setDisplay("Chief Complaint Section");
         return type;
     }
+
     static CodeableConcept getAllergySectionType() {
         CodeableConcept type = new CodeableConcept();
         Coding coding = type.addCoding();
@@ -198,7 +204,14 @@ static CodeableConcept getAllergySectionType() {
         return type;
     }
 
-
+    static CodeableConcept getImmunizationRecommendationSectionType() {
+        CodeableConcept type = new CodeableConcept();
+        Coding coding = type.addCoding();
+        coding.setSystem(Constants.EKA_SCT_SYSTEM);
+        coding.setCode("41000179103");
+        coding.setDisplay("Immunization Recommendation");
+        return type;
+    }
 
     static void addToBundleEntry(Bundle bundle, Resource resource, boolean useIdPart) {
         String resourceType = resource.getResourceType().toString();
@@ -322,6 +335,33 @@ static Immunization getImmunization(Vaccine vaccine, Date date, String orgPrefix
         return immunization;
     }
 
+    static ImmunizationRecommendation getImmunizationRecommendation(Vaccine vaccine, TargetDisease targetDisease, Date date){
+        ImmunizationRecommendation immunizationRecommendation = new ImmunizationRecommendation();
+        immunizationRecommendation.setId(UUID.randomUUID().toString());
+        immunizationRecommendation.setDate(date);
+        var immunizationRecommendationComponent = immunizationRecommendation.addRecommendation();
+        immunizationRecommendationComponent.addVaccineCode(getCodeableConcept(vaccine.getCode(), vaccine.getName(), null));
+        immunizationRecommendationComponent.setTargetDisease(getCodeableConcept(targetDisease.getCode(), targetDisease.getName(), null));
+
+        var dateCriterion = immunizationRecommendationComponent.addDateCriterion();
+        dateCriterion.setCode(getCodeableConcept("30980-7", "Date vaccine due", null));
+        dateCriterion.setValue(date);
+
+        return immunizationRecommendation;
+    }
+
+    static DiagnosticReport getDiagnosticReport(Date date) {
+        DiagnosticReport diagnosticReport = new DiagnosticReport();
+        diagnosticReport.setId(UUID.randomUUID().toString());
+
+        DateTimeType dateTimeType = new DateTimeType();
+        dateTimeType.setValue(Utils.getFutureTime(date, 60));
+        diagnosticReport.setStatus(DiagnosticReport.DiagnosticReportStatus.FINAL);
+        diagnosticReport.setCode(FHIRUtils.getDiagnosticTestCode(SimpleDiagnosticTest.getRandomTest()));
+        diagnosticReport.setConclusion("Refer to Doctor. To be correlated with further study.");
+        return diagnosticReport;
+    }
+
     static MedicationRequest createMedicationRequest(Practitioner author,
                                                      Date date,
                                                      Medicine med,

src/main/java/in/projecteka/utils/data/ImmunizationGenerator.java

@@ -1,19 +1,24 @@
 package in.projecteka.utils.data;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
 import in.projecteka.utils.DocRequest;
 import in.projecteka.utils.data.model.Doctor;
+import in.projecteka.utils.data.model.Obs;
+import in.projecteka.utils.data.model.SimpleCondition;
 import in.projecteka.utils.data.model.Vaccine;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Composition;
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Immunization;
+import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceType;
 
 import java.nio.file.Path;
@@ -32,7 +37,7 @@ public class ImmunizationGenerator implements DocumentGenerator {
     private Properties patients;
 
     public void init() throws Exception {
-        immunizationProps = Utils.loadFromFile("/immunization.properties");
+        immunizationProps = Utils.loadFromFile("/immunization-vaccines.properties");
         doctors = Utils.loadFromFile("/practitioners.properties");
         patients = Utils.loadFromFile("/patients.properties");
     }
@@ -42,7 +47,7 @@ public void execute(DocRequest request) throws Exception {
         LocalDateTime dateTime = request.getFromDate().toInstant().atZone(ZoneId.systemDefault()).toLocalDateTime();
         for (int i = 0; i < request.getNumber(); i++) {
             Date date = Utils.getNextDate(dateTime, i);
-            Bundle bundle = createImmunizationBundle(date, request.getPatientName(), request.getHipPrefix(), request.getPatientId());
+            Bundle bundle = createImmunizationBundle(date, request.getPatientName(), request.getHipPrefix(), request.getPatientId(), fhirContext.newJsonParser());
             String encodedString = fhirContext.newJsonParser().encodeResourceToString(bundle);
             List<Bundle.BundleEntryComponent> patientEntries =
                     bundle.getEntry().stream()
@@ -60,7 +65,7 @@ public void execute(DocRequest request) throws Exception {
         }
     }
 
-    private Bundle createImmunizationBundle(Date date, String patientName, String hipPrefix, String patientId) throws Exception {
+    private Bundle createImmunizationBundle(Date date, String patientName, String hipPrefix, String patientId, IParser parser) throws Exception {
         Bundle bundle = FHIRUtils.createBundle(date, hipPrefix);
         Patient patientResource = FHIRUtils.getPatientResource(patientName, patientId, patients);
         Reference patientRef = createPatientReference(patientResource);
@@ -106,6 +111,31 @@ private Bundle createImmunizationBundle(Date date, String patientName, String hi
             FHIRUtils.addToBundleEntry(bundle, organization, true);
             immunization.setManufacturer(FHIRUtils.getReferenceToResource(organization));
 
+            //Reason reference
+            if(Utils.randomBool()) {
+                int randomReasonRefNumber = Utils.randomInt(1,2);
+                Resource reasonResource = FHIRUtils.createCondition(SimpleCondition.getRandomCondition(), date);
+
+                if(randomReasonRefNumber == 1){
+                    reasonResource = getObservation(parser);
+                }
+
+                if(randomReasonRefNumber == 2){
+                    var diagnosticReport = FHIRUtils.getDiagnosticReport(date);
+                    diagnosticReport.addResultsInterpreter(FHIRUtils.getReferenceToResource(author));
+                    reasonResource = diagnosticReport;
+                }
+
+                FHIRUtils.addToBundleEntry(bundle, reasonResource, false);
+                immunization.addReasonReference(FHIRUtils.getReferenceToResource(reasonResource));
+            }
+
+            if(Utils.randomBool()){
+                Observation observation = getObservation(parser);
+                FHIRUtils.addToBundleEntry(bundle, observation, false);
+                immunization.addReaction().setDetail(FHIRUtils.getReferenceToResource(observation));
+            }
+
             immunization.setPatient(patientRef);
             FHIRUtils.addToBundleEntry(bundle, immunization, false);
             section.getEntry().add(FHIRUtils.getReferenceToResource(immunization));
@@ -125,4 +155,10 @@ private Reference createPatientReference(Patient patientResource) {
         return patientRef;
     }
 
+    private Observation getObservation(IParser parser) {
+        Observation observation = parser.parseResource(Observation.class, Obs.getObservationResString());
+        observation.setId(UUID.randomUUID().toString());
+        return observation;
+    }
+
 }

src/main/java/in/projecteka/utils/data/OPConsultationGenerator.java

@@ -9,7 +9,10 @@
 import in.projecteka.utils.data.model.SimpleAllergy;
 import in.projecteka.utils.data.model.SimpleCondition;
 import in.projecteka.utils.data.model.SimpleDiagnosticTest;
+import in.projecteka.utils.data.model.TargetDisease;
+import in.projecteka.utils.data.model.Vaccine;
 import lombok.SneakyThrows;
+import org.apache.commons.lang3.RandomUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.AllergyIntolerance;
 import org.hl7.fhir.r4.model.Annotation;
@@ -23,6 +26,7 @@
 import org.hl7.fhir.r4.model.DiagnosticReport;
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.ImmunizationRecommendation;
 import org.hl7.fhir.r4.model.Medication;
 import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.Observation;
@@ -58,12 +62,16 @@ public class OPConsultationGenerator implements  DocumentGenerator {
     private Properties doctors;
     private Properties patients;
     private Properties medicationProps;
+    private Properties immunizationVaccineProps;
+    private Properties immunizationDiseaseProps;
 
     @Override
     public void init() throws Exception {
         doctors = Utils.loadFromFile("/practitioners.properties");
         patients = Utils.loadFromFile("/patients.properties");
         medicationProps = Utils.loadFromFile("/medications.properties");
+        immunizationDiseaseProps = Utils.loadFromFile("/immunization-diseases.properties");
+        immunizationVaccineProps = Utils.loadFromFile("/immunization-vaccines.properties");
     }
 
     @Override
@@ -137,22 +145,23 @@ private Bundle createOPConsultationBundle(Date date, String patientName, String
         Reference referenceToResource = FHIRUtils.getReferenceToResource(encounter);
         opDoc.setEncounter(referenceToResource);
 
-        generateSections(hipPrefix, jsonParser, bundle, opDoc, patientResource);
+        generateSections(hipPrefix, jsonParser, bundle, opDoc, patientResource, date);
         return bundle;
     }
 
     protected String getCompositionDocumentTitle() {
         return "OP Consultation Document";
     }
 
-    protected void generateSections(String hipPrefix, IParser jsonParser, Bundle bundle, Composition opDoc, Patient patientResource) {
+    protected void generateSections(String hipPrefix, IParser jsonParser, Bundle bundle, Composition opDoc, Patient patientResource, Date date) {
         createChiefComplaintsSection(bundle, opDoc, patientResource);
         createAllergiesSection(bundle, opDoc, patientResource, jsonParser);
         createMedicalHistorySection(bundle, opDoc, patientResource); //TODO
         createSymptomSection(bundle, opDoc, patientResource); //TODO
         createObservationSection(bundle, opDoc, patientResource, jsonParser);
         createInvestigationSection(bundle, opDoc, patientResource); //TODO
         createPrescriptionSection(bundle, opDoc, patientResource);
+        createImmunizationRecordSection(bundle, opDoc, patientResource, date);
         createDocumentsSection(bundle, opDoc, patientResource, hipPrefix);
         createProcedureSection(bundle, opDoc, patientResource, hipPrefix);
         createDiagnosticReportSection(bundle, opDoc, patientResource, jsonParser, hipPrefix);
@@ -461,6 +470,21 @@ protected void createAllergiesSection(Bundle bundle, Composition composition, Pa
         section.getEntry().add(FHIRUtils.getReferenceToResource(medicationAllergy));
     }
 
+    @SneakyThrows
+    protected void createImmunizationRecordSection(Bundle bundle, Composition composition, Patient patient, Date date) {
+        Composition.SectionComponent section = composition.addSection();
+        section.setTitle("Immunization Recommendation");
+        section.setCode(FHIRUtils.getImmunizationRecommendationSectionType());
+        var vaccineIndex = RandomUtils.nextInt(1, 11);
+        var diseaseIndex = RandomUtils.nextInt(1, 10);
+        Vaccine vaccine = Vaccine.parse((String) immunizationVaccineProps.get(String.valueOf(vaccineIndex)));
+        TargetDisease targetDisease = TargetDisease.parse((String) immunizationDiseaseProps.get(String.valueOf(diseaseIndex)));
+        ImmunizationRecommendation immunizationRecommendation = FHIRUtils.getImmunizationRecommendation(vaccine, targetDisease, date);
+        immunizationRecommendation.setPatient(FHIRUtils.getReferenceToPatient(patient));
+        FHIRUtils.addToBundleEntry(bundle, immunizationRecommendation, true);
+        section.getEntry().add(FHIRUtils.getReferenceToResource(immunizationRecommendation));
+    }
+
     @SneakyThrows
     protected void createMedicalHistorySection(Bundle bundle, Composition composition, Patient patient) {
         return;

src/main/java/in/projecteka/utils/data/model/TargetDisease.java

@@ -0,0 +1,17 @@
+package in.projecteka.utils.data.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+@Data
+@AllArgsConstructor
+public class TargetDisease {
+    String code;
+    String name;
+
+    public static TargetDisease parse(String details) {
+        String[] parts = details.split(",");
+        return new TargetDisease(parts[0].trim(), parts[1].trim());
+    }
+
+}

src/main/resources/immunization-diseases.properties

@@ -0,0 +1,9 @@
+1=1857005, Gestational rubella syndrome
+2=397430003, Diphtheria due to Corynebacterium diphtheriae
+3=14189004, Measles
+4=36989005, Mumps
+5=36653000, Rubella
+6=76902006, Tetanus
+7=709410003, Haemophilus influenzae type b infection
+8=27836007, Pertussis
+9=398102009, Acute poliomyelitis

src/main/resources/patients.properties

@@ -6,4 +6,5 @@ singhal=Navajot Singhal, female, NCC1702, navjSinghal85, navajotSinghal.1985
 mane=Sadio Mane, male, LIVNO10, sadiomane92, sadiomane.1992
 salah=Mohamed Salah, male, LIVNO11, mohamedsalah92, mohamedsalah.1992
 firmino=Roberto Firmino, male, LIVNO09, robertofirmino91, robertofirmino.1991
-david=David James, male, LIVNO14, davidjames93, davidjames.1993
+david=David James, male, LIVNO14, davidjames93, davidjames.1993
+kabir=Kabir Singh, male, RVH1012, kabirsingh99, kabirsingh.1992