Addeed Practitioner & Medication Request Resources to Patient export.…

… Created MockEncounterRepository.java for testing purposes.
FEMR · Mar 2, 2025 · 4e8ce1b · 4e8ce1b
1 parent 775a240
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Showing 3 changed files with 190 additions and 6 deletions.
diff --git a/app/femr/business/services/system/FhirExportService.java b/app/femr/business/services/system/FhirExportService.java
@@ -5,13 +5,17 @@
 import ca.uhn.fhir.util.BundleBuilder;
 import com.google.inject.Inject;
 import femr.business.services.core.IFhirExportService;
+import femr.data.daos.core.IEncounterRepository;
 import femr.data.daos.core.IPatientRepository;
-import femr.data.models.core.IPatient;
+import femr.data.daos.core.IPrescriptionRepository;
+import femr.data.daos.core.IUserRepository;
+import femr.data.daos.system.UserRepository;
+import femr.data.models.core.*;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.r5.model.*;
 
-import java.util.ArrayList;
-import java.util.Collections;
+import java.util.*;
+
 
 /**
  * Converts between fEMR data models and FHIR models.
@@ -21,10 +25,14 @@ public class FhirExportService implements IFhirExportService {
     private static final FhirContext fhirContext = FhirContext.forR5();
 
     IPatientRepository patientRepository;
+    IEncounterRepository encounterRepository;
+    IPrescriptionRepository prescriptionRepository;
 
     @Inject
-    public FhirExportService(IPatientRepository patientRepository) {
+    public FhirExportService(IPatientRepository patientRepository, IEncounterRepository encounterRepository, IPrescriptionRepository prescriptionRepository) {
         this.patientRepository = patientRepository;
+        this.encounterRepository = encounterRepository;
+        this.prescriptionRepository = prescriptionRepository;
     }
 
     private BundleBuilder buildPatientBundle(int patientId) {
@@ -85,13 +93,93 @@ private void addPatientData(BundleBuilder bundleBuilder, int patientId) {
             fhirPatient.setAddress(Collections.singletonList(address));
         }
 
+        // Gather all encounters
+        List<? extends IPatientEncounter> encounters = encounterRepository.retrievePatientEncountersByPatientIdAsc(patientId);
+
+        // To ensure we don't add duplicate practitioners
+        Set<Integer> addedUserIds = new HashSet<>();
+
+        // Similarly, but for medication IDs
+        Set<Integer> addedMedIds = new HashSet<>();
+
+        for (IPatientEncounter encounter : encounters) {
+            List<? extends IPatientPrescription> prescriptions = prescriptionRepository.retrieveUnreplacedPrescriptionsByEncounterId(encounter.getId());
+
+            for (IPatientPrescription prescription : prescriptions) {
+                addMedicationRequestForPrescription(bundleBuilder, prescription, patientId, addedMedIds);
+            }
+
+            IUser nurse = encounter.getNurse();
+            IUser physician = encounter.getDoctor();
+            IUser pharmacist = encounter.getPharmacist();
+
+            // If nurse is present and not yet added, add them
+            if (nurse != null && !addedUserIds.contains(nurse.getId())) {
+                addPractitionerData(bundleBuilder, nurse, "Nurse");
+                addedUserIds.add(nurse.getId());
+            }
+
+            // If physician is present and not yet added, add them
+            if (physician != null && !addedUserIds.contains(physician.getId())) {
+                addPractitionerData(bundleBuilder, physician, "Physician");
+                addedUserIds.add(physician.getId());
+            }
+
+            // If pharmacist is present and not yet added, add them
+            if (pharmacist != null && !addedUserIds.contains(pharmacist.getId())) {
+                addPractitionerData(bundleBuilder, pharmacist, "Pharmacist");
+                addedUserIds.add(pharmacist.getId());
+            }
+        }
+
         // city is omitted as it is where the patient is treated and not
         // a property of the patient itself. So it will go with the encounter model.
 
         // TODO: add photo
 
     }
 
+    private void addMedicationRequestForPrescription(BundleBuilder bundleBuilder, IPatientPrescription prescription, int patientId, Set<Integer> addedMedIds) {
+        IMedication domainMedication = prescription.getMedication();
+
+        if (domainMedication == null) {
+            // If there's no medication info, we can't build the FHIR resources
+            return;
+        }
+
+        // Only add Medication resource if we haven't already.
+        int medId = domainMedication.getId();
+        if (!addedMedIds.contains(medId)) {
+            // Create a Medication resource
+            Medication fhirMedication = new Medication();
+            // Ex. "Medication-123"
+            fhirMedication.setId("Medication-" + medId);
+            fhirMedication.setCode(new CodeableConcept().setText(domainMedication.getName()));
+
+            // Add to bundle
+            IBase medEntry = bundleBuilder.addEntry();
+            bundleBuilder.addToEntry(medEntry, "resource", fhirMedication);
+
+            // Mark this medId as added
+            addedMedIds.add(medId);
+        }
+
+        // Now we create a MedicationRequest referencing that Medication
+        MedicationRequest fhirMedRequest = new MedicationRequest();
+        // Ex. "MedicationRequest-13"
+        fhirMedRequest.setId("MedicationRequest-" + prescription.getId());
+        // Assign references
+        CodeableReference medCodeableRef = new CodeableReference();
+        medCodeableRef.setReference(new Reference("Medication-" + medId));
+        fhirMedRequest.setMedication(medCodeableRef);
+
+        // Linking to patient
+        fhirMedRequest.setSubject(new Reference("Patient/" + patientId));
+
+        IBase requestEntry = bundleBuilder.addEntry();
+        bundleBuilder.addToEntry(requestEntry, "resource", fhirMedRequest);
+    }
+
     /**
      * @param patientSex either male or female, or some other string, or null.
      *                   Hopefully that doesn't happen.
@@ -111,6 +199,36 @@ private static Enumerations.AdministrativeGender getAdministrativeGender(String
         }
     }
 
+    /**
+     * Helper method for creating Practitioner resources out of IUsers & adding them to a Bundle.
+     * @param prefix  A string which describes the Practitioner's specific role. Physician, Nurse, Pharmacist...
+     */
+    private void addPractitionerData(BundleBuilder bundleBuilder, IUser user, String prefix) {
+        // Creating Practitioner resource and assigning it a unique ID:
+        Practitioner fhirPractitioner = new Practitioner();
+        // Ex. User 42 (Nurse)
+        fhirPractitioner.setId("User " + user.getId() + " (" + prefix + ")");
+
+        // Populating name
+        HumanName name = new HumanName();
+        name.setFamily(user.getLastName());
+        name.addGiven(user.getFirstName());
+        name.addPrefix(prefix);
+        fhirPractitioner.setName(Collections.singletonList(name));
+
+        // If the practitioner has an email, add it as a ContactPoint.
+        if (user.getEmail() != null) {
+            ContactPoint emailContact = new ContactPoint();
+            emailContact.setSystem(ContactPoint.ContactPointSystem.EMAIL);
+            emailContact.setValue(user.getEmail());
+            fhirPractitioner.setTelecom(Collections.singletonList(emailContact));
+        }
+
+        // Add to bundle
+        IBase entry = bundleBuilder.addEntry();
+        bundleBuilder.addToEntry(entry, "resource", fhirPractitioner);
+    }
+
     private String toJson(BundleBuilder bundleBuilder) {
         // Create a parser
         IParser parser = fhirContext.newJsonParser();

diff --git a/test/femr/business/services/TestFhirExportService.java b/test/femr/business/services/TestFhirExportService.java
@@ -1,8 +1,13 @@
 package femr.business.services;
 
 import femr.business.services.system.FhirExportService;
+import femr.data.daos.core.IEncounterRepository;
 import femr.data.daos.core.IPatientRepository;
+import femr.data.daos.core.IPrescriptionRepository;
+import femr.data.daos.system.EncounterRepository;
+import mock.femr.data.daos.MockEncounterRepository;
 import mock.femr.data.daos.MockPatientRepository;
+import mock.femr.data.daos.MockPrescriptionRepository;
 import mock.femr.data.models.MockPatient;
 import org.junit.Test;
 import org.json.*;
@@ -16,19 +21,23 @@ public class TestFhirExportService {
     @Test
     public void smokeTestBlankDocument() {
         IPatientRepository patientRepository = new MockPatientRepository();
-        FhirExportService export = new FhirExportService(patientRepository);
+        IEncounterRepository encounterRepository = new MockEncounterRepository();
+        IPrescriptionRepository prescriptionRepository = new MockPrescriptionRepository();
+        FhirExportService export = new FhirExportService(patientRepository, encounterRepository, prescriptionRepository);
 
         System.out.println(export.exportPatient(1));
     }
 
     @Test
     public void nonStandardSex() {
         MockPatientRepository patientRepository = new MockPatientRepository();
+        IEncounterRepository encounterRepository = new MockEncounterRepository();
+        IPrescriptionRepository prescriptionRepository = new MockPrescriptionRepository();
         patientRepository.mockPatient = new MockPatient();
         patientRepository.mockPatient.setSex("SOMETHING NOT M or F");
 
 
-        FhirExportService export = new FhirExportService(patientRepository);
+        FhirExportService export = new FhirExportService(patientRepository, encounterRepository, prescriptionRepository);
 
         String jsonString = export.exportPatient(1);
 

diff --git a/test/mock/femr/data/daos/MockEncounterRepository.java b/test/mock/femr/data/daos/MockEncounterRepository.java
@@ -0,0 +1,57 @@
+package mock.femr.data.daos;
+
+import femr.data.daos.core.IEncounterRepository;
+import femr.data.models.core.IPatientEncounter;
+import org.joda.time.DateTime;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class MockEncounterRepository implements IEncounterRepository {
+    public List<IPatientEncounter> mockEncounters = new ArrayList<>();
+
+    @Override
+    public IPatientEncounter createPatientEncounter(int patientID, DateTime date, int userId, Integer patientAgeClassificationId, Integer tripId, String languageCode) {
+        return null;
+    }
+
+    @Override
+    public IPatientEncounter deletePatientEncounter(int encounterId, String reason, int userId) {
+        return null;
+    }
+
+    @Override
+    public List<? extends IPatientEncounter> retrievePatientEncounters(DateTime from, DateTime to, Integer tripId) {
+        return null;
+    }
+
+    @Override
+    public IPatientEncounter retrievePatientEncounterById(int id) {
+        return null;
+    }
+
+    @Override
+    public List<? extends IPatientEncounter> retrievePatientEncountersByPatientIdAsc(int patientId) {
+        return mockEncounters;
+    }
+
+    @Override
+    public List<? extends IPatientEncounter> retrievePatientEncountersByPatientIdDesc(int patientId) {
+        return mockEncounters;
+    }
+
+    @Override
+    public IPatientEncounter savePatientEncounterMedicalCheckin(int encounterId, int userId, DateTime date) {
+        return null;
+    }
+
+    @Override
+    public IPatientEncounter savePatientEncounterPharmacyCheckin(int encounterId, int userId, DateTime date) {
+        return null;
+    }
+
+    @Override
+    public IPatientEncounter savePatientEncounterDiabetesScreening(int encounterId, int userId, DateTime date, Boolean isScreened) {
+        return null;
+    }
+}