fhir 1st

@@ -92,8 +92,12 @@ android {
 
     packagingOptions {
         //exclude 'lib/armeabi-v7a/libc++_shared.so' // 过滤该文件
+        exclude 'META-INF/DEPENDENCIES'
+        exclude 'META-INF/LICENSE'
+        exclude 'META-INF/LICENSE.txt'
+        exclude 'META-INF/NOTICE'
+        exclude 'META-INF/NOTICE.txt'
     }
-
 }
 
 String getDate() {
@@ -148,4 +152,7 @@ dependencies {
     compileOnly files('syslibs/framework.jar')
 
 //    implementation("com.google.android.fhir:engine:1.0.0")
+//    implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:5.4.0'
+    implementation 'ca.uhn.hapi.fhir:hapi-fhir-android:5.5.1'
+    implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:5.5.1'
 }

+package com.sw.laryngoscope.model;
+
+public class PatientAddressModel {
+    private String city;
+    private String state;
+    private String country;
+
+    public PatientAddressModel(String city,String state,String country){
+        this.city = city;
+        this.state = state;
+        this.country = country;
+    }
+
+    public String getFullAddress(){
+        return  city + " City" + "\n" + state + "," + country;
+    }
+}

+package com.sw.laryngoscope.model;
+
+import android.text.format.DateFormat;
+
+import com.sw.laryngoscope.model.observation.BloodPressureObservationModel;
+import com.sw.laryngoscope.model.observation.ObservationModel;
+import com.sw.laryngoscope.model.observation.ObservationType;
+
+import org.hl7.fhir.r4.model.Enumerations;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+
+public class PatientModel {
+    private String patientID;
+    private String name;
+    private Date birthDate;
+    private Enumerations.AdministrativeGender gender;
+    private PatientAddressModel address;
+
+    private HashMap<ObservationType, ObservationModel> observationReadings;
+    private HashMap<ObservationType, Boolean> isMonitored;
+    private ArrayList<BloodPressureObservationModel> latestBPReadings;
+
+    /**
+     * Constructor
+     * @param patientID Unique patient ID from the FHIR server
+     * @param name name of the patient
+     */
+    public PatientModel(String patientID, String name, Date birthDate, Enumerations.AdministrativeGender gender, PatientAddressModel address) {
+        this.patientID = patientID;
+        this.name = name;
+        this.birthDate = birthDate;
+        this.gender = gender;
+        this.address = address;
+        observationReadings = new HashMap<>();
+        isMonitored = new HashMap<>();
+        latestBPReadings = new ArrayList<>();
+        initialiseMonitoredObservations();
+    }
+
+    public String getPatientID() {
+        return patientID;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getBirthDate() {
+        return DateFormat.format("yyyy.MM.dd", birthDate).toString();
+    }
+
+    public String getGender() {
+        return gender.toString();
+    }
+
+    public PatientAddressModel getAddress() {
+        return address;
+    }
+
+    public void setObservation(ObservationType type, ObservationModel observation) {
+        observationReadings.put(type, observation);
+    }
+
+    public ObservationModel getObservationReading(ObservationType type) {
+        return observationReadings.get(type);
+    }
+
+    public void monitorObservation(ObservationType type, Boolean check) {
+        isMonitored.put(type, check);
+    }
+
+    public Boolean isObservationMonitored(ObservationType type) {
+        return isMonitored.get(type);
+    }
+
+    private void initialiseMonitoredObservations() {
+        for (ObservationType type: ObservationType.values()) {
+            monitorObservation(type, false);
+        }
+    }
+
+    public void addLatestBPReadings(ArrayList<BloodPressureObservationModel> readings) {
+        latestBPReadings = readings;
+    }
+
+    public ArrayList<BloodPressureObservationModel> getLatestBPReadings() {
+        return latestBPReadings;
+    }
+
+}

+package com.sw.laryngoscope.model.observation;
+
+import org.hl7.fhir.r4.model.Observation;
+
+public class BloodPressureObservationModel extends ObservationModel{
+    public BloodPressureObservationModel(Observation observation) {
+        super(observation);
+    }
+
+    @Override
+    public String getValue() {
+        return observation.getValueQuantity().getValue().toString();
+    }
+
+    public String getSystolic() { return observation.getComponent().get(1).getValueQuantity().getValue().toString(); }
+
+    public String getDiastolic() { return observation.getComponent().get(0).getValueQuantity().getValue().toString(); }
+
+    @Override
+    public String getUnit() {
+        return observation.getComponent().get(0).getValueQuantity().getUnit();
+    }
+
+    @Override
+    public String getDateTime() { return observation.getEffectiveDateTimeType().asStringValue(); }
+}

+package com.sw.laryngoscope.model.observation;
+
+import org.hl7.fhir.r4.model.Observation;
+
+public class CholesterolObservationModel extends ObservationModel{
+    public CholesterolObservationModel(Observation observation) {
+        super(observation);
+    }
+
+    @Override
+    public String getValue() {
+        return observation.getValueQuantity().getValue().toString();
+    }
+
+    @Override
+    public String getUnit() {
+        return observation.getValueQuantity().getUnit();
+    }
+
+    @Override
+    public String getDateTime() { return observation.getEffectiveDateTimeType().asStringValue(); }
+}

+package com.sw.laryngoscope.model.observation;
+
+import org.hl7.fhir.r4.model.Observation;
+
+public class ObservationModel {
+    protected Observation observation;
+
+    ObservationModel(Observation observation) {
+        this.observation = observation;
+    }
+
+    /**
+     * Return the Observation value
+     * @return double
+     */
+    public abstract String getValue();
+
+    /**
+     * Get the unit type for the Observation
+     */
+    public abstract String getUnit();
+
+    /**
+     * Get the effective DateTime
+     * @return effective date time
+     */
+    public abstract String getDateTime();
+}

+package com.sw.laryngoscope.model.observation;
+
+public enum ObservationType {
+    CHOLESTEROL, BLOOD_PRESSURE;
+    private String observationCode;
+
+    static {
+        CHOLESTEROL.observationCode = "2093-3";
+        BLOOD_PRESSURE.observationCode = "55284-4";
+    }
+
+    public String getObservationCode() {
+        return observationCode;
+    }
+}

+package com.sw.laryngoscope.service;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+
+public class FhirService {
+    protected IGenericClient client;
+
+    public FhirService(){
+        FhirContext ctx = FhirContext.forR4();
+
+        //Server url
+        String BASE_URL = "https://hapi.fhir.org/" + "baseR4";
+        client = ctx.newRestfulGenericClient(BASE_URL);
+        // increase timeout
+        ctx.getRestfulClientFactory().setConnectTimeout(60*1000);
+        ctx.getRestfulClientFactory().setSocketTimeout(60*1000);
+
+    }
+}

+package com.sw.laryngoscope.service.repository;
+
+import com.sw.laryngoscope.model.observation.BloodPressureObservationModel;
+import com.sw.laryngoscope.model.observation.CholesterolObservationModel;
+import com.sw.laryngoscope.model.observation.ObservationModel;
+import com.sw.laryngoscope.model.observation.ObservationType;
+import com.sw.laryngoscope.service.FhirService;
+
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Observation;
+
+import java.util.ArrayList;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+
+public class ObservationRepositoryFactory extends FhirService {
+    private IGenericClient client = super.client;
+
+    private Observation getObservation(String patientId,String code){
+        Bundle bundle = client.search()
+                .forResource(Observation.class)
+                .where(Observation.PATIENT.hasId(patientId))
+                .and(Observation.CODE.exactly().code(code))
+                .sort().descending(Observation.DATE)
+                .returnBundle(Bundle.class)
+                .execute();
+
+        return (Observation) (bundle.getEntry().get(0).getResource());
+    }
+
+    public ObservationModel getObservationModel(String patientId, ObservationType type){
+        switch (type){
+            case CHOLESTEROL:
+                return createCholesterolModel(patientId);
+            case BLOOD_PRESSURE:
+                return createBloodPressureModel(patientId);
+            default:
+                throw new IllegalArgumentException("Observation type invalid");
+        }
+    }
+
+    private CholesterolObservationModel createCholesterolModel(String patientId){
+        return new CholesterolObservationModel(getObservation(patientId, ObservationType.CHOLESTEROL.getObservationCode()));
+    }
+
+    private BloodPressureObservationModel createBloodPressureModel(String patientId) {
+        return new BloodPressureObservationModel(getObservation(patientId, ObservationType.BLOOD_PRESSURE.getObservationCode()));
+    }
+
+    /**
+     * Returns an ArrayList of n latest readings
+     * @param patientId patient id
+     * @param code observation code
+     * @param n latest n readings
+     * @return ArrayList of readings
+     */
+    private ArrayList<Observation> getLatestObservationReadings(String patientId, String code, int n) {
+        ArrayList<Observation> latestReadings = new ArrayList<>();
+        Bundle bundle = client.search()
+                .forResource(Observation.class)
+                .where(Observation.PATIENT.hasId(patientId))
+                .and(Observation.CODE.exactly().code(code))
+                .sort().descending(Observation.DATE)
+                .returnBundle(Bundle.class)
+                .execute();
+
+        for (int i = 0; i < Math.min(n, bundle.getTotal()); i++) {
+            latestReadings.add((Observation) (bundle.getEntry().get(i)).getResource());
+        }
+        return latestReadings;
+    }
+
+    public ArrayList<BloodPressureObservationModel> getLatestBloodPressureReadings(String patientId, int n) {
+        ArrayList<BloodPressureObservationModel> bpReadings = new ArrayList<>();
+        for (Observation observation: getLatestObservationReadings(patientId, ObservationType.BLOOD_PRESSURE.getObservationCode(), n)) {
+            bpReadings.add(new BloodPressureObservationModel(observation));
+        }
+        return bpReadings;
+    }
+}

+package com.sw.laryngoscope.service.repository;
+
+import com.sw.laryngoscope.model.PatientAddressModel;
+import com.sw.laryngoscope.model.PatientModel;
+import com.sw.laryngoscope.service.FhirService;
+
+import org.hl7.fhir.r4.model.Bundle;
+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.Patient;
+
+import java.util.ArrayList;
+import java.util.Date;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.gclient.TokenClientParam;
+
+public class PatientRepository extends FhirService {
+    private String practitionerId;
+    private IGenericClient client = super.client;
+
+    public PatientRepository(String practitionerId) {
+        this.practitionerId = practitionerId;
+    }
+    /**
+     * Get all patients treated by the practitioner
+     * @return ArrayList of patients
+     */
+    public ArrayList<PatientModel> getAllPatients() {
+        // store patient references
+        ArrayList<String> patientReferences = new ArrayList<>();
+        // store patients
+        ArrayList<PatientModel> patientModels = new ArrayList<>();
+
+        // search for all encounters with the practitioner identifier
+        Bundle bundle = client.search().forResource(Encounter.class)
+                .where(new TokenClientParam("participant.identifier")
+                        .exactly().systemAndCode("http://hl7.org/fhir/sid/us-npi", practitionerId))
+                .returnBundle(Bundle.class)
+                .count(100) // not too many searches to prevent overloading the server
+                .execute();
+
+        // get all patient references
+        bundle.getEntry().forEach((entry) -> patientReferences.add(
+                (((Encounter) entry.getResource()).getSubject()).getReference()));
+
+        Bundle patientBundle;
+
+        // go through each patient reference and get the patient
+        for (String id: patientReferences) {
+            patientBundle = client.search()
+                    .forResource(Patient.class)
+                    .where(Patient.RES_ID.exactly().identifier(id))
+                    .returnBundle(Bundle.class)
+                    .execute();
+
+            Patient patient = (Patient) (patientBundle.getEntry().get(0)).getResource();
+
+            // human name documentation: https://www.hl7.org/fhir/DSTU2/datatypes-definitions.html#HumanName
+            HumanName humanName = patient.getName().get(0);
+            // prefix ie. Mr/ Mrs, given name ie. first & middle names, family ie. surname
+            String patientName = humanName.getPrefixAsSingleString() + " "
+                    + humanName.getGivenAsSingleString() + " " + humanName.getFamily();
+
+            // get birth date
+            Date birthDate = patient.getBirthDate();
+
+            // get gender
+            Enumerations.AdministrativeGender gender = patient.getGender();
+
+            // get address
+            PatientAddressModel patientAddress = new PatientAddressModel(patient.getAddress().get(0).getCity(),
+                    patient.getAddress().get(0).getState(), patient.getAddress().get(0).getCountry());
+
+            patientModels.add(new PatientModel(id, patientName, birthDate, gender, patientAddress));
+        }
+
+        return patientModels;
+    }
+}