update with recent changes

api/pom.xml

@@ -47,5 +47,10 @@
             <scope>provided</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.json</groupId>
+            <artifactId>json</artifactId>
+        </dependency>
+
     </dependencies>
 </project>

api/src/main/java/org/openmrs/module/ohricore/OHRICoreActivator.java

@@ -11,16 +11,14 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-
 import org.openmrs.api.context.Context;
 import org.openmrs.api.db.ContextDAO;
 import org.openmrs.module.BaseModuleActivator;
 import org.openmrs.module.ohricore.task.QueryLabResultsTask;
+import org.openmrs.module.ohricore.task.UpdateLuceneIndexesTask;
 import org.openmrs.scheduler.SchedulerService;
 import org.openmrs.scheduler.TaskDefinition;
 
-import org.springframework.core.task.TaskExecutor;
-
 /**
  * This class contains the logic that is run every time this module is either started or shutdown
  */
@@ -36,9 +34,6 @@ public OHRICoreActivator() {
 	 * @see #started()
 	 */
 	public void started() {
-		ContextDAO contextDAO = (ContextDAO) Context.getRegisteredComponents(ContextDAO.class).get(0);
-		// Refresh Lucene indexes
-		contextDAO.updateSearchIndex();
 		log.info("Started OHRICore");
 	}
 
@@ -57,7 +52,14 @@ public void contextRefreshed() {
 		String taskClassName = QueryLabResultsTask.class.getName();
 		String description = "Query Lab Results Task - DISI";
 
+		String namibiaLuceneIndexUpdateTaskName = "Update Namibia Lucene Indexes";
+		Long namibiaLuceneRepeatInterval = 31536000L; //second
+		String namibiaLuceneTaskClassName = UpdateLuceneIndexesTask.class.getName();
+		String namibiaLuceneDescription = "Update Namibia Lucene Indexes task";
+
 		addTask(taskName, taskClassName, repeatInterval, description);
+		addTask(namibiaLuceneIndexUpdateTaskName, namibiaLuceneTaskClassName, namibiaLuceneRepeatInterval,
+		    namibiaLuceneDescription);
 	}
 
 	@Override
@@ -67,7 +69,13 @@ public void stopped() {
 
 	@Override
 	public void willRefreshContext() {
+
 		super.willRefreshContext();
+		/*
+		System.out.println("Refresh Lucene indexes...");
+		ContextDAO contextDAO = Context.getRegisteredComponents(ContextDAO.class).get(0);
+		contextDAO.updateSearchIndex();// Refresh Lucene indexes
+		*/
 	}
 
 	@Override

api/src/main/java/org/openmrs/module/ohricore/OhriCoreConstant.java

@@ -7,6 +7,8 @@ public final class OhriCoreConstant {
 
 	public static final String MUTEX_QUERY_LABRESULTS = "QUERY LAB RESULTS MUTEX";
 
+	public static final String MUTEX_UPDATE_LUCENE_INDEXES = "UPDATE LUCENE INDEXES MUTEX";
+
 	public static final String FHIR_SANDBOX_URL = "https://oh-route.gicsandbox.org/fhir";
 
 	public static final String FHIR_COMPLETED_OHRI_TASKS = "/Task?owner=Organization/101283&status=completed&_count=999";
@@ -67,10 +69,22 @@ public final class OhriCoreConstant {
 
 	public static final String OHRI_ENCOUNTER_SYSTEM = "OHRI_ENCOUNTER_UUID";
 
+	public static final String NATIONAL_ID_SYSTEM = "http://ohie.org/National_ID";
+
+	public static final String HEALTH_ID_SYSTEM = "http://ohie.org/Health_ID";
+
+	public static final String HEALTH_FACILITY_ID_SYSTEM = "http://ohie.org/Health_Facility";
+
 	public static final String GP_PARENT_SERVER_URL = "ohricore.fhir.sandbox.url";
 
 	public static final String GP_PARENT_SERVER_USERNAME = "";
 
+	public static final String GP_MPI_SERVER_URL = "ohricore.mpi.namibia.server.url";
+
+	public static final String GP_MPI_CLIENT_ID = "ohricore.mpi.namibia.server.clientid";
+
+	public static final String GP_MPI_CLIENT_SECRET = "ohricore.mpi.namibia.server.clientsecret";
+
 	public static final String CONCEPT_MAPPING_CIEL = "CIEL";
 
 	public static final String CONCEPT_MAPPING_LOINC = "LOINC";

api/src/main/java/org/openmrs/module/ohricore/Token.java

@@ -0,0 +1,70 @@
+package org.openmrs.module.ohricore;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+/**
+ * @author smallGod date: 30/11/2022
+ */
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class Token {
+
+	@JsonProperty("access_token")
+	private String accessToken;
+
+	@JsonProperty("id_token")
+	private String idToken;
+
+	@JsonProperty("token_type")
+	private String tokenType;
+
+	@JsonProperty("expires_in")
+	private String expiresIn;
+
+	@JsonProperty("refresh_token")
+	private String refreshToken;
+
+	public Token() {
+	}
+
+	public String getAccessToken() {
+		return accessToken;
+	}
+
+	public void setAccessToken(String accessToken) {
+		this.accessToken = accessToken;
+	}
+
+	public String getIdToken() {
+		return idToken;
+	}
+
+	public void setIdToken(String idToken) {
+		this.idToken = idToken;
+	}
+
+	public String getTokenType() {
+		return tokenType;
+	}
+
+	public void setTokenType(String tokenType) {
+		this.tokenType = tokenType;
+	}
+
+	public String getExpiresIn() {
+		return expiresIn;
+	}
+
+	public void setExpiresIn(String expiresIn) {
+		this.expiresIn = expiresIn;
+	}
+
+	public String getRefreshToken() {
+		return refreshToken;
+	}
+
+	public void setRefreshToken(String refreshToken) {
+		this.refreshToken = refreshToken;
+	}
+}

api/src/main/java/org/openmrs/module/ohricore/aop/EncounterInterceptorAdvice.java

@@ -53,7 +53,7 @@ public void afterReturning(Object returnValue, Method methodInvoked, Object[] me
 
                         List<OHRIComputedConcept> ohriComputedConcepts = OHRIComputedConceptsFactory.getComputedConcepts(encounter);
                         for (OHRIComputedConcept computedConcept : ohriComputedConcepts) {
-                            computedConcept.computeAndPersistObs(encounter);
+                            //computedConcept.computeAndPersistObs(encounter); //Disable computed obs here: SG - Sept.11.2022
                         }
 
                         //TODO: Re-factor this code into a separate neat file

api/src/main/java/org/openmrs/module/ohricore/aop/PatientInterceptorAdvice.java

@@ -0,0 +1,111 @@
+package org.openmrs.module.ohricore.aop;
+
+import org.hl7.fhir.r4.model.Address;
+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.Patient;
+import org.hl7.fhir.r4.model.StringType;
+import org.openmrs.Location;
+import org.openmrs.PatientIdentifier;
+import org.openmrs.PatientIdentifierType;
+import org.openmrs.PersonAddress;
+import org.openmrs.api.context.Context;
+import org.openmrs.module.ohricore.engine.ConceptComputeTrigger;
+import org.openmrs.module.ohricore.fhir.FhirClient;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.aop.AfterReturningAdvice;
+
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * @author smallGod date: 30/11/2022
+ */
+public class PatientInterceptorAdvice implements AfterReturningAdvice {
+
+	private static final Logger log = LoggerFactory.getLogger(PatientInterceptorAdvice.class);
+
+	@Override
+    public void afterReturning(Object returnValue, Method methodInvoked, Object[] methodArgs, Object target)
+            throws Throwable {
+
+        System.out.println("After returning Patient Save in EMR");
+        try {
+            if (methodInvoked.getName().equals(ConceptComputeTrigger.SAVE_PATIENT)) {
+
+                System.out.println("Save Patient method()...");
+
+                for (Object arg : methodArgs) {
+                    if (arg instanceof org.openmrs.Patient) {
+
+                        org.openmrs.Patient patient = (org.openmrs.Patient) arg;
+                        Patient newPatient = new Patient();
+
+                        Enumerations.AdministrativeGender patientGender;
+                        String gender = patient.getGender();
+                        switch (gender) {
+                            case "M":
+                                patientGender = Enumerations.AdministrativeGender.MALE;
+                                break;
+                            case "F":
+                                patientGender = Enumerations.AdministrativeGender.FEMALE;
+                                break;
+                            default:
+                                patientGender = Enumerations.AdministrativeGender.UNKNOWN;
+                                break;
+                        }
+//check if health id exists on MPI (send if doesn't exist) otherwise don't
+// -> add global property for health ID
+// expose endpoint for search
+                        HumanName name = new HumanName();
+                        name.setFamily(patient.getFamilyName());
+                        name.setGiven(Collections.singletonList(new StringType(patient.getGivenName())));
+                        name.setUse(HumanName.NameUse.USUAL);
+
+                        Set<PersonAddress> personAddresses = patient.getAddresses();
+                        List<Address> addresses = new ArrayList<>();
+                        for (PersonAddress personAddress : personAddresses) {
+
+                            Address address = new Address();
+                            address.setUse(Address.AddressUse.HOME);
+                            address.setCountry(personAddress.getCountry());
+                            address.setCity(personAddress.getAddress1());
+                            address.setState(personAddress.getCountry());
+                            addresses.add(new Address());
+                        }
+
+                        List<PatientIdentifier> patientIds = patient.getActiveIdentifiers();
+                        List<Identifier> identifiers = new ArrayList<>();
+                        for (PatientIdentifier id : patientIds) {
+                            Identifier identifier = new Identifier();
+                            identifier.setSystem("urn:oid:3.9");//TODO: don't hardcode
+                            identifier.setValue(id.getIdentifier());
+                            identifiers.add(identifier);
+                        }
+
+                        newPatient.setIdentifier(identifiers);
+                        newPatient.setGender(patientGender);
+                        newPatient.setName(Collections.singletonList(name));
+                        newPatient.setBirthDate(patient.getBirthdate());
+                        newPatient.setAddress(addresses);
+
+                        //String response = FhirClient.postMPIRequest(newPatient);
+                        List<PatientIdentifier> newPatientIds = FhirClient.postPatient(newPatient);
+                        for (PatientIdentifier patientId : newPatientIds) {
+                            patientId.setPatient(patient);
+                            Context.getPatientService().savePatientIdentifier(patientId);
+                        }
+                    }
+                }
+            }
+        } catch (Exception e) {
+            log.error("An un-expected Error occurred while registering a patient: " + e.getMessage());
+            e.printStackTrace();
+        }
+    }
+}

api/src/main/java/org/openmrs/module/ohricore/api/MPIClientPatient.java

@@ -0,0 +1,11 @@
+package org.openmrs.module.ohricore.api;
+
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import org.hl7.fhir.r4.model.Patient;
+
+/**
+ * @author smallGod
+ */
+
+@ResourceDef(name = "MPIPatient", profile = "http://hl7.org/fhir/StructureDefinition/Patient")
+public class MPIClientPatient extends Patient {}

api/src/main/java/org/openmrs/module/ohricore/api/MPIClientService.java

@@ -0,0 +1,14 @@
+package org.openmrs.module.ohricore.api;
+
+import org.hl7.fhir.r4.model.Patient;
+import org.openmrs.module.fhir2.api.FhirService;
+
+import javax.annotation.Nonnull;
+
+/**
+ * @author smallGod
+ */
+public interface MPIClientService extends FhirService<MPIClientPatient> {
+
+	MPIClientPatient getByHealthId(@Nonnull String healthId);
+}

api/src/main/java/org/openmrs/module/ohricore/api/impl/MPIClientServiceImpl.java

@@ -0,0 +1,45 @@
+package org.openmrs.module.ohricore.api.impl;
+
+import org.openmrs.module.fhir2.api.dao.FhirDao;
+import org.openmrs.module.fhir2.api.impl.BaseFhirService;
+import org.openmrs.module.ohricore.api.MPIClientPatient;
+import org.openmrs.module.ohricore.api.MPIClientService;
+import org.openmrs.module.ohricore.api.translator.MPIClientPatientTranslator;
+import org.openmrs.module.ohricore.fhir.FhirClient;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.annotation.Nonnull;
+
+/**
+ * @author smallGod
+ */
+
+@Component
+@Transactional
+public class MPIClientServiceImpl extends BaseFhirService<MPIClientPatient, org.openmrs.Patient> implements MPIClientService {
+
+	@Autowired
+	private MPIClientPatientTranslator translator;
+
+	@Override
+	protected FhirDao<org.openmrs.Patient> getDao() {
+		return null;
+	}
+
+	@Override
+	public MPIClientPatient getByHealthId(@Nonnull String healthId) {
+		org.openmrs.Patient patient = FhirClient.getPatient(healthId);
+		return getTranslator().toFhirResource(patient);
+	}
+
+	@Override
+	public MPIClientPatientTranslator getTranslator() {
+		return translator;
+	}
+
+	public void setTranslator(MPIClientPatientTranslator translator) {
+		this.translator = translator;
+	}
+}