Refactor

src/main/java/net/ihe/gazelle/servlet/ChHapiFhirServer.java → src/main/java/net/ihe/gazelle/adapter/servlet/ChHapiFhirServer.java

-package net.ihe.gazelle.servlet;
+package net.ihe.gazelle.adapter.servlet;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -14,8 +14,8 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import net.ihe.gazelle.interceptor.LegacyLoggingInterceptor;
-import net.ihe.gazelle.provider.ChPatientResourceProvider;
+import net.ihe.gazelle.business.interceptor.LegacyLoggingInterceptor;
+import net.ihe.gazelle.business.provider.ChPatientResourceProvider;
 
 /**
  * This servlet is the actual FHIR server itself

src/main/java/net/ihe/gazelle/adapter/servlet/IheHapiFhirServer.java

+package net.ihe.gazelle.adapter.servlet;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
+import ca.uhn.fhir.narrative.INarrativeGenerator;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import net.ihe.gazelle.business.provider.IhePatientResourceProvider;
+import javax.servlet.annotation.WebServlet;
+import java.util.ArrayList;
+import java.util.List;
+
+
+@WebServlet(urlPatterns = {"/fhir_ihe/*"}, displayName = "FHIR Server IHE")
+public class IheHapiFhirServer extends RestfulServer {
+
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Constructor
+     */
+    public IheHapiFhirServer() {
+        super(FhirContext.forR4());
+    }
+
+    /**
+     * This method is called automatically when the
+     * servlet is initializing.
+     */
+    @Override
+    public void initialize() {
+        /*
+         * Two resource providers are defined. Each one handles a specific
+         * type of resource.
+         */
+        List<IResourceProvider> providers = new ArrayList<IResourceProvider>();
+        providers.add(new IhePatientResourceProvider());
+        setResourceProviders(providers);
+
+        //creating an interceptor to log in console an error occurring
+        LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
+        loggingInterceptor.setLoggerName("test.accesslog");
+        loggingInterceptor.setMessageFormat("Source[$remoteAddr] Operation[${operationType}"
+                + "${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");
+
+        registerInterceptor(loggingInterceptor);
+
+        //creating an interceptor for special exception to dump the stack trace in the logs.
+        ExceptionHandlingInterceptor exceptionInterceptor = new ExceptionHandlingInterceptor();
+        exceptionInterceptor.setReturnStackTracesForExceptionTypes(InternalErrorException.class, NullPointerException.class);
+        registerInterceptor(exceptionInterceptor);
+
+        /*
+         * Use a narrative generator. This is a completely optional step,
+         * but can be useful as it causes HAPI to generate narratives for
+         * resources which don't otherwise have one.
+         */
+        INarrativeGenerator narrativeGen = new DefaultThymeleafNarrativeGenerator();
+        getFhirContext().setNarrativeGenerator(narrativeGen);
+
+    }
+
+}

src/main/java/net/ihe/gazelle/interceptor/LegacyLoggingInterceptor.java → src/main/java/net/ihe/gazelle/business/interceptor/LegacyLoggingInterceptor.java

-package net.ihe.gazelle.interceptor;
+package net.ihe.gazelle.business.interceptor;
 
 import java.io.IOException;
 

src/main/java/net/ihe/gazelle/interceptor/NewLoggingInterceptor.java → src/main/java/net/ihe/gazelle/business/interceptor/NewLoggingInterceptor.java

-package net.ihe.gazelle.interceptor;
+package net.ihe.gazelle.business.interceptor;
 
 import ca.uhn.fhir.interceptor.api.Hook;
 import ca.uhn.fhir.interceptor.api.Pointcut;

src/main/java/net/ihe/gazelle/provider/ChPatientResourceProvider.java → src/main/java/net/ihe/gazelle/business/provider/ChPatientResourceProvider.java

-package net.ihe.gazelle.provider;
+package net.ihe.gazelle.business.provider;
 
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -181,7 +181,7 @@ public class ChPatientResourceProvider implements IResourceProvider {
 	@Operation(name="$ihe-pix", idempotent = true)
 	public Parameters findPatientsByIdentifier(@OperationParam(name = "sourceIdentifier") TokenParam sourceIdentifier, 
 			@OperationParam(name = "targetSystem") StringAndListParam targetSystem) 
-					throws PatientResourceProviderException, ForbiddenOperationException, ResourceNotFoundException { 
+					throws PatientResourceProviderException, ForbiddenOperationException, ResourceNotFoundException {
 
 		Parameters results = new Parameters();
 
@@ -461,10 +461,10 @@ public class ChPatientResourceProvider implements IResourceProvider {
 	/**
 	 * Method used to generate a Parameter Component representing an error in the the Fhir Resource Model
 	 * Permits to display the error.
-	 *  
+	 *
 	 * @param errorType : the code of the error as a String.
 	 * Will be translated as an OperationOutcome.IssueType
-	 * @return A ParametersParameterComponent representing the http error as a Fhir resource 
+	 * @return A ParametersParameterComponent representing the http error as a Fhir resource
 	 */
 	private ParametersParameterComponent generateErrorReturn(String errorCode) {
 		OperationOutcome error = new OperationOutcome();

src/main/java/net/ihe/gazelle/business/provider/IhePatientResourceProvider.java

+package net.ihe.gazelle.business.provider;
+
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.rest.param.StringOrListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import net.ihe.gazelle.app.patientregistryapi.application.SearchCrossReferenceException;
+import net.ihe.gazelle.app.patientregistryapi.business.EntityIdentifier;
+import net.ihe.gazelle.app.patientregistryapi.business.PatientAliases;
+import net.ihe.gazelle.app.patientregistryapi.business.PersonName;
+import net.ihe.gazelle.app.patientregistryxrefsearchclient.adapter.XRefSearchClient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.Address.AddressUse;
+import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.r4.model.HumanName.NameUse;
+import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.*;
+
+/**
+ * This is a resource provider which stores Patient resources in memory using a HashMap. This is obviously not a production-ready solution for many
+ * reasons,
+ * but it is useful to help illustrate how to build a fully-functional server.
+ */
+public class IhePatientResourceProvider implements IResourceProvider {
+    /**
+     * The getResourceType method comes from IResourceProvider, and must be overridden to indicate what type of resource this provider supplies.
+     */
+    @Override
+    public Class<? extends IBaseResource> getResourceType() {
+        return Patient.class;
+    }
+
+    private static final Logger patientLogger = LoggerFactory.getLogger(IhePatientResourceProvider.class);
+
+    /**
+     * This map has a resource ID as a key, and each key maps to a Deque list containing all versions of the resource with that ID.
+     */
+    private Map<Long, Deque<Patient>> myIdToPatientVersions = new HashMap<Long, Deque<Patient>>();
+
+
+    /**
+     * Search method for a Patient using the source identifier required parameter
+     * and an optional list of target system
+     *
+     * @param sourceIdentifierParam : the source identifier of the patient, should be formatted "urn:oid:x.x.x.x.x.x.x.x.x.x|value"
+     * @param targetSystemParam:    the target System(s) we want to find the Patient on, should be formatted "urn:oid:x.x.x.x.x.x.x.x.x.x,urn:oid:x
+     *                              .x.x.x
+     *                              .x.x.x.x.x.x,"
+     * @return a Parameters element composed of a list of target identifier for every Patient found, and an url to the Patient in the server.
+     */
+    @Operation(name = "$ihe-pix", idempotent = true)
+    public Parameters findPatientsByIdentifier(@OperationParam(name = "sourceIdentifier", min = 1, max = 1) TokenParam sourceIdentifierParam,
+                                               @OperationParam(name = "targetSystem") StringAndListParam targetSystemParam) throws PatientResourceProviderException, ForbiddenOperationException, ResourceNotFoundException {
+
+        EntityIdentifier sourceIdentifier = createEntityIdentifierFromSourceIdentifier(sourceIdentifierParam);
+        List<String> targetSystemList = createTargetSystemListFromParam(targetSystemParam);
+
+
+        Parameters results = new Parameters();
+
+        PatientAliases response;
+
+        int log = 0;
+
+        try {
+            URL url = new URL("https://qualification.ihe-europe.net/patient-registry/CrossReferenceService/xref-processing-service?wsdl");
+            XRefSearchClient searchClient = new XRefSearchClient(url);
+            patientLogger.info(targetSystemList.toString());
+
+            response = searchClient.search(sourceIdentifier, targetSystemList);
+            patientLogger.info(Integer.toString(log++));
+
+
+        } catch (MalformedURLException e) {
+            throw new PatientResourceProviderException("Could not find target url for Patient Registry, The given URL might be wrong.", e);
+        } catch (SearchCrossReferenceException e) {
+
+            //results.addParameter(generateErrorReturn("code-invalid"));
+            return results;
+            //throw new ResourceNotFoundException("Could not find Patient in Patient Registry");
+        }
+
+        patientLogger.info(Integer.toString(log++));
+
+        if (response.getMembers().size() == 0) {
+          //  results.addParameter(generateErrorReturn("notfound"));
+            return results;
+            //throw new ResourceNotFoundException("No crossReferenced Patient found.");
+        }
+
+        patientLogger.info("Number of patents found : " + response.getMembers().size());
+
+        for (net.ihe.gazelle.app.patientregistryapi.business.Patient pat : response.getMembers()) {
+
+//            long id = myNextId++;
+
+            patientLogger.info(pat.getNames().get(0).getFamily());
+
+            Patient translated = this.translatePatientToR4(pat);
+
+            for (EntityIdentifier entity : pat.getIdentifiers()) {
+                patientLogger.info(Integer.toString(log++));
+
+                Identifier r4Identifier = new Identifier();
+                r4Identifier.setSystem(entity.getSystemIdentifier());
+                r4Identifier.setValue(entity.getValue());
+                translated.addIdentifier(r4Identifier);
+
+                ParametersParameterComponent alias = new ParametersParameterComponent();
+                alias.setName("target Identifier");
+                alias.setValue(r4Identifier);
+                results.addParameter(alias);
+
+            }
+
+            ParametersParameterComponent targetId = new ParametersParameterComponent();
+            targetId.setName("targetId");
+            Reference ref = new Reference();
+//            targetId.setValue(ref);
+
+            results.addParameter(targetId);
+            patientLogger.info(Integer.toString(log++));
+
+          //  translated.setId(Long.toString(id));
+            LinkedList<Patient> listToAdd = new LinkedList<>();
+            listToAdd.add(translated);
+        //    myIdToPatientVersions.put(id, listToAdd);
+
+        }
+     //   results.setId(Long.toString(myNextId++));
+        patientLogger.info(Integer.toString(log++));
+        return results;
+    }
+
+    @Search
+    public List<Patient> findPatientsUsingArbitraryCriteria() {
+        LinkedList<Patient> retVal = new LinkedList<Patient>();
+
+        for (Deque<Patient> nextPatientList : myIdToPatientVersions.values()) {
+            Patient nextPatient = nextPatientList.getLast();
+            retVal.add(nextPatient);
+        }
+
+        return retVal;
+    }
+
+
+    /**
+     * Private Method called to translate a Patient between the model in Patient Registry to the fhir model
+     * We need to translate a Patient in order to have it in the list of Patient contained in the fhir server
+     * To later have access to it (through an URL given when searched)
+     *
+     * @param patReg : the Patient in the Patient Registry Model
+     * @return the same Patient translated in the FHIR r4 model.
+     */
+    private Patient translatePatientToR4(net.ihe.gazelle.app.patientregistryapi.business.Patient patReg) {
+
+        Patient translatedPatient = new Patient();
+
+        translatedPatient.setActive(patReg.isActive());
+        List<HumanName> nameList = new ArrayList<>();
+        for (PersonName pName : patReg.getNames()) {
+            HumanName name = new HumanName();
+            name.setFamily(pName.getFamily());
+            List<StringType> givenNames = new ArrayList<>();
+            for (String given : pName.getGivens()) {
+                givenNames.add(new StringType(given));
+            }
+            name.setGiven(givenNames);
+            name.addPrefix(pName.getPrefix());
+            name.addSuffix(pName.getSuffix());
+            name.setUse(NameUse.fromCode(pName.getUse()));
+            nameList.add(name);
+        }
+        translatedPatient.setName(nameList);
+        translatedPatient.setGender(AdministrativeGender.fromCode(patReg.getGender().toString().toLowerCase()));
+        List<Address> addresses = new ArrayList<>();
+        for (net.ihe.gazelle.app.patientregistryapi.business.Address pAddress : patReg.getAddresses()) {
+            Address address = new Address();
+            address.setUse(AddressUse.fromCode(pAddress.getUse().toString().toLowerCase()));
+            address.setCity(pAddress.getCity());
+            address.setCountry(pAddress.getCountryIso3());
+            address.setPostalCode(pAddress.getPostalCode());
+            address.setState(pAddress.getState());
+            for (String addressLine : pAddress.getLines())
+                address.addLine(addressLine);
+            addresses.add(address);
+        }
+        translatedPatient.setAddress(addresses);
+        translatedPatient.setBirthDate(patReg.getDateOfBirth());
+
+        return translatedPatient;
+
+    }
+
+    private EntityIdentifier createEntityIdentifierFromSourceIdentifier(TokenParam sourceIdentifier) {
+        if (sourceIdentifier == null) {
+            throw new InvalidRequestException("Invalid request : sourceIdentifier is a mandatory parameter");
+        }
+        String sourceIdentifierSystem = sourceIdentifier.getSystem();
+        String sourceIdentifierValue = sourceIdentifier.getValue();
+        if (sourceIdentifierSystem == null) {
+            throw new InvalidRequestException("Invalid request : sourceIdentifier is wrong");
+        }
+        if (sourceIdentifierValue == null) {
+            throw new InvalidRequestException("Invalid request : sourceIdentifier is wrong");
+        }
+        if (sourceIdentifierSystem.isBlank() || sourceIdentifierValue.isBlank()) {
+            throw new InvalidRequestException("Invalid request : sourceIdentifier is wrong");
+        }
+        patientLogger.info("Searching Patient with given sourceIdentifier: " + sourceIdentifier);
+
+        EntityIdentifier wellFormedEntityIdentifier = new EntityIdentifier();
+        if (sourceIdentifierSystem.contains("urn:oid:")) {
+            wellFormedEntityIdentifier.setSystemIdentifier(sourceIdentifierSystem.replace("urn:oid:", ""));
+            wellFormedEntityIdentifier.setType("ISO");
+            wellFormedEntityIdentifier.setValue(sourceIdentifierValue);
+        } else if (sourceIdentifierSystem.contains("http")) {
+            wellFormedEntityIdentifier.setSystemIdentifier(sourceIdentifierSystem);
+            wellFormedEntityIdentifier.setType("ISO");
+            wellFormedEntityIdentifier.setValue(sourceIdentifierValue);
+        } else {
+            throw new InvalidRequestException("Invalid request : sourceIdentifier system is malformed");
+        }
+        return wellFormedEntityIdentifier;
+    }
+
+    private List<String> createTargetSystemListFromParam(StringAndListParam targetSystemParam) {
+        List<String> targetSystemList = new ArrayList<>();
+        if (targetSystemParam != null) {
+            for (StringOrListParam listParam : targetSystemParam.getValuesAsQueryTokens()) {
+                List<StringParam> queryStrings = listParam.getValuesAsQueryTokens();
+                for (StringParam singleParam : queryStrings) {
+                    String singleParamValue = singleParam.getValue();
+                    if (singleParamValue.contains("urn:oid:")) {
+                        singleParamValue = singleParamValue.replace("urn:oid:", "");
+                    }
+                    if (singleParamValue.equals("")) {
+                        throw new InvalidRequestException("Invalid request : targetDomain can not be empty");
+                    }
+                    targetSystemList.add(singleParamValue);
+                }
+            }
+        }
+        return targetSystemList;
+    }
+
+}

src/main/java/net/ihe/gazelle/provider/PatientResourceProviderException.java → src/main/java/net/ihe/gazelle/business/provider/PatientResourceProviderException.java

-package net.ihe.gazelle.provider;
+package net.ihe.gazelle.business.provider;
 
 public class PatientResourceProviderException extends Exception {
 	

src/main/java/net/ihe/gazelle/provider/IhePatientResourceProvider.java

-package net.ihe.gazelle.provider;
-
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Address;
-import org.hl7.fhir.r4.model.Address.AddressUse;
-import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.r4.model.HumanName;
-import org.hl7.fhir.r4.model.HumanName.NameUse;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Identifier;
-import org.hl7.fhir.r4.model.InstantType;
-import org.hl7.fhir.r4.model.OperationOutcome;
-import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
-import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.StringType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.parser.DataFormatException;
-import ca.uhn.fhir.rest.annotation.Create;
-import ca.uhn.fhir.rest.annotation.IdParam;
-import ca.uhn.fhir.rest.annotation.Operation;
-import ca.uhn.fhir.rest.annotation.OperationParam;
-import ca.uhn.fhir.rest.annotation.Read;
-import ca.uhn.fhir.rest.annotation.RequiredParam;
-import ca.uhn.fhir.rest.annotation.ResourceParam;
-import ca.uhn.fhir.rest.annotation.Search;
-import ca.uhn.fhir.rest.annotation.Update;
-import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.rest.param.StringAndListParam;
-import ca.uhn.fhir.rest.param.StringOrListParam;
-import ca.uhn.fhir.rest.param.StringParam;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
-import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
-import net.ihe.gazelle.app.patientregistryapi.application.SearchCrossReferenceException;
-import net.ihe.gazelle.app.patientregistryapi.business.EntityIdentifier;
-import net.ihe.gazelle.app.patientregistryapi.business.PatientAliases;
-import net.ihe.gazelle.app.patientregistryapi.business.PersonName;
-import net.ihe.gazelle.app.patientregistryxrefsearchclient.adapter.XRefSearchClient;
-
-/**
- * This is a resource provider which stores Patient resources in memory using a HashMap. This is obviously not a production-ready solution for many reasons,
- * but it is useful to help illustrate how to build a fully-functional server.
- */
-public class IhePatientResourceProvider implements IResourceProvider {
-
-	private static final Logger patientLogger = LoggerFactory.getLogger(IhePatientResourceProvider.class);
-
-	/**
-	 * This map has a resource ID as a key, and each key maps to a Deque list containing all versions of the resource with that ID.
-	 */
-	private Map<Long, Deque<Patient>> myIdToPatientVersions = new HashMap<Long, Deque<Patient>>();
-
-	/**
-	 * This is used to generate new IDs
-	 */
-	private long myNextId = 1;
-
-	/**
-	 * Constructor, which pre-populates the provider with one resource instance.
-	 */
-	public IhePatientResourceProvider() {
-		long resourceId = myNextId++;
-
-		Patient patient = new Patient();
-		patient.setId(Long.toString(resourceId));
-		patient.addIdentifier();
-		patient.getIdentifier().get(0).setSystem("urn:oid");
-		patient.getIdentifier().get(0).setValue("00002");
-		patient.addName().setFamily("Test");
-		patient.getName().get(0).addGiven("PatientOne");
-		patient.setGender(AdministrativeGender.FEMALE);
-
-		LinkedList<Patient> list = new LinkedList<Patient>();
-		list.add(patient);
-
-
-		myIdToPatientVersions.put(resourceId, list);
-
-	}
-
-	/**
-	 * Stores a new version of the patient in memory so that it can be retrieved later.
-	 *
-	 * @param thePatient The patient resource to store
-	 * @param theId      The ID of the patient to retrieve
-	 */
-	private void addNewVersion(Patient thePatient, Long theId) {
-		if (!myIdToPatientVersions.containsKey(theId)) {
-			myIdToPatientVersions.put(theId, new LinkedList<Patient>());
-		}
-
-		thePatient.getMeta().setLastUpdatedElement(InstantType.withCurrentTime());
-
-		Deque<Patient> existingVersions = myIdToPatientVersions.get(theId);
-
-		// We just use the current number of versions as the next version number
-		String newVersion = Integer.toString(existingVersions.size());
-
-		// Create an ID with the new version and assign it back to the resource
-		IdType newId = new IdType("Patient", Long.toString(theId), newVersion);
-		thePatient.setId(newId);
-
-		existingVersions.add(thePatient);
-	}
-
-	/**
-	 * The "@Create" annotation indicates that this method implements "create=type", which adds a
-	 * new instance of a resource to the server.
-	 */
-	@Create()
-	public MethodOutcome createPatient(@ResourceParam Patient thePatient) {
-		validateResource(thePatient);
-
-		// Here we are just generating IDs sequentially
-		long id = myNextId++;
-
-		addNewVersion(thePatient, id);
-
-		// Let the caller know the ID of the newly created resource
-		return new MethodOutcome(new IdType(id));
-	}
-
-	/**
-	 * The "@Search" annotation indicates that this method supports the search operation. You may have many different method annotated with this annotation, to support many different search criteria.
-	 * This example searches by family name.
-	 *
-	 * @param theFamilyName This operation takes one parameter which is the search criteria. It is annotated with the "@Required" annotation. This annotation takes one argument, a string containing the name of
-	 *                      the search criteria. The datatype here is StringDt, but there are other possible parameter types depending on the specific search criteria.
-	 * @return This method returns a list of Patients. This list may contain multiple matching resources, or it may also be empty.
-	 */
-	@Search()
-	public List<Patient> findPatientsByName(@RequiredParam(name = Patient.SP_FAMILY) StringType theFamilyName) {
-		LinkedList<Patient> retVal = new LinkedList<Patient>();
-
-		/*
-		 * Look for all patients matching the name
-		 */
-		for (Deque<Patient> nextPatientList : myIdToPatientVersions.values()) {
-			Patient nextPatient = nextPatientList.getLast();
-			NAMELOOP:
-				for (HumanName nextName : nextPatient.getName()) {
-					String nextFamily = nextName.getFamily();
-					if (theFamilyName.equals(nextFamily)) {
-						retVal.add(nextPatient);
-						break NAMELOOP;
-					}
-				}
-		}
-
-		return retVal;
-	}
-
-	/**
-	 * Search method for a Patient using the source identifier required parameter
-	 * and an optional list of target system
-	 * 
-	 * @param sourceIdentifier : the source identifier of the patient, should be formated "urn:oid:x.x.x.x.x.x.x.x.x.x|value"
-	 * @param targetSystem: the target System(s) we want to find the Patient on, should be formated "urn:oid:x.x.x.x.x.x.x.x.x.x,urn:oid:x.x.x.x.x.x.x.x.x.x,"
-	 * 
-	 * @return a Parameters element composed of a list of target identifier for every Patient found, and an url to the Patient in the server.
-	 */
-	@Operation(name="$ihe-pix", idempotent = true)
-	public Parameters findPatientsByIdentifier(@OperationParam(name = "sourceIdentifier",min = 1,max = 1) TokenParam sourceIdentifier,
-			@OperationParam(name = "targetSystem") StringAndListParam targetSystem) throws PatientResourceProviderException, ForbiddenOperationException, ResourceNotFoundException {
-
-		Parameters results = new Parameters();
-
-		patientLogger.info("Searching Patient " + sourceIdentifier);
-
-		PatientAliases response = new PatientAliases();
-
-		int log = 0;
-		if (sourceIdentifier ==null){
-			throw new InvalidRequestException("Missing parameter");
-		}
-		try {
-			URL url = new URL("https://qualification.ihe-europe.net/patient-registry/CrossReferenceService/xref-processing-service?wsdl");
-
-			XRefSearchClient searchClient = new XRefSearchClient(url);
-
-			EntityIdentifier wellFormedEntityIdentifier = new EntityIdentifier();
-
-
-			if (sourceIdentifier.getSystem().contains("urn:oid:")) {
-				wellFormedEntityIdentifier.setSystemIdentifier(sourceIdentifier.getSystem().replace("urn:oid:", ""));
-				wellFormedEntityIdentifier.setType("ISO");
-			}
-
-			wellFormedEntityIdentifier.setValue(sourceIdentifier.getValue());
-			patientLogger.info(wellFormedEntityIdentifier.getValue());
-
-			List<String> listTargetSystem = new ArrayList<String>();
-			if (null != targetSystem) {
-				for (StringOrListParam nextList : targetSystem.getValuesAsQueryTokens()) {
-					List<StringParam> queryStrings = nextList.getValuesAsQueryTokens();
-					for (StringParam singleParam : queryStrings) {
-						if (singleParam.getValue().equals("")) {
-							results.addParameter(generateErrorReturn("code-invalid"));
-							return results;
-							//throw new ForbiddenOperationException("Won't accept empty targetSystem");
-						}
-						listTargetSystem.add(singleParam.getValue());
-					}
-				}
-			}
-
-
-			patientLogger.info(listTargetSystem.toString());
-
-			response = searchClient.search(wellFormedEntityIdentifier, listTargetSystem);
-			patientLogger.info(Integer.toString(log++));
-
-
-		} catch (MalformedURLException e) {
-			throw new PatientResourceProviderException("Could not find target url for Patient Registry, The given URL might be wrong.", e);
-		} catch (SearchCrossReferenceException e) {
-
-			results.addParameter(generateErrorReturn("code-invalid"));
-			return results;
-			//throw new ResourceNotFoundException("Could not find Patient in Patient Registry");
-		}
-
-		patientLogger.info(Integer.toString(log++));
-
-		if ( response.getMembers().size() == 0 ) {
-			results.addParameter(generateErrorReturn("notfound"));
-			return results;
-			//throw new ResourceNotFoundException("No crossReferenced Patient found.");
-		}
-
-		patientLogger.info("Number of patents found : " + response.getMembers().size());
-
-		for (net.ihe.gazelle.app.patientregistryapi.business.Patient pat : response.getMembers()) {
-
-			long id = myNextId++;
-
-			patientLogger.info(pat.getNames().get(0).getFamily());
-
-			Patient translated = this.translatePatientToR4(pat);
-
-			for (EntityIdentifier entity : pat.getIdentifiers()) {
-				patientLogger.info(Integer.toString(log++));
-
-				Identifier r4Identifier = new Identifier();
-				r4Identifier.setSystem(entity.getSystemIdentifier());
-				r4Identifier.setValue(entity.getValue());
-				translated.addIdentifier(r4Identifier);
-
-				ParametersParameterComponent alias = new ParametersParameterComponent();
-				alias.setName("target Identifier");
-				alias.setValue(r4Identifier);
-				results.addParameter(alias);
-
-			}
-
-			ParametersParameterComponent targetId = new ParametersParameterComponent();
-			targetId.setName("targetId");
-			Reference ref = new Reference();
-			ref.setReference("pixm_fhir_server/fhir/Patient/" + id);
-			targetId.setValue(ref);
-
-			results.addParameter(targetId);
-			patientLogger.info(Integer.toString(log++));
-
-			translated.setId(Long.toString(id));
-			LinkedList<Patient> listToAdd = new LinkedList<>();
-			listToAdd.add(translated);
-			myIdToPatientVersions.put(id, listToAdd);
-
-		}
-		results.setId(Long.toString(myNextId++));
-		patientLogger.info(Integer.toString(log++));
-		return results;
-	}
-
-	@Search
-	public List<Patient> findPatientsUsingArbitraryCriteria() {
-		LinkedList<Patient> retVal = new LinkedList<Patient>();
-
-		for (Deque<Patient> nextPatientList : myIdToPatientVersions.values()) {
-			Patient nextPatient = nextPatientList.getLast();
-			retVal.add(nextPatient);
-		}
-
-		return retVal;
-	}
-
-
-	/**
-	 * The getResourceType method comes from IResourceProvider, and must be overridden to indicate what type of resource this provider supplies.
-	 */
-	@Override
-	public Class<? extends IBaseResource> getResourceType() {
-		return Patient.class;
-	}
-
-	/**
-	 * This is the "read" operation. The "@Read" annotation indicates that this method supports the read and/or vread operation.
-	 * <p>
-	 * Read operations take a single parameter annotated with the {@link IdParam} paramater, and should return a single resource instance.
-	 * </p>
-	 *
-	 * @param theId The read operation takes one parameter, which must be of type IdDt and must be annotated with the "@Read.IdParam" annotation.
-	 * @return Returns a resource matching this identifier, or null if none exists.
-	 */
-	@Read(version = true)
-	public Patient readPatient(@IdParam IdType theId) {
-
-		Deque<Patient> retVal;
-		patientLogger.warn("ReadingPatient " + theId.getIdPart());
-		try {
-			retVal = myIdToPatientVersions.get(theId.getIdPartAsLong());
-		} catch (NumberFormatException e) {
-			/*
-			 * If we can't parse the ID as a long, it's not valid so this is an unknown resource
-			 */
-			throw new ResourceNotFoundException(theId);
-		}
-
-		if (retVal == null) {
-			throw new ResourceNotFoundException(theId);
-		}
-		if (theId.hasVersionIdPart() == false) {
-			return retVal.getLast();
-		} else {
-			patientLogger.info("Patient found");
-			for (Patient nextVersion : retVal) {
-				String nextVersionId = nextVersion.getIdElement().getVersionIdPart();
-				if (theId.getVersionIdPart().equals(nextVersionId)) {
-					return nextVersion;
-				}
-			}
-			patientLogger.warn("Could not find ressource");
-			// No matching version
-			throw new ResourceNotFoundException("Unknown version: " + theId.getValue());
-		}
-
-	}
-
-	/**
-	 * The "@Update" annotation indicates that this method supports replacing an existing
-	 * resource (by ID) with a new instance of that resource.
-	 *
-	 * @param theId      This is the ID of the patient to update
-	 * @param thePatient This is the actual resource to save
-	 * @return This method returns a "MethodOutcome"
-	 */
-	@Update()
-	public MethodOutcome updatePatient(@IdParam IdType theId, @ResourceParam Patient thePatient) {
-		validateResource(thePatient);
-
-		Long id;
-		try {
-			id = theId.getIdPartAsLong();
-		} catch (DataFormatException e) {
-			throw new InvalidRequestException("Invalid ID " + theId.getValue() + " - Must be numeric");
-		}
-
-		/*
-		 * Throw an exception (HTTP 404) if the ID is not known
-		 */
-		if (!myIdToPatientVersions.containsKey(id)) {
-			throw new ResourceNotFoundException(theId);
-		}
-
-		addNewVersion(thePatient, id);
-
-		return new MethodOutcome();
-	}
-
-	/**
-	 * This method just provides simple business validation for resources we are storing.
-	 *
-	 * @param thePatient The patient to validate
-	 */
-	private void validateResource(Patient thePatient) {
-		/*
-		 * Our server will have a rule that patients must have a family name or we will reject them
-		 */
-		if (thePatient.getNameFirstRep().getFamily().isEmpty()) {
-			OperationOutcome outcome = new OperationOutcome();
-			outcome.addIssue().setSeverity(IssueSeverity.FATAL).setDiagnostics("No family name provided, Patient resources must have at least one family name.");
-			throw new UnprocessableEntityException(FhirContext.forDstu3(), outcome);
-		}
-	}
-
-	/**
-	 * Private Method called to translate a Patient between the model in Patient Registry to the fhir model
-	 * We need to translate a Patient in order to have it in the list of Patient contained in the fhir server
-	 * To later have access to it (through an URL given when searched)
-	 * 
-	 * @param patReg : the Patient in the Patient Registry Model
-	 * @return the same Patient translated in the FHIR r4 model.
-	 */
-	private Patient translatePatientToR4(net.ihe.gazelle.app.patientregistryapi.business.Patient patReg) {
-
-		Patient translatedPatient = new Patient();
-
-		translatedPatient.setActive(patReg.isActive());
-		List<HumanName> nameList = new ArrayList<>();
-		for (PersonName pName : patReg.getNames()) { 
-			HumanName name = new HumanName();
-			name.setFamily(pName.getFamily());
-			List<StringType> givenNames = new ArrayList<>();
-			for (String given : pName.getGivens()) {
-				givenNames.add(new StringType(given));
-			}
-			name.setGiven(givenNames);
-			name.addPrefix(pName.getPrefix());
-			name.addSuffix(pName.getSuffix());
-			name.setUse(NameUse.fromCode(pName.getUse()));
-			nameList.add(name);
-		}
-		translatedPatient.setName(nameList);
-		translatedPatient.setGender(AdministrativeGender.fromCode(patReg.getGender().toString().toLowerCase()));
-		List<Address> addresses = new ArrayList<>();
-		for (net.ihe.gazelle.app.patientregistryapi.business.Address pAddress : patReg.getAddresses()) {
-			Address address = new Address();
-			address.setUse(AddressUse.fromCode(pAddress.getUse().toString().toLowerCase()));
-			address.setCity(pAddress.getCity());
-			address.setCountry(pAddress.getCountryIso3());
-			address.setPostalCode(pAddress.getPostalCode());
-			address.setState(pAddress.getState());
-			for(String addressLine : pAddress.getLines()) 
-				address.addLine(addressLine);	
-			addresses.add(address);
-		}
-		translatedPatient.setAddress(addresses);
-		translatedPatient.setBirthDate(patReg.getDateOfBirth());
-
-		return translatedPatient;
-
-	}
-
-	/**
-	 * Method used to generate a Parameter Component representing an error in the the Fhir Resource Model
-	 * Permits to display the error.
-	 *  
-	 * @param errorType : the code of the error as a String.
-	 * Will be translated as an OperationOutcome.IssueType
-	 * @return A ParametersParameterComponent representing the http error as a Fhir resource 
-	 */
-	private ParametersParameterComponent generateErrorReturn(String errorType) {
-		OperationOutcome error = new OperationOutcome();
-		OperationOutcomeIssueComponent issue = new OperationOutcomeIssueComponent();
-		issue.setCode(OperationOutcome.IssueType.fromCode(errorType));
-		error.addIssue(issue);
-		ParametersParameterComponent errorReturned = new ParametersParameterComponent();
-		errorReturned.setResource(error);
-		return errorReturned;
-	}
-
-
-}

src/main/java/net/ihe/gazelle/servlet/IheHapiFhirServer.java

-package net.ihe.gazelle.servlet;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.servlet.annotation.WebServlet;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
-import ca.uhn.fhir.narrative.INarrativeGenerator;
-import ca.uhn.fhir.rest.server.IResourceProvider;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import net.ihe.gazelle.interceptor.LegacyLoggingInterceptor;
-import net.ihe.gazelle.provider.IhePatientResourceProvider;
-
-/**
- * This servlet is the actual FHIR server itself
- */
-@WebServlet(urlPatterns= {"/fhir_ihe/*"}, displayName="FHIR Server IHE")
-public class IheHapiFhirServer extends RestfulServer {
-
-	private static final long serialVersionUID = 1L;
-
-	/**
-	 * Constructor
-	 */
-	public IheHapiFhirServer() {
-		super(FhirContext.forR4()); // This is an R4 server
-	}
-	
-	/**
-	 * This method is called automatically when the
-	 * servlet is initializing.
-	 */
-	@Override
-	public void initialize() {
-		/*
-		 * Two resource providers are defined. Each one handles a specific
-		 * type of resource.
-		 */
-		List<IResourceProvider> providers = new ArrayList<IResourceProvider>();
-		providers.add(new IhePatientResourceProvider());
-		setResourceProviders(providers);
-		
-		//creating an interceptor to log in console an error occurring
-		LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
-		loggingInterceptor.setLoggerName("test.accesslog");
-		loggingInterceptor.setMessageFormat("Source[$remoteAddr] Operation[${operationType}"
-				+ "${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}]");
-		
-		registerInterceptor(loggingInterceptor);
-		
-		//creating an interceptor for special excpetion to dump the stack trace in the logs.
-		ExceptionHandlingInterceptor exceptionInterceptor = new ExceptionHandlingInterceptor();
-		exceptionInterceptor.setReturnStackTracesForExceptionTypes(InternalErrorException.class, NullPointerException.class);		
-		registerInterceptor(exceptionInterceptor);
-
-		/*
-		 * Use a narrative generator. This is a completely optional step, 
-		 * but can be useful as it causes HAPI to generate narratives for
-		 * resources which don't otherwise have one.
-		 */
-		INarrativeGenerator narrativeGen = new DefaultThymeleafNarrativeGenerator();
-		getFhirContext().setNarrativeGenerator(narrativeGen);
-		
-	}
-
-}

src/test/java/net/ihe/gazelle/provider/ProviderTestClass.java

 package net.ihe.gazelle.provider;
 
+import net.ihe.gazelle.business.provider.IhePatientResourceProvider;
+import net.ihe.gazelle.business.provider.PatientResourceProviderException;
 import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.StringType;
 import org.junit.Assert;
 import org.junit.jupiter.api.Test;
 
-import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.param.StringAndListParam;
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
-import net.ihe.gazelle.provider.IhePatientResourceProvider;
-import net.ihe.gazelle.provider.PatientResourceProviderException;
 
 public class ProviderTestClass {
 	
 	public static final IhePatientResourceProvider provider = new IhePatientResourceProvider();
 	
-	@Test
-	public void createPatientTest() {
-		Patient pat = new Patient();
-		MethodOutcome ret = provider.createPatient(pat);
-		Assert.assertNotNull(ret);
-	}
-	
+//	@Test
+//	public void createPatientTest() {
+//		Patient pat = new Patient();
+//		MethodOutcome ret = provider.createPatient(pat);
+//		Assert.assertNotNull(ret);
+//	}
 	
 	
-	@Test
-	public void findPatientsByNameTest() {
-		StringType param = new StringType("WALTERS");
-		Assert.assertNotNull(provider.findPatientsByName(param));
-	}
 	
+//	@Test
+//	public void findPatientsByNameTest() {
+//		StringType param = new StringType("WALTERS");
+//		Assert.assertNotNull(provider.findPatientsByName(param));
+//	}
+//
 	@Test
 	public void findPatientsByIdentifierTest() {
 		TokenParam sourceIdentifier = new TokenParam();
@@ -60,14 +57,14 @@ public class ProviderTestClass {
 		Assert.assertNotNull(provider.findPatientsUsingArbitraryCriteria());
 	}
 	
-	@Test
-	public void readPatientTest() {
-		IdType param = new IdType();
-		param.setId("3");
-		
-		Assert.assertNotNull(provider.readPatient(param));
-	}
-	
+//	@Test
+//	public void readPatientTest() {
+//		IdType param = new IdType();
+//		param.setId("3");
+//
+//		Assert.assertNotNull(provider.readPatient(param));
+//	}
+//
 	@Test
 	public void updatePatientTest() {
 		IdType idParam = new IdType();