Add java doc and fix bug

src/main/java/net/ihe/gazelle/adapter/preferences/Namespaces.java

@@ -12,14 +12,16 @@ public enum Namespaces {
 
     /**
      * Default constructor for the class. Defines the value of the value in the JNDI context. This aims to be used by the Preferences Module.
-     * @param value     value of the value in the JNDI context.
+     *
+     * @param value value of the value in the JNDI context.
      */
-    Namespaces(String value){
+    Namespaces(String value) {
         this.value = value;
     }
 
     /**
      * Getter for the value property.
+     *
      * @return the value of the value property.
      */
     public String getValue() {

src/main/java/net/ihe/gazelle/adapter/preferences/OperationalPreferencesPIXm.java

@@ -11,7 +11,7 @@ public class OperationalPreferencesPIXm implements OperationalPreferencesClientA
     @Override
     public Map<String, List<String>> wantedMandatoryPreferences() {
         Map<String, List<String>> mandatoryPreferences = new HashMap<>();
-        List<String> deploymentPreferences = new ArrayList<>() ;
+        List<String> deploymentPreferences = new ArrayList<>();
 
         deploymentPreferences.add(Preferences.XREF_PATREG.toString());
 

src/main/java/net/ihe/gazelle/adapter/preferences/Preferences.java

 package net.ihe.gazelle.adapter.preferences;
 
 public enum Preferences {
-    XREF_PATREG(Namespaces.DEPLOYMENT,"xrefpatientregistry.url"),
-    PATIENT_PATREG(Namespaces.DEPLOYMENT,"patientregistry.url");
+    XREF_PATREG(Namespaces.DEPLOYMENT, "xrefpatientregistry.url"),
+    PATIENT_PATREG(Namespaces.DEPLOYMENT, "patientregistry.url");
 
     private Namespaces namespace;
     private String key;
@@ -10,16 +10,18 @@ public enum Preferences {
     /**
      * Default constructor for the class. Defines the value of the Preference's key. It can then be used throughout the application to retrieve the
      * preference value.
-     * @param namespace     value of the namespace where the Preference is defined.
-     * @param key           value of the Preference's key.
+     *
+     * @param namespace value of the namespace where the Preference is defined.
+     * @param key       value of the Preference's key.
      */
-    Preferences(Namespaces namespace, String key){
+    Preferences(Namespaces namespace, String key) {
         this.namespace = namespace;
         this.key = key;
     }
 
     /**
      * Getter for the namespace property.
+     *
      * @return the value of the namespace property.
      */
     public Namespaces getNamespace() {
@@ -28,6 +30,7 @@ public enum Preferences {
 
     /**
      * Getter for the key property.
+     *
      * @return the value of the key property.
      */
     public String getKey() {

src/main/java/net/ihe/gazelle/application/PatientRegistryXRefSearchClient.java

@@ -108,7 +108,7 @@ public class PatientRegistryXRefSearchClient {
                 throw new SearchCrossReferenceException("Can't connect to patient registry !");
             }
         }
-        if (serverUrl==null){
+        if (serverUrl == null) {
             getUrlOfServer();
         }
 
@@ -116,10 +116,11 @@ public class PatientRegistryXRefSearchClient {
 
     /**
      * Proceed to the request using the XReferencePatientRegistry client and  prepare the fhir response
+     *
      * @param sourceIdentifier Identity of the patient
      * @param targetSystemList targetSystem we want to retrieve through PatientRegistry
      * @return Fhir response that contain the target identity
-     * @throws SearchCrossReferenceException  if the client can not be initialized
+     * @throws SearchCrossReferenceException if the client can not be initialized
      */
     public Parameters process(EntityIdentifier sourceIdentifier, List<String> targetSystemList) throws SearchCrossReferenceException {
         initializeSearchClient();
@@ -130,12 +131,14 @@ public class PatientRegistryXRefSearchClient {
             switch (searchCrossReferenceException.getCause().getMessage()) {
                 case ERROR_IN_THE_SOURCE_IDENTIFIER_SYSTEM_DOES_NOT_EXIT:
                 case THE_SYSTEM_IDENTIFIER_FROM_SOURCE_IDENTIFIER_CANNOT_BE_NULL_OR_EMPTY:
-                    throw new InvalidRequestException(SOURCE_IDENTIFIER_ASSIGNING_AUTHORITY_NOT_FOUND, generateOperationOutcome("code-invalid",SOURCE_IDENTIFIER_ASSIGNING_AUTHORITY_NOT_FOUND));
+                    throw new InvalidRequestException(SOURCE_IDENTIFIER_ASSIGNING_AUTHORITY_NOT_FOUND, generateOperationOutcome("code-invalid",
+                            SOURCE_IDENTIFIER_ASSIGNING_AUTHORITY_NOT_FOUND));
                 case ERROR_IN_THE_SOURCE_IDENTIFIER_IT_DOES_NOT_MATCH_ANY_PATIENT:
                 case ERROR_IN_THE_SOURCE_IDENTIFIER_IT_DOES_NOT_MATCH_ANY_IDENTITY:
-                    throw new ResourceNotFoundException(SOURCE_IDENTIFIER_PATIENT_IDENTIFIER_NOT_FOUND, generateOperationOutcome("not-found",SOURCE_IDENTIFIER_PATIENT_IDENTIFIER_NOT_FOUND));
+                    throw new ResourceNotFoundException(SOURCE_IDENTIFIER_PATIENT_IDENTIFIER_NOT_FOUND, generateOperationOutcome("not-found",
+                            SOURCE_IDENTIFIER_PATIENT_IDENTIFIER_NOT_FOUND));
                 case ONE_OF_THE_TARGET_DOMAIN_DOES_NOT_EXIST:
-                    throw new ForbiddenOperationException(TARGET_SYSTEM_NOT_FOUND, generateOperationOutcome("code-invalid",TARGET_SYSTEM_NOT_FOUND));
+                    throw new ForbiddenOperationException(TARGET_SYSTEM_NOT_FOUND, generateOperationOutcome("code-invalid", TARGET_SYSTEM_NOT_FOUND));
                 default:
                     throw new InternalErrorException("An internal error occurred", searchCrossReferenceException);
             }
@@ -166,7 +169,7 @@ public class PatientRegistryXRefSearchClient {
             Parameters.ParametersParameterComponent targetId = new Parameters.ParametersParameterComponent();
             targetId.setName("targetId");
             Reference ref = new Reference();
-            ref.setReference("https://"+serverUrl+"/pixm-connector/fhir_ihe/Patient/" + pat.getUuid());
+            ref.setReference("https://" + serverUrl + "/pixm-connector/fhir_ihe/Patient/" + pat.getUuid());
             targetId.setValue(ref);
 
             parameters.addParameter(targetId);
@@ -179,6 +182,7 @@ public class PatientRegistryXRefSearchClient {
     /**
      * Method to construct the fhir response, return true if the entityIdentifier match a targetSystem and false otherwise
      * It returns true is the targetSystem list is empty.
+     *
      * @param targetSystemList
      * @param entityIdentifierSystem
      * @return boolean
@@ -198,11 +202,12 @@ public class PatientRegistryXRefSearchClient {
 
     /**
      * Method to generate the Error outcome in the response
-     * @param codeString Code of the error catch
+     *
+     * @param codeString  Code of the error catch
      * @param diagnostics origin of the issue
      * @return generated Operation outcome for the Fhir response
      */
-    private OperationOutcome generateOperationOutcome(String codeString,String diagnostics) {
+    private OperationOutcome generateOperationOutcome(String codeString, String diagnostics) {
         OperationOutcome code = new OperationOutcome();
         OperationOutcome.OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
         issue.setSeverity(OperationOutcome.IssueSeverity.ERROR);
@@ -215,7 +220,7 @@ public class PatientRegistryXRefSearchClient {
     /**
      * The method is used to retrieve the url of the current server.
      */
-    private void getUrlOfServer(){
+    private void getUrlOfServer() {
         InetAddress ip;
         try {
             ip = InetAddress.getLocalHost();

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

@@ -9,10 +9,7 @@ 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 ca.uhn.fhir.rest.server.exceptions.*;
 import net.ihe.gazelle.app.patientregistryapi.application.SearchCrossReferenceException;
 import net.ihe.gazelle.app.patientregistryapi.business.EntityIdentifier;
 import net.ihe.gazelle.app.patientregistryapi.business.PersonName;
@@ -171,7 +168,7 @@ public class ChPatientResourceProvider implements IResourceProvider {
         try {
             parametersResults = patientRegistryXRefSearchClient.process(sourceIdentifier, targetSystemList);
         } catch (SearchCrossReferenceException e) {
-            e.printStackTrace();
+            throw new InternalErrorException(e);
         }
         return parametersResults;
     }

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

@@ -8,11 +8,11 @@ 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.InternalErrorException;
 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.patientregistryxrefsearchclient.adapter.XRefSearchProcessResponseException;
 import net.ihe.gazelle.application.PatientRegistryXRefSearchClient;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Parameters;
@@ -68,7 +68,7 @@ public class IhePatientResourceProvider implements IResourceProvider {
         try {
             parametersResults = patientRegistryXRefSearchClient.process(sourceIdentifier, targetSystemList);
         } catch (SearchCrossReferenceException e) {
-            e.printStackTrace();
+           throw new InternalErrorException(e);
         }
 
         return parametersResults;