clean code fixing sonar issues

src/main/java/com/systelab/seed/BaseException.java

@@ -1,5 +1,8 @@
 package com.systelab.seed;
 
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+
 /**
  * SeedException wraps all checked standard Java exception and enriches them with a custom error code.
  * You can use this code to retrieve localized error messages and to link to our online documentation.
@@ -9,18 +12,16 @@ public class BaseException extends Exception {
     private static final long serialVersionUID = 3714428835173293220L;
     private final ErrorCode errorCode;
 
+    @AllArgsConstructor
+    @Getter
     public enum ErrorCode {
         ALLERGY_ALREADY_EXIST(5),
         ALLERGY_NOT_FOUND(4),
         PATIENT_NOT_FOUND(3),
         USER_NOT_FOUND(2),
         DEFAULT_ERROR(1);
 
-        private final int errorCode;
-
-        ErrorCode(int errorCode) {
-            this.errorCode = errorCode;
-        }
+       private final int code;
     }
 
     public BaseException(ErrorCode code) {
@@ -33,16 +34,6 @@ public BaseException(String message, Throwable cause, ErrorCode code) {
         this.errorCode = code;
     }
 
-    public BaseException(String message, ErrorCode code) {
-        super(message);
-        this.errorCode = code;
-    }
-
-    public BaseException(Throwable cause, ErrorCode code) {
-        super(cause);
-        this.errorCode = code;
-    }
-
     public ErrorCode getCode() {
         return this.errorCode;
     }

src/main/java/com/systelab/seed/allergy/entity/Allergy.java

@@ -7,7 +7,6 @@
 import lombok.NoArgsConstructor;
 
 import javax.persistence.Entity;
-import javax.persistence.NamedQueries;
 import javax.persistence.NamedQuery;
 import javax.persistence.Table;
 import javax.validation.constraints.NotNull;
@@ -20,8 +19,8 @@
 @NoArgsConstructor
 @AllArgsConstructor
 @Table(name = "allergy")
-@NamedQueries({@NamedQuery(name = com.systelab.seed.allergy.entity.Allergy.FIND_ALL, query = "SELECT a FROM Allergy a ORDER BY a.name"),
-        @NamedQuery(name = com.systelab.seed.allergy.entity.Allergy.ALL_COUNT, query = "SELECT COUNT(a.id) FROM Allergy a")})
+@NamedQuery(name = com.systelab.seed.allergy.entity.Allergy.FIND_ALL, query = "SELECT a FROM Allergy a ORDER BY a.name")
+@NamedQuery(name = com.systelab.seed.allergy.entity.Allergy.ALL_COUNT, query = "SELECT COUNT(a.id) FROM Allergy a")
 public class Allergy extends BaseEntity {
     public static final String FIND_ALL = "Allergy.findAll";
     public static final String ALL_COUNT = "Allergy.allCount";

src/main/java/com/systelab/seed/infrastructure/auth/TokenAuthenticationFilter.java

@@ -40,7 +40,9 @@ public class TokenAuthenticationFilter implements ContainerRequestFilter {
     public void filter(ContainerRequestContext requestContext) {
 
         try {
-            logger.info(requestContext.getUriInfo().getRequestUri().toString());
+            if (logger.isInfoEnabled()){
+                logger.info(requestContext.getUriInfo().getRequestUri().toString());
+            }
             String userRole = tokenGenerator.getRoleFromToken(getTokenFromHeader(requestContext));
             if (!methodIsAllowed(resourceInfo.getResourceMethod(), userRole)) {
                 requestContext.abortWith(Response.status(Response.Status.UNAUTHORIZED).build());

src/main/java/com/systelab/seed/infrastructure/security/RequestRateLimiterFilter.java

@@ -77,7 +77,7 @@ private AtomicRateLimiter getLimiter(String key) {
 
   private void logLimitExceeded(UriInfo uriInfo, String byAddress) {
     String path = uriInfo.getAbsolutePath().getPath();
-    logger.warn("Overloaded {0} request {1}; discarding it", new Object[]{byAddress, path});
+    logger.warn("Overloaded {} request {}; discarding it", byAddress, path);
   }
 
   private String getRateExceededMessage(AtomicRateLimiter rateLimiter) {

src/main/java/com/systelab/seed/infrastructure/security/implementation/SHA256PasswordDigest.java

@@ -3,27 +3,22 @@
 import com.systelab.seed.BaseException;
 import com.systelab.seed.infrastructure.security.PasswordDigest;
 
-import java.io.UnsupportedEncodingException;
+import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.Base64;
-import javax.inject.Inject;
-import org.slf4j.Logger;
 
 
 public class SHA256PasswordDigest implements PasswordDigest {
-    @Inject
-    private Logger logger;
 
     @Override
     public String digest(String plainTextPassword) throws BaseException {
         try {
             MessageDigest md = MessageDigest.getInstance("SHA-256");
-            md.update(plainTextPassword.getBytes("UTF-8"));
+            md.update(plainTextPassword.getBytes(StandardCharsets.UTF_8));
             byte[] passwordDigest = md.digest();
             return new String(Base64.getEncoder().encode(passwordDigest));
-        } catch (NoSuchAlgorithmException | UnsupportedEncodingException e) {
-            logger.error(e.getMessage(), e);
+        } catch (NoSuchAlgorithmException e) {
             throw new BaseException("Incorrect algorithm implementation", e, BaseException.ErrorCode.DEFAULT_ERROR);
         }
     }

src/main/java/com/systelab/seed/patient/boundary/bean/DeleteOldPatientsTimerBean.java

@@ -20,7 +20,7 @@ public class DeleteOldPatientsTimerBean {
     private Logger logger;
 
     @Inject
-    PatientMaintenanceServiceHealthCheck healthCheck;
+    private PatientMaintenanceServiceHealthCheck healthCheck;
 
     @EJB
     private PatientService patientService;
@@ -54,7 +54,7 @@ private void createTimer() {
     }
 
     private void cancelAnyRunningTimer() {
-        timerService.getTimers().stream().forEach((timer) -> {
+        timerService.getTimers().stream().forEach(timer -> {
             logger.info("Found running timer with info: {}, cancelling it", timer.getInfo());
             timer.cancel();
         });

src/main/java/com/systelab/seed/patient/boundary/health/PatientMaintenanceServiceHealthCheck.java

@@ -23,11 +23,11 @@ public HealthCheckResponse call() {
         return working ? builder.up().build() : builder.down().build();
     }
 
-    public void setWorking(boolean working) {
-        this.working = working;
+    public synchronized void setWorking(boolean working) {
+        PatientMaintenanceServiceHealthCheck.working = working;
     }
 
-    public void setLastExecution(LocalDateTime lastExecution) {
-        this.lastExecution = lastExecution;
+    public synchronized void setLastExecution(LocalDateTime lastExecution) {
+        PatientMaintenanceServiceHealthCheck.lastExecution = lastExecution;
     }
 }

src/main/java/com/systelab/seed/patient/control/BodyMassIndexCalculator.java

@@ -2,6 +2,10 @@
 
 public class BodyMassIndexCalculator {
 
+    private BodyMassIndexCalculator()
+    {
+    }
+
     private static boolean isValidWeight(Double value) {
         return value != null && Double.isFinite(value) && value > 1;
     }

src/main/java/com/systelab/seed/patient/control/MedicalRecordNumberService.java

@@ -12,11 +12,13 @@
 interface IdentityClient {
 
     @RequestLine("GET /identity/v1/medical-record-number")
-    public String getMedicalRecordNumber();
+    String getMedicalRecordNumber();
 }
 
 public class MedicalRecordNumberService {
 
+    private  static final String UNDEFINED = "UNDEFINED";
+
     @Inject
     private Logger logger;
 
@@ -26,14 +28,15 @@ public class MedicalRecordNumberService {
 
     public String getMedicalRecordNumber() {
 
-        logger.info(String.format("medicalRecordNumberServiceUrl: %s", medicalRecordNumberServiceUrl));
-
+        if (logger.isInfoEnabled()){
+            logger.info(String.format("medicalRecordNumberServiceUrl: %s", medicalRecordNumberServiceUrl));
+        }
         IdentityClient client = HystrixFeign.builder().target(IdentityClient.class, medicalRecordNumberServiceUrl, MedicalRecordNumberService::defaultMedicalRecordNumber);
         return client.getMedicalRecordNumber();
     }
 
     private static String defaultMedicalRecordNumber() {
-        return "UNDEFINED";
+        return UNDEFINED;
     }
 
 }

src/main/java/com/systelab/seed/patient/control/PatientWorkbookGenerator.java

@@ -25,7 +25,7 @@ private void addPatientToWorkBook(Sheet sheet, int rowIndex, Patient patient) {
         Row row = sheet.createRow(rowIndex);
         createCell(row, colNum++, patient.getName());
         createCell(row, colNum++, patient.getSurname());
-        createCell(row, colNum++, patient.getEmail());
+        createCell(row, colNum, patient.getEmail());
     }
 
     private void createCell(Row row, int colIndex, String value) {

src/main/java/com/systelab/seed/patient/control/RealtimePatientTracking.java

@@ -51,7 +51,7 @@ public void onPatientCreated(@Observes @PatientCreated Patient patient) {
         try (JsonGenerator generator = Json.createGenerator(writer)) {
             generator.writeStartObject().write("patientid", patient.getId().toString()).write("patientname", patient.getName()).writeEnd();
         }
-        sessions.forEach((session) -> sendMessageToSession(session, writer.toString()));
+        sessions.forEach(session -> sendMessageToSession(session, writer.toString()));
     }
 
     private void sendMessageToSession(Session session, String json) {

src/main/java/com/systelab/seed/patient/entity/Patient.java

@@ -30,9 +30,9 @@
 @NoArgsConstructor
 @AllArgsConstructor
 @Table(name = "patient")
-@NamedQueries({@NamedQuery(name = Patient.FIND_ALL, query = "SELECT p FROM Patient p ORDER BY p.surname"),
-        @NamedQuery(name = Patient.ALL_COUNT, query = "SELECT COUNT(p.id) FROM Patient p"),
-        @NamedQuery(name = Patient.DEACTIVATE, query = "UPDATE Patient p SET p.active = FALSE WHERE p.modificationTime < :modificationTime")})
+@NamedQuery(name = Patient.FIND_ALL, query = "SELECT p FROM Patient p ORDER BY p.surname")
+@NamedQuery(name = Patient.ALL_COUNT, query = "SELECT COUNT(p.id) FROM Patient p")
+@NamedQuery(name = Patient.DEACTIVATE, query = "UPDATE Patient p SET p.active = FALSE WHERE p.modificationTime < :modificationTime")
 public class Patient extends BaseEntity {
     public static final String FIND_ALL = "Patient.findAll";
     public static final String ALL_COUNT = "Patient.allCount";

src/main/java/com/systelab/seed/patientallergy/boundary/PatientAllergyResource.java

@@ -74,10 +74,7 @@ public Response addAllergyToPatient(@PathParam("uid") String uid, @RequestBody(d
         } catch (PatientNotFoundException ex) {
             logger.error(PatientAllergyResource.INVALID_PATIENT_ERROR_MESSAGE, ex);
             return Response.status(Status.NOT_FOUND).build();
-        } catch (AllergyNotFoundException ex) {
-            logger.error(PatientAllergyResource.INVALID_ALLERGY_ERROR_MESSAGE, ex);
-            return Response.status(Status.NOT_FOUND).build();
-        } catch (AllergyAlreadyExistException ex) {
+        } catch (AllergyNotFoundException | AllergyAlreadyExistException ex) {
             logger.error(PatientAllergyResource.INVALID_ALLERGY_ERROR_MESSAGE, ex);
             return Response.status(Status.NOT_FOUND).build();
         }

src/main/java/com/systelab/seed/user/entity/User.java

@@ -16,9 +16,9 @@
 @EqualsAndHashCode(callSuper = true)
 @AllArgsConstructor
 @Table(name = "SeedUser")
-@NamedQueries({@NamedQuery(name = User.FIND_ALL, query = "SELECT u FROM User u ORDER BY u.surname DESC"), @NamedQuery(name = User.FIND_BY_LOGIN_PASSWORD, query = "SELECT u FROM User u WHERE u.login = :login AND u.password = :password"),
-        @NamedQuery(name = User.ALL_COUNT, query = "SELECT COUNT(u.id) FROM User u")})
-
+@NamedQuery(name = User.FIND_ALL, query = "SELECT u FROM User u ORDER BY u.surname DESC")
+@NamedQuery(name = User.FIND_BY_LOGIN_PASSWORD, query = "SELECT u FROM User u WHERE u.login = :login AND u.password = :password")
+@NamedQuery(name = User.ALL_COUNT, query = "SELECT COUNT(u.id) FROM User u")
 @XmlRootElement
 public class User extends BaseEntity {
     public static final String FIND_ALL = "User.findAll";

src/main/webapp/swagger/oauth2-redirect.html

@@ -1,5 +1,8 @@
 <!doctype html>
 <html lang="en-US">
+<head>
+    <title>OAUTH redirect</title>
+</head>
 <body onload="run()">
 </body>
 </html>

src/test/java/com/systelab/seed/RESTResourceTest.java

@@ -11,7 +11,7 @@
 
 import static io.restassured.RestAssured.given;
 
-public class RESTResourceTest {
+public abstract class RESTResourceTest {
 
     protected static final String AUTHORIZATION_HEADER = "Authorization";
 

src/test/java/com/systelab/seed/allergy/AllergyResourceTest.java

@@ -19,7 +19,7 @@
 
 @TmsLink("TC0002_AllergyManagement_IntegrationTest")
 @Feature("Allergy Test Suite.\n\nGoal:\nThe goal of this TC is to verify that the Allergies management actions (CRUD) behave as expected according the specifications and the input values.\n\nEnvironment:\n...\nPreconditions:\nN/A.")
-public class AllergyResourceTest extends RESTResourceTest {
+class AllergyResourceTest extends RESTResourceTest {
 
     private Response doCreateAllergy(Allergy allergy){
         return given().body(allergy).when().post("/allergies/allergy");
@@ -61,7 +61,7 @@ private void checkAllergyData(Allergy expected, Allergy actual){
 
     @Description("Create a new allergy with name, sign and symptoms")
     @Test
-    public void testCreateAllergy() {
+    void testCreateAllergy() {
         String expectedName = "Tree pollen";
         String expectedSigns = "Watering eyes";
 
@@ -75,7 +75,7 @@ public void testCreateAllergy() {
 
     @Description("Create a new allergy with all information")
     @Test
-    public void testCreateAllergyAllInfo() {
+    void testCreateAllergyAllInfo() {
         String expectedName = "Tree pollen";
         String expectedSigns = "Watering eyes";
         String expectedSymptoms = "Sneezing";
@@ -98,15 +98,15 @@ private void testCreateInvalidAllergy(Allergy allergy) {
 
     @Description("Create a Allergy with invalid data: mandatory fields empty (name, signs)")
     @Test
-    public void testCreateInvalidAllergyMandatoryFieldsEmpty() {
+    void testCreateInvalidAllergyMandatoryFieldsEmpty() {
         testCreateInvalidAllergy(getAllergyData("", "", "Sneezing"));
         testCreateInvalidAllergy(getAllergyData("", "Sneezing", "Sneezing"));
         testCreateInvalidAllergy(getAllergyData("Pollen", "", "Sneezing"));
     }
 
     @Description("Create a Allergy with invalid data: name, signs or symptoms field too long")
     @Test
-    public void testCreateInvalidAllergyTooLongText() {
+    void testCreateInvalidAllergyTooLongText() {
         String tooLongString = "thisStringIsIntendedToCauseAnExceptionBecauseOfItsExcessiveLengthTheMostLongStringAllowedMustHaveLessThanTeoHundredAndFiftyFiveCharactersThisShouldBeVerifiedInEveryTextFieldToEnsureTheLimitationIsWorkingProperlyThisStringOnlyHasEnglishLettersButMoreScenarios";
         testCreateInvalidAllergy(getAllergyData(tooLongString, "Watering eyes", "Sneezing"));
         testCreateInvalidAllergy(getAllergyData("Tree pollen", tooLongString, "Sneezing"));
@@ -134,7 +134,7 @@ private void createSomeAllergies(int numberOfAllergies) {
 
     @Description("Get a list of allergies")
     @Test
-    public void testGetAllergyList() {
+    void testGetAllergyList() {
         int numberOfAllergies = 5;
 
         Response responseBefore = doGetAllergyList();
@@ -156,7 +156,7 @@ public void testGetAllergyList() {
 
     @Description("Get a Allergy by id")
     @Test
-    public void testGetAllergy() {
+    void testGetAllergy() {
         Allergy allergy = getAllergyData("Tree pollen", "Watering eyes", "Dry, red and cracked skin");
         Response responseCre = doCreateAllergy(allergy);
         Allergy allergyCreated = responseCre.then().assertThat().statusCode(200)
@@ -174,7 +174,7 @@ public void testGetAllergy() {
 
     @Description("Get a allergy with an non-existing id")
     @Test
-    public void testGetUnexistingAllergy() {
+    void testGetUnexistingAllergy() {
         int statusCode = given()
                 .when().get("/allergies/38400000-8cf0-11bd-b23e-10b96e4ef00d")
                 .then()
@@ -184,7 +184,7 @@ public void testGetUnexistingAllergy() {
 
     @Description("Delete a allergy by id")
     @Test
-    public void testDeleteAllergy() {
+    void testDeleteAllergy() {
         Allergy allergy = getAllergyData("Tree pollen", "Watering eyes", "Dry, red and cracked skin");
         Response responseCre = doCreateAllergy(allergy);
         Allergy allergyCreated = responseCre.then().assertThat().statusCode(200)
@@ -205,7 +205,7 @@ public void testDeleteAllergy() {
 
     @Description("Delete non-existing Allergy")
     @Test
-    public void testDeleteUnexistingAllergy() {
+    void testDeleteUnexistingAllergy() {
         int statusCode = given()
                 .when().delete("/allergies/38400000-8cf0-11bd-b23e-10b96e4ef00d")
                 .then()
@@ -215,7 +215,7 @@ public void testDeleteUnexistingAllergy() {
 
     @Description("Update a allergy by id")
     @Test
-    public void testUpdateAllergy() {
+    void testUpdateAllergy() {
         Allergy allergy = getAllergyData("Tree pollen", "Watering eyes", "Dry, red and cracked skin");
         Response responseCre = doCreateAllergy(allergy);
         Allergy allergyCreated = responseCre.then().assertThat().statusCode(200)
@@ -234,7 +234,7 @@ public void testUpdateAllergy() {
 
     @Description("Update non-existent allergy, that is Create new Allergy")
     @Test
-    public void testUpdateUnexistingAllergy() {
+    void testUpdateUnexistingAllergy() {
         Allergy allergy = getAllergyData("Tree pollen", "Watering eyes", "Dry, red and cracked skin");
         Allergy allergyCreated = given().body(allergy)
                 .when().put("/allergies/38400000-8cf0-11bd-b23e-10b96e4ef00d")