Merge pull request #910 from qbicsoftware/development

Prepare smaller 1.6.1 release with minor improvements

Author: KochTobi

application-commons/src/main/java/life/qbic/application/commons/ApplicationException.java

@@ -17,7 +17,7 @@
 public class ApplicationException extends RuntimeException {
 
   private final ErrorCode errorCode;
-  private final ErrorParameters errorParameters;
+  private final transient ErrorParameters errorParameters;
 
   public ApplicationException() {
     this(ErrorCode.GENERAL, ErrorParameters.empty());

broadcasting/src/main/java/life/qbic/broadcasting/Exchange.java

@@ -169,7 +169,7 @@ public void subscribe(MessageSubscriber subscriber, String topic) {
    */
   static class Topic {
 
-    private final String topic;
+    private final String value;
 
     private final Set<MessageSubscriber> subscribers;
 
@@ -185,7 +185,7 @@ static Topic create(String topic) {
 
     protected Topic(String topic) {
       super();
-      this.topic = topic;
+      this.value = topic;
       subscribers = new HashSet<>();
     }
 
@@ -198,11 +198,11 @@ synchronized void removeSubscriber(MessageSubscriber subscriber) {
     }
 
     boolean matchesTopic(String topic) {
-      return this.topic.equalsIgnoreCase(topic);
+      return this.value.equalsIgnoreCase(topic);
     }
 
     synchronized void informAllSubscribers(String message, MessageParameters messageParameters) {
-      if (messageParameters.messageType.equalsIgnoreCase(topic)) {
+      if (messageParameters.messageType.equalsIgnoreCase(value)) {
         informSubscribers(message, messageParameters);
       }
     }

docs/processes/Sample_registration_process.svg

@@ -1,8 +1,4 @@
 package life.qbic.domain.concepts
-
-
-import java.time.Instant
-
 /**
  * <b><class short description - 1 Line!></b>
  *

domain-concept/src/test/groovy/life/qbic/domain/concepts/TestEvent.groovy

@@ -33,11 +33,11 @@ public IdentityEmailServiceProvider(EmailServiceProvider emailServiceProvider) {
   @Override
   public void send(Subject subject, Recipient recipient, Content content)
       throws CommunicationException {
-    Optional.ofNullable(subject)
+    subject = Optional.ofNullable(subject)
         .orElseThrow(() -> new CommunicationException("No subject provided."));
-    Optional.ofNullable(recipient)
+    recipient = Optional.ofNullable(recipient)
         .orElseThrow(() -> new CommunicationException("No recipient provided."));
-    Optional.ofNullable(content)
+    content = Optional.ofNullable(content)
         .orElseThrow(() -> new CommunicationException("No content provided."));
 
     try {

email-service-provider/src/main/java/life/qbic/infrastructure/email/identity/IdentityEmailServiceProvider.java

@@ -64,7 +64,7 @@ public ApplicationResponse registerUser(final String fullName, String userName,
 
     var userDomainService = DomainRegistry.instance().userDomainService();
     if (userDomainService.isEmpty()) {
-      throw new RuntimeException("User registration failed.");
+      throw new ApplicationException("User registration failed.");
     }
 
     var userEmail = EmailAddress.from(email);
@@ -98,7 +98,7 @@ public ApplicationResponse registerOpenIdUser(String fullName, String userName,
 
     var userDomainService = DomainRegistry.instance().userDomainService();
     if (userDomainService.isEmpty()) {
-      throw new RuntimeException("User registration failed.");
+      throw new ApplicationException("User registration failed.");
     }
 
     var userEmail = EmailAddress.from(email);
@@ -301,6 +301,7 @@ public static class UserNameNotAvailableException extends ApplicationException {
     private static final long serialVersionUID = 4409722243047442583L;
 
     public UserNameNotAvailableException() {
+      super();
     }
   }
 

identity/src/main/java/life/qbic/identity/application/user/IdentityService.java

@@ -2,6 +2,7 @@
 
 import java.net.MalformedURLException;
 import java.net.URL;
+import life.qbic.application.commons.ApplicationException;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
@@ -46,7 +47,7 @@ public String emailConfirmationUrl(String userId) {
             URL url = new URL(protocol, host, port, pathWithQuery);
             return url.toExternalForm();
         } catch (MalformedURLException e) {
-            throw new RuntimeException("Link creation failed.", e);
+            throw new ApplicationException("Link creation failed.", e);
         }
 
     }

identity/src/main/java/life/qbic/identity/application/user/policy/EmailConfirmationLinkSupplier.java

@@ -61,7 +61,6 @@ public Result<ExperimentId, RuntimeException> addExperimentToProject(ProjectId p
       String specimenIconLabel) {
       requireNonNull(projectId, "project id must not be null during experiment creation");
       if (experimentName.isBlank()) {
-        //ToDo Add Iterator for multiple experiments?
         experimentName = "Unnamed Experiment";
       }
       if (CollectionUtils.isEmpty(species)) {

project-management/src/main/java/life/qbic/projectmanagement/application/AddExperimentToProjectService.java

@@ -1,7 +1,6 @@
 package life.qbic.projectmanagement.application;
 
 import static java.util.Objects.isNull;
-import static life.qbic.logging.service.LoggerFactory.logger;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -11,7 +10,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import life.qbic.logging.api.Logger;
+import life.qbic.application.commons.ApplicationException;
 import life.qbic.projectmanagement.application.ProjectOverview.UserInfo;
 
 /**
@@ -24,8 +23,6 @@
 public class CollaboratorUserInfosConverter implements
     AttributeConverter<List<UserInfo>, String> {
 
-  private static final Logger log = logger(CollaboratorUserInfosConverter.class);
-
   private final ObjectMapper objectMapper = new ObjectMapper();
 
   @Override
@@ -41,7 +38,7 @@ public String convertToDatabaseColumn(List<UserInfo> attribute) {
       return outputStream.toString();
     } catch (IOException e) {
       // we need to throw to prevent data loss
-      throw new RuntimeException(
+      throw new ApplicationException(
           "Unexpected problems writing project collaborators to the database", e);
     }
   }
@@ -58,7 +55,7 @@ public List<UserInfo> convertToEntityAttribute(String dbData) {
       );
     } catch (JsonProcessingException e) {
       // we need to throw to prevent data loss
-      throw new RuntimeException("Unexpected failure parsing project collaborators from database",
+      throw new ApplicationException("Unexpected failure parsing project collaborators from database",
           e);
     }
 

project-management/src/main/java/life/qbic/projectmanagement/application/CollaboratorUserInfosConverter.java

@@ -11,7 +11,6 @@ public class ContactRepository {
 
   @PostFilter("hasAnyAuthority('ROLE_ADMIN')")
   public List<Contact> findAll() {
-      //TODO implement
       return dummyContacts();
   }