Merge pull request #402 from qbicsoftware/release/2023-10-17

Release 2023 10 17

database-connector/src/main/java/life/qbic/projectmanagement/experiment/persistence/BatchJpaRepository.java

@@ -8,7 +8,7 @@
 import life.qbic.projectmanagement.domain.project.repository.BatchRepository;
 import life.qbic.projectmanagement.domain.project.sample.Batch;
 import life.qbic.projectmanagement.domain.project.sample.BatchId;
-import life.qbic.projectmanagement.domain.project.service.BatchDomainService.ResponseCode;
+import life.qbic.projectmanagement.application.batch.BatchRegistrationService.ResponseCode;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 

domain-concept/src/main/java/life/qbic/domain/concepts/communication/Attachment.java

@@ -0,0 +1,12 @@
+package life.qbic.domain.concepts.communication;
+
+/**
+ * <b>MailAttachment</b>
+ *
+ * <p>Encapsulates information about an attachment, e.g. a file added to an email</p>
+ *
+ * @since 1.0.0
+ */
+public record Attachment(String content, String name) {
+
+}

domain-concept/src/main/java/life/qbic/domain/concepts/communication/CommunicationService.java

@@ -9,6 +9,22 @@
  */
 public interface CommunicationService {
 
+  /**
+   * Sends a message (e.g. email) to a recipient
+   * @param subject The subject of the message
+   * @param recipient The Recipient of the message
+   * @param content The Content of the message
+   * @throws CommunicationException
+   */
   void send(Subject subject, Recipient recipient, Content content) throws CommunicationException;
 
+  /**
+   * Sends a message (e.g. email) with an attached file to a recipient
+   * @param subject The subject of the message
+   * @param recipient The Recipient of the message
+   * @param content The Content of the message
+   * @param attachment An Attachment object denoting name and content of the attached file
+   * @throws CommunicationException
+   */
+  void send(Subject subject, Recipient recipient, Content content, Attachment attachment) throws CommunicationException;
 }

newshandler/src/main/java/life/qbic/newshandler/usermanagement/email/EmailCommunicationService.java

@@ -1,11 +1,20 @@
 package life.qbic.newshandler.usermanagement.email;
 
+import jakarta.activation.DataHandler;
+import jakarta.activation.DataSource;
+import jakarta.mail.BodyPart;
 import jakarta.mail.Message.RecipientType;
 import jakarta.mail.MessagingException;
+import jakarta.mail.Multipart;
 import jakarta.mail.Transport;
 import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeBodyPart;
 import jakarta.mail.internet.MimeMessage;
+import jakarta.mail.internet.MimeMultipart;
+import jakarta.mail.util.ByteArrayDataSource;
+import java.io.UnsupportedEncodingException;
 import java.util.Objects;
+import life.qbic.domain.concepts.communication.Attachment;
 import life.qbic.domain.concepts.communication.CommunicationException;
 import life.qbic.domain.concepts.communication.CommunicationService;
 import life.qbic.domain.concepts.communication.Content;
@@ -27,7 +36,7 @@ public class EmailCommunicationService implements CommunicationService {
   private static final Logger log = LoggerFactory.logger(
       EmailCommunicationService.class);
   private static final String NO_REPLY_ADDRESS = "[email protected]";
-
+  private static final String NOTIFICATION_FAILED = "Notification of recipient failed!";
   private static final String SIGNATURE = """
       
       With kind regards,
@@ -54,17 +63,63 @@ public void send(Subject subject, Recipient recipient, Content content) {
           "Sending email with subject %s to %s".formatted(subject.content(), recipient.address()));
     } catch (MessagingException e) {
       log.error("Could not send email to " + recipient.address(), e);
-      throw new CommunicationException("Notification of recipient failed!");
+      throw new CommunicationException(NOTIFICATION_FAILED);
     }
   }
 
-  private MimeMessage setupMessage(Subject subject, Recipient recipient, Content content)
+  @Override
+  public void send(Subject subject, Recipient recipient, Content content, Attachment attachment) {
+    try {
+      var message = setupMessageWithAttachment(subject, recipient, content, attachment);
+      Transport.send(message);
+      log.debug(
+          "Sending email with subject %s to %s".formatted(subject.content(), recipient.address()));
+    } catch (MessagingException e) {
+      log.error("Could not send email to " + recipient.address(), e);
+      throw new CommunicationException(NOTIFICATION_FAILED);
+    } catch (UnsupportedEncodingException e) {
+      log.error("Could not create attachment for email to " + recipient.address(), e);
+      throw new CommunicationException(NOTIFICATION_FAILED);
+    }
+  }
+
+  private MimeMessage setupMessageWithoutContent(Subject subject, Recipient recipient)
       throws MessagingException {
     var message = this.mailServerConfiguration.mimeMessage();
     message.setFrom(new InternetAddress(NO_REPLY_ADDRESS));
-    message.setContent(combineMessageWithRegards(content).content(), "text/plain");
     message.setRecipient(RecipientType.TO, new InternetAddress(recipient.address()));
     message.setSubject(subject.content());
     return message;
   }
+
+  private MimeMessage setupMessage(Subject subject, Recipient recipient, Content content)
+      throws MessagingException {
+    var message = setupMessageWithoutContent(subject, recipient);
+    message.setContent(combineMessageWithRegards(content).content(), "text/plain");
+    return message;
+  }
+
+  private MimeMessage setupMessageWithAttachment(Subject subject, Recipient recipient,
+      Content content, Attachment attachment)
+      throws MessagingException, UnsupportedEncodingException {
+
+    var message = setupMessageWithoutContent(subject, recipient);
+
+    BodyPart messageBodyPart = new MimeBodyPart();
+    messageBodyPart.setContent(combineMessageWithRegards(content).content(), "text/plain");
+
+    Multipart multipart = new MimeMultipart();
+    multipart.addBodyPart(messageBodyPart);
+
+    BodyPart attachmentPart = new MimeBodyPart();
+    DataSource dataSource = new ByteArrayDataSource(attachment.content().getBytes("UTF-8"),
+        "application/octet-stream");
+    attachmentPart.setDataHandler(new DataHandler(dataSource));
+    attachmentPart.setFileName(attachment.name());
+    multipart.addBodyPart(attachmentPart);
+
+    message.setContent(multipart);
+    return message;
+  }
+
 }

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/AppContextProvider.java

@@ -16,6 +16,14 @@ public interface AppContextProvider {
    * @return a fully resolvable URL
    * @since 1.0.0
    */
-  String urlToProject(String projectId);
 
+  String urlToProject(String projectId);
+  /**
+   * Returns a resolvable URL to the target project's sample page resource in the application.
+   *
+   * @param projectId the project id
+   * @return a fully resolvable URL
+   * @since 1.0.0
+   */
+  String urlToSamplePage(String projectId);
 }

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/Messages.java

@@ -13,6 +13,38 @@ private Messages() {
 
   }
 
+  /**
+   * A pre-formatted message that informs a user about newly created samples and their identifiers
+   * in the data manager.
+   *
+   * @param fullNameUser the name of the user to inform for addressing them politely
+   * @param projectTitle the title of the project, will be in the message to inform the user about
+   *                     which project they have been granted access with
+   * @param batchName    the name of the batch that was added
+   * @param sampleUri   a uniform resource identifier of the sample page of this project, that the
+   *                    recipient can use to access the newly registered samples
+   * @return the filled out template message
+   * @since 1.0.0
+   */
+  public static String samplesAddedToProject(String fullNameUser, String projectTitle,
+      String batchName, String sampleUri) {
+    return String.format("""
+        Dear %s,
+                      
+        the new batch ('%s') of samples has been added to the project:
+               
+        '%s'
+            
+        Sample information and QBiC identifiers have been added to the Data Manager.
+        These identifiers uniquely characterize each added sample. They will be used to attach data
+        for each of the samples, as soon as it has been measured and uploaded.
+
+        Please click the link below to access the sample information after login:
+            
+        %s
+        """, fullNameUser, batchName, projectTitle, sampleUri);
+  }
+
   /**
    * A pre-formatted message that informs a user about their new access grant to a project in the
    * data manager.
@@ -24,7 +56,7 @@ private Messages() {
    *                     access the project
    * @return the filled out template message
    * @since 1.0.0
-   */
+      */
   public static String projectAccessToUser(String fullNameUser, String projectTitle,
       String projectUri) {
     return String.format("""

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/authorization/acl/ProjectAccessService.java

@@ -21,6 +21,14 @@ public interface ProjectAccessService {
    */
   List<String> listUsers(ProjectId projectId);
 
+  /**
+   * Lists all active users which have a permission within the specific project
+   *
+   * @param projectId the identifier of the project
+   * @return a list of user ids of active users that are associated with the project
+   */
+  List<String> listActiveUsers(ProjectId projectId);
+
   /**
    * Lists all users which have a permission on the project
    *

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/authorization/acl/ProjectAccessServiceImpl.java

@@ -2,6 +2,7 @@
 
 import static java.util.Objects.requireNonNull;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.function.Predicate;
 import life.qbic.projectmanagement.application.authorization.QbicUserDetails;
@@ -19,6 +20,7 @@
 import org.springframework.security.acls.model.Permission;
 import org.springframework.security.acls.model.Sid;
 import org.springframework.security.core.GrantedAuthority;
+import org.springframework.security.core.userdetails.UserDetails;
 import org.springframework.security.core.userdetails.UserDetailsService;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -43,7 +45,18 @@ public List<String> listUsers(ProjectId projectId) {
         .filter(it -> it instanceof QbicUserDetails)
         .map(it -> (QbicUserDetails) it)
         .map(QbicUserDetails::getUserId)
-        .toList();
+        .distinct().toList();
+  }
+
+  @Transactional
+  @Override
+  public List<String> listActiveUsers(ProjectId projectId) {
+    return listUsernames(projectId).stream().map(userDetailsService::loadUserByUsername)
+        .filter(it -> it instanceof QbicUserDetails)
+        .map(it -> (QbicUserDetails) it)
+        .filter(QbicUserDetails::isEnabled)
+        .map(QbicUserDetails::getUserId)
+        .distinct().toList();
   }
 
   @Transactional

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/batch/BatchRegistrationService.java

@@ -1,36 +1,66 @@
 package life.qbic.projectmanagement.application.batch;
 
+import static org.slf4j.LoggerFactory.getLogger;
+
+import java.util.Objects;
 import life.qbic.application.commons.Result;
+import life.qbic.projectmanagement.application.ProjectInformationService;
+import life.qbic.projectmanagement.domain.project.ProjectId;
 import life.qbic.projectmanagement.domain.project.repository.BatchRepository;
 import life.qbic.projectmanagement.domain.project.sample.Batch;
 import life.qbic.projectmanagement.domain.project.sample.BatchId;
 import life.qbic.projectmanagement.domain.project.sample.SampleId;
+import life.qbic.projectmanagement.domain.project.service.BatchDomainService;
+import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 /**
- * <b><class short description - 1 Line!></b>
- *
- * <p><More detailed description - When to use, what it solves, etc.></p>
+ * <b>Batch Registration Service</b>
+ * <p>
+ * Service that handles {@link Batch} creation and deletion events, that need to dispatch domain
+ * events.
  *
- * @since <version tag>
+ * @since 1.0.0
  */
 @Service
 public class BatchRegistrationService {
 
   private final BatchRepository batchRepository;
+  private final BatchDomainService batchDomainService;
+  private final ProjectInformationService projectInformationService;
+  private static final Logger log = getLogger(BatchRegistrationService.class);
 
-  public BatchRegistrationService(@Autowired BatchRepository batchRepository) {
-    this.batchRepository = batchRepository;
+  @Autowired
+  public BatchRegistrationService(BatchRepository batchRepository,
+      BatchDomainService batchDomainService, ProjectInformationService projectInformationService) {
+    this.batchRepository = Objects.requireNonNull(batchRepository);
+    this.batchDomainService = Objects.requireNonNull(batchDomainService);
+    this.projectInformationService = Objects.requireNonNull(projectInformationService);
   }
 
-  public Result<BatchId, ResponseCode> registerBatch(String label, boolean isPilot) {
-    Batch batch = Batch.create(label, isPilot);
-    var result = batchRepository.add(batch);
-    if (result.isError()) {
+  /**
+   * Registers a new batch of samples that serves as reference for sample processing in the lab for
+   * measurement and analysis purposes.
+   *
+   * @param label   a human-readable semantic descriptor of the batch
+   * @param isPilot a flag that indicates the batch to describe as pilot submission batch. Pilots
+   *                are usually followed by a complete batch that represents the measurements of the
+   *                complete experiment.
+   * @param projectId id of the project this batch is added to
+   * @return a result object with the response. If the registration failed, a response code will be
+   * provided.
+   * @since 1.0.0
+   */
+  public Result<BatchId, ResponseCode> registerBatch(String label, boolean isPilot,
+      ProjectId projectId) {
+    var project = projectInformationService.find(projectId);
+    if (project.isEmpty()) {
+      log.error("Batch registration aborted. Reason: project with id:"+projectId+" was not found");
       return Result.fromError(ResponseCode.BATCH_CREATION_FAILED);
     }
-    return Result.fromValue(batch.batchId());
+    String projectTitle = project.get().getProjectIntent().projectTitle().title();
+    return batchDomainService.register(label, isPilot, projectTitle, projectId);
   }
 
   public Result<BatchId, ResponseCode> addSampleToBatch(SampleId sampleId, BatchId batchId) {
@@ -48,11 +78,12 @@ public Result<BatchId, ResponseCode> addSampleToBatch(SampleId sampleId, BatchId
     }
   }
 
+
   public enum ResponseCode {
     BATCH_UPDATE_FAILED,
     BATCH_NOT_FOUND,
-    BATCH_CREATION_FAILED
-
+    BATCH_CREATION_FAILED,
+    BATCH_REGISTRATION_FAILED
   }
 
 }

projectmanagement-domain/src/main/java/life/qbic/projectmanagement/application/policy/BatchRegisteredPolicy.java

@@ -0,0 +1,35 @@
+package life.qbic.projectmanagement.application.policy;
+
+import life.qbic.domain.concepts.DomainEventDispatcher;
+import life.qbic.projectmanagement.application.policy.directive.InformUsersAboutBatchRegistration;
+
+/**
+ * <b>Policy: Batch Registered</b>
+ * <p>
+ * A collection of all directives that need to be executed after a new batch of
+ * samples has been registered for measurement.
+ * <p>
+ * The policy subscribes to events of type
+ * {@link life.qbic.projectmanagement.domain.project.sample.event.BatchRegistered} and ensures the
+ * registration of all business required directives.
+ *
+ * @since 1.0.0
+ */
+public class BatchRegisteredPolicy {
+
+  private final InformUsersAboutBatchRegistration informUsers;
+
+  /**
+   * Creates an instance of a {@link BatchRegisteredPolicy} object.
+   * <p>
+   * All directives will be created and subscribed upon instantiation.
+   *
+   * @param informUsers directive to inform users of a project about the new samples of a batch
+   *                         {@link life.qbic.projectmanagement.domain.project.sample.Batch}
+   * @since 1.0.0
+   */
+  public BatchRegisteredPolicy(InformUsersAboutBatchRegistration informUsers) {
+    this.informUsers = informUsers;
+    DomainEventDispatcher.instance().subscribe(this.informUsers);
+  }
+}