Merge pull request #168 from qbicsoftware/release/0.12.0

Release 0.12.0

Author: Steffengreiner

.gitignore

@@ -19,7 +19,6 @@ logs
 */webapp/frontend/index.html
 */package.json
 */tsconfig.json
-*/types.d.ts
 */webpack.config.js
 */webpack.generated.js
 
@@ -31,3 +30,11 @@ error-screenshots/
 */webapp/frontend/generated/theme.d.ts
 */package-lock.json
 /logs/
+
+# Ignore Vite generated files created since vaadin 23.2
+/frontend/index.html
+/frontend/generated/index.ts
+/vaadinfrontend/types.d.ts
+/frontend/generated/vaadin.ts
+/frontend/generated/vaadin-featureflags.ts
+/vaadinfrontend/vite.config.ts

README.md

@@ -132,16 +132,31 @@ default configuration.
 service.host.name=${DM_SERVICE_HOST:localhost}
 service.host.protocol=${DM_HOST_PROTOCOL:https}
 service.host.port=${DM_SERVICE_PORT:-1}
-
 # route for mail confirmation consumption
 email-confirmation-endpoint=${EMAIL_CONFIRMATION_ENDPOINT:login}
 email-confirmation-parameter=${EMAIL_CONFIRMATION_PARAMETER:confirm-email}
-
 # route for password reset
 password-reset-endpoint=${PASSWORD_RESET_ENDPOINT:new-password}
 password-reset-parameter=${PASSWORD_RESET_PARAMETER:user-id}
 ```
 
+Since the application will retrieve experimental design values from a list of defined vocabularies
+a connection to the datasource containing this information is necessary:
+
+| environment variable         | description                              |
+|------------------------------|------------------------------------------|
+| `OPENBIS_DATASOURCE_URL`     | The vocabulary database host API address |
+| `OPENBIS_USER_NAME`          | The vocabulary database user name        |
+| `OPENBIS_USER_PASSWORD`      | The vocabulary database password         |
+
+The application properties file could look like the following:
+
+```properties
+openbis.user.name=${OPENBIS_USER_NAME:openbis-username}
+openbis.user.password=${OPENBIS_USER_PASSWORD:openbis-password}
+openbis.datasource.url=${OPENBIS_DATASOURCE_URL:openbis-url}
+```
+
 #### Properties
 
 The environment variables can either be set in the runtime configuration of your IDE or directly in
@@ -162,26 +177,26 @@ spring.datasource.driver-class-name=${USER_DB_DRIVER:com.mysql.cj.jdbc.Driver}
 spring.datasource.username=${USER_DB_USER_NAME:myusername}
 spring.datasource.password=${USER_DB_USER_PW:astrongpassphrase!}
 spring.jpa.hibernate.ddl-auto=update
-
 # mail configuration
 spring.mail.username=${MAIL_USERNAME}
 spring.mail.password=${MAIL_PASSWORD}
 spring.mail.host=${MAIL_HOST:smtp.gmail.com}
 spring.mail.default-encoding=UTF-8
 spring.mail.port=${MAIL_PORT:587}
-
 # global service route configuration for mail interaction requests
 service.host.name=${DM_SERVICE_HOST:localhost}
 service.host.protocol=${DM_HOST_PROTOCOL:https}
 service.host.port=${DM_SERVICE_PORT:-1}
-
 # route for mail confirmation consumption
 email-confirmation-endpoint=${EMAIL_CONFIRMATION_ENDPOINT:login}
 email-confirmation-parameter=${EMAIL_CONFIRMATION_PARAMETER:confirm-email}
-
 # route for password reset
 password-reset-endpoint=${PASSWORD_RESET_ENDPOINT:new-password}
 password-reset-parameter=${PASSWORD_RESET_PARAMETER:user-id}
+# openbis-client credentials
+openbis.user.name=${OPENBIS_USER_NAME:openbis-username}
+openbis.user.password=${OPENBIS_USER_PASSWORD:openbis-password}
+openbis.datasource.url=${OPENBIS_DATASOURCE_URL:openbis-url}
 
 ```
 

mariadb-connector/pom.xml database-connector/pom.xml

@@ -9,7 +9,7 @@
   </parent>
   <modelVersion>4.0.0</modelVersion>
 
-  <artifactId>mariadb-connector</artifactId>
+  <artifactId>database-connector</artifactId>
   <dependencyManagement>
     <dependencies>
       <dependency>
@@ -26,6 +26,11 @@
       <version>0.11.1</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>life.qbic</groupId>
+      <artifactId>openbis-client-lib</artifactId>
+      <version>1.5.0</version>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-data-jpa</artifactId>

mariadb-connector/src/main/java/life/qbic/authentication/persistence/QbicUserRepo.java database-connector/src/main/java/life/qbic/authentication/persistence/QbicUserRepo.java

@@ -23,7 +23,7 @@ public class ProjectPreviewJpaRepository implements ProjectPreviewLookup {
 
   private final ProjectPreviewRepository projectPreviewRepository;
 
-  public ProjectPreviewJpaRepository(@Autowired ProjectPreviewRepository projectPreviewRepository) {
+  public ProjectPreviewJpaRepository(ProjectPreviewRepository projectPreviewRepository) {
     Objects.requireNonNull(projectPreviewRepository);
     this.projectPreviewRepository = projectPreviewRepository;
   }

mariadb-connector/src/main/java/life/qbic/authentication/persistence/UserJpaRepository.java database-connector/src/main/java/life/qbic/authentication/persistence/UserJpaRepository.java

@@ -1,7 +1,11 @@
 package life.qbic.projectmanagement.persistence;
 
+import static life.qbic.logging.service.LoggerFactory.logger;
+
 import java.util.List;
 import java.util.Optional;
+import life.qbic.logging.api.Logger;
+import life.qbic.projectmanagement.application.ProjectCreationService;
 import life.qbic.projectmanagement.domain.project.Project;
 import life.qbic.projectmanagement.domain.project.ProjectCode;
 import life.qbic.projectmanagement.domain.project.ProjectId;
@@ -12,7 +16,7 @@
 
 
 /**
- * <b>Project JPA repository</b>
+ * <b>Project repository implementation</b>
  *
  * <p>Implementation for the {@link ProjectRepository} interface.
  *
@@ -24,25 +28,39 @@
  * dependency
  * upon creation.
  *
+ * Also handles project storage in openBIS through {@link QbicProjectDataRepo}
+ *
  * @since 1.0.0
  */
 @Component
 @Scope("singleton")
-public class ProjectJpaRepository implements ProjectRepository {
+public class ProjectRepositoryImpl implements ProjectRepository {
 
+  private static final Logger log = logger(ProjectRepositoryImpl.class);
   private final QbicProjectRepo projectRepo;
+  private final QbicProjectDataRepo projectDataRepo;
 
   @Autowired
-  public ProjectJpaRepository(QbicProjectRepo projectRepo) {
+  public ProjectRepositoryImpl(QbicProjectRepo projectRepo, QbicProjectDataRepo projectDataRepo) {
     this.projectRepo = projectRepo;
+    this.projectDataRepo = projectDataRepo;
   }
 
   @Override
   public void add(Project project) {
-    if (doesProjectExistWithId(project.getId())) {
+    ProjectCode projectCode = project.getProjectCode();
+    if (doesProjectExistWithId(project.getId()) || projectDataRepo.projectExists(projectCode)) {
       throw new ProjectExistsException();
     }
     projectRepo.save(project);
+
+    try {
+      projectDataRepo.add(project.getProjectCode());
+    } catch (Exception e) {
+      log.error("Could not add project to openBIS. Removing project from repository, as well.");
+      projectRepo.delete(project);
+      throw e;
+    }
   }
 
   @Override

mariadb-connector/src/main/java/life/qbic/finance/persistence/OfferPreviewRepository.java database-connector/src/main/java/life/qbic/finance/persistence/OfferPreviewRepository.java

@@ -0,0 +1,33 @@
+package life.qbic.projectmanagement.persistence;
+
+import life.qbic.projectmanagement.domain.project.Project;
+import life.qbic.projectmanagement.domain.project.ProjectCode;
+
+
+/**
+ * <b>Project Data Storage Interface</b>
+ *
+ * <p>Provides access to the persistence layer that handles the {@link Project} data storage.
+ *
+ * @since 1.0.0
+ */
+public interface QbicProjectDataRepo {
+
+  /**
+   * Creates a reference to a {@link Project} in the data repository to connect project data.
+   *
+   * @param projectCode the {@link ProjectCode} of the project reference to store
+   * @since 1.0.0
+   */
+  void add(ProjectCode projectCode);
+
+  /**
+   * Searches for projects that contain the provided project code
+   *
+   * @param projectCode the {@link ProjectCode} to search for in the data repository
+   * @return true, if a project with that code already exists in the system, false if not
+   * @since 1.0.0
+   */
+  boolean projectExists(ProjectCode projectCode);
+
+}

mariadb-connector/src/main/java/life/qbic/finance/persistence/OfferRepository.java database-connector/src/main/java/life/qbic/finance/persistence/OfferRepository.java

@@ -29,15 +29,6 @@ public class Person {
   @Column(name = "referenceId")
   private String referenceId;
 
-  public void setId(Long id) {
-    this.id = id;
-  }
-
-  @Id
-  public Long getId() {
-    return id;
-  }
-
   public String fullName() {
     return this.firstName + " " + this.lastName;
   }
@@ -49,36 +40,4 @@ public String referenceId() {
   public String emailAddress() {
     return this.email;
   }
-
-  private String getFirstName() {
-    return firstName;
-  }
-
-  private void setFirstName(String firstName) {
-    this.firstName = firstName;
-  }
-
-  private String getLastName() {
-    return lastName;
-  }
-
-  private void setLastName(String lastName) {
-    this.lastName = lastName;
-  }
-
-  private String getEmail() {
-    return email;
-  }
-
-  private void setEmail(String email) {
-    this.email = email;
-  }
-
-  private String getReferenceId() {
-    return referenceId;
-  }
-
-  private void setReferenceId(String referenceId) {
-    this.referenceId = referenceId;
-  }
 }

mariadb-connector/src/main/java/life/qbic/finance/persistence/SimpleOfferSearchService.java database-connector/src/main/java/life/qbic/finance/persistence/SimpleOfferSearchService.java

@@ -17,7 +17,7 @@ public class PersonReferenceJpaRepository implements PersonLookupService {
 
   private final PersonRepo personRepo;
 
-  public PersonReferenceJpaRepository(@Autowired PersonRepo personRepo) {
+  public PersonReferenceJpaRepository(PersonRepo personRepo) {
     this.personRepo = personRepo;
   }