Release 1.1.4 #247 from qbicsoftware/development

Fixed loading time and filtered project samples

Author: jenniferboedker

pom.xml

@@ -21,7 +21,7 @@
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>
 
-    <groovy.version>3.0.8</groovy.version>
+    <groovy.version>3.0.12</groovy.version>
 
     <log4j.version>2.17.1</log4j.version>
 
@@ -133,7 +133,7 @@
       <dependency>
         <groupId>life.qbic</groupId>
         <artifactId>data-model-lib</artifactId>
-        <version>2.15.0</version>
+        <version>2.20.0</version>
       </dependency>
       <dependency>
         <groupId>org.apache.logging.log4j</groupId>

sample-tracking-status-overview-app/pom.xml

@@ -32,8 +32,9 @@
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>8.0.28</version>
+            <version>8.0.30</version>
         </dependency>
+
         <!-- https://mvnrepository.com/artifact/com.liferay.portal/portal-service -->
         <dependency>
             <groupId>com.liferay.portal</groupId>
@@ -52,8 +53,11 @@
             <artifactId>jackson-databind</artifactId>
             <version>2.13.3</version>
         </dependency>
-
-
+        <dependency>
+            <groupId>com.fasterxml.jackson.datatype</groupId>
+            <artifactId>jackson-datatype-jsr310</artifactId>
+            <version>2.13.3</version>
+        </dependency>
         <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
         <dependency>
             <groupId>org.slf4j</groupId>
@@ -103,9 +107,15 @@
         <dependency>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-resources-plugin</artifactId>
-            <version>3.2.0</version>
+            <version>3.3.0</version>
             <type>maven-plugin</type>
         </dependency>
+        <!-- https://mvnrepository.com/artifact/org.apache.httpcomponents.client5/httpclient5 -->
+        <dependency>
+            <groupId>org.apache.httpcomponents.client5</groupId>
+            <artifactId>httpclient5</artifactId>
+            <version>5.1.3</version>
+        </dependency>
         <dependency>
             <groupId>life.qbic</groupId>
             <artifactId>openbis-api</artifactId>

sample-tracking-status-overview-app/src/main/groovy/life/qbic/portal/sampletracking/Constants.groovy

@@ -1,51 +1,25 @@
 package life.qbic.portal.sampletracking
 
 import com.vaadin.ui.VerticalLayout
-import life.qbic.business.project.Project
-import life.qbic.business.project.load.*
-import life.qbic.business.project.subscribe.SubscribeProject
-import life.qbic.business.project.subscribe.SubscribeProjectOutput
-import life.qbic.business.project.subscribe.Subscriber
-import life.qbic.business.project.subscribe.SubscriptionDataSource
-import life.qbic.business.samples.count.CountSamples
-import life.qbic.business.samples.count.CountSamplesDataSource
-import life.qbic.business.samples.count.CountSamplesOutput
-import life.qbic.business.samples.count.StatusCount
-import life.qbic.business.samples.download.DownloadSamples
-import life.qbic.business.samples.download.DownloadSamplesDataSource
-import life.qbic.business.samples.download.DownloadSamplesOutput
-import life.qbic.business.samples.info.GetSamplesInfo
-import life.qbic.business.samples.info.GetSamplesInfoDataSource
-import life.qbic.business.samples.info.GetSamplesInfoOutput
-import life.qbic.business.samples.info.SampleStatusDataSource
+import groovy.transform.CompileStatic
+import life.qbic.business.subscribe.Subscriber
 import life.qbic.datamodel.dtos.portal.PortalUser
-import life.qbic.portal.sampletracking.communication.notification.MessageBroker
-import life.qbic.portal.sampletracking.communication.notification.NotificationService
-import life.qbic.portal.sampletracking.components.MainPage
-import life.qbic.portal.sampletracking.components.NotificationHandler
-import life.qbic.portal.sampletracking.components.ViewModel
-import life.qbic.portal.sampletracking.components.projectoverview.CountSamplesPresenter
-import life.qbic.portal.sampletracking.components.projectoverview.LoadProjectsPresenter
-import life.qbic.portal.sampletracking.components.projectoverview.ProjectView
-import life.qbic.portal.sampletracking.components.projectoverview.download.DownloadProjectController
-import life.qbic.portal.sampletracking.components.projectoverview.download.ManifestPresenter
-import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscribeProjectController
-import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscribeProjectPresenter
-import life.qbic.portal.sampletracking.components.sampleoverview.SampleOverviewController
-import life.qbic.portal.sampletracking.components.sampleoverview.SampleView
-import life.qbic.portal.sampletracking.datasources.Credentials
-import life.qbic.portal.sampletracking.datasources.OpenBisConnector
-import life.qbic.portal.sampletracking.datasources.database.DatabaseSession
-import life.qbic.portal.sampletracking.datasources.samples.SamplesDbConnector
-import life.qbic.portal.sampletracking.datasources.subscriptions.SubscriptionsDbConnector
-import life.qbic.portal.sampletracking.resource.ResourceService
-import life.qbic.portal.sampletracking.resource.project.ProjectResourceService
-import life.qbic.portal.sampletracking.resource.status.StatusCountResourceService
-import life.qbic.portal.sampletracking.services.sample.SampleTracking
-import life.qbic.portal.sampletracking.services.sample.SampleTrackingService
+import life.qbic.portal.sampletracking.data.*
+import life.qbic.portal.sampletracking.data.database.DatabaseSession
+import life.qbic.portal.sampletracking.view.MainView
+import life.qbic.portal.sampletracking.view.notifications.NotificationCenter
+import life.qbic.portal.sampletracking.view.notifications.NotificationHandler
+import life.qbic.portal.sampletracking.view.projects.ProjectStatusComponentProvider
+import life.qbic.portal.sampletracking.view.projects.ProjectView
+import life.qbic.portal.sampletracking.view.projects.SubscriptionCheckboxProvider
+import life.qbic.portal.sampletracking.view.samples.SampleStatusComponentProvider
+import life.qbic.portal.sampletracking.view.samples.SampleView
 import life.qbic.portal.utils.ConfigurationManager
 import life.qbic.portal.utils.ConfigurationManagerFactory
 
+import java.util.concurrent.ExecutorService
+import java.util.concurrent.Executors
+
 import static java.util.Objects.requireNonNull
 
 /**
@@ -58,38 +32,34 @@ import static java.util.Objects.requireNonNull
  * @since 1.0.0
  *
  */
+@CompileStatic
 class DependencyManager {
-    private VerticalLayout portletView
     private ConfigurationManager configurationManager
     private final PortalUser portalUser
-    private final NotificationHandler notificationHandler
-
-    private LoadProjectsDataSource loadProjectsDataSource
-    private LastChangedDateDataSource lastChangedDateDataSource
-    private CountSamplesDataSource countSamplesDataSource
-    private GetSamplesInfoDataSource getSamplesInfoDataSource
-    private DownloadSamplesDataSource downloadSamplesDataSource
-    private SubscriptionDataSource subscriptionDataSource
-    private SubscribedProjectsDataSource subscribedProjectsDataSource
-    private SampleStatusDataSource sampleStatusDataSource
-
-    private ResourceService<Project> projectResourceService
-    private ResourceService<StatusCount> statusCountService
-    private NotificationService notificationService
+
     private Subscriber subscriptionUser
 
-    DependencyManager(PortalUser user) {
+    private static final int PROJECT_LOADING_THREAD_COUNT = 2
+    private static final int SAMPLE_LOADING_THREAD_COUNT = 2
+    private final ExecutorService projectLoadingExecutor = Executors.newFixedThreadPool(PROJECT_LOADING_THREAD_COUNT)
+    private final ExecutorService sampleLoadingExecutor = Executors.newFixedThreadPool(SAMPLE_LOADING_THREAD_COUNT)
+
+
+  private OpenBisConnector openBisConnector
+  private ProjectStatusComponentProvider projectStatusComponentProvider
+  private SampleStatusComponentProvider sampleStatusComponentProvider
+  private SubscriptionCheckboxProvider subscriptionCheckboxProvider
+  private SampleTrackingConnector sampleTrackingConnector
+  private SubscriptionDatabaseConnector subscriptionDatabaseConnector
+  private NotificationCenter notificationCenter
+
+  DependencyManager(PortalUser user) {
         portalUser = user
         subscriptionUser = subscriberFor(portalUser)
         // Load the app environment configuration
         configurationManager = ConfigurationManagerFactory.getInstance()
 
         initializeDependencies()
-        notificationHandler = new NotificationHandler(notificationService)
-
-        populateProjectService()
-        portletView = setupPortletView()
-        populateStatusCountService()
     }
 
     private static Subscriber subscriberFor(PortalUser portalUser) {
@@ -101,15 +71,11 @@ class DependencyManager {
 
 
     private void initializeDependencies() {
-        setupDatabaseConnections()
-        setupServices()
+      setupDatabaseConnections()
+      setupOpenBisConnection()
+      setupSampleTracking()
     }
 
-    private void setupServices() {
-        projectResourceService = new ProjectResourceService()
-        statusCountService = new StatusCountResourceService()
-        notificationService = new MessageBroker()
-    }
 
     private void setupDatabaseConnections() {
         String user = requireNonNull(configurationManager.getMysqlUser(), "Mysql user missing.")
@@ -119,108 +85,97 @@ class DependencyManager {
         String sqlDatabase = requireNonNull(configurationManager.getMysqlDB(), "Mysql database name missing.")
 
         DatabaseSession.init(user, password, host, port, sqlDatabase)
-        SampleTrackingService service = setUpTrackingService()
-        SamplesDbConnector samplesDbConnector = new SamplesDbConnector(DatabaseSession.getInstance(),service)
-        countSamplesDataSource = samplesDbConnector
-        downloadSamplesDataSource = samplesDbConnector
-        lastChangedDateDataSource = samplesDbConnector
-        sampleStatusDataSource = samplesDbConnector
-
-        Credentials openBisCredentials = new Credentials(
-                user: configurationManager.getDataSourceUser(),
-                password: configurationManager.getDataSourcePassword()
-        )
-        OpenBisConnector openBisConnector = new OpenBisConnector(openBisCredentials, portalUser, configurationManager.getDataSourceUrl() + "/openbis/openbis")
-        loadProjectsDataSource = openBisConnector
-        lastChangedDateDataSource = samplesDbConnector
-
-        subscriptionDataSource = new SubscriptionsDbConnector(DatabaseSession.getInstance())
-        getSamplesInfoDataSource = openBisConnector
-
-
-        SubscriptionsDbConnector subscriptionsDbConnector = new SubscriptionsDbConnector(DatabaseSession.getInstance())
-        subscriptionDataSource = subscriptionsDbConnector
-        subscribedProjectsDataSource = subscriptionsDbConnector
-    }
-
-    private SampleTrackingService setUpTrackingService(){
-        String serviceURL = requireNonNull(configurationManager.getSampleTrackingServiceUrl())
-        def user = requireNonNull(configurationManager.getServiceUser())
+        subscriptionDatabaseConnector= new SubscriptionDatabaseConnector(DatabaseSession.getInstance(), subscriptionUser)
 
-        Credentials credentials = new Credentials(
-                user: user.name,
-                password: user.password
-        )
+    }
 
-        return new SampleTracking(serviceURL, credentials)
+  private void setupOpenBisConnection() {
+    Credentials openBisCredentials = new Credentials(
+            user: configurationManager.getDataSourceUser(),
+            password: configurationManager.getDataSourcePassword()
+    )
+    this.openBisConnector = new OpenBisConnector(openBisCredentials, portalUser, configurationManager.getDataSourceUrl() + "/openbis/openbis")
+  }
+
+  private void setupSampleTracking() {
+    if (Objects.nonNull(sampleTrackingConnector)) {
+      return
     }
+    def credentials = new Credentials(configurationManager.getServiceUser().name,
+            configurationManager.getServiceUser().password)
+    sampleTrackingConnector = new SampleTrackingConnector(configurationManager.getSampleTrackingServiceUrl(),
+            "/v2/samples",
+            "/status",
+            "/v2/projects",
+            credentials, getNgsSampleRepository())
+  }
 
     /**
      * @return the main view of the application
      * @since 1.0.0
      */
     VerticalLayout getPortletView() {
-        return portletView
+      def projectView = new ProjectView(getProjectRepository(), getSubscriptionRepository(), getSampleStatusSummaryProvider(), getSubscriptionCheckboxProvider(), getDownloadManifestProvider())
+      def sampleView = new SampleView(getSampleRepository(), getSampleStatusComponentProvider())
+      return new MainView(projectView, sampleView, notificationCenter)
     }
 
-    private VerticalLayout setupPortletView() {
-        ViewModel viewModel = new ViewModel(projectResourceService, statusCountService)
-        SampleView sampleView = new SampleView(viewModel, notificationService)
-        ProjectView projectView = new ProjectView(viewModel, setupSubscribeProjectUseCase(), notificationService, subscriptionUser, setupDownloadProjectUseCase(viewModel))
-        SampleOverviewController sampleOverviewController = setupProjectSamplesUseCase(sampleView.getPresenter())
-
-        MainPage mainPage = new MainPage(projectView, sampleView, viewModel, sampleOverviewController)
+  ProjectRepository getProjectRepository() {
+    return openBisConnector
+  }
 
-        return mainPage
-    }
+  SampleRepository getSampleRepository() {
+    return openBisConnector
+  }
 
-    private SampleOverviewController setupProjectSamplesUseCase(GetSamplesInfoOutput output) {
-        GetSamplesInfo getSamplesInfo = new GetSamplesInfo(sampleStatusDataSource, downloadSamplesDataSource, getSamplesInfoDataSource, output)
-        return new SampleOverviewController(getSamplesInfo)
+  SampleStatusComponentProvider getSampleStatusComponentProvider() {
+    if (Objects.nonNull(sampleStatusComponentProvider)) {
+      return sampleStatusComponentProvider
     }
+    sampleStatusComponentProvider = new SampleStatusComponentProvider(sampleLoadingExecutor, getSampleStatusProvider())
+    return sampleStatusComponentProvider
+  }
 
-    private DownloadProjectController setupDownloadProjectUseCase(ViewModel viewModel) {
-        DownloadSamplesOutput output = new ManifestPresenter(notificationService, viewModel)
-        DownloadSamples downloadSamples = new DownloadSamples(downloadSamplesDataSource, output)
-
-        return new DownloadProjectController(downloadSamples)
+  ProjectStatusComponentProvider getSampleStatusSummaryProvider() {
+    if (Objects.nonNull(projectStatusComponentProvider)) {
+      return projectStatusComponentProvider
     }
-
-    private SubscribeProjectController setupSubscribeProjectUseCase() {
-        SubscribeProjectOutput output = new SubscribeProjectPresenter(projectResourceService, notificationService)
-        SubscribeProject subscribeProject = new SubscribeProject(subscriptionDataSource, output)
-        return new SubscribeProjectController(subscribeProject)
+    projectStatusComponentProvider = new ProjectStatusComponentProvider(projectLoadingExecutor, getProjectStatusProvider())
+    return projectStatusComponentProvider
+  }
+  SampleStatusProvider getSampleStatusProvider() {
+    return sampleTrackingConnector
+  }
+
+  ProjectStatusProvider getProjectStatusProvider() {
+    return sampleTrackingConnector
+  }
+
+  SubscriptionRepository getSubscriptionRepository() {
+    return subscriptionDatabaseConnector
+  }
+
+  SubscriptionCheckboxProvider getSubscriptionCheckboxProvider() {
+    if (Objects.nonNull(subscriptionCheckboxProvider)) {
+      return subscriptionCheckboxProvider
     }
+    subscriptionCheckboxProvider = new SubscriptionCheckboxProvider(getSubscriptionRepository(), getNotificationHandler())
+    return subscriptionCheckboxProvider
+  }
 
-    /**
-     * Triggers the project loading initially to have data in the service
-     * This is to be called after the view was initialized
-     */
-    private void populateProjectService() {
-        LoadProjectsOutput output = new LoadProjectsPresenter(projectResourceService, notificationService)
-        LoadProjectsInput loadProjects = new LoadProjects(loadProjectsDataSource, output, lastChangedDateDataSource, subscribedProjectsDataSource)
-        loadProjects.withSubscriptions(subscriptionUser)
+  NotificationHandler getNotificationHandler() {
+    if (Objects.nonNull(notificationCenter)) {
+      return notificationCenter
     }
+    notificationCenter = new NotificationCenter()
+    return notificationCenter
+  }
 
-    /**
-     * Triggers the project status count loading initially to have data in the service
-     */
-    private void populateStatusCountService() {
-        CountSamplesOutput output = new CountSamplesPresenter(notificationService, statusCountService)
-        CountSamples countSamples = new CountSamples(countSamplesDataSource, output)
-        List<String> projectCodes = projectResourceService.iterator().collect {
-            return it.code
-        }
-        projectCodes.each {
-            countSamples.countSamplesPerStatus(it)
-        }
-    }
+  DownloadManifestProvider getDownloadManifestProvider() {
+    return sampleTrackingConnector
+  }
 
-    /**
-     * Returns the global notification center
-     * @return a notification center that handles app notifications
-     */
-    NotificationHandler getNotificationCenter() {
-        return notificationHandler
-    }
+  NgsSampleRepository getNgsSampleRepository() {
+    return openBisConnector
+  }
 }