Release 1.0.0 Beta.11 #207

Release 1.0.0 beta.11

Author: jenniferboedker

.designer/designer-theme.css

@@ -4,6 +4,31 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
+1.0.0-beta.11 (2022-01-26)
+---------------------------
+
+**Added**
+
+* Changed notification style (#191)
+
+* Add sorting by subscription and last updated (#204)
+
+* Implement searchbar for projects and samples (#205)
+
+* Add filtering by status (#199)
+
+**Fixed**
+
+* Update overall UI design (#198)
+
+* Add tooltips and cursor change for better UX (#201)
+
+**Dependencies**
+
+* ``life.qbic:data-model-lib:2.12.0`` -> ``2.15.0``
+
+**Deprecated**
+
 1.0.0-beta.10 (2022-01-18)
 ---------------------------
 

CHANGELOG.rst

@@ -21,7 +21,7 @@ You can run the application in a ``testing`` mode:
 
 .. code-block:: bash
 
-  mvn clean jetty:run -Denvironment=testing -Demail=<email> -Dauth_id=<auth provider id>
+  mvn clean jetty:run -Denvironment=testing -Demail=<email> -Dauth_id=<auth provider id> -Dfirst_name=<first name> -Dlast_name=<last name>
 
 You also see, that you need to provide two more properties then, ``email`` and ``auth_id``. The email property is used
 to generate your portal-user id, the auth-id is the one that is provided by the authentication provider after successful login into the portal.

README.rst

@@ -57,9 +57,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.0.0-beta.9'
+version = '1.0.0-beta.11-SNAPSHOT'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0-beta.9'
+release = '1.0.0-beta.11-SNAPSHOT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/conf.py

@@ -10,7 +10,7 @@
   </modules>
   <artifactId>sample-tracking-status-overview</artifactId>
   <groupId>life.qbic</groupId>
-  <version>1.0.0-beta.10</version> <!-- <<QUBE_FORCE_BUMP>> -->
+  <version>1.0.0-beta.11</version> <!-- <<QUBE_FORCE_BUMP>> -->
   <name>Sample Tracking Status Overview</name>
   <url>https://github.com/qbicsoftware/sample-tracking-status-overview</url>
   <description>Gives a visual overview of sample statuses</description>
@@ -133,7 +133,7 @@
       <dependency>
         <groupId>life.qbic</groupId>
         <artifactId>data-model-lib</artifactId>
-        <version>2.12.0</version>
+        <version>2.15.0</version>
       </dependency>
       <dependency>
         <groupId>org.apache.logging.log4j</groupId>

pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>sample-tracking-status-overview</artifactId>
         <groupId>life.qbic</groupId>
-        <version>1.0.0-beta.10</version>
+        <version>1.0.0-beta.11</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <packaging>war</packaging>
@@ -16,7 +16,7 @@
         <dependency>
             <groupId>life.qbic</groupId>
             <artifactId>sample-tracking-status-overview-domain</artifactId>
-            <version>1.0.0-beta.10</version>
+            <version>1.0.0-beta.11</version>
             <scope>compile</scope>
         </dependency>
         <dependency>

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

@@ -22,11 +22,14 @@ 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.AppView
+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.ProjectOverviewView
 import life.qbic.portal.sampletracking.components.projectoverview.ProjectOverviewViewModel
+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.samplelist.FailedQCSamplesController
@@ -35,6 +38,7 @@ import life.qbic.portal.sampletracking.components.projectoverview.subscribe.Subs
 import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscribeProjectPresenter
 import life.qbic.portal.sampletracking.components.sampleoverview.SampleOverviewView
 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
@@ -55,7 +59,7 @@ import life.qbic.portal.utils.ConfigurationManagerFactory
  *
  * @since 1.0.0
  *
-*/
+ */
 class DependencyManager {
     private VerticalLayout portletView
     private ConfigurationManager configurationManager
@@ -149,55 +153,25 @@ class DependencyManager {
     }
 
     private VerticalLayout setupPortletView() {
-        ProjectOverviewView projectOverviewView = createProjectOverviewView()
-        SampleOverviewView sampleOverviewView = new SampleOverviewView(notificationService)
-        SampleOverviewController projectSamplesController = setupProjectSamplesUseCase(sampleOverviewView.getPresenter())
+        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)
 
-        AppView mainView = new AppView(projectOverviewView, sampleOverviewView, projectSamplesController)
-        return mainView
-    }
-
-    /**
-     * Creates a new ProjectOverviewView using
-     * <ul>
-     *     <li>{@link #projectResourceService}</li>
-     *     <li>{@link #statusCountService}</li>
-     * </ul>
-     * @return a new ProjectOverviewView
-     */
-    private ProjectOverviewView createProjectOverviewView() {
-        ProjectOverviewViewModel viewModel = new ProjectOverviewViewModel(projectResourceService, statusCountService,
-                this.subscriptionUser)
-        SubscribeProjectController subscribeProjectController = setupSubscribeProjectUseCase()
-        DownloadProjectController downloadController = setupDownloadProjectUseCase(viewModel)
-
-        FailedQCSamplesView failedQCSamplesView = new FailedQCSamplesView(notificationService)
-        FailedQCSamplesController failedQCSamplesController = setupFailedQCUseCase(failedQCSamplesView.getPresenter())
-
-        ProjectOverviewView view = new ProjectOverviewView(notificationService,
-                viewModel,
-                downloadController,
-                failedQCSamplesView,
-                failedQCSamplesController,
-                subscribeProjectController)
-        return view
+        return mainPage
     }
 
     private SampleOverviewController setupProjectSamplesUseCase(GetSamplesInfoOutput output) {
         GetSamplesInfo getSamplesInfo = new GetSamplesInfo(sampleStatusDataSource, downloadSamplesDataSource, getSamplesInfoDataSource, output)
         return new SampleOverviewController(getSamplesInfo)
     }
 
-    private FailedQCSamplesController setupFailedQCUseCase(GetSamplesInfoOutput output){
-        GetSamplesInfo getSamplesInfo = new GetSamplesInfo(sampleStatusDataSource, downloadSamplesDataSource,getSamplesInfoDataSource, output)
-        return new FailedQCSamplesController(getSamplesInfo)
-    }
-
-    private DownloadProjectController setupDownloadProjectUseCase(ProjectOverviewViewModel viewModel) {
+    private DownloadProjectController setupDownloadProjectUseCase(ViewModel viewModel) {
         DownloadSamplesOutput output = new ManifestPresenter(notificationService, viewModel)
         DownloadSamples downloadSamples = new DownloadSamples(downloadSamplesDataSource, output)
-        
+
         return new DownloadProjectController(downloadSamples)
     }
 
@@ -213,7 +187,7 @@ class DependencyManager {
      */
     private void populateProjectService() {
         LoadProjectsOutput output = new LoadProjectsPresenter(projectResourceService, notificationService)
-        LoadProjectsInput loadProjects = new LoadProjects(loadProjectsDataSource, output, lastChangedDateDataSource, subscribedProjectsDataSource )
+        LoadProjectsInput loadProjects = new LoadProjects(loadProjectsDataSource, output, lastChangedDateDataSource, subscribedProjectsDataSource)
         loadProjects.withSubscriptions(subscriptionUser)
     }
 
@@ -231,7 +205,7 @@ class DependencyManager {
         }
     }
 
-        /**
+    /**
      * Returns the global notification center
      * @return a notification center that handles app notifications
      */

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

@@ -37,7 +37,7 @@ class StatusOverviewApp extends QBiCPortletUI {
         // The constructor MUST NOT fail since the user does not get any feedback otherwise.
         try {
             PortalUser user = loadUser()
-            log.info("Loading portlet for user: $user.userId - $user.authProviderId")
+            log.info("Loading portlet for user: $user.userId - $user.firstName $user.lastName ($user.authProviderId)")
             dependencyManager = new DependencyManager(user)
             notificationCenter = dependencyManager.getNotificationCenter()
         } catch (Exception e) {

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

@@ -1,15 +1,12 @@
 package life.qbic.portal.sampletracking.components
 
-import com.vaadin.ui.Button
+
 import com.vaadin.ui.Component
-import com.vaadin.ui.Grid
 import com.vaadin.ui.HorizontalLayout
 import com.vaadin.ui.Label
 import com.vaadin.ui.VerticalLayout
-import com.vaadin.ui.components.grid.ItemClickListener
 import com.vaadin.ui.themes.ValoTheme
 import life.qbic.portal.sampletracking.components.projectoverview.ProjectOverviewView
-import life.qbic.portal.sampletracking.components.projectoverview.ProjectSummary
 import life.qbic.portal.sampletracking.components.sampleoverview.SampleOverviewController
 import life.qbic.portal.sampletracking.components.sampleoverview.SampleOverviewView
 import life.qbic.portal.sampletracking.components.toggle.ToggleButton
@@ -28,14 +25,14 @@ class AppView extends VerticalLayout {
     private final SampleOverviewController sampleOverviewController
 
     private final HorizontalLayout hotbar = new HorizontalLayout()
-    protected final Label titleLabel = new Label("Sample Status Portlet")
+    protected final Label appTitleLabel = new Label("Sample Status Viewer")
     private final ToggleButton projectSampleToggle
 
     AppView(ProjectOverviewView projectOverviewView, SampleOverviewView sampleOverviewView, SampleOverviewController sampleOverviewController) {
         this.setMargin(true)
         this.setSpacing(true)
 
-        titleLabel.addStyleName(ValoTheme.LABEL_HUGE)
+        appTitleLabel.addStyleName(ValoTheme.LABEL_HUGE)
 
         this.projectOverviewView = projectOverviewView
         this.sampleOverviewView = sampleOverviewView
@@ -52,11 +49,11 @@ class AppView extends VerticalLayout {
         showProjectView(true)
         showSampleView(false)
 
-        this.addComponents(titleLabel, createSpacer(2, Unit.EM), hotbar, projectOverviewView, sampleOverviewView)
+        this.addComponents(appTitleLabel, createSpacer(2, Unit.EM), hotbar, projectOverviewView, sampleOverviewView)
     }
 
 
-    private void listenToProjectSelectionChange(){
+    private void listenToProjectSelectionChange() {
         projectOverviewView.onSelectedProjectChange({
             if (it) {
                 projectSampleToggle.setEnabled(true)
@@ -71,13 +68,11 @@ class AppView extends VerticalLayout {
     private void showProjectView(Boolean visible) {
         projectOverviewView.setVisible(visible)
         projectOverviewView.getHotbar().setVisible(visible)
-        if (visible) this.titleLabel.value = projectOverviewView.getTitle()
     }
 
     private void showSampleView(Boolean visible) {
         sampleOverviewView.setVisible(visible)
         sampleOverviewView.getHotbar().setVisible(visible)
-        if (visible) this.titleLabel.value = sampleOverviewView.getTitle()
     }
 
     private void addHotbarItem(HorizontalLayout item) {

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

@@ -0,0 +1,42 @@
+package life.qbic.portal.sampletracking.components;
+
+import life.qbic.portal.sampletracking.components.projectoverview.ProjectView;
+import com.vaadin.ui.VerticalLayout
+import life.qbic.portal.sampletracking.components.sampleoverview.SampleOverviewController;
+import life.qbic.portal.sampletracking.components.sampleoverview.SampleView
+
+
+class MainPage extends VerticalLayout {
+
+    private final ProjectView projectView
+    private final SampleView sampleView
+    private final ViewModel viewModel
+    private final SampleOverviewController controller
+
+    MainPage(ProjectView projectLayout, SampleView sampleLayout, ViewModel viewModel, SampleOverviewController sampleOverviewController) {
+        this.projectView = projectLayout
+        this.sampleView = sampleLayout
+        this.viewModel = viewModel
+        this.controller = sampleOverviewController
+
+        this.addComponents(projectLayout, sampleLayout)
+        sampleLayout.setVisible(false)
+
+        listenToProjectSelectionChange()
+    }
+
+    private void listenToProjectSelectionChange() {
+        projectView.onSelectedProjectChange({
+            if (it) {
+                controller.getSamplesFor(it.code)
+            } else {
+                sampleView.reset()
+            }
+        })
+
+        viewModel.addPropertyChangeListener("projectViewEnabled", {
+            projectView.setVisible(viewModel.projectViewEnabled)
+            sampleView.setVisible(!viewModel.projectViewEnabled)
+        })
+    }
+}

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

@@ -23,7 +23,7 @@ class NotificationHandler {
     }
 
     private static void showMessage(String message, Type type) {
-        Notification notification = new Notification(message, type)
+        StyledNotification notification = new StyledNotification(message, type)
         if (Page.getCurrent()) {
             notification.show(Page.getCurrent())
         } else {
@@ -33,8 +33,8 @@ class NotificationHandler {
 
 
     void subscribeToService() {
-        notificationService.subscribe({showMessage(it, Type.ERROR_MESSAGE)}, Topic.NOTIFICATION_FAILURE)
-        notificationService.subscribe({showMessage(it, Type.HUMANIZED_MESSAGE)}, Topic.NOTIFICATION_SUCCESS)
-        notificationService.subscribe({showMessage(it, Type.ASSISTIVE_NOTIFICATION)}, Topic.NOTIFICATION_INFO)
+        notificationService.subscribe({ showMessage(it, Type.ERROR_MESSAGE) }, Topic.NOTIFICATION_FAILURE)
+        notificationService.subscribe({ showMessage(it, Type.HUMANIZED_MESSAGE) }, Topic.NOTIFICATION_SUCCESS)
+        notificationService.subscribe({ showMessage(it, Type.ASSISTIVE_NOTIFICATION) }, Topic.NOTIFICATION_INFO)
     }
 }

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

@@ -9,7 +9,7 @@ class StyledNotification extends Notification {
 
     StyledNotification(String caption) {
         super(caption)
-        setNotificationProperties()
+        setNotificationProperties(Type.HUMANIZED_MESSAGE)
     }
 
     StyledNotification(String caption, Type type) {