1.0.0-beta.8 #185

Release 1.0.0 beta.8 containing security fixes, colored sample statuses, and adapts to the new DB structure

Author: jenniferboedker

.github/workflows/sync_project.yml

@@ -4,6 +4,31 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
+1.0.0-beta.8 (2021-12-22)
+---------------------------
+
+**Added**
+
+* Color sample status (#177)
+
+* Use person table instead of subscriber (#183)
+
+**Fixed**
+
+* Manifest file download is reset correctly after project selection change (`#169 <https://github.com/qbicsoftware/sample-tracking-status-overview/pull/169>`_)
+
+* CVE-2021-45105
+
+* CVE-2021-33609
+
+**Dependencies**
+
+* ``org.apache.logging.log4j:log4j-core:2.16.0`` -> ``2.17.0``
+
+* ``org.apache.logging.log4j:log4j-api:2.16.0`` -> ``2.17.0``
+
+* ``com.vaadin:vaadin-bom:8.14.0`` -> ``8.14.1``
+
 1.0.0-beta.7 (2021-12-15)
 ---------------------------
 
@@ -16,6 +41,7 @@ This project adheres to `Semantic Versioning <https://semver.org/>`_.
 **Dependencies**
 
 * ``org.apache.logging.log4j:log4j-core:2.15.0`` -> ``2.16.0``
+
 * ``org.apache.logging.log4j:log4j-api:2.15.0`` -> ``2.16.0``
 
 1.0.0-beta.6 (2021-12-13)
@@ -30,6 +56,7 @@ This project adheres to `Semantic Versioning <https://semver.org/>`_.
 **Dependencies**
 
 * ``org.apache.logging.log4j:log4j-core:2.13.2`` -> ``2.15.0``
+
 * ``org.apache.logging.log4j:log4j-api:2.13.2`` -> ``2.15.0``
 
 **Deprecated**

.qube.yml

@@ -57,9 +57,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.0.0-beta.6'
+version = '1.0.0-beta.8'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0-beta.6'
+release = '1.0.0-beta.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

CHANGELOG.rst

@@ -2,17 +2,17 @@
 <project
   xmlns="http://maven.apache.org/POM/4.0.0"
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <modules>
     <module>sample-tracking-status-overview-app</module>
     <module>sample-tracking-status-overview-domain</module>
   </modules>
   <artifactId>sample-tracking-status-overview</artifactId>
   <groupId>life.qbic</groupId>
-  <version>1.0.0-beta.7</version> <!-- <<QUBE_FORCE_BUMP>> -->
+  <version>1.0.0-beta.8</version> <!-- <<QUBE_FORCE_BUMP>> -->
   <name>Sample Tracking Status Overview</name>
-  <url>http://github.com/qbicsoftware/sample-tracking-status-overview</url>
+  <url>https://github.com/qbicsoftware/sample-tracking-status-overview</url>
   <description>Gives a visual overview of sample statuses</description>
   <packaging>pom</packaging>
   <!-- we only need to tell maven where to find our parent pom and other QBiC dependencies -->
@@ -23,7 +23,9 @@
 
     <groovy.version>3.0.8</groovy.version>
 
-    <vaadin.version>8.14.0</vaadin.version>
+    <log4j.version>2.17.0</log4j.version>
+
+    <vaadin.version>8.14.1</vaadin.version>
     <vaadin.plugin.version>8.14.0</vaadin.plugin.version>
   </properties>
 
@@ -136,12 +138,12 @@
       <dependency>
         <groupId>org.apache.logging.log4j</groupId>
         <artifactId>log4j-api</artifactId>
-        <version>2.16.0</version>
+        <version>${log4j.version}</version>
       </dependency>
       <dependency>
         <groupId>org.apache.logging.log4j</groupId>
         <artifactId>log4j-core</artifactId>
-        <version>2.16.0</version>
+        <version>${log4j.version}</version>
       </dependency>
     </dependencies>
   </dependencyManagement>

docs/conf.py

@@ -5,21 +5,18 @@
     <parent>
         <artifactId>sample-tracking-status-overview</artifactId>
         <groupId>life.qbic</groupId>
-        <version>1.0.0-beta.7</version> <!-- <<QUBE_FORCE_BUMP>> -->
+        <version>1.0.0-beta.8</version> <!-- <<QUBE_FORCE_BUMP>> -->
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <packaging>war</packaging>
-    <properties>
-        <log4j.version>2.16.0</log4j.version>
-    </properties>
     <artifactId>sample-tracking-status-overview-app</artifactId>
     <name>The sample tracking status overview portlet</name>
     <url>http://github.com/qbicsoftware/sample-tracking-status-overview</url>
     <dependencies>
         <dependency>
             <groupId>life.qbic</groupId>
             <artifactId>sample-tracking-status-overview-domain</artifactId>
-            <version>1.0.0-beta.7</version> <!-- <<QUBE_FORCE_BUMP>> -->
+            <version>1.0.0-beta.8</version> <!-- <<QUBE_FORCE_BUMP>> -->
             <scope>compile</scope>
         </dependency>
         <dependency>

pom.xml

@@ -93,6 +93,7 @@ class DependencyManager {
     private static Subscriber subscriberFor(PortalUser portalUser) {
         return new Subscriber(portalUser.firstName,
                 portalUser.lastName,
+                portalUser.title.value,
                 portalUser.emailAddress)
     }
 

qube.cfg

@@ -4,6 +4,7 @@ import com.vaadin.data.provider.DataProvider
 import com.vaadin.data.provider.ListDataProvider
 import com.vaadin.event.selection.SingleSelectionEvent
 import com.vaadin.icons.VaadinIcons
+import com.vaadin.server.ClientConnector
 import com.vaadin.server.FileDownloader
 import com.vaadin.server.StreamResource
 import com.vaadin.shared.ui.ContentMode
@@ -23,8 +24,8 @@ import life.qbic.portal.sampletracking.components.projectoverview.samplelist.Fai
 import life.qbic.portal.sampletracking.components.projectoverview.samplelist.FailedQCSamplesView
 import life.qbic.portal.sampletracking.components.projectoverview.statusdisplay.SampleCount
 import life.qbic.portal.sampletracking.components.projectoverview.statusdisplay.State
-import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscriptionCheckboxFactory
 import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscribeProjectController
+import life.qbic.portal.sampletracking.components.projectoverview.subscribe.SubscriptionCheckboxFactory
 
 import java.util.function.Consumer
 
@@ -56,7 +57,6 @@ class ProjectOverviewView extends VerticalLayout implements HasHotbar, HasTitle
     private static final Collection<String> columnIdsWithFilters = ["ProjectCode", "ProjectTitle"]
 
     final static int MAX_CODE_COLUMN_WIDTH = 400
-    private FileDownloader fileDownloader
     private HorizontalLayout projectButtonBar = new HorizontalLayout()
 
     ProjectOverviewView(NotificationService notificationService, ProjectOverviewViewModel viewModel, DownloadProjectController downloadProjectController
@@ -171,21 +171,26 @@ class ProjectOverviewView extends VerticalLayout implements HasHotbar, HasTitle
     private Button setupDownloadButton() {
         Button downloadManifestAction = new Button("Download Manifest", VaadinIcons.DOWNLOAD)
         viewModel.addPropertyChangeListener("generatedManifest", {
-            if (isDownloadAvailable()) {
-                this.fileDownloader = new FileDownloader(new StreamResource({viewModel.getManifestInputStream()}, "manifest.txt"))
-                this.fileDownloader.extend(downloadManifestAction)
-            } else {
-                if (this.fileDownloader) {
-                    if (downloadManifestAction.extensions.contains(fileDownloader)) {
-                        downloadManifestAction.removeExtension(this.fileDownloader)
-                    }
+            if (it.getOldValue() != it.getNewValue()) {
+                removeFileDownloaders(downloadManifestAction)
+                if (it.newValue) {
+                    FileDownloader fileDownloader = new FileDownloader(new StreamResource({viewModel.getManifestInputStream()}, "manifest.txt"))
+                    fileDownloader.extend(downloadManifestAction)
                 }
             }
         })
         enableWhenDownloadIsAvailable(downloadManifestAction)
         return downloadManifestAction
     }
 
+    private static void removeFileDownloaders(ClientConnector clientConnector) {
+        def fileDownloaders = clientConnector.extensions.stream()
+                .filter((extension) -> extension instanceof FileDownloader)
+                .collect()
+        fileDownloaders.forEach(clientConnector::removeExtension)
+    }
+
+
     private void setupProjects() {
         projectGrid = new Grid<ProjectSummary>()
         fillProjectsGrid()

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

@@ -49,8 +49,9 @@ class SubscribeProjectPresenter implements SubscribeProjectOutput {
      */
     @Override
     void subscriptionFailed(Subscriber subscriber, String projectCode) {
+        //todo this message might not be meaningful to the user, e.g. if a person entry is missing
         String message = "An unexpected error occured while trying to subscribe to project ${projectCode}. " +
-                    "Please contact ${Constants.CONTACT_HELPDESK}."
+                    "${Constants.CONTACT_HELPDESK}."
         notificationService.publishFailure(message)
     }
 
@@ -78,8 +79,9 @@ class SubscribeProjectPresenter implements SubscribeProjectOutput {
      */
     @Override
     void unsubscriptionFailed(Subscriber subscriber, String projectCode) {
+        //todo this message might not be meaningful to the user
         String message = "An unexpected error occured while trying to unsubscribe from project ${projectCode}. " +
-                    "Please contact ${Constants.CONTACT_HELPDESK}."
+                    "${Constants.CONTACT_HELPDESK}."
         notificationService.publishFailure(message)
     }
 }

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

@@ -7,10 +7,13 @@ import com.vaadin.ui.HorizontalLayout
 import com.vaadin.ui.VerticalLayout
 import life.qbic.business.samples.Sample
 import life.qbic.business.samples.info.GetSamplesInfoOutput
+import life.qbic.datamodel.samples.Status
 import life.qbic.portal.sampletracking.communication.notification.NotificationService
 import life.qbic.portal.sampletracking.components.HasHotbar
 import life.qbic.portal.sampletracking.components.HasTitle
 import life.qbic.portal.sampletracking.components.Resettable
+import life.qbic.portal.sampletracking.components.projectoverview.statusdisplay.SampleCount
+import life.qbic.portal.sampletracking.components.projectoverview.statusdisplay.State
 
 /**
  * <b>A view component showing a list of samples</b>
@@ -51,13 +54,24 @@ class SampleOverviewView extends VerticalLayout implements HasHotbar, HasTitle,
         ListDataProvider<Sample> dataProvider = ListDataProvider.ofCollection(samples)
         samplesGrid.addColumn(Sample::getCode).setCaption("Sample Code").setId("SampleCode")
         samplesGrid.addColumn(Sample::getName).setCaption("Sample Name").setId("SampleName")
-        samplesGrid.addColumn(Sample::getStatus).setCaption("Sample Status").setId("SampleStatus")
+        samplesGrid.addColumn(Sample::getStatus).setCaption("Sample Status").setId("SampleStatus").setStyleGenerator({Sample sample -> determineColor(sample.status)})
         samplesGrid.setSelectionMode(Grid.SelectionMode.NONE)
         samplesGrid.setDataProvider(dataProvider)
         samplesGrid.setHeightMode(HeightMode.ROW)
         return samplesGrid
     }
 
+    private static String determineColor(Status status) {
+        switch (status){
+            case Status.DATA_AVAILABLE:
+                return State.COMPLETED.getCssClass()
+            case Status.SAMPLE_QC_FAIL:
+                return State.FAILED.getCssClass()
+            default:
+                return State.IN_PROGRESS.getCssClass()
+        }
+    }
+
     /**
      * Model for this view component
      */