From 5ac4971785d5c6e4bd2fda05fe2d0f1834dfda9f Mon Sep 17 00:00:00 2001
From: wow-such-code <andreas.friedrich@uni-tuebingen.de>
Date: Mon, 5 Sep 2022 15:16:34 +0200
Subject: [PATCH 1/4] Prepare version 1.13.0 (#59)

* use latest version of exp design lib (#54)

* only allow unique header columns for metadata update (#53)

Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>

* Add message if space already exists, re-enable button (#55)

* remove parent pom (#49)

* v1.6.0 of utils lib

* fix workflows

Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>
Co-authored-by: Tobias Koch <KochTobi@users.noreply.github.com>
Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de>

* add description for imaging support option (#57)

* improve UI messages (#56)
---
 .github/ISSUE_TEMPLATE/bug_report.md          |  28 ---
 .github/ISSUE_TEMPLATE/feature_request.md     |  20 --
 .github/ISSUE_TEMPLATE/general_question.md    |  13 --
 .github/workflows/build-package.yml           |   4 +-
 .github/workflows/codeql-analysis.yml         |  81 ++++----
 .github/workflows/nexus-publish-snapshots.yml |   2 +-
 .github/workflows/run-tests.yml               |   2 +-
 CHANGELOG.rst                                 |  11 ++
 docs/conf.py                                  |   4 +-
 pom.xml                                       | 181 +++++++++++++++++-
 .../qbic/portal/portlet/ProjectWizardUI.java  |   5 +-
 .../steps/ProjectContextStep.java             |   5 +-
 .../steps/SummaryRegisterStep.java            |   2 +-
 .../ProjectInformationComponent.java          |   2 +-
 .../uicomponents/UploadComponent.java         |   1 +
 .../qbic/projectwizard/views/AdminView.java   |   7 +-
 .../views/MetadataUploadView.java             |  32 +++-
 17 files changed, 266 insertions(+), 134 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md
 delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md
 delete mode 100644 .github/ISSUE_TEMPLATE/general_question.md

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index d162979e..00000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,28 +0,0 @@
----
-name: Bug report
-about: Create a bug report to help us improve
-title: 'Bug Summary'
-labels: 'bug'
-assignees: ''
-
----
-
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**To Reproduce**
-Steps to reproduce the behavior:
-1. ...
-2. ...
-3. ...
-
-**Expected behavior**
-A clear and concise description of what you expected to happen.
-
-**System [please complete the following information]:**
- - OS: e.g. [Ubuntu 18.04]
- - Language Version: [e.g. Python 3.8]
- - Virtual environment: [e.g. Conda]
-
-**Additional context**
-Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index 3bed8fc2..00000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-name: Feature request
-about: Suggest a new feature
-title: 'Feature Request Summary'
-labels: 'enhancement'
-assignees: ''
-
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when ...
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
-
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
diff --git a/.github/ISSUE_TEMPLATE/general_question.md b/.github/ISSUE_TEMPLATE/general_question.md
deleted file mode 100644
index 37c39b39..00000000
--- a/.github/ISSUE_TEMPLATE/general_question.md
+++ /dev/null
@@ -1,13 +0,0 @@
----
-name: General question
-about: Ask a question about anything related to this project
-title: 'Question'
-labels: 'question'
-assignees: ''
-
----
-
-**Question**
-
-Please ask your question here. It can be about the usage of this project, the internals, the implementation or whatever interests you.
-Please use the BUG template for bugs and the FEATURE REQUEST template for feature requests.
diff --git a/.github/workflows/build-package.yml b/.github/workflows/build-package.yml
index fcf076fb..d616186c 100644
--- a/.github/workflows/build-package.yml
+++ b/.github/workflows/build-package.yml
@@ -3,7 +3,7 @@ name: Build Maven Package
 on:
   push:
     branches:
-      - '*'
+      - '**'
   pull_request:
     # The branches below must be a subset of the branches above
     branches: [ main, master ]
@@ -18,7 +18,6 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 1.8
-
       - name: Load local Maven repository cache
         uses: actions/cache@v2
         with:
@@ -26,6 +25,5 @@ jobs:
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
           restore-keys: |
             ${{ runner.os }}-maven-
-
       - name: Run mvn package
         run: mvn -B package --file pom.xml
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 5a03f334..803f763e 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -13,16 +13,15 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ master, development, patch/*, release/*, hotfix/* ]
+    branches: [ main, master, development, release/*, hotfix/* ]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ master ]
+    branches: [ main, master ]
   schedule:
     - cron: '21 1 * * 4'
 
 jobs:
   analyze:
-    name: analyze
     runs-on: ubuntu-latest
     permissions:
       actions: read
@@ -37,47 +36,47 @@ jobs:
         # Learn more about CodeQL language support at https://git.io/codeql-language-support
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
-      with:
-        java-version: 1.8
-        settings-path: ${{ github.workspace }}
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.8
+          settings-path: ${{ github.workspace }}
 
-    - name: Load local Maven repository cache
-      uses: actions/cache@v2
-      with:
-        path: ~/.m2/repository
-        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-        restore-keys: |
-           ${{ runner.os }}-maven-
-           
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v1
 
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      #- run: |
+      #   make bootstrap
+      #   make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1
diff --git a/.github/workflows/nexus-publish-snapshots.yml b/.github/workflows/nexus-publish-snapshots.yml
index 4fc649bc..f5af5f15 100644
--- a/.github/workflows/nexus-publish-snapshots.yml
+++ b/.github/workflows/nexus-publish-snapshots.yml
@@ -10,7 +10,7 @@ on:
       - development
 
 jobs:
-  publish_snapshots:
+  publish_snapshot:
 
     runs-on: ubuntu-latest
 
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index ab4e81d9..5708a258 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -3,7 +3,7 @@ name: Run Maven Tests
 on:
   push:
     branches:
-      - '*'
+      - '**'
   pull_request:
     # The branches below must be a subset of the branches above
     branches: [ main, master ]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index d99eb434..d1038007 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -4,6 +4,17 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
+1.13.0-SNAPSHOT (2021-06-07)
+----------------------------
+
+**Added**
+
+**Fixed**
+
+**Dependencies**
+
+**Deprecated**
+
 1.12.6 (2022-01-04)
 -------------------
 
diff --git a/docs/conf.py b/docs/conf.py
index aedbdf64..2833094c 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -55,9 +55,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.12.2'
+version = '1.13.0-SNAPSHOT'
 # The full version, including alpha/beta/rc tags.
-release = '1.12.2'
+release = '1.13.0-SNAPSHOT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/pom.xml b/pom.xml
index 90d17d88..41bddf0a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,21 +4,37 @@
 	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">
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>projectwizard-portlet</artifactId>
-	<version>1.12.7</version>
+	<groupId>life.qbic</groupId>
+	<version>1.13.0-SNAPSHOT</version>
 	<name>ProjectWizard Portlet</name>
 	<url>https://github.com/qbicsoftware/projectwizard-portlet</url>
 	<description>Creates hierarchical experiments using factorial design.</description>
 	<packaging>war</packaging>
-	<parent>
-		<groupId>life.qbic</groupId>
-		<artifactId>portlet-parent-pom</artifactId>
-		<version>3.1.4</version>
-	</parent>
 	<properties>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
 		<vaadin.version>7.7.28</vaadin.version>
 		<vaadin.plugin.version>7.7.28</vaadin.plugin.version>
 		<log4j.version>2.17.1</log4j.version>
+		<liferay.version>6.2.5</liferay.version>
+		<liferay.maven.plugin.version>6.2.5</liferay.maven.plugin.version>
+		<jetty.plugin.version>9.4.10.v20180503</jetty.plugin.version>
+		<jetty.scanIntervalSeconds>2</jetty.scanIntervalSeconds>
 	</properties>
+	<distributionManagement>
+		<repository>
+			<uniqueVersion>true</uniqueVersion>
+			<id>nexus-releases</id>
+			<name>QBiC Releases</name>
+			<url>https://qbic-repo.qbic.uni-tuebingen.de/repository/maven-releases</url>
+		</repository>
+		<snapshotRepository>
+			<uniqueVersion>false</uniqueVersion>
+			<id>nexus-snapshots</id>
+			<name>QBiC Snapshots</name>
+			<url>https://qbic-repo.qbic.uni-tuebingen.de/repository/maven-snapshots</url>
+		</snapshotRepository>
+	</distributionManagement>
 	<repositories>
 		<repository>
 			<releases>
@@ -73,6 +89,27 @@
 		</repository>
 	</repositories>
 	<dependencies>
+		<!-- Vaadin -->
+		<dependency>
+			<groupId>com.vaadin</groupId>
+			<artifactId>vaadin-server</artifactId>
+			<version>${vaadin.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.vaadin</groupId>
+			<artifactId>vaadin-client-compiled</artifactId>
+			<version>${vaadin.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.vaadin</groupId>
+			<artifactId>vaadin-client</artifactId>
+			<version>${vaadin.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.vaadin</groupId>
+			<artifactId>vaadin-themes</artifactId>
+			<version>${vaadin.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
@@ -88,9 +125,16 @@
 			<artifactId>core-utils-lib</artifactId>
 			<version>1.7.0</version>
 		</dependency>
+		<dependency>
+			<groupId>com.liferay.portal</groupId>
+			<artifactId>portal-service</artifactId>
+			<version>${liferay.version}</version>
+			<scope>provided</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.mariadb.jdbc</groupId>
 			<artifactId>mariadb-java-client</artifactId>
+			<version>2.7.5</version>
 		</dependency>
 		<!-- needed since isa-creator-lib uses old version leading to portlet compilation 
 			error -->
@@ -103,7 +147,7 @@
 		<dependency>
 			<groupId>life.qbic</groupId>
 			<artifactId>experimental-design-lib</artifactId>
-			<version>0.20.1</version>
+			<version>0.20.2</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
 		<dependency>
@@ -166,4 +210,127 @@
 			</exclusions>
 		</dependency>
 	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>com.vaadin</groupId>
+				<artifactId>vaadin-maven-plugin</artifactId>
+				<version>${vaadin.plugin.version}</version>
+				<configuration>
+					<extraJvmArgs>-Xmx1024m -Xss1024k</extraJvmArgs>
+					<!-- We are doing "inplace" but into subdir VAADIN/widgetsets. This 
+						way compatible with Vaadin eclipse plugin. -->
+					<webappDirectory>${basedir}/src/main/webapp/VAADIN/widgetsets</webappDirectory>
+					<hostedWebapp>${basedir}/src/main/webapp/VAADIN/widgetsets</hostedWebapp>
+					<!-- Most Vaadin apps don't need this stuff, guide that to target -->
+					<persistentunitcachedir>${project.build.directory}</persistentunitcachedir>
+					<deploy>${project.build.directory}/gwt-deploy</deploy>
+					<!-- Compile report is not typically needed either, saves hundreds of 
+						disk -->
+					<compileReport>false</compileReport>
+					<noServer>true</noServer>
+					<!-- Remove draftCompile when project is ready -->
+					<draftCompile>false</draftCompile>
+					<style>OBF</style>
+				</configuration>
+				<executions>
+					<execution>
+						<configuration>
+							<!-- if you don't specify any modules, the plugin will find them -->
+						</configuration>
+						<goals>
+							<goal>clean</goal>
+							<goal>resources</goal>
+							<goal>update-theme</goal>
+							<goal>update-widgetset</goal>
+							<goal>compile-theme</goal>
+							<goal>compile</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.eclipse.jetty</groupId>
+				<artifactId>jetty-maven-plugin</artifactId>
+				<version>${jetty.plugin.version}</version>
+				<configuration>
+					<!-- Jetty's hot deploy enabled has been enabled by default! If you 
+						want to disable jetty's hot deploy feature, activate the 'jetty-cold-deploy' 
+						profile via the command line: mvn -P jetty-cold-deploy Or, alternatively, 
+						you can change your settings.xml to permanently activate this profile. For 
+						more information on how to permanently activate a property, see: https://maven.apache.org/settings.html#Profiles 
+						For more information about the origin of this long comment, see: https://github.com/qbicsoftware/parent-poms/issues/4 -->
+					<scanIntervalSeconds>${jetty.scanIntervalSeconds}</scanIntervalSeconds>
+					<useProvidedScope>true</useProvidedScope>
+					<stopPort>8005</stopPort>
+					<stopKey>STOP</stopKey>
+				</configuration>
+				<executions>
+					<execution>
+						<id>start-jetty</id>
+						<phase>pre-integration-test</phase>
+						<goals>
+							<goal>start</goal>
+						</goals>
+						<configuration>
+							<scanIntervalSeconds>${jetty.scanIntervalSeconds}</scanIntervalSeconds>
+						</configuration>
+					</execution>
+					<execution>
+						<id>stop-jetty</id>
+						<phase>post-integration-test</phase>
+						<goals>
+							<goal>stop</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<!-- enable resource filtering for war files -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-war-plugin</artifactId>
+				<version>3.2.2</version>
+				<configuration>
+					<nonFilteredFileExtensions>
+						<nonFilteredFileExtension>docx</nonFilteredFileExtension>
+						<nonFilteredFileExtension>pdf</nonFilteredFileExtension>
+					</nonFilteredFileExtensions>
+					<failOnMissingWebXml>true</failOnMissingWebXml>
+					<!-- Exclude an unnecessary file generated by the GWT compiler. -->
+					<packagingExcludes>WEB-INF/classes/VAADIN/widgetsets/WEB-INF/**</packagingExcludes>
+					<webResources>
+						<resource>
+							<filtering>true</filtering>
+							<directory>src/main/resources</directory>
+							<targetPath>WEB-INF/classes</targetPath>
+						</resource>
+						<resource>
+							<filtering>true</filtering>
+							<directory>src/main/webapp/WEB-INF</directory>
+							<targetPath>WEB-INF</targetPath>
+						</resource>
+					</webResources>
+				</configuration>
+			</plugin>
+			<!--portal plugins -->
+			<plugin>
+				<groupId>com.liferay.maven.plugins</groupId>
+				<artifactId>liferay-maven-plugin</artifactId>
+				<version>${liferay.maven.plugin.version}</version>
+				<configuration>
+					<autoDeployDir>${liferay.auto.deploy.dir}</autoDeployDir>
+					<appServerDeployDir>${liferay.app.server.deploy.dir}</appServerDeployDir>
+					<appServerLibGlobalDir>${liferay.app.server.lib.global.dir}</appServerLibGlobalDir>
+					<appServerPortalDir>${liferay.app.server.portal.dir}</appServerPortalDir>
+					<liferayVersion>${liferay.version}</liferayVersion>
+					<pluginType>portlet</pluginType>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.8.0</version>
+			</plugin>
+		</plugins>
+	</build>
 </project> 
diff --git a/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java b/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
index bc53c96d..c4fc3700 100644
--- a/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
+++ b/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
@@ -19,11 +19,11 @@
 import org.vaadin.teemu.wizards.event.WizardStepSetChangedEvent;
 import com.liferay.portal.model.User;
 import com.liferay.portal.model.UserGroup;
+import com.vaadin.ui.themes.ValoTheme;
 import com.vaadin.annotations.Theme;
 import com.vaadin.annotations.Widgetset;
 import com.vaadin.server.FontAwesome;
 import com.vaadin.server.VaadinRequest;
-import com.vaadin.ui.themes.ValoTheme;
 import com.vaadin.ui.Label;
 import com.vaadin.ui.Layout;
 import com.vaadin.ui.TabSheet;
@@ -51,7 +51,6 @@
 import life.qbic.projectwizard.views.AdminView;
 import life.qbic.projectwizard.views.MetadataUploadView;
 
-
 @Theme("mytheme")
 @Widgetset("life.qbic.portlet.AppWidgetSet")
 public class ProjectWizardUI extends QBiCPortletUI {
@@ -88,7 +87,7 @@ protected Layout getPortletContent(final VaadinRequest request) {
     if (PortalUtils.isLiferayPortlet()) {
       // read in the configuration file
       logger.info("Wizard is running on Liferay and user is logged in.");
-      userID = PortalUtils.getUser().getScreenName();
+      userID = PortalUtils.getScreenName();
     } else {
       if (development) {
         logger.warn("Checks for local dev version successful. User is granted admin status.");
diff --git a/src/main/java/life/qbic/projectwizard/steps/ProjectContextStep.java b/src/main/java/life/qbic/projectwizard/steps/ProjectContextStep.java
index cb1e331c..ef415efd 100644
--- a/src/main/java/life/qbic/projectwizard/steps/ProjectContextStep.java
+++ b/src/main/java/life/qbic/projectwizard/steps/ProjectContextStep.java
@@ -70,9 +70,8 @@ public class ProjectContextStep implements WizardStep {
   private CheckBox pilotBox;
 
   /**
-   * Create a new Context Step for the wizard
-   * 
-   * @param newProjectCode
+   *
+   * @param projSelect ProjectInformationComponent storing project name and basic metadata
    */
   public ProjectContextStep(ProjectInformationComponent projSelect) {
     main = new VerticalLayout();
diff --git a/src/main/java/life/qbic/projectwizard/steps/SummaryRegisterStep.java b/src/main/java/life/qbic/projectwizard/steps/SummaryRegisterStep.java
index 57ee8a1f..5b647d1f 100644
--- a/src/main/java/life/qbic/projectwizard/steps/SummaryRegisterStep.java
+++ b/src/main/java/life/qbic/projectwizard/steps/SummaryRegisterStep.java
@@ -100,7 +100,7 @@ public SummaryRegisterStep() {
     main.addComponent(Styles.questionize(tsvInfo,
         "You can download a technical spreadsheet to register your samples at a later time instead. More informative spreadsheets are available in the next step.",
         "TSV Download"));
-
+    
     Container cont = new IndexedContainer();
     cont.addContainerProperty("caption", String.class, "");
     cont.getContainerProperty(cont.addItem(), "caption").setValue(paidOption);
diff --git a/src/main/java/life/qbic/projectwizard/uicomponents/ProjectInformationComponent.java b/src/main/java/life/qbic/projectwizard/uicomponents/ProjectInformationComponent.java
index 80a71cc1..46ceb9a4 100644
--- a/src/main/java/life/qbic/projectwizard/uicomponents/ProjectInformationComponent.java
+++ b/src/main/java/life/qbic/projectwizard/uicomponents/ProjectInformationComponent.java
@@ -79,7 +79,7 @@ public ProjectInformationComponent(List<String> spaces, Set<String> people) {
     addComponent(Styles.questionize(spaceBox, "Name of the project", "Project Name"));
 
     imgCheck = new CheckBox("Imaging Support");
-    addComponent(imgCheck);
+    addComponent(Styles.questionize(imgCheck, "Needs to be checked to store imaging data in Omero", "Imaging Support"));
 
     ComboBox prBox = new ComboBox("Sub-Project");
     prBox.setStyleName(Styles.boxTheme);
diff --git a/src/main/java/life/qbic/projectwizard/uicomponents/UploadComponent.java b/src/main/java/life/qbic/projectwizard/uicomponents/UploadComponent.java
index 842afb78..22eac226 100644
--- a/src/main/java/life/qbic/projectwizard/uicomponents/UploadComponent.java
+++ b/src/main/java/life/qbic/projectwizard/uicomponents/UploadComponent.java
@@ -153,6 +153,7 @@ public void uploadFailed(FailedEvent event) {
     } else {
       StringWriter sw = new StringWriter();
       PrintWriter pw = new PrintWriter(sw);
+
       if (event.getReason() != null)
         event.getReason().printStackTrace(pw);
       logger.error("Upload cancelled due to error.");
diff --git a/src/main/java/life/qbic/projectwizard/views/AdminView.java b/src/main/java/life/qbic/projectwizard/views/AdminView.java
index 5376ff79..5eca86c3 100644
--- a/src/main/java/life/qbic/projectwizard/views/AdminView.java
+++ b/src/main/java/life/qbic/projectwizard/views/AdminView.java
@@ -167,8 +167,13 @@ public void buttonClick(ClickEvent event) {
                   "There seems to have been a problem while creating the space. Do the specified users already exist in openbis? If not, create them.",
                   NotificationType.ERROR);
             }
-            createSpace.setEnabled(true);
+
+          } else {
+            Styles.notification("Problem creating space",
+                    "This space already exists.",
+                    NotificationType.DEFAULT);
           }
+          createSpace.setEnabled(true);
         }
       }
     });
diff --git a/src/main/java/life/qbic/projectwizard/views/MetadataUploadView.java b/src/main/java/life/qbic/projectwizard/views/MetadataUploadView.java
index dc3854dd..d5761c47 100644
--- a/src/main/java/life/qbic/projectwizard/views/MetadataUploadView.java
+++ b/src/main/java/life/qbic/projectwizard/views/MetadataUploadView.java
@@ -173,7 +173,7 @@ public MetadataUploadView(IOpenBisClient openbis, Vocabularies vocabularies,
     addComponent(separatorSelection);
     separatorSelection.select("Tab");
     separatorSelection.setVisible(false);
-    upload = new UploadComponent("Upload Metadata (tab-separated)", "Upload",
+    upload = new UploadComponent("Upload Metadata", "Upload",
         ProjectWizardUI.tmpFolder, user, 200000);
     upload.setVisible(false);
     addComponent(upload);
@@ -219,9 +219,10 @@ public void valueChange(ValueChangeEvent event) {
 
       @Override
       public void uploadFinished(FinishedEvent event) {
-        if (upload.wasSuccess())
+        if (upload.wasSuccess()) {
           try {
-            send.setVisible(parseTSV(upload.getFile()));
+            boolean isTsvParsed = parseTSV(upload.getFile());
+            send.setVisible(isTsvParsed);
             reload.setVisible(true);
           } catch (IOException e) {
             e.printStackTrace();
@@ -229,6 +230,7 @@ public void uploadFinished(FinishedEvent event) {
             // TODO Auto-generated catch block
             e.printStackTrace();
           }
+        }
       }
     });
 
@@ -240,6 +242,7 @@ public void buttonClick(ClickEvent event) {
         ingestTable(new MetadataUpdateReadyRunnable(view), progressBar, progressInfo);
         send.setEnabled(false);
       }
+
     });
   }
 
@@ -543,6 +546,17 @@ public void selectedTabChange(SelectedTabChangeEvent event) {
     }
     reader.close();
     String[] header = data.get(0);
+
+    Set<String> uniqueHeaders = new HashSet<>();
+    for (String currentHeader : header) {
+      if(!uniqueHeaders.add(currentHeader)) {
+        error = "Column names in your upload must be unique.";
+        Styles.notification(String.format("Duplicate header found: %s", currentHeader), error, NotificationType.ERROR);
+        reader.close();
+        return false;
+      }
+    }
+
     data.remove(0);
     int barcodeCol = -1;
     String projectCode = "";
@@ -557,7 +571,7 @@ public void selectedTabChange(SelectedTabChangeEvent event) {
     }
     if (barcodeCol == -1) {
       error =
-          "No barcode column found. Make sure one column contains QBiC Barcodes to map your information to existing samples!";
+          "No barcode column found or first sample code is wrong. Make sure one column contains QBiC Barcodes to map your information to existing samples!";
       Styles.notification("File Incomplete", error, NotificationType.ERROR);
       return false;
     }
@@ -571,8 +585,7 @@ public void selectedTabChange(SelectedTabChangeEvent event) {
       }
       barcodeCol = 0;
     }
-    List<Sample> projectSamples =
-        openbis.getSamplesOfProject(projectCode);
+    List<Sample> projectSamples = openbis.getSamplesOfProject(projectCode);
 
     codesToSamples = new HashMap<String, Sample>();
     Map<String, List<String>> sampleTypeToAttributes = new HashMap<String, List<String>>();
@@ -652,9 +665,9 @@ public void selectedTabChange(SelectedTabChangeEvent event) {
       row.add("Properties -->");
       for (int i = 1; i < header.length; i++) {
         String headline = header[i];
-        List<String> sortedOtions = new ArrayList<>(options);
-        Collections.sort(sortedOtions);
-        ComboBox attributeOptions = new ComboBox("", sortedOtions);
+        List<String> sortedOptions = new ArrayList<>(options);
+        Collections.sort(sortedOptions);
+        ComboBox attributeOptions = new ComboBox("", sortedOptions);
         attributeOptions.setStyleName(Styles.boxTheme);
         attributeOptions.setImmediate(true);
         attributeOptions.setInputPrompt("<Select Attribute>");
@@ -759,6 +772,7 @@ public void valueChange(ValueChangeEvent event) {
     }
     addComponent(send);
     addComponent(progressBar);
+
     return true;
   }
 

From 1a0a565bff9c68836638bfe10971492414155c3e Mon Sep 17 00:00:00 2001
From: wow-such-code <andreas.friedrich@uni-tuebingen.de>
Date: Tue, 6 Sep 2022 16:10:06 +0200
Subject: [PATCH 2/4] fix image resource path using portlet.properties (#61)

* build image resource path using portlets.properties
---
 pom.xml                                            |  2 +-
 .../life/qbic/portal/portlet/ProjectWizardUI.java  | 14 ++++++--------
 .../projectwizard/views/ExperimentImportView.java  |  4 ++--
 src/main/resources/portlet.properties              |  1 +
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/pom.xml b/pom.xml
index 41bddf0a..7fd975c4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>projectwizard-portlet</artifactId>
 	<groupId>life.qbic</groupId>
-	<version>1.13.0-SNAPSHOT</version>
+	<version>1.13.0</version>
 	<name>ProjectWizard Portlet</name>
 	<url>https://github.com/qbicsoftware/projectwizard-portlet</url>
 	<description>Creates hierarchical experiments using factorial design.</description>
diff --git a/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java b/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
index c4fc3700..b3af1187 100644
--- a/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
+++ b/src/main/java/life/qbic/portal/portlet/ProjectWizardUI.java
@@ -9,6 +9,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
+
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vaadin.teemu.wizards.Wizard;
@@ -33,8 +34,6 @@
 import life.qbic.omero.BasicOMEROClient;
 import life.qbic.openbis.openbisclient.IOpenBisClient;
 import life.qbic.openbis.openbisclient.OpenBisClient;
-import life.qbic.portal.portlet.QBiCPortletUI;
-import life.qbic.portal.samplegraph.GraphPage;
 import life.qbic.portal.utils.ConfigurationManager;
 import life.qbic.portal.utils.ConfigurationManagerFactory;
 import life.qbic.portal.utils.PortalUtils;
@@ -64,7 +63,7 @@ public class ProjectWizardUI extends QBiCPortletUI {
   List<String> expTypes = new ArrayList<String>(
       Arrays.asList("Q_EXPERIMENTAL_DESIGN", "Q_SAMPLE_EXTRACTION", "Q_SAMPLE_PREPARATION"));
 
-  private Logger logger = LogManager.getLogger(ProjectWizardUI.class);
+  private final static Logger logger = LogManager.getLogger(ProjectWizardUI.class);
 
   private ConfigurationManager config;
 
@@ -284,17 +283,16 @@ public static String getPathToVaadinFolder() {
     if (PortalUtils.isLiferayPortlet()) {
       Properties prop = new Properties();
       // workaround
-      GraphPage p = new GraphPage();
-      InputStream in = p.getClass().getClassLoader()
-          .getResourceAsStream("WEB-INF/liferay-plugin-package.properties");
+      InputStream in = ProjectWizardUI.class.getClassLoader()
+          .getResourceAsStream("portlet.properties");
       try {
         prop.load(in);
         in.close();
       } catch (IOException e1) {
-        // TODO Auto-generated catch block
+        logger.error("Could not load portlet.properties");
         e1.printStackTrace();
       }
-      String portletName = prop.getProperty("name");
+      String portletName = prop.getProperty("artifact.id");
 
       URI location = UI.getCurrent().getPage().getLocation();
       // http
diff --git a/src/main/java/life/qbic/projectwizard/views/ExperimentImportView.java b/src/main/java/life/qbic/projectwizard/views/ExperimentImportView.java
index 26c39cf8..60b2cfda 100644
--- a/src/main/java/life/qbic/projectwizard/views/ExperimentImportView.java
+++ b/src/main/java/life/qbic/projectwizard/views/ExperimentImportView.java
@@ -160,8 +160,8 @@ public void buttonClick(ClickEvent event) {
 
       Resource res =
           new ExternalResource(ProjectWizardUI.getPathToVaadinFolder() + "img/isatools.png");
-      Image imNotYourC_Pal = new Image(null, res);
-      layout.addComponent(imNotYourC_Pal);
+      Image isaTools = new Image(null, res);
+      layout.addComponent(isaTools);
 
       subWindow.setContent(layout);
       // Center it in the browser window
diff --git a/src/main/resources/portlet.properties b/src/main/resources/portlet.properties
index 4cb0e4a2..62944429 100644
--- a/src/main/resources/portlet.properties
+++ b/src/main/resources/portlet.properties
@@ -3,3 +3,4 @@ include-and-override=${liferay.home}/qbic-ext.properties
 # Do not modify the values. These are automatically resolved by maven during the build.
 version=${project.version}
 repository.url=${project.url}
+artifact.id=${artifactId}

From bab3251241cf46807ecd9596a2ae582d933bf256 Mon Sep 17 00:00:00 2001
From: Tobias Koch <KochTobi@users.noreply.github.com>
Date: Thu, 1 Jun 2023 16:48:49 +0200
Subject: [PATCH 3/4] Update GitHub Actions (#63)

Updates all actions to the latest version using node.js 16.
The label action was replaced by a maintained action.
---
 .github/dependabot.yml                        | 11 ++++++++++
 .github/labeler.yml                           | 13 ++++++++++++
 .github/pr-labels.yml                         |  3 ---
 .../{build-package.yml => build_package.yml}  | 12 ++++++-----
 .github/workflows/codeql-analysis.yml         | 17 ++++++++--------
 .github/workflows/create-release.yml          | 20 ++++++++++---------
 .github/workflows/label-pull-requests.yml     | 12 ++++++-----
 .github/workflows/nexus-publish-snapshots.yml | 12 ++++++-----
 .../{run-tests.yml => run_tests.yml}          | 13 +++++++-----
 9 files changed, 73 insertions(+), 40 deletions(-)
 create mode 100644 .github/dependabot.yml
 create mode 100644 .github/labeler.yml
 delete mode 100644 .github/pr-labels.yml
 rename .github/workflows/{build-package.yml => build_package.yml} (71%)
 rename .github/workflows/{run-tests.yml => run_tests.yml} (65%)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..90e05c40
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/labeler.yml b/.github/labeler.yml
new file mode 100644
index 00000000..fdd0f42b
--- /dev/null
+++ b/.github/labeler.yml
@@ -0,0 +1,13 @@
+feature:
+  - any:
+      - head-branch: [ '^feature' ]
+fix:
+  - any:
+      - head-branch: [ '^fix', '^hotfix' ]
+chore:
+  - any:
+      - head-branch: [ '^chore', '^documentation', '^docs', '^ci', '^refactor' ]
+release:
+  - all:
+      - base-branch: [ 'main', 'master' ]
+      - head-branch: [ 'development', 'dev' ]
diff --git a/.github/pr-labels.yml b/.github/pr-labels.yml
deleted file mode 100644
index f95cf6e9..00000000
--- a/.github/pr-labels.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-feature: ['feature/*', 'feat/*']
-fix: ['fix/*', 'hotfix']
-chore: ['chore/*', 'documentation/*', 'docs/*', 'ci/*', 'refactor/*']
diff --git a/.github/workflows/build-package.yml b/.github/workflows/build_package.yml
similarity index 71%
rename from .github/workflows/build-package.yml
rename to .github/workflows/build_package.yml
index d616186c..77c5fe5c 100644
--- a/.github/workflows/build-package.yml
+++ b/.github/workflows/build_package.yml
@@ -13,13 +13,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
         with:
-          java-version: 1.8
+          distribution: 'zulu'
+          java-version: '8'
       - name: Load local Maven repository cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 803f763e..1b1841d8 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -37,15 +37,16 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
+        uses: actions/checkout@v3
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
         with:
-          java-version: 1.8
+          distribution: 'zulu'
+          java-version: '8'
           settings-path: ${{ github.workspace }}
 
       - name: Load local Maven repository cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
@@ -54,7 +55,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v1
+        uses: github/codeql-action/init@v2
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -65,7 +66,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v1
+        uses: github/codeql-action/autobuild@v2
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 https://git.io/JvXDl
@@ -79,4 +80,4 @@ jobs:
       #   make release
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v1
+        uses: github/codeql-action/analyze@v2
diff --git a/.github/workflows/create-release.yml b/.github/workflows/create-release.yml
index 82efca7d..ed38abf1 100644
--- a/.github/workflows/create-release.yml
+++ b/.github/workflows/create-release.yml
@@ -11,15 +11,17 @@ jobs:
   release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
         with:
-          java-version: 1.8
+          distribution: 'zulu'
+          java-version: '8'
           settings-path: ${{ github.workspace }}
 
       - name: Load local Maven repository cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
@@ -42,7 +44,7 @@ jobs:
           && !( contains(github.event.inputs.versionTag, 'alpha')
           || contains(github.event.inputs.versionTag, 'beta')
           || contains(github.event.inputs.versionTag, 'rc')) }}
-        uses: actions/github-script@v4.0.2
+        uses: actions/github-script@v6
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |
@@ -56,7 +58,7 @@ jobs:
           && ( contains(github.event.inputs.versionTag, 'alpha')
           || contains(github.event.inputs.versionTag, 'beta')
           || contains(github.event.inputs.versionTag, 'rc')) }}
-        uses: actions/github-script@v4.0.2
+        uses: actions/github-script@v6
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |
@@ -85,12 +87,12 @@ jobs:
         run: git push
 
       - name: Open PR with version bump
-        uses: actions/github-script@v4.0.2
+        uses: actions/github-script@v6
         with:
           github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
           script: |
             await github.request(`POST /repos/${{ github.repository }}/pulls`, {
               title: 'Update version to ${{ github.event.inputs.versionTag }}',
               head: 'release/set-version-to-${{ github.event.inputs.versionTag }}',
-              base: 'master'
+              base: 'main'
             });
diff --git a/.github/workflows/label-pull-requests.yml b/.github/workflows/label-pull-requests.yml
index b03eee14..931ff6da 100644
--- a/.github/workflows/label-pull-requests.yml
+++ b/.github/workflows/label-pull-requests.yml
@@ -1,15 +1,17 @@
 name: Label Pull Requests
 
+permissions:
+  contents: read
+  pull-requests: write
+
 on:
   pull_request:
     types: [ opened, edited ]
 
 jobs:
-  label:
+  Assign-Label-To-Pull-Request:
     runs-on: ubuntu-latest
     steps:
-      - uses: TimonVS/pr-labeler-action@v3
+      - uses: actions/labeler@v5.0.0-alpha.1
         with:
-          configuration-path: .github/pr-labels.yml # optional, .github/pr-labeler.yml is the default value
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/nexus-publish-snapshots.yml b/.github/workflows/nexus-publish-snapshots.yml
index f5af5f15..9d98c352 100644
--- a/.github/workflows/nexus-publish-snapshots.yml
+++ b/.github/workflows/nexus-publish-snapshots.yml
@@ -15,15 +15,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
         with:
-          java-version: 1.8
+          distribution: 'zulu'
+          java-version: '8'
           settings-path: ${{ github.workspace }}
 
       - name: Load local Maven repository cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run_tests.yml
similarity index 65%
rename from .github/workflows/run-tests.yml
rename to .github/workflows/run_tests.yml
index 5708a258..a5e32810 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -13,14 +13,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 1.8
-        uses: actions/setup-java@v1
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
         with:
-          java-version: 1.8
+          distribution: 'zulu'
+          java-version: '8'
+          settings-path: ${{ github.workspace }}
 
       - name: Load local Maven repository cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}

From d46eb536c501e4ebd2d92c64e77c41de58e96736 Mon Sep 17 00:00:00 2001
From: Johnny Q5 <50356506+JohnnyQ5@users.noreply.github.com>
Date: Wed, 12 Jul 2023 15:47:23 +0200
Subject: [PATCH 4/4] Set version to 1.13.1 (#62)

Co-authored-by: wow-such-code <andreas.friedrich@uni-tuebingen.de>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 7fd975c4..c696f185 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>projectwizard-portlet</artifactId>
 	<groupId>life.qbic</groupId>
-	<version>1.13.0</version>
+	<version>1.13.1</version>
 	<name>ProjectWizard Portlet</name>
 	<url>https://github.com/qbicsoftware/projectwizard-portlet</url>
 	<description>Creates hierarchical experiments using factorial design.</description>