Merge pull request #64 from qbicsoftware/main

main to dev

.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"

.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' ]

.github/workflows/build-package.yml → .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') }}

.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

.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'
             });

.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 }}"

.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') }}

.github/workflows/run-tests.yml → .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') }}

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>1.13.1</version>
 	<name>ProjectWizard Portlet</name>
 	<url>https://github.com/qbicsoftware/projectwizard-portlet</url>
 	<description>Creates hierarchical experiments using factorial design.</description>

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

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

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}