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 # ℹī¸ 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') }} diff --git a/pom.xml b/pom.xml index 41bddf0a..c696f185 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ 4.0.0 projectwizard-portlet life.qbic - 1.13.0-SNAPSHOT + 1.13.1 ProjectWizard Portlet https://github.com/qbicsoftware/projectwizard-portlet Creates hierarchical experiments using factorial design. 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 expTypes = new ArrayList( 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}