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
# âšī¸ Command-line programs to run using the OS shell.
# đ 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}