diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..405cc4f --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,54 @@ +# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Java CI with Maven + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + +jobs: + build-ubuntu: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: '17' + distribution: 'temurin' + cache: maven + - name: Cache SonarCloud packages + uses: actions/cache@v3 + with: + path: ~/.sonar/cache + key: ${{ runner.os }}-sonar + restore-keys: ${{ runner.os }}-sonar + - name: Build and analyze + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any + SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} + run: | + xvfb-run mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=3D-e-Chem_knime-gpcrdb + build-windows: + runs-on: windows-latest + steps: + - uses: actions/checkout@v3 + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + java-version: '17' + distribution: 'temurin' + cache: maven + - name: Build and analyze + run: | + mvn -B verify diff --git a/.mvn/extensions.xml b/.mvn/extensions.xml new file mode 100644 index 0000000..3fceb34 --- /dev/null +++ b/.mvn/extensions.xml @@ -0,0 +1,8 @@ + + + + org.eclipse.tycho + tycho-build + 2.7.5 + + diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index c849dc2..0000000 --- a/.travis.yml +++ /dev/null @@ -1,12 +0,0 @@ -language: java -jdk: openjdk8 -cache: - directories: - - $HOME/.m2 - - $HOME/jpm -install: mvn package -B -script: xvfb-run mvn verify -B -after_success: - - curl -sL https://github.com/jpm4j/jpm4j.installers/raw/master/dist/biz.aQute.jpm.run.jar > ~/.m2/jpm4j.jar - - java -jar $HOME/.m2/jpm4j.jar -u install com.codacy:codacy-coverage-reporter:assembly - - $HOME/jpm/bin/codacy-coverage-reporter -l Java -r tests/target/jacoco/report/jacoco.xml diff --git a/CHANGELOG.md b/CHANGELOG.md index 85e2c82..7eb5954 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,12 @@ Formatted as described on http://keepachangelog.com/. ## [Unreleased] +## [1.4.3] - 2023-11-21 + +### Changes + +- Requires KNIME 5.1 + ## [1.4.2] - 2020-04-06 Nodes in existing workflows giving not found errors should be replaced. diff --git a/README.md b/README.md index 0a2fe78..38b3bbd 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,9 @@ # GPCRDB node for KNIME -[![Build Status](https://travis-ci.org/3D-e-Chem/knime-gpcrdb.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-gpcrdb) -[![Build status](https://ci.appveyor.com/api/projects/status/4n4bjgaq04dbem0u?svg=true)](https://ci.appveyor.com/project/3D-e-Chem/knime-gpcrdb) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/116701411bee4b92a9f265f1a0a9efaf)](https://www.codacy.com/app/3D-e-Chem/knime-gpcrdb?utm_source=github.com&utm_medium=referral&utm_content=3D-e-Chem/knime-gpcrdb&utm_campaign=Badge_Grade) -[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/116701411bee4b92a9f265f1a0a9efaf)](https://www.codacy.com/app/3D-e-Chem/knime-gpcrdb?utm_source=github.com&utm_medium=referral&utm_content=3D-e-Chem/knime-gpcrdb&utm_campaign=Badge_Coverage) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3257985.svg)](https://doi.org/10.5281/zenodo.3257985) +[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-gpcrdb&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-gpcrdb) +[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-gpcrdb&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-gpcrdb) +[![Java CI with Maven](https://github.com/3D-e-Chem/knime-gpcrdb/actions/workflows/ci.yml/badge.svg)](https://github.com/3D-e-Chem/knime-gpcrdb/actions/workflows/ci.yml) KNIME plugin for retrieving data from [https://gpcrdb.org](https://gpcrdb.org), GPCRdb website contains data, web tools and diagrams for G protein-coupled receptors (GPCRs). @@ -12,13 +11,13 @@ KNIME plugin for retrieving data from [https://gpcrdb.org](https://gpcrdb.org), Requirements: -* KNIME, https://www.knime.org, version 4.0 or higher +* KNIME, https://www.knime.org, version 5.1 or higher Steps to get GPCRDB nodes inside KNIME: 1. Goto Help > Install new software ... menu 2. Press add button -3. Fill text fields with `https://3d-e-chem.github.io/updates` +3. Fill text fields with `https://3d-e-chem.github.io/updates/5.1` 4. Select --all sites-- in work with pulldown 5. Open KNIME 3D-e-Chem Contributions folder 6. Select GPCRDB @@ -43,11 +42,11 @@ An Eclipse update site will be made in `p2/target/repository` repository. Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup: -1. Install Java 8 -2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/release/2018-12/r/eclipse-ide-rcp-and-rap-developers) -3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs +1. Install Java 17 +2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/installer) +3. Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs 4. Import this repo as an Existing Maven project -5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the `KNIME Analytics Platform (4.0) - nl.esciencecenter.e3dchem.knime.molviewer.targetplatform/KNIME-AP-4.0.target` target definition. +5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the `KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.molviewer.targetplatform/KNIME-AP-5.1.target` target definition. During import the Tycho Eclipse providers must be installed. diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 7e66b48..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,16 +0,0 @@ -version: 1.0.{build} -cache: C:\Users\appveyor\.m2 -build_script: -- cmd: mvn package -B -test_script: -- cmd: mvn verify -B -artifacts: -- path: p2\target\*.zip - name: Update site -on_finish: -- ps: >- - $url = "https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)" - - Get-ChildItem "tests/target/surefire-reports/" -Filter *.xml | Foreach-Object{ - (New-Object 'System.Net.WebClient').UploadFile($url, $_.FullName) - } diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index b8d2a6d..b04933a 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -3,10 +3,10 @@ Bundle-ManifestVersion: 2 Bundle-Name: GPCRDB Nodes Bundle-SymbolicName: nl.esciencecenter.e3dchem.gpcrdb;singleton:=true Bundle-Version: 1.4.2.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.8 -Require-Bundle: org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", - org.knime.json;bundle-version="[4.0.0,5.0.0)", +Bundle-RequiredExecutionEnvironment: JavaSE-17 +Require-Bundle: org.knime.core;bundle-version="[4.0.0,6.0.0)", + org.knime.base;bundle-version="[4.0.0,6.0.0)", + org.knime.json;bundle-version="[4.0.0,6.0.0)", nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)" Export-Package: nl.esciencecenter.e3dchem.gpcrdb, nl.esciencecenter.e3dchem.gpcrdb.client, diff --git a/plugin/pom.xml b/plugin/pom.xml index e379be0..d419fa0 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -10,5 +10,9 @@ nl.esciencecenter.e3dchem.gpcrdb eclipse-plugin + + ../tests/target/jacoco/report/jacoco.xml + ../tests/target/surefire-reports + 1.4.2-SNAPSHOT diff --git a/pom.xml b/pom.xml index 815c301..5cac60b 100644 --- a/pom.xml +++ b/pom.xml @@ -25,8 +25,8 @@ - Travis CI - http://travis-ci.org/3D-e-Chem/knime-gpcrdb + GitHub actions + https://github.com/3D-e-Chem/knime-gpcrdb/actions @@ -42,15 +42,34 @@ - 1.4.0 - 1.4.0 + 2.7.5 + ${tycho.version} -Xmx512m + 0.8.10 + 17 + 3.10.1 UTF-8 UTF-8 - KNIME-AP-4.0 + 5.1 + KNIME-AP-${knime.version} scm:git:https://github.com/3D-e-Chem/knime-gpcrdb.git https://sonarcloud.io 3d-e-chem + + --add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED + --add-opens=java.base/sun.security.ssl=ALL-UNNAMED + --add-opens=java.base/sun.security.util=ALL-UNNAMED + --add-opens=java.base/java.lang=ALL-UNNAMED + --add-opens=java.base/java.lang.invoke=ALL-UNNAMED + --add-opens=java.base/java.net=ALL-UNNAMED + --add-opens=java.base/java.nio=ALL-UNNAMED + --add-opens=java.base/java.nio.channels=ALL-UNNAMED + --add-opens=java.base/java.util=ALL-UNNAMED + --add-opens=java.base/sun.nio.ch=ALL-UNNAMED + --add-opens=java.base/sun.nio=ALL-UNNAMED + --add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED + --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED + -Dmisc.io.testing=true diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-5.1.target similarity index 66% rename from targetplatform/KNIME-AP-4.0.target rename to targetplatform/KNIME-AP-5.1.target index c5a8109..30782ff 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-5.1.target @@ -1,7 +1,8 @@ - + + - + @@ -11,19 +12,19 @@ - + - + + + + + + - - - - - - - + + -server -Dsun.java2d.d3d=false -Dosgi.classloader.lock=classname @@ -38,4 +39,4 @@ -Dsun.net.client.defaultReadTimeout=0 -Dorg.eclipse.swt.internal.gtk.disablePrinting - \ No newline at end of file + diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index 2dcaf0d..283296b 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -3,14 +3,14 @@ Bundle-ManifestVersion: 2 Bundle-Name: Tests Bundle-SymbolicName: nl.esciencecenter.e3dchem.gpcrdb.tests Bundle-Version: 1.4.2.qualifier -Bundle-RequiredExecutionEnvironment: JavaSE-1.7 +Bundle-RequiredExecutionEnvironment: JavaSE-17 Require-Bundle: org.junit;bundle-version="4.12.0", nl.esciencecenter.e3dchem.gpcrdb, nl.esciencecenter.e3dchem.knime.testing.plugin;bundle-version="[1.0.0,2.0.0)", - org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.json;bundle-version="[4.0.0,5.0.0)", - org.knime.testing;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)" + org.knime.core;bundle-version="[4.0.0,6.0.0)", + org.knime.json;bundle-version="[4.0.0,6.0.0)", + org.knime.testing;bundle-version="[4.0.0,6.0.0)", + org.knime.base;bundle-version="[4.0.0,6.0.0)" Bundle-Vendor: Netherlands eScience Center Bundle-ClassPath: lib/mockito-all-1.10.19.jar, lib/jackson-core-2.4.2.jar, diff --git a/tests/pom.xml b/tests/pom.xml index 89e88dd..8abca06 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -17,7 +17,7 @@ org.jacoco jacoco-maven-plugin - 0.7.8 + ${jacoco.version} @@ -39,7 +39,7 @@ org.jacoco org.jacoco.ant - 0.7.8 + ${jacoco.version} ant-contrib @@ -107,7 +107,48 @@ tycho-surefire-plugin ${tycho.version} - ${tycho.testArgLine} ${tycho.test.jvmArgs} + ${tycho.testArgLine} + ${tycho.test.jvmArgs} + ${knime.ini.testArgs} + + + + + org.eclipse.tycho + target-platform-configuration + ${tycho.version} + + + + + + eclipse-feature + org.knime.features.clfixes + 0.0.0 + + + eclipse-feature + org.knime.features.workbench + 0.0.0 + + + eclipse-feature + org.knime.features.core + 0.0.0 + + + eclipse-feature + org.knime.features.testing.application + 0.0.0 + + + eclipse-feature + org.knime.features.base + 0.0.0 + + +