3D-e-Chem · sverhoeven · Nov 21, 2023 · Nov 21, 2023 · Nov 21, 2023 · Nov 21, 2023
diff --git a/.github/workflows/ci.yml 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
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<extensions>
+    <extension>
+        <groupId>org.eclipse.tycho</groupId>
+        <artifactId>tycho-build</artifactId>
+        <version>2.7.5</version>
+    </extension>
+</extensions>
diff --git a/.travis.yml b/.travis.yml
diff --git 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
@@ -1,24 +1,23 @@
 # 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&amp;utm_medium=referral&amp;utm_content=3D-e-Chem/knime-gpcrdb&amp;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&amp;utm_medium=referral&amp;utm_content=3D-e-Chem/knime-gpcrdb&amp;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).
 
 ## Installation
 
 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
diff --git 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
@@ -10,5 +10,9 @@
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.gpcrdb</artifactId>
 	<packaging>eclipse-plugin</packaging>
+	<properties>
+	    <sonar.coverage.jacoco.xmlReportPaths>../tests/target/jacoco/report/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>
+		<sonar.junit.reportsPath>../tests/target/surefire-reports</sonar.junit.reportsPath>
+	</properties>
 <version>1.4.2-SNAPSHOT</version>
 </project>
diff --git a/pom.xml b/pom.xml
@@ -25,8 +25,8 @@
 	</issueManagement>
 
 	<ciManagement>
-		<system>Travis CI</system>
-		<url>http://travis-ci.org/3D-e-Chem/knime-gpcrdb</url>
+		<system>GitHub actions</system>
+		<url>https://github.com/3D-e-Chem/knime-gpcrdb/actions</url>
 	</ciManagement>
 
 	<modules>
@@ -42,15 +42,34 @@
 	</prerequisites>
 
 	<properties>
-		<tycho.version>1.4.0</tycho.version>
-		<tycho.extras.version>1.4.0</tycho.extras.version>
+		<tycho.version>2.7.5</tycho.version>
+		<tycho.extras.version>${tycho.version}</tycho.extras.version>
 		<tycho.test.jvmArgs>-Xmx512m</tycho.test.jvmArgs>
+		<jacoco.version>0.8.10</jacoco.version>
+		<java.version>17</java.version>
+		<maven.compiler.version>3.10.1</maven.compiler.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <target.file>KNIME-AP-4.0</target.file>
+        <knime.version>5.1</knime.version>
+		<target.file>KNIME-AP-${knime.version}</target.file>
 		<tycho.scmUrl>scm:git:https://github.com/3D-e-Chem/knime-gpcrdb.git</tycho.scmUrl>
 		<sonar.host.url>https://sonarcloud.io</sonar.host.url>
 		<sonar.organization>3d-e-chem</sonar.organization>
+		<!-- following required if running mvn from JDK17 -->
+		<knime.ini.testArgs>--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</knime.ini.testArgs>
 	</properties>
 	<build>
 		<plugins>

diff --git a/targetplatform/KNIME-AP-4.0.target → targetplatform/KNIME-AP-5.1.target b/targetplatform/KNIME-AP-4.0.target → targetplatform/KNIME-AP-5.1.target
@@ -1,7 +1,8 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><?pde version="3.8"?><target name="KNIME Analytics Platform (4.0)" sequenceNumber="1512743962">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?pde version="3.8"?><target name="KNIME Analytics Platform (5.1)" sequenceNumber="1512743962">
 <locations>
 <location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
-<unit id="com.knime.features.explorer.serverspace.feature.group" version="0.0.0"/>
+<!-- unit id="com.knime.features.explorer.serverspace.feature.group" version="0.0.0"/ -->
 <unit id="org.knime.features.base.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.dbdrivers.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.ensembles.feature.group" version="0.0.0"/>
@@ -11,19 +12,19 @@
 <unit id="org.knime.features.js.quickforms.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.json.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.personalproductivity.feature.group" version="0.0.0"/>
-<unit id="org.knime.features.testingapplication.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.testing.application.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.xml.feature.group" version="0.0.0"/>
 <unit id="org.knime.targetPlatform.feature.group" version="0.0.0"/>
-<repository location="https://update.knime.org/analytics-platform/4.0/"/>
+<repository location="https://update.knime.org/analytics-platform/5.1/"/>
+</location>
+<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+	<unit id="nl.esciencecenter.e3dchem.knime.testing.plugin" version="0.0.0"/>
+	<unit id="nl.esciencecenter.e3dchem.plugin" version="0.0.0"/>
+	<repository location="https://3d-e-chem.github.io/updates/5.1/"/>
 </location>
-	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
-		<unit id="nl.esciencecenter.e3dchem.knime.testing.plugin" version="0.0.0"/>
-		<unit id="nl.esciencecenter.e3dchem.plugin" version="0.0.0"/>
-		<repository location="https://3d-e-chem.github.io/updates"/>
-	</location>
 </locations>
-<targetJRE path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
-<launcherArgs>
+<targetJRE path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17"/>
+	<launcherArgs>
 <vmArgs>-server
 -Dsun.java2d.d3d=false
 -Dosgi.classloader.lock=classname
@@ -38,4 +39,4 @@
 -Dsun.net.client.defaultReadTimeout=0
 -Dorg.eclipse.swt.internal.gtk.disablePrinting</vmArgs>
 </launcherArgs>
-</target>
+</target>
diff --git 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
@@ -17,7 +17,7 @@
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.8</version>
+				<version>${jacoco.version}</version>
 				<executions>
 					<execution>
 						<goals>
@@ -39,7 +39,7 @@
 					<dependency>
 						<groupId>org.jacoco</groupId>
 						<artifactId>org.jacoco.ant</artifactId>
-						<version>0.7.8</version>
+						<version>${jacoco.version}</version>
 					</dependency>
 					<dependency>
 						<groupId>ant-contrib</groupId>
@@ -107,7 +107,48 @@
 				<artifactId>tycho-surefire-plugin</artifactId>
 				<version>${tycho.version}</version>
 				<configuration>
-					<argLine>${tycho.testArgLine} ${tycho.test.jvmArgs}</argLine>
+					<argLine>${tycho.testArgLine} 
+						${tycho.test.jvmArgs} 
+						${knime.ini.testArgs}</argLine>
+				</configuration>
+
+			</plugin>
+			<plugin>
+				<groupId>org.eclipse.tycho</groupId>
+				<artifactId>target-platform-configuration</artifactId>
+				<version>${tycho.version}</version>
+				<configuration>
+					<dependency-resolution>
+						<!-- These additional dependencies ensure that the test
+	   	 				platform generated by tycho can start correctly -->
+						<extraRequirements>
+							<requirement>
+								<type>eclipse-feature</type>
+								<id>org.knime.features.clfixes</id>
+								<versionRange>0.0.0</versionRange>
+							</requirement>
+							<requirement>
+								<type>eclipse-feature</type>
+								<id>org.knime.features.workbench</id>
+								<versionRange>0.0.0</versionRange>
+							</requirement>
+							<requirement>
+								<type>eclipse-feature</type>
+								<id>org.knime.features.core</id>
+								<versionRange>0.0.0</versionRange>
+							</requirement>
+							<requirement>
+								<type>eclipse-feature</type>
+								<id>org.knime.features.testing.application</id>
+								<versionRange>0.0.0</versionRange>
+							</requirement>
+							<requirement>
+								<type>eclipse-feature</type>
+								<id>org.knime.features.base</id>
+								<versionRange>0.0.0</versionRange>
+							</requirement>
+						</extraRequirements>
+					</dependency-resolution>
 				</configuration>
 
 			</plugin>