Merge pull request #13 from 3D-e-Chem/knime51

KNIME 5.1 support

.github/workflows/ci.yml

@@ -0,0 +1,40 @@
+# 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:
+    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-sstea

.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>

CHANGELOG.md

@@ -5,6 +5,12 @@ Formatted as described on http://keepachangelog.com/
 
 ## [Unreleased]
 
+## [1.0.7] - 2023-11-21
+
+### Changes
+
+- Require KNIME 5.1
+
 ## [1.0.6] - 2019-06-26
 
 ### Changes

README.md

@@ -4,10 +4,9 @@ The ss-TEA can identify specific ligand binding residue positions for any recept
 
 See reference at https://doi.org/10.1186/1471-2105-12-332 for a description of the score.
 
-[![Build Status](https://travis-ci.org/3D-e-Chem/knime-sstea.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-sstea)
 [![DOI](https://zenodo.org/badge/19641/3D-e-Chem/knime-sstea.svg)](https://zenodo.org/badge/latestdoi/19641/3D-e-Chem/knime-sstea)
-[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sstea%3Anl.esciencecenter.e3dchem.sstea&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sstea%3Anl.esciencecenter.e3dchem.sstea)
-[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sstea%3Anl.esciencecenter.e3dchem.sstea&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sstea%3Anl.esciencecenter.e3dchem.sstea)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-sstea&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-sstea)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-sstea&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-sstea)
 
 # Installation
 
@@ -19,7 +18,7 @@ Steps install ss-TEA KNIME node:
 
 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 ss-TEA
@@ -44,11 +43,11 @@ 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.sstea.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.sstea.targetplatform/KNIME-AP-5.1.target` target definition.
 
 During import the Tycho Eclipse providers must be installed.
 

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.sstea.feature"
       label="ss-TEA"
-      version="1.0.6.qualifier"
+      version="1.0.7.qualifier"
       provider-name="Netherlands eScience Center">
 
    <description url="https://github.com/3D-e-Chem/knime-sstea">

feature/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.6-SNAPSHOT</version>
+		<version>1.0.7-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.sstea.feature</artifactId>

p2/category.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature-1.0.5.jar" id="nl.esciencecenter.e3dchem.sstea.feature" version="1.0.6.qualifier">
+   <feature url="features/nl.esciencecenter.e3dchem.sstea.feature-1.0.5.jar" id="nl.esciencecenter.e3dchem.sstea.feature" version="1.0.7.qualifier">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
    <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">

p2/pom.xml

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
         <groupId>nl.esciencecenter.e3dchem.sstea</groupId>
-        <version>1.0.6-SNAPSHOT</version>
+        <version>1.0.7-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.sstea.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,10 +2,10 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Subfamily specific two entropy analysis score
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sstea.plugin;singleton:=true
-Bundle-Version: 1.0.6.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)",
+Bundle-Version: 1.0.7.qualifier
+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)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-Vendor: Netherlands eScience Center
 Bundle-Activator: nl.esciencecenter.e3dchem.sstea.NodePlugin

plugin/pom.xml

@@ -6,12 +6,12 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.6-SNAPSHOT</version>
+		<version>1.0.7-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.sstea.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>
 	<properties>
-		<sonar.jacoco.reportPaths>../tests/target/jacoco.exec</sonar.jacoco.reportPaths>
+		<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>
 </project>

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>nl.esciencecenter.e3dchem.sstea</groupId>
     <artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-    <version>1.0.6-SNAPSHOT</version>
+    <version>1.0.7-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <organization>
@@ -23,8 +23,8 @@
     </issueManagement>
 
     <ciManagement>
-        <system>Travis CI</system>
-        <url>http://travis-ci.org/3D-e-Chem/knime-sstea</url>
+        <system>GitHub Actions</system>
+        <url>https://github.com/3D-e-Chem/knime-sstea/actions</url>
     </ciManagement>
 
     <modules>
@@ -40,16 +40,35 @@
     </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>${tycho.version}</tycho.extras.version>
         <tycho.test.platformArgs/>
         <tycho.test.jvmArgs>-Xmx512m</tycho.test.jvmArgs>
+        <jacoco.version>0.8.10</jacoco.version>
+		<java.version>17</java.version>
+        <maven.compiler.version>3.10.1</maven.compiler.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <target.file>KNIME-AP-4.0</target.file>
+		<knime.version>5.1</knime.version>
+		<target.file>KNIME-AP-${knime.version}</target.file>
         <tycho.scmUrl>scm:git:https://github.com/3D-e-Chem/knime-sstea.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>

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>

targetplatform/pom.xml

@@ -20,7 +20,7 @@ Contributors:
 	<parent>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
-		<version>1.0.6-SNAPSHOT</version>
+		<version>1.0.7-SNAPSHOT</version>
 	</parent>
 
 </project>

tests/META-INF/MANIFEST.MF

@@ -2,12 +2,12 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Tests
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sstea.tests
-Bundle-Version: 1.0.6.qualifier
+Bundle-Version: 1.0.7.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.junit;bundle-version="4.12.0",
- org.knime.core;bundle-version="[4.0.0,5.0.0)",
- org.knime.base;bundle-version="[4.0.0,5.0.0)",
- org.knime.testing;bundle-version="[4.0.0,5.0.0)",
+ org.knime.core;bundle-version="[4.0.0,6.0.0)",
+ org.knime.base;bundle-version="[4.0.0,6.0.0)",
+ org.knime.testing;bundle-version="[4.0.0,6.0.0)",
  nl.esciencecenter.e3dchem.knime.testing.plugin;bundle-version="[1.0.0,2.0.0)",
  nl.esciencecenter.e3dchem.sstea.plugin
 Bundle-Vendor: Netherlands eScience Center

tests/pom.xml

@@ -6,7 +6,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sstea</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sstea</artifactId>
-		<version>1.0.6-SNAPSHOT</version>
+		<version>1.0.7-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.sstea.tests</artifactId>
@@ -17,7 +17,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.8</version>
+				<version>${jacoco.version}</version>
 				<executions>
 					<execution>
 						<goals>
@@ -39,7 +39,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 					<dependency>
 						<groupId>org.jacoco</groupId>
 						<artifactId>org.jacoco.ant</artifactId>
-						<version>0.7.8</version>
+						<version>${jacoco.version}</version>
 					</dependency>
 					<dependency>
 						<groupId>ant-contrib</groupId>
@@ -86,6 +86,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 													</structure>
 													<html destdir="${project.basedir}/target/jacoco/report" />
 													<xml destfile="${project.basedir}/target/jacoco/report/jacoco.xml" />
+													<csv destfile="${project.basedir}/target/jacoco/report/jacoco.csv" />
 												</jacoco-report>
 											</try>
 											<catch>
@@ -108,9 +109,48 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xs
 				<version>${tycho.version}</version>
 				<configuration>
 					<useUIHarness>true</useUIHarness>
-					<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>
 		</plugins>
 	</build>