Merge pull request #18 from 3D-e-Chem/knime51

Support KNIME 5.1

.github/workflows/build.yml

@@ -5,10 +5,10 @@ name: Java CI with Maven
 
 on:
   push:
+    branches:
+      - master
   pull_request:
-    types:
-      - "opened"
-      - "reopened"
+    types: [opened, synchronize, reopened]
 
 jobs:
   build:
@@ -17,47 +17,27 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - uses: actions/checkout@v3
       with:
-        java-version: 1.8
-    - name: Setup miniconda
-      uses: conda-incubator/setup-miniconda@v2
+        fetch-depth: 0
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
       with:
-        auto-update-conda: true
-        activate-environment: test
-        python-version: 3.8
-    - name: Cache Maven packages
-      uses: actions/cache@v2
+        java-version: 17
+        distribution: 'temurin'
+        cache: maven
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        path: ~/.m2
-        key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }}
-        restore-keys: ${{ runner.os }}-m2
-    - name: Cache conda deps
-      uses: actions/cache@v2
-      with:
-        path: |
-          ~/conda_pkgs_dir
-          ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('.github/workflows/build.yml') }}
-        restore-keys: ${{ runner.os }}-pip
-    - name: OS dependencies
-      run: sudo apt-get install xvfb
-    - name: Conda dependencies
-      run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf
+        environment-name: test-env
+        create-args: >-
+          python=3.10
+          rdkit
     - name: Python dependencies
       run: pip install sygma
     - name: Build with Maven
       run: mvn -B package
-    - name: Run tests
-      run: xvfb-run mvn verify -B
-    - name: Set up JDK 11 for SonarCloud analysis
-      uses: actions/setup-java@v1
-      with:
-        java-version: 11
-    - name: SonarCloud analysis
+    - name: Build and analyze
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
         SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-      run: mvn sonar:sonar
+      run: xvfb-run mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=3D-e-Chem_knime-sygma

.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

@@ -6,6 +6,13 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [3.0.0] - 2023-11-23
+
+### Changed
+
+- Support KNIME 5.1
+- Replaced `knime-python-wrapper` dependency with calling `sygma` executable.
+
 ## [2.0.0] - 2021-02-12
 
 ### Fixed

CITATION.cff

@@ -15,6 +15,5 @@ authors:
 - given-names: Albert
   family-names: J. Kooistra
   affiliation: UMC Nijmegen
-date-released: 2021-02-12
 repository-code: https://github.com/3D-e-Chem/knime-sygma
 license: GPL-3.0

README.md

@@ -3,22 +3,22 @@
 The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) nodes for the **Sy**stematic **G**eneration of potential **M**et**a**bolites.
 
 [![Java CI with Maven](https://github.com/3D-e-Chem/knime-sygma/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/3D-e-Chem/knime-sygma/actions?query=workflow%3A%22Java+CI+with+Maven%22)
-[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma)
-[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-sygma&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-sygma)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-sygma&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-sygma)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4537282.svg)](https://doi.org/10.5281/zenodo.4537282)
 
 # Installation
 
 Requirements:
 
-- KNIME, https://www.knime.org, version 4.0 or higher
-- SyGMa Python library, https://github.com/3D-e-Chem/sygma
+- KNIME, https://www.knime.org, version 5.1 or higher
+- SyGMa Python executable, https://github.com/3D-e-Chem/sygma
 
 Steps to get the SyGMa KNIME nodes inside KNIME:
 
 1. Goto Help > Install new software ... menu
 2. Press add button
-3. Fill text fields with the `https://3d-e-chem.github.io/updates` update site url.
+3. Fill text fields with the `https://3d-e-chem.github.io/updates/5.1` update site url.
 4. Select --all sites-- in `work with` pulldown
 5. Select the node
 6. Install software
@@ -45,11 +45,11 @@ The update site can be used to perform a local installation.
 
 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.sygma.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.sygma.targetplatform/KNIME-AP-5.1.target` target definition.
 6. A KNIME Analytics Platform instance can be started by right clicking on the `targetplatform/KNIME\ Analytics\ Platform.launch` file and selecting `Run As → KNIME Analytics Platform`. The KNIME instance will contain the target platform together with all extensions defined in the workspace.
 
 During import the Tycho Eclipse providers must be installed.
@@ -88,4 +88,4 @@ This can be skipped by running maven offline using `mvn -o`.
 10. Update Zenodo entry
 11. Correct authors
 12. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
-13. Update CITIATION.cff with new DOI
+13. Update CITATION.cff with new DOI

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.sygma.feature"
       label="Sygma KNIME nodes"
-      version="2.0.0.qualifier"
+      version="3.0.0.qualifier"
       provider-name="Netherlands eScience Center">
 
   <description url="https://github.com/3D-e-Chem/knime-sygma">

feature/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sygma</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
-		<version>2.0.0-SNAPSHOT</version>
+		<version>3.0.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.sygma.feature</artifactId>

p2/category.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature id="nl.esciencecenter.e3dchem.sygma.feature" version="2.0.0.qualifier">
+   <feature id="nl.esciencecenter.e3dchem.sygma.feature" version="3.0.0.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

@@ -4,7 +4,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
         <groupId>nl.esciencecenter.e3dchem.sygma</groupId>
-        <version>2.0.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.sygma.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,19 +2,15 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Sygma KNIME nodes
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.plugin;singleton:=true
-Bundle-Version: 2.0.0.qualifier
-Bundle-RequiredExecutionEnvironment: JavaSE-1.8
+Bundle-Version: 3.0.0.qualifier
+Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-Activator: nl.esciencecenter.e3dchem.sygma.Activator
 Bundle-Vendor: Netherlands eScience Center
 Require-Bundle: org.eclipse.core.runtime,
- org.knime.workbench.core;bundle-version="[4.3.0,5.0.0)",
- org.knime.workbench.repository;bundle-version="[4.3.0,5.0.0)",
- org.knime.base;bundle-version="[4.3.0,5.0.0)",
- org.rdkit.knime.types,
- org.knime.chem.types;bundle-version="[4.3.0,5.0.0)",
- nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.4,3.0.0)",
+ org.knime.workbench.core;bundle-version="[4.3.0,6.0.0)",
+ org.knime.workbench.repository;bundle-version="[4.3.0,6.0.0)",
+ org.knime.base;bundle-version="[4.3.0,6.0.0)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: .
 Export-Package: nl.esciencecenter.e3dchem.sygma
-Import-Package: org.knime.python2.config

plugin/pom.xml

@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sygma</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
-		<version>2.0.0-SNAPSHOT</version>
+		<version>3.0.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.sygma.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>

plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesConfig.java

@@ -1,64 +1,38 @@
 package nl.esciencecenter.e3dchem.sygma;
 
-import java.util.Set;
-
 import org.knime.core.node.InvalidSettingsException;
 import org.knime.core.node.NodeSettingsRO;
 import org.knime.core.node.NodeSettingsWO;
 import org.knime.core.node.defaultnodesettings.SettingsModelIntegerBounded;
 import org.knime.core.node.defaultnodesettings.SettingsModelString;
-import org.knime.core.node.workflow.FlowVariable;
-
-import nl.esciencecenter.e3dchem.python.PythonWrapperNodeConfig;
-
-public class PredictMetabolitesConfig extends PythonWrapperNodeConfig {
-	private static final String CFGKEY_PHASE1CYCLES = "phase1_cycles";
-	private static final int DEFAULT_PHASE1CYCLES = 2;
-	private static final String CFGKEY_PHASE2CYCLES = "phase2_cycles";
-	private static final int DEFAULT_PHASE2CYCLES = 1;
-	private static final String CFG_PARENTSCOLNAME = "parents_column_name";
 
-	private final SettingsModelString parentsColumnName = new SettingsModelString(CFG_PARENTSCOLNAME, null);
+public class PredictMetabolitesConfig {
+	private SettingsModelString sygmaPath = new SettingsModelString("sygmaPath", "sygma");
+	private SettingsModelString parentsColumnName = new SettingsModelString("parents_column_name", null);
+	private SettingsModelIntegerBounded phase1cycles = new SettingsModelIntegerBounded("phase1_cycles",
+			2, 0, 100);
+	private SettingsModelIntegerBounded phase2cycles = new SettingsModelIntegerBounded("phase2_cycles",
+			1, 0, 100);
 
-	private final SettingsModelIntegerBounded phase1cycles = new SettingsModelIntegerBounded(CFGKEY_PHASE1CYCLES,
-			DEFAULT_PHASE1CYCLES, 0, 100);
-
-	private final SettingsModelIntegerBounded phase2cycles = new SettingsModelIntegerBounded(CFGKEY_PHASE2CYCLES,
-			DEFAULT_PHASE2CYCLES, 0, 100);
-
-	public PredictMetabolitesConfig(String[] inputTables, String[] outputTables) {
-		super(inputTables, outputTables);
-		addRequiredModule("sygma");
-	}
-
-	public PredictMetabolitesConfig() {
-		super();
-		addRequiredModule("sygma");
-	}
-
-	@Override
-	public void saveTo(final NodeSettingsWO settings) {
-		super.saveTo(settings);
+	public void saveSettingsTo(NodeSettingsWO settings) {
 		phase1cycles.saveSettingsTo(settings);
 		phase2cycles.saveSettingsTo(settings);
 		parentsColumnName.saveSettingsTo(settings);
+		sygmaPath.saveSettingsTo(settings);
 	}
 
-	@Override
-	public void loadFrom(final NodeSettingsRO settings) throws InvalidSettingsException {
+	public void loadValidatedSettingsFrom(NodeSettingsRO settings) throws InvalidSettingsException {
 		phase1cycles.loadSettingsFrom(settings);
 		phase2cycles.loadSettingsFrom(settings);
 		parentsColumnName.loadSettingsFrom(settings);
-		super.loadFrom(settings);
+		sygmaPath.loadSettingsFrom(settings);
 	}
 
-	@Override
-	public Set<FlowVariable> getOptionsValues() {
-		Set<FlowVariable> variables = super.getOptionsValues();
-		variables.add(new FlowVariable(CFGKEY_PHASE1CYCLES, phase1cycles.getIntValue()));
-		variables.add(new FlowVariable(CFGKEY_PHASE2CYCLES, phase2cycles.getIntValue()));
-		variables.add(new FlowVariable(CFG_PARENTSCOLNAME, parentsColumnName.getStringValue()));
-		return variables;
+	public void validateSettings(NodeSettingsRO settings) throws InvalidSettingsException {
+		phase1cycles.validateSettings(settings);
+		phase2cycles.validateSettings(settings);
+		parentsColumnName.validateSettings(settings);
+		sygmaPath.validateSettings(settings);
 	}
 
 	public SettingsModelIntegerBounded getPhase1cycles() {
@@ -72,4 +46,8 @@ public SettingsModelIntegerBounded getPhase2cycles() {
 	public SettingsModelString getParentsColumnName() {
 		return parentsColumnName;
 	}
+
+	public SettingsModelString getSygmaPath() {
+		return sygmaPath;
+	}
 }