Merge pull request #17 from 3D-e-Chem/knime-43

Support KNIME 4.3

.github/workflows/build.yml

@@ -0,0 +1,63 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Java CI with Maven
+
+on:
+  push:
+  pull_request:
+    types:
+      - "opened"
+      - "reopened"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 1.8
+      uses: actions/setup-java@v1
+      with:
+        java-version: 1.8
+    - name: Setup miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        activate-environment: test
+        python-version: 3.8
+    - name: Cache Maven packages
+      uses: actions/cache@v2
+      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
+    - 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
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      run: mvn sonar:sonar

CHANGELOG.md

@@ -1,10 +1,21 @@
 # Change Log
+
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [2.0.0] - 2021-02-12
+
+### Fixed
+
+- Support KNIME 4.3 ([#16](https://github.com/3D-e-Chem/knime-sygma/issues/16) [5](https://github.com/3D-e-Chem/knime-python-wrapper/issues/5))
+
+### Removed
+
+- Support for KNIME versions older than 4.3
+
 ## [1.2.1] - 2019-06-27
 
 ### Changes
@@ -91,3 +102,17 @@ Switched to GPLv3 license due to license of [Python wrapper](https://github.com/
 
 Initial release.
 Skeleton generated by https://github.com/3D-e-Chem/knime-python-node-archetype
+
+[unreleased]: https://github.com/3D-e-Chem/knime-sygma/compare/v2.0.0...HEAD
+[2.0.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.2.1...v2.2.0
+[1.2.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.2.0...v1.2.1
+[1.2.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.5...v1.2.0
+[1.1.5]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.4...v1.1.5
+[1.1.4]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.3...v1.1.4
+[1.1.3]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.2...v1.1.3
+[1.1.2]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.1...v1.1.2
+[1.1.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.0...v1.1.1
+[1.1.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.2...v1.1.0
+[1.0.2]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/3D-e-Chem/knime-sygma/releases/tag/v1.0.0

README.md

@@ -2,7 +2,7 @@
 
 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.
 
-[![Build Status](https://travis-ci.org/3D-e-Chem/knime-sygma.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-sygma)
+[![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)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1168387.svg)](https://doi.org/10.5281/zenodo.1168387)
@@ -11,8 +11,8 @@ The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) n
 
 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 4.0 or higher
+- SyGMa Python library, https://github.com/3D-e-Chem/sygma
 
 Steps to get the SyGMa KNIME nodes inside KNIME:
 
@@ -81,12 +81,11 @@ This can be skipped by running maven offline using `mvn -o`.
 3. Run tests with `mvn verify`
 4. Optionally, test node by installing it in KNIME from a local update site
 5. Append new release to an update site
-  1. Make clone of an update site repo
-  2. Append release to the update site with `mvn install -Dtarget.update.site=<path to update site>`
-6. Commit and push changes in this repo and update site repo.
-7. Create a GitHub release
-8. Update Zenodo entry
-  1. Correct authors
-9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
-10. Update CITIATION.cff with new DOI
-
+6. Make clone of an update site repo
+7. Append release to the update site with `mvn install -Dtarget.update.site=<path to update site>`
+8. Commit and push changes in this repo and update site repo.
+9. Create a GitHub release
+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

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.sygma.feature"
       label="Sygma KNIME nodes"
-      version="1.2.1.qualifier"
+      version="2.0.0.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>1.2.1-SNAPSHOT</version>
+		<version>2.0.0-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="1.2.1.qualifier">
+   <feature id="nl.esciencecenter.e3dchem.sygma.feature" version="2.0.0.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>1.2.1-SNAPSHOT</version>
+        <version>2.0.0-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.sygma.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,17 +2,17 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Sygma KNIME nodes
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.plugin;singleton:=true
-Bundle-Version: 1.2.1.qualifier
+Bundle-Version: 2.0.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Activator: nl.esciencecenter.e3dchem.sygma.Activator
 Bundle-Vendor: Netherlands eScience Center
 Require-Bundle: org.eclipse.core.runtime,
- org.knime.workbench.core;bundle-version="[4.0.0,5.0.0)",
- org.knime.workbench.repository;bundle-version="[4.0.0,5.0.0)",
- org.knime.base;bundle-version="[4.0.0,5.0.0)",
+ 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="[4.0.0,5.0.0)",
- nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.1,3.0.0)",
+ 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)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: .

plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.sygma</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
-		<version>1.2.1-SNAPSHOT</version>
+		<version>2.0.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.sygma.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>

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

@@ -49,15 +49,23 @@ protected PredictMetabolitesDialog() {
 	public void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
 			throws NotConfigurableException {
 		super.loadAdditionalSettingsFrom(settings, specs);
-		config.loadFromInDialog(settings);
+		try {
+			config.loadFromInDialog(settings);
+		} catch (InvalidSettingsException e) {
+			// swallow error
+		}
 		pythonOptions.loadSettingsFrom(config);
 	}
 
 	@Override
 	public void loadAdditionalSettingsFrom(NodeSettingsRO settings, DataTableSpec[] specs)
 			throws NotConfigurableException {
 		super.loadAdditionalSettingsFrom(settings, specs);
-		config.loadFromInDialog(settings);
+		try {
+			config.loadFromInDialog(settings);
+		} catch (InvalidSettingsException e) {
+			// swallow error
+		}
 		pythonOptions.loadSettingsFrom(config);
 	}
 

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>nl.esciencecenter.e3dchem.sygma</groupId>
 	<artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
-	<version>1.2.1-SNAPSHOT</version>
+	<version>2.0.0-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<scm>

targetplatform/KNIME-AP-4.0.target

@@ -2,6 +2,7 @@
 <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="org.knime.features.core.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"/>
@@ -11,12 +12,12 @@
 <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.features.chem.types.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.python2.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/4.3/"/>
 </location>
 	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
 		<unit id="nl.esciencecenter.e3dchem.knime.testing.plugin" version="0.0.0"/>
@@ -26,7 +27,7 @@
 	</location>
 	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
 		<unit id="org.rdkit.knime.feature.feature.group" version="0.0.0"/>
-		<repository location="http://update.knime.org/community-contributions/trusted/4.0/"/>
+		<repository location="http://update.knime.org/community-contributions/trusted/4.3/"/>
 	</location>
 </locations>
 <targetJRE path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
@@ -35,7 +36,7 @@
 -Dsun.java2d.d3d=false
 -Dosgi.classloader.lock=classname
 -XX:+UnlockDiagnosticVMOptions
--XX:+UnsyncloadClass 
+-XX:+UnsyncloadClass
 -XX:+UseG1GC
 -ea
 -Dorg.eclipse.swt.internal.gtk.cairoGraphics=false

targetplatform/pom.xml

@@ -20,7 +20,7 @@ Contributors:
 	<parent>
 		<artifactId>nl.esciencecenter.e3dchem.sygma</artifactId>
 		<groupId>nl.esciencecenter.e3dchem.sygma</groupId>
-		<version>1.2.1-SNAPSHOT</version>
+		<version>2.0.0-SNAPSHOT</version>
 	</parent>
 
 </project>

tests/META-INF/MANIFEST.MF

@@ -2,17 +2,17 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Tests
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.tests
-Bundle-Version: 1.2.1.qualifier
+Bundle-Version: 2.0.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.junit,
- 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="[4.3.0,5.0.0)",
+ org.knime.base;bundle-version="[4.3.0,5.0.0)",
+ org.knime.testing;bundle-version="[4.3.0,5.0.0)",
  org.rdkit.knime.nodes,
- org.knime.chem.base;bundle-version="[4.0.0,5.0.0)",
- org.knime.python2.serde.flatbuffers;bundle-version="[4.0.0,5.0.0)",
+ org.knime.chem.base;bundle-version="[4.3.0,5.0.0)",
+ org.knime.python2.serde.flatbuffers;bundle-version="[4.3.0,5.0.0)",
  nl.esciencecenter.e3dchem.knime.testing.plugin;bundle-version="[1.0.0,2.0.0)",
- nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.3,3.0.0)",
+ nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.4,3.0.0)",
  nl.esciencecenter.e3dchem.sygma.plugin
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ClassPath: .