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Merge pull request #34 from 3D-e-Chem/knime51
KNIME 5.1 support
2 parents 02cb22c + 8c12c20 commit 8d14679

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‎.github/workflows/build.yml‎

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on:
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push:
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branches:
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- master
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pull_request:
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types:
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- "opened"
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- "reopened"
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types: [opened, synchronize, reopened]
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jobs:
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build:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v2
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- name: Set up JDK 1.8
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uses: actions/setup-java@v1
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- uses: actions/checkout@v3
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with:
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java-version: 1.8
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- name: Cache Maven packages
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uses: actions/cache@v2
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fetch-depth: 0
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- name: Set up JDK 17
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uses: actions/setup-java@v3
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with:
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path: ~/.m2
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key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }}
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restore-keys: ${{ runner.os }}-m2
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- name: OS dependencies
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run: sudo apt-get install xvfb
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- name: Build with Maven
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run: mvn -B package
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- name: Run tests
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run: xvfb-run mvn verify -B
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- name: Set up JDK 11 for SonarCloud analysis
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uses: actions/setup-java@v1
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with:
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java-version: 11
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- name: SonarCloud analysis
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run: mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN
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java-version: 17
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distribution: 'temurin'
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cache: maven
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- name: Build and analyze
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
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run: xvfb-run mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=3D-e-Chem_knime-kripodb

‎.mvn/extensions.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<extensions>
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<extension>
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<groupId>org.eclipse.tycho</groupId>
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<artifactId>tycho-build</artifactId>
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<version>2.7.5</version>
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</extension>
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</extensions>

‎CHANGELOG.md‎

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## Unreleased
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## [3.0.1] - 2023-11-22
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### Changed
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- Require KNIME 5.1
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## [3.0.0] - 2021-02-12
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## Removed
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### Removed
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- Python based nodes in favour of web service nodes ([#25](https://github.com/3D-e-Chem/knime-kripodb/issues/25))
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- Python templates to use KripoDB package
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- Example workflow on Github repo.
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[unreleased]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.5.0...HEAD
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[unreleased]: https://github.com/3D-e-Chem/knime-kripodb/compare/v3.0.1...HEAD
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[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v3.0.0...v3.0.1
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[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.5.0...v3.0.0
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[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.4.2...v2.5.0
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[2.4.2]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.1...v2.4.2
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[2.4.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.0...v2.3.1

‎CITATION.cff‎

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family-names: Verhoeven
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affiliation: Netherlands eScience Center
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orcid: https://orcid.org/0000-0002-5821-2060
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date-released: 2019-07-02
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repository-code: https://github.com/3D-e-Chem/knime-kripodb
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license: GPL-3.0

‎README.md‎

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[KNIME](http://www.knime.org) nodes for KripoDB (https://github.com/3D-e-Chem/kripodb).
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[![Java CI with Maven](https://github.com/3D-e-Chem/knime-kripodb/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/3D-e-Chem/knime-kripodb/actions?query=workflow%3A%22Java+CI+with+Maven%22)
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[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb)
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[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb)
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[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-kripodb&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-kripodb)
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[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=3D-e-Chem_knime-kripodb&metric=coverage)](https://sonarcloud.io/summary/new_code?id=3D-e-Chem_knime-kripodb)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597262.svg)](https://doi.org/10.5281/zenodo.597262)
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# Installation
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Requirements:
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- KNIME, https://www.knime.org, version 4.0 or higher
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- KNIME, https://www.knime.org, version 5.1 or higher
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Optionally:
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1. Goto Help > Install new software ... menu
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2. Press add button
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3. Fill text fields with `https://3d-e-chem.github.io/updates`
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3. Fill text fields with `https://3d-e-chem.github.io/updates/5.1`
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4. Select --all sites-- in work with pulldown
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5. Open KNIME 3D-e-Chem Contributions folder
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6. Select KripoDB
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Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
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1. Install Java 8
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2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/release/2018-12/r/eclipse-ide-rcp-and-rap-developers)
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3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
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1. Install Java 17
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2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/installer)
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3. Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs
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4. Import this repo as an Existing Maven project
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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.kripodb.targetplatform/KNIME-AP-4.0.target` target definition.
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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.kripodb.targetplatform/KNIME-AP-5.1.target` target definition.
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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.
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During import the Tycho Eclipse providers must be installed.

‎feature/feature.xml‎

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<feature
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id="nl.esciencecenter.e3dchem.kripodb.feature"
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label="KripoDB nodes for KNIME"
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version="3.0.0.qualifier"
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version="3.0.1.qualifier"
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provider-name="Netherlands eScience Center">
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<description url="https://github.com/3D-e-Chem/knime-kripodb">
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<discovery label="KripoDB" url="https://github.com/3D-e-Chem/kripodb"/>
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</url>
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<requires>
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<import feature="org.rdkit.knime.binaries.feature" version="0.0.0"/>
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</requires>
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<plugin
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id="nl.esciencecenter.e3dchem.kripodb.plugin"
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download-size="0"

‎feature/pom.xml‎

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<parent>
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<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
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<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
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<version>3.0.0-SNAPSHOT</version>
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<version>3.0.1-SNAPSHOT</version>
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</parent>
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<artifactId>nl.esciencecenter.e3dchem.kripodb.feature</artifactId>

‎p2/category.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<site>
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<feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="3.0.0.qualifier">
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<feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="3.0.1.qualifier">
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<category name="nl.esciencecenter.3D-e-Chem"/>
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</feature>
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<category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">

‎p2/pom.xml‎

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<parent>
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<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
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<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
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<version>3.0.0-SNAPSHOT</version>
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<version>3.0.1-SNAPSHOT</version>
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</parent>
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<artifactId>nl.esciencecenter.e3dchem.kripodb.p2</artifactId>
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<packaging>eclipse-repository</packaging>

‎plugin/META-INF/MANIFEST.MF‎

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Bundle-ManifestVersion: 2
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Bundle-Name: 3D-e-Chem KNIME KripoDB nodes
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Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.plugin;singleton:=true
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Bundle-Version: 3.0.0.qualifier
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Bundle-RequiredExecutionEnvironment: JavaSE-1.8
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Bundle-Version: 3.0.1.qualifier
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Bundle-RequiredExecutionEnvironment: JavaSE-17
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Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator
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Require-Bundle: org.knime.core;bundle-version="[4.0.0,5.0.0)",
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org.knime.base;bundle-version="[4.0.0,5.0.0)",
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org.knime.chem.types;bundle-version="[4.0.0,5.0.0)",
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org.rdkit.knime.types,
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Require-Bundle: org.knime.core;bundle-version="[4.0.0,6.0.0)",
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org.knime.base;bundle-version="[4.0.0,6.0.0)",
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org.knime.chem.types;bundle-version="[4.0.0,6.0.0)",
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org.rdkit.knime.types;bundle-version="[4.6.1,5.0.0)",
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nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)",
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nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)"
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Bundle-Vendor: Netherlands eScience Center

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