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Support KNIME 5.1
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‎.github/workflows/build.yml‎

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@@ -5,10 +5,10 @@ name: Java CI with Maven
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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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@@ -5,15 +5,15 @@ KRIPO stands for [Key Representation of Interaction in POckets](http://dx.doi.or
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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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<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"

‎plugin/META-INF/MANIFEST.MF‎

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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-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

‎plugin/pom.xml‎

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<artifactId>nl.esciencecenter.e3dchem.kripodb.plugin</artifactId>
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<packaging>eclipse-plugin</packaging>
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<properties>
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<sonar.jacoco.reportPaths>../tests/target/jacoco.exec</sonar.jacoco.reportPaths>
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<sonar.coverage.jacoco.xmlReportPaths>../tests/target/report/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>
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<sonar.junit.reportsPath>../tests/target/surefire-reports</sonar.junit.reportsPath>
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<!-- exclude the generate client code from sonar cloud analysis -->
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<sonar.exclusions>src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/**/*</sonar.exclusions>

‎pom.xml‎

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</issueManagement>
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<ciManagement>
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<system>Travis CI</system>
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<url>http://travis-ci.org/3D-e-Chem/knime-kripodb</url>
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<system>GitHub actions</system>
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<url>https://github.com/3D-e-Chem/knime-kripodb/actions</url>
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</ciManagement>
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<modules>
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</prerequisites>
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<properties>
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<tycho.version>1.4.0</tycho.version>
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<tycho.extras.version>1.4.0</tycho.extras.version>
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<tycho.version>2.7.5</tycho.version>
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<tycho.extras.version>${tycho.version}</tycho.extras.version>
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<tycho.test.jvmArgs>-Xmx512m</tycho.test.jvmArgs>
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<jacoco.version>0.8.10</jacoco.version>
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<java.version>17</java.version>
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<maven.compiler.version>3.10.1</maven.compiler.version>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
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<tycho.scmUrl>scm:git:https://github.com/3D-e-Chem/knime-kripodb.git</tycho.scmUrl>
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<target.file>KNIME-AP-4.0</target.file>
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<knime.version>5.1</knime.version>
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<target.file>KNIME-AP-${knime.version}</target.file>
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<sonar.host.url>https://sonarcloud.io</sonar.host.url>
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<sonar.organization>3d-e-chem</sonar.organization>
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<!-- following required if running mvn from JDK17 -->
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<knime.ini.testArgs>--add-opens=java.security.jgss/sun.security.jgss.krb5=ALL-UNNAMED
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--add-opens=java.base/sun.security.ssl=ALL-UNNAMED
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--add-opens=java.base/sun.security.util=ALL-UNNAMED
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--add-opens=java.base/java.lang=ALL-UNNAMED
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--add-opens=java.base/java.lang.invoke=ALL-UNNAMED
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--add-opens=java.base/java.net=ALL-UNNAMED
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--add-opens=java.base/java.nio=ALL-UNNAMED
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--add-opens=java.base/java.nio.channels=ALL-UNNAMED
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--add-opens=java.base/java.util=ALL-UNNAMED
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--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
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--add-opens=java.base/sun.nio=ALL-UNNAMED
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--add-opens=java.desktop/javax.swing.plaf.basic=ALL-UNNAMED
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--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED
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-Dmisc.io.testing=true</knime.ini.testArgs>
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</properties>
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<build>
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<plugins>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.eclipse.tycho.extras</groupId>
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<artifactId>tycho-pack200a-plugin</artifactId>
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<version>${tycho.extras.version}</version>
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</plugin>
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</plugins>
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<pluginManagement>
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<plugins>

‎targetplatform/KNIME Analytics Platform.launch‎

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<stringAttribute key="location" value="${workspace_loc}/../runtime-KNIME"/>
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<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
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<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="true"/>
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<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
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<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17"/>
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<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="-os ${target.os} -ws ${target.ws} -arch ${target.arch} -nl ${target.nl} -consoleLog"/>
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<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.pde.ui.workbenchClasspathProvider"/>
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<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-server&#10;-Dsun.java2d.d3d=false&#10;-Dosgi.classloader.lock=classname&#10;-XX:+UnlockDiagnosticVMOptions&#10;-XX:+UnsyncloadClass&#10;-XX:+UseG1GC&#10;-Dknime.enable.fastload=true&#10;-ea&#10;-Dorg.eclipse.swt.internal.gtk.cairoGraphics=false&#10;-Dorg.eclipse.swt.internal.gtk.useCairo=false&#10;-Dorg.eclipse.swt.browser.IEVersion=12001&#10;-Dsun.awt.noerasebackground=true&#10;-Dorg.eclipse.swt.internal.gtk.disablePrinting&#10;-Xmx2G"/>

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