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Moved Python wrapper from knime-kripodb nodes to own repo.
See https://github.com/3D-e-Chem/knime-kripodb
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‎.gitignore‎

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*.class
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*.pyc
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# Mobile Tools for Java (J2ME)
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.mtj.tmp/
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
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hs_err_pid*
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# Eclipse project
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.settings/
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.project
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target
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.classpath
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swagger-codegen-cli-*.jar

‎.travis.yml‎

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sudo: false
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language: java
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jdk: oraclejdk8
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cache:
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directories:
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- $HOME/.m2
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install: mvn package -B
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script: mvn verify -B

‎CHANGELOG.md‎

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# Change Log
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All notable changes to this project will be documented in this file.
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This project adheres to [Semantic Versioning](http://semver.org/).
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The file is formatted as described on http://keepachangelog.com/.
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## [Unreleased]

‎LICENSE‎

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‎README.md‎

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Abstract Python wrapper KNIME node and helpers.
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Used for development of KNIME nodes calling Python scripts.
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[![Build Status](https://travis-ci.org/3D-e-Chem/knime-python-wrapper.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-python-wrapper)
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The nodes in Scripting>Python folder of the node repository (nodes part of the `KNIME Python integration` plugin) the end-user needs to paste Python code in a text area in the node dialog.
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Nodes derived from this repo will have a Python script included in their jar file and the dialog of the node will contain no source code text area.
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The included Python script is not editable by the end-user, but can read options from dialog like the input column name.
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# Usage
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Requirements:
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* KNIME SDK, https://www.knime.org, version 3.1 or higher
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Instructions for KNIME node developers that want to call a Python script.
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Several steps must be performed:
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[1. Add update site](#1-add-update-site)
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[2. Add dependency](#2-add-dependency)
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[3. Implement node](#3-implement-node)
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[4. Write tests](#4-write-tests)
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## 1. Add update site
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The releases of this repository are available in the `https://3d-e-chem.github.io/updates` update site.
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Configure KNIME SDK by adding the `https://3d-e-chem.github.io/updates` update site in Preferences > Install/Update > Available Software Sites.
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To make use of in a Tycho based project add to the `<repositories>` tag of the `pom.xml` file the following:
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```
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<repository>
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<id>3d-e-chem</id>
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<layout>p2</layout>
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<url>https://3d-e-chem.github.io/updates</url>
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</repository>
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```
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## 2. Add dependency
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To implement the node a dependency is needed for the plugin add tests.
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To do this add `nl.esciencecenter.e3dchem.knime.python` as a required plugin to the `plugin/META-INF/MANIFEST.MF` and `tests/META-INF/MANIFEST.MF` file.
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## 3. Implement node
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Create your node config class extended from the `nl.esciencecenter.e3dchem.python.PythonWrapperNodeConfig` class.
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Add fields you want to have in the node dialog and be available inside the Python script inside the `options` dictionary.
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Create your node model class extended from the `nl.esciencecenter.e3dchem.python.PythonWrapperNodeModel` class.
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Overwrite the `python_code_filename` and `required_python_packages` fields in the constructor.
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## 4. Write tests
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To run tests which execute the node it is needed to setup `KNIME Python integration` plugin.
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This can be done by calling `PythonWrapperTestUtils.materializeKNIMEPythonUtils()` in `@BeforeClass` method of a test case.
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# Build
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```
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mvn verify
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```
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An Eclipse update site will be made in `p2/target/repository` repository.
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The update site can be used to perform a local installation.
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# Development
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Development of code in this repository.
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Steps to get development environment setup:
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1. Download KNIME SDK from https://www.knime.org/downloads/overview
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2. Install/Extract/start KNIME SDK
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3. Start SDK
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4. Install m2e (Maven integration for Eclipse) + KNIME Python Integration
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1. Goto Help > Install new software ...
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2. Make sure Update site is http://update.knime.org/analytics-platform/3.1 is in the pull down list otherwise add it
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3. Select --all sites-- in work with pulldown
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4. Select m2e (Maven integration for Eclipse)
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5. Select `KNIME Python Integration`
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6. Install software & restart
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5. Import this repo as an Existing Maven project
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During import the Tycho Eclipse providers must be installed.
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# New release
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1. Update versions in pom files with `mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>` command.
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2. Manually update version of "source" feature in `p2/category.xml` file.
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3. Commit and push changes
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3. Create package with `mvn package`, will create update site in `p2/target/repository`
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4. Append new release to an update site
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1. Make clone of an update site repo
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2. Append release to the update site with `mvn install -Dtarget.update.site=<path to update site>`
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5. Commit and push changes in this repo and update site repo.

‎p2/category.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<site>
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<bundle id="nl.esciencecenter.e3dchem.python.plugin" version="1.0.0">
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<category name="nl.esciencecenter.3D-e-Chem"/>
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</bundle>
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<bundle id="nl.esciencecenter.e3dchem.python.plugin.source" version="1.0.0">
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<category name="nl.esciencecenter.3D-e-Chem.sources"/>
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</bundle>
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<category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">
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<description>
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3D-e-Chem: Collection KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
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</description>
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</category-def>
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<category-def name="nl.esciencecenter.3D-e-Chem.sources" label="KNIME 3D-e-Chem Contributions Sources">
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<description>
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3D-e-Chem Sources: Sources of KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
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</description>
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</category-def>
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</site>

‎p2/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>nl.esciencecenter.e3dchem.python</artifactId>
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<groupId>nl.esciencecenter.e3dchem.python</groupId>
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<version>1.0.0</version>
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</parent>
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<artifactId>nl.esciencecenter.e3dchem.python.p2</artifactId>
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<packaging>eclipse-repository</packaging>
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<build>
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<plugins>
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<plugin>
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<groupId>org.eclipse.tycho.extras</groupId>
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<artifactId>tycho-p2-extras-plugin</artifactId>
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<version>${tycho.extras.version}</version>
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<executions>
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<execution>
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<id>add-to-update-site</id>
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<phase>install</phase>
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<goals>
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<goal>mirror</goal>
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</goals>
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<configuration>
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<source>
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<repository>
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<url>${project.build.directory}/repository</url>
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</repository>
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</source>
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<destination>${target.update.site}</destination>
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<append>true</append>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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</project>

‎plugin/META-INF/MANIFEST.MF‎

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Manifest-Version: 1.0
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Bundle-ManifestVersion: 2
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Bundle-Name: Abstract Python wrapper KNIME node and helpers
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Bundle-SymbolicName: nl.esciencecenter.e3dchem.python.plugin;singleton:=true
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Bundle-Version: 1.0.0
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Bundle-RequiredExecutionEnvironment: JavaSE-1.8
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Bundle-Vendor: Netherlands eScience Center
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Require-Bundle: org.knime.core;bundle-version="[3.1.0,4.0.0)",
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org.knime.base;bundle-version="[3.1.0,4.0.0)",
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org.knime.python;bundle-version="[3.1.0,4.0.0)"
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Bundle-ClassPath: .
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Export-Package: nl.esciencecenter.e3dchem.python

‎plugin/build.properties‎

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source.. = src/java/
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output.. = target/classes/
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bin.includes = META-INF/,\
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.,\
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plugin.xml

‎plugin/plugin.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<?eclipse version="3.0"?>
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<plugin>
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<!-- No extensions provided, plugin used to get Python Wrapper dependency inside another project to run implement nodes which call Python scripts -->
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</plugin>

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