knime-plants

KNIME nodes to configure, run and analyze PLANTS protein-ligand docking

PLANTS homepage at http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html

This project uses Eclipse Tycho to perform build steps.

License

Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-biochemie/pharmazie/pharmazeutische-chemie/pd-dr-t-exner/research/plants.html). When installing the plugin you have to accept this license agreement, you agree to use the included PLANTS executable only for academic usage. To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.

The PLANTS KNIME nodes themselves have the Apache 2.0 license.

Installation

Requirements:

• KNIME, https://www.knime.org, version 3.3 or higher

Steps to get the PLANTS KNIME node 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.
4. Select --all sites-- in work with pulldown
5. Select the node
6. Install software
7. Restart KNIME

Usage

1. Create a new KNIME workflow.
2. Find node in Node navigator panel.
3. Drag node to workflow canvas.

Examples

The examples/ folder contains example KNIME workflows.

Build

mvn verify

An Eclipse update site will be made in p2/target/repository directory. The update site can be used to perform a local installation.

Development

Steps to get development environment setup:

1. Download KNIME SDK from https://www.knime.org/downloads/overview
2. Install/Extract/start KNIME SDK
3. Start SDK

4. Install m2e (Maven integration for Eclipse) + KNIME Testing framework + Vernalis + SWTBot

   1. Goto Window -> Preferences -> Install/Update -> Available Software Sites

   2. Make sure the following Software Sites (or a version of them) are present otherwise add them:

      • http://update.knime.org/analytics-platform/3.3
      • http://update.knime.org/community-contributions/trusted/3.3
      • https://3d-e-chem.github.io/updates
      • http://download.eclipse.org/eclipse/updates/4.6
      • http://download.eclipse.org/releases/neon
      • http://download.eclipse.org/technology/swtbot/releases/latest/

   3. Goto Help -> Check for updates

   4. Install any updates found & restart
   5. Goto Help > Install new software ...
   6. Select --All Available sites-- in work with pulldown
   7. Wait for list to be filled, Pending... should disappear

   8. Select the following items:

      • m2e (Maven integration for Eclipse)
      • Test Knime workflows from a Junit test
      • Splash & node category for 3D-e-Chem KNIME nodes
      • Vernalis
      • SWTBot for Eclipse Testing
      • SWtBot JUnit Headless launchers for Eclipse

   9. Install software & restart

5. Import this repo as an Existing Maven project

After the import the Maven plugin connections must be setup, a Discover m2e connections dialog will popup to install all requested connectors, after the installation restart eclipse.

Meta nodes

This plugin uses metanodes as it's public nodes. The are created in the following way:

1. The meta nodes are first created and tested inside the example workflows in the examples/ directory.
2. The name and customDescription field inside examples/**/workflow.knime is filled.
3. The examples are fully run and committed
4. The meta nodes are internally completely reset, so we don't ship public nodes with example data in them.
5. The meta nodes from the example workflows are then copied to the plugin/src/knime/ directory.
6. The meta nodes are added to the plugin/plugin.xml as PersistedMetaNode in the org.knime.workbench.repository.metanode extension.
7. The examples are checked-out to their fully run state.

Tests

Tests for the node are in tests/src directory. Tests can be executed with mvn verify, they will be run in a separate KNIME environment. Test results will be written to test/target/surefire-reports directory. Code coverage reports (html+xml) can be found in the tests/target/jacoco/report/ directory.

There are no tests for the meta nodes as they are copied from the plugin to a workflow each time, which would make the test test itself.

Unit tests

Unit tests written in Junit4 format can be put in tests/src/java.

Workflow tests

See https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow

Speed up builds

Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites. This can be skipped by running maven offline using mvn -o.

New release

1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
2. Create package with mvn package, will create update site in p2/target/repository
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
   2. Correct license
   3. Add https://doi.org/10.1007/11839088_22 as is referenced by this upload related identifier
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