WikiPathways KNIME Nodes

These nodes are based on the KNIME node skeleton with sample code as described here.

This project uses Eclipse Tycho to perform build steps.

Installation

Requirements:

• KNIME, https://www.knime.org, version 3.5 or higher

Steps to get the WikiPathwaysNode KNIME node inside KNIME:

1. Goto Help > Install new software ... menu
2. Press add button
3. Fill text fields with url of update site which contains this node.
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.

Build

To build the node extension and verify the tests run with the following command:

mvn verify

Make sure all code is commited as the snapshot version is determined by git commit timestamp.

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

Continuous Integration

Configuration files to run Continuous Integration builds on Linux (Travis-CI), OS X (Travis-CI) and Windows (AppVeyor) are present.

See ./.travis.yml file how to trigger a Travis-CI build for every push or pull request. Also see ./.travis.yml file how to perform a SonarCloud analysis and code coverage.

See ./appveyor.yml file how to run on https://www.appveyor.com .

Development

Steps to get development environment setup:

1. Download KNIME SDK from https://www.knime.org/downloads/overview

2. Install/extract KNIME SDK

3. Start KNIME SDK

4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit

   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/3.5
   • http://download.eclipse.org/eclipse/updates/4.6
   • http://download.eclipse.org/releases/neon
   • https://3d-e-chem.github.io/updates (only required for 3D-e-Chem node)
   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 (includes Incubating components)
   • Test KNIME workflows from a Junit test
   • Splash & node category for 3D-e-Chem KNIME nodes (only required for 3D-e-Chem node)
   9. Install software & restart

5. Import this repo as an Existing Maven project

During import the Tycho Eclipse providers must be installed, Eclipse will ask for your permission.

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.

The tests can be run against a different KNIME version using mvn verify -Dknime.version=3.5 where 3.5 is the major.minor version of KNIME.

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
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. Correct license
13. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release