KNIME nodes for Sygma
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README.md

SyGMa KNIME nodes

The SyGMa KNIME nodes for the Systematic Generation of potential Metabolites.

Build Status SonarCloud Gate SonarCloud Coverage DOI

Installation

Requirements:

Steps to get the SyGMa KNIME nodes 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.

See example workflow in examples folder.

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) + Python wrapper + Test workflows in JUnit + 3D-e-Chem node category + RDKit

    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:
    1. Goto Help -> Check for updates
    2. Install any updates found & restart
    3. Goto Help > Install new software ...
    4. Select --All Available sites-- in work with pulldown
    5. Wait for list to be filled, Pending... should disappear
    6. Select the following items:
    • Abstract Python wrapper KNIME node and helpers
    • Test Knime workflows from a Junit test
    • Splash & node category for 3D-e-Chem KNIME nodes
    • RDKit KNIME integration
    • KNIME Base Chemistry Types & Nodes
    • Test Knime workflows from a Junit test
    1. 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.

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.

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. Commit and push changes
  3. Create package with mvn package, will create update site in p2/target/repository
  4. Append new release to an update site
  5. Make clone of an update site repo
  6. Append release to the update site with mvn install -Dtarget.update.site=<path to update site>
  7. Commit and push changes in this repo and update site repo.
  8. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release