kunchenli / knime-silicos-it

KNIME nodes and example workflows for software made by Silicos-it, ie. align-it, shape-it

knime-silicosit

KNIME nodes and example workflows for software made by Silicos-it like shape-it to align molecules based on shape and align-it to align molecules based on their pharmacophore.

This project uses Eclipse Tycho to perform build steps.

Installation

Requirements:

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

Steps to get the Silicos-it KNIME node inside KNIME:

1. Goto Help > Install new software ... menu
2. Press add button
3. Fill text fields with https://3d-e-chem.github.io/updates
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.

Continuous Integration

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

See ./.travis.yml file how to trigger a Travis-CI build for every push or pull request.

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) + Test workflows in JUnit + Chem base + Python

   1. Goto Help > Install new software ...
   2. Make sure Update site http://update.knime.org/analytics-platform/3.3 and https://3d-e-chem.github.io/updates are in the pull down list otherwise add them
   3. Select --all sites-- in work with pulldown
   4. Select m2e (Maven integration for Eclipse)
   5. Select Test Knime workflows from a Junit test
   6. Select Splash & node category for 3D-e-Chem KNIME nodes
   7. Select KNIME Base Chemistry Types & Nodes
   8. Select KNIME Python Integration
   9. Install software & restart

5. Import this repo as an Existing Maven project

During import the Tycho Eclipse providers must be installed.

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
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