https://github.com/egonw/knime-wikipathways

KNIME nodes for WikiPathways.
https://github.com/egonw/knime-wikipathways

biological-data-analysis knime pathway-analysis wikipathways workflow

Last synced: 8 months ago
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KNIME nodes for WikiPathways.

• Host: GitHub
• URL: https://github.com/egonw/knime-wikipathways
• Owner: egonw
• Created: 2018-02-22T13:03:57.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-03-21T13:22:44.000Z (about 8 years ago)
• Last Synced: 2025-01-22T17:11:33.596Z (over 1 year ago)
• Topics: biological-data-analysis, knime, pathway-analysis, wikipathways, workflow
• Language: Java
• Size: 46.9 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md

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README

          
# WikiPathways KNIME Nodes

These nodes are based on the KNIME node skeleton with sample code as described [here](https://tech.knime.org/developer-guide).

[![Build Status](https://travis-ci.org/egonw/knime-wikipathways.svg?branch=master)](https://travis-ci.org/egonw/knime-wikipathways)

[![SonarCloud Gate](https://sonarcloud.io/api/badges/gate?key=org.wikipathways:org.wikipathways.knime)](https://sonarcloud.io/dashboard?id=org.wikipathways:org.wikipathways.knime)

[![SonarCloud Coverage](https://sonarcloud.io/api/badges/measure?key=org.wikipathways:org.wikipathways.knime&metric=coverage)](https://sonarcloud.io/component_measures/domain/Coverage?id=org.wikipathways:org.wikipathways.knime)

This project uses [Eclipse Tycho](https://www.eclipse.org/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](https://sonarcloud.io/) 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=-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=`

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

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