GPCRDB node for KNIME

KNIME plugin for retrieving data from https://gpcrdb.org, GPCRdb website contains data, web tools and diagrams for G protein-coupled receptors (GPCRs).

Installation

Requirements:

• KNIME, https://www.knime.org, version 5.1 or higher

Steps to get GPCRDB nodes 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/5.1
4. Select --all sites-- in work with pulldown
5. Open KNIME 3D-e-Chem Contributions folder
6. Select GPCRDB
7. Install software & restart

Usage

See example workflow in examples folder.

Build

Requires Maven and JDK 8.

mvn verify

Jar has been made in plugin/target folder. An Eclipse update site will be made in p2/target/repository repository.

Development

Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:

1. Install Java 17
2. Install Eclipse for RCP and RAP developers
3. Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs
4. Import this repo as an Existing Maven project
5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.molviewer.targetplatform/KNIME-AP-5.1.target target definition.

During import the Tycho Eclipse providers must be installed.

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. Test node by installing it from local update site
5. Append new release to 3D-e-Chem update site
   1. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
   2. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
6. Commit and push changes in this repo and 3D-e-Chem.github.io repo
7. Create a Github release
8. Update Zenodo entry
   1. Fix authors
   2. Fix 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

Create GPCRDB client

1. Download swagger code generator

wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.3.0/swagger-codegen-cli-2.3.0.jar

2. Download and unpack the swagger rewriter

3. Generate a Swagger spec for the client

Install the swagger rewriter from https://github.com/3D-e-Chem/swagger-rewriter

swagger-rewriter/bin/swagger-rewriter \
https://gpcrdb.org/services/reference/api-docs/ \
client-config/swagger-rewriter.config.yml \
client-config/gpcrdb.swagger-spec.json

3.1 Optionally, make manual changes to client-config/gpcrdb.swagger-spec.json

4. Generate a client for GPCRDB web service using the rewritten spec

java -jar swagger-codegen-cli-2.3.0.jar generate \
--input-spec client-config/gpcrdb.swagger-spec.json \
--output client \
--lang java \
--config client-config/swagger-codegen.config.json

5. Compile client

cd client
mvn package

6. Make client jar and it's dependencies available in plugin

cp -r target/lib/* target/*jar ../plugin/lib/

7. Remove test dependencies

rm plugin/lib/*-tests.jar plugin/lib/junit* plugin/lib/hamcrest*

8. Update plugin/META-INF/MANIFEST.MF, plugin/build.properties files to reflect contents of lib/

Create stub recordings for integration tests

The test workflow are tested against a mocked web server and not the actual https://gpcrdb.org site. The mock server is called WireMock and normally gives empty responses. To have WireMock server return filled responses, stubs stored in tests/src/test/resources/ directory must be provided. The stubs can be recorded by starting a WireMock server in recording mode by:

java -jar tests/lib/wiremock-standalone-2.5.0.jar --proxy-all="https://gpcrdb.org/" \
--port=8089 --record-mappings --verbose --root-dir=tests/src/test/resources/

Then in a KNIME workflow in the GPCRDB nodes set the base path to http://localhost:8089. Executing the workflow will fetch data from https://gpcrdb.org/ via the WireMock server and cause new stubs to be recorded in the tests/src/test/resources/ directory.

To run the test workflows from inside KNIME desktop environment start the WireMock server in mock mode by:

java -jar tests/lib/wiremock-standalone-2.5.0.jar --port=8089 --verbose --root-dir=tests/src/test/resources/

Then import the test workflows in tests/src/knime/ directory, select the workflow in the KNIME explorer and in the context menu (right-click) select Run as workflow test.

References

• V Isberg, S Mordalski, C Munk, K Rataj, K Harpsøe, AS Hauser, B Vroling, AJ Bojarski, G Vriend, DE Gloriam. “GPCRdb: an information system for G protein-coupled receptors”, 2016, Nucleic Acids Res., 44, D356-D364. 10.1093/nar/gkv1178
• V Isberg, B Vroling, R van der Kant, K Li, G Vriend* and DE Gloriam*, “GPCRDB: an information system for G protein-coupled receptors”, 2014, Nucleic Acids Res., 42 (D1), D422-D425. 10.1093/nar/gkv1178