KripoDB KNIME nodes

KRIPO stands for Key Representation of Interaction in POckets.

KNIME nodes for KripoDB (https://github.com/3D-e-Chem/kripodb).

Installation

Requirements:

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

Optionally:

• KripoDB Python package & data files, https://github.com/3D-e-Chem/kripodb, required to start local running kripo web service instead of the public one.

Steps to get KripoDB 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 KripoDB
7. Install software & restart

Usage

See a minimal example workflow at examples/Knime-KripoDB-example.zip. The workflow can be run by importing it into KNIME as an archive.

Other workflows using the KripoDB nodes can be found at https://github.com/3D-e-Chem/workflows

Development

Development requirements:

• Maven, https://maven.apache.org

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.kripodb.targetplatform/KNIME-AP-5.1.target target definition.
6. A KNIME Analytics Platform instance can be started by right clicking on the targetplatform/KNIME\ Analytics\ Platform.launch file and selecting Run As → KNIME Analytics Platform. The KNIME instance will contain the target platform together with all extensions defined in the workspace.

During import the Tycho Eclipse providers must be installed.

Build

mvn package

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

Tests

mvn verify

Tests in tests module will have been run with results in test/target/surefire-reports directory. There are unit tests and workflow tests both are executed in the KNIME eclipse application. See https://github.com/3D-e-Chem/knime-testflow for more information about workflow tests.

Create web service client

The web service client is generated using Swagger Code Generator and stored inside plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/ directory.

1. Start KripoDB webservice

kripodb serve data/similarities.frozen.h5 data/fragments.sqlite data/pharmacophores.h5

2. Download swagger code generator

wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.2.3/swagger-codegen-cli-2.2.3.jar

3. Generate a client for KripoDB web service

java -jar swagger-codegen-cli-2.2.3.jar generate \
--input-spec http://localhost:8084/kripo/swagger.json \
--output client \
--lang java \
--config swagger-codegen.config.json

4. Compile client

cd client
mvn package

5. Populate plugin with client source code and dependencies

mkdir ../plugin/lib
cp target/lib/gson-* target/lib/logging-interceptor-* target/lib/ok* target/lib/swagger-annotations-* ../plugin/lib/
rm -r ../plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client
cp -r src/main/java/nl/esciencecenter/e3dchem/kripodb/ws/client ../plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/

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

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
6. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
7. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
8. Commit and push changes in this repo and 3D-e-Chem.github.io repo
9. Create a Github release
10. Update Zenodo entry
11. Correct authors
12. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as is cited by this upload entry.
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
14. Update CITIATION.cff with new DOI

Create stub recordings for integration tests

The test workflow are tested against a mocked web server and not the actual http://3d-e-chem.vu-compmedchem.nl/kripodb 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="http://3d-e-chem.vu-compmedchem.nl/" \
--port=8089 --record-mappings --verbose --root-dir=tests/src/test/resources/
java -jar tests/lib/wiremock-standalone-2.5.0.jar --proxy-all="http://localhost:8084/" \
--port=8089 --record-mappings --verbose --root-dir=tests/src/test/resources/

Then in a KNIME workflow in the KripoDB nodes set the base path to http://localhost:8089. Executing the workflow will fetch data from http://3d-e-chem.vu-compmedchem.nl/kripodb 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 enviroment 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.