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

Optionally:

• KripoDB Python package & data files, https://github.com/3D-e-Chem/kripodb, required when nodes which use local Kripo files are used. Nodes which talk to web service work without the KripoDB Python package.

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
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

Make sure the Python used by KNIME is the same the Python with kripodb package installed.

Development

Development requirements:

• Maven, https://maven.apache.org

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) + KNIME Python Integration + RDKit KNIME integration + KNIME Testing framework + 3D-e-Chem node category

   1. Goto Help > Install new software ...
   2. Make sure Update site is https://3d-e-chem.github.io/updates , http://download.eclipse.org/releases/neon/ , http://update.knime.org/analytics-platform/3.1 and http://update.knime.org/community-contributions/trusted/3.1 are in the pull down list otherwise add it
   3. Select --all sites-- in work with pulldown
   4. Select m2e (Maven integration for Eclipse)
   5. Select RDKit KNIME integration
   6. Select Abstract Python wrapper KNIME node and helpers
   7. Select Test Knime workflows from a Junit test
   8. Select Splash & node category for 3D-e-Chem KNIME nodes
   9. Install software & restart

5. Import this repo as an Existing Maven project

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
   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
   3. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as is cited by this upload entry.
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 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.