Knime node for KripoDB package
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Latest commit 4606e48 Apr 4, 2018

README.md

KripoDB KNIME nodes

KRIPO stands for Key Representation of Interaction in POckets.

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

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Installation

Requirements:

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:

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
  1. 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
  1. 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
  1. Compile client
cd client
mvn package
  1. 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/
  1. 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. Fix authors
  12. Fix license
  13. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as is cited by this upload entry.
  14. 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.