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Development

Building

The makefile contains the necessary commands to build the verticox+ package.

If you wish to build the vantage6 docker image from scratch, use: 

make docker

Testing

There are several types of tests in this repository: - Unit tests - Integration test - vantage6 tests

Unit tests

The unit tests for the python components can be found in python/tests and can be run with pytest. The unit tests for the java components are found in java/src/test and can be run with maven.

Integration test

The files for the integration test can be found in integration/. It contains configuration files for the java components, a data directory with a small dataset, a docker-compose file to run all components, and a .env-example file that can be used to create your specific .env file. The .env file is required to indicate the absolute path to the directory that contains the jar file for the java components after you built them with maven.

The integration test can be run with docker compose up.

Vantage6 tests

The main vantage6 test is the script python/tests/test_verticox_v6.py. This can be run as a command-line tool and has parameters to configure the test to your needs:

./test_verticox_v6.py --help
Usage: test_verticox_v6.py [OPTIONS] host port user password

Arguments:
  host
  port
  user
  password

Options:
  --image=STR          (default: harbor2.vantage6.ai/algorithms/verticox:latest)
  --method=STR         (default: fit)
  --private-key=STR

Other actions:
  -h, --help          Show the help

You could run the test on a local vantage6 network. You have to make sure your nodes have access to data that is suitable for survival analysis.

./test_verticox_v6.py http://localhost 7601 dev_admin password

Further development

If this code would be developed further, it would be good to add the following features:

Sample size threshold

In order to further prevent data leakage, a threshold should be added to prevent the analysis from being run if the sample size is below a certain threshold.

Upgrade to latest vantage6 version

The current version of vantage6 that is being used is 4.7.1. In order to make it compatible with the latest version, the code should comply with the new client api.