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Testing

These instructions describe some basic functionality tests and the ingestion of a test dataset to ensure your local installation is working properly.

Automatic testing

The easiest way to test your local installation is to run the integration tests.

This requires:

  • An activated conda environment (candig) showing up on the left of your command line.
  • Installation of some extra python requirements.

This can be done automatically:

Terminal window
source ./etc/venv/activate.sh

or separately:

Terminal window
cd CanDIGv2
conda activate candig
pip install -r etc/venv/requirements

Run the tests with:

Terminal window
make test-integration

Manual tests

These tests assume you are on a local deployment with default .env values. If not, you will need to update some of the values to suit your deployment. Check that you can see the data portal in your browser at http://candig.docker.internal:5080. If not, refer to the instructions in the deployment guide.

Check that you can generate a bearer token for user2 with the following call, substituting usernames, secrets and passwords from env.sh.

Terminal window
## user2 bearer token
curl -X "POST" "http://candig.docker.internal:8080/auth/realms/candig/protocol/openid-connect/token" \
     -H 'Content-Type: application/x-www-form-urlencoded; charset=utf-8' \
     --data-urlencode "client_id="$CANDIG_CLIENT_ID \
     --data-urlencode "client_secret="$CANDIG_CLIENT_SECRET \
     --data-urlencode "grant_type=password" \
     --data-urlencode "username="$CANDIG_NOT_ADMIN2_USER \
     --data-urlencode "password="$CANDIG_NOT_ADMIN2_PASSWORD \
     --data-urlencode "scope=openid"

Federation Service Errors

The federation service is required to run most CanDIG operations. It is included with make install-all, but sometimes glitches. Federation errors look like:

Terminal window
FAILED etc/tests/test_integration.py::test_server_count - assert 0 > 0
FAILED etc/tests/test_integration.py::test_services_count - assert 0 > 0
FAILED etc/tests/test_integration.py::test_federation_call - AssertionError: assert 'results' in {'error': 'There was a problem proxying the request'}
FAILED etc/tests/test_integration.py::test_add_server - IndexError: list index out of range

To solve these errors:

  1. Ensure federation is in the list of CANDIG_AUTH_MODULES in .env (though it is present by default).

  2. If you already have federation running, restart the container with:

Terminal window
make clean-federation
make build-federation
make compose-federation

Ingest the synthetic clinical dataset

Synthetic data is ingested as part of the integration tests. By default, this data is deleted after tests are run. If you’d like to keep the data in the platform, ensure the KEEP_TEST_DATA variable in your .env file is set to true.

If you would like to ingest the data separately, follow the clinical ingest and genomic ingest instructions using the test files in lib/candig-ingest/candigv2-ingest/tests, using small_dataset_clinical_ingest.json for clinical ingest and small_dataset_genomic_ingest.json for genomic ingest.

You should now see the ingested data in the data portal.