Testing, Development, and Contributing¶

Testing¶

Tripal Apollo uses Tripal Test Suite to make configuring PHPUnit to work with Drupal and Tripal easy. Tripal Test Suite documentation is available here: https://tripaltestsuite.readthedocs.io/en/latest/

Creating a Development Environment¶

The travis CI environment uses the Docker compose file in this repository to launch a Tripal site and Apollo site. You can simply use this configuration locally!

An example setup:

# extract the example dataset
tar -xvf example_data/yeast.tar.gz -C example_data/
composer install
docker-compose up -d
## Set the APOLLO_URL variable.
APOLLO_URL=http://localhost:8888
export APOLLO_URL
/bin/bash setup/set_travis_apollo.sh

If you only need an Apollo container, it can be run via docker run:

# extract the example dataset
tar -xvf example_data/yeast.tar.gz -C example_data/
# run an Apollo container
docker run -it -v ${PWD}/example_data/:/data  -p 8888:8080 quay.io/gmod/docker-apollo:2.1.0

## Set the APOLLO_URL variable.
APOLLO_URL=http://localhost:8888
export APOLLO_URL
#run the setup script, which will create the organism and groups in the Apollo instance.
/bin/bash setup/set_travis_apollo.sh

Note

The Apollo credentials for this container are:

username: admin@local.host
password: password

Setting up Tripal Test Suite¶

Prior to running test suite, you must run composer install and copy tests/example.env to tests/.env. Note we define an extra variable in tests/example.env: APOLLO_URL=http://localhost:8888. This MUST include http:// and it must point at your Apollo instance for tests to work.

See https://tripaltestsuite.readthedocs.io/en/latest/environment.html?highlight=.env for general information on setting up Test Suite.

Contributing¶

Tripal Apollo is open source and distributed via the GPL 3 license. If you have questions, feature requests, or a desire to contribute, please post to the github issues board here: https://github.com/NAL-i5K/tripal_apollo/issues