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migrating_to_2_11.md

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Migrating to BentoV2 2.11

BentoV2 2.11 introduces a new pre-built gateway image, a new Keycloak image version, and a new management tool called bentoctl which replaces the Makefile.

Shut down the old cluster

The Makefile will likely no longer work, so stop the containers using the docker command or GUI.

Move certificates

Certificates have been relocated from lib/gateway/certs to ./certs, since Keycloak now terminates SSL at the Keycloak server itself instead of the gateway.

To move certs, run:

mv ./lib/gateway/certs/* ./certs/

Move development repos (optional; can just let bentoctl re-clone instead)

Development repositories are now located in ./repos.

Repositories should be relocated and renamed after the docker compose service name. For example, for web:

mv lib/web/bento_web repos/web

Updating local environment variables

A new configuration variable has been added in BentoV2 2.11. Here is what you will need to set in your local.env file:

# Set this to a random secret value
BENTOV2_SESSION_SECRET=some-long-random-string

# These used to be set by default in bento.env, but now needs explicit setting in local.env
BENTOV2_KATSU_APP_SECRET=some-long-random-string
BENTOV2_KATSU_DB_PASSWORD=some-long-random-string

# This used to be set by default in bento.env; same as above
BENTOV2_GOHAN_ES_PASSWORD=some-long-random-string

Remove any lines which look like the following:

BENTOV2_FEDERATION_PROD_DEBUG=true
BENTOV2_FEDERATION_DEV_DEBUG=true

The default development value for BENTOV2_ROOT_DATA_DIR was changed to ./data; this should not affect an existing setup.

Create a Python 3.8+ (preferably 3.10+) virtual environment and install bentoctl requirements

bentoctl is a Python script, and requires some external dependencies, which we can put in a virtual environment.

python3 -m venv ./env  # create env folder with virtual environment inside
source ./env/bin/activate  # activate the virtual environment
pip install -r requirements.txt  # install bentoctl requirements
./bentoctl.bash --help  # Make sure bentoctl works and look at the available commands

Make bentoctl alias (optional; Linux/macOS)

To make interacting with the CLI quicker, consider adding an alias for calling bentoctl.bash, putting the following in your .bash_aliases, .bash_profile or .zshrc file:

Bash/ZSH:

alias bentoctl="./bentoctl.bash"

From here, you can use bentoctl instead of ./bentoctl.bash to manage BentoV2.

Install Docker Compose Plugin (if needed)

On Ubuntu, for example:

apt-get install docker-compose-plugin

See this StackOverflow post.

Create new Docker networks

v2.11 adds several new Docker networks in an effort to better isolate services from each other to provide better security. To create these if needed, run:

./bentoctl.bash init-docker

Don't worry; this is idempotent and will not fail if any required network already exists.

Pull new images

v2.11 needs a bunch of new service images, as specified by etc/bento.env. To update the images using the new bentoctl tool, run:

./bentoctl.bash pull

Start the new cluster

./bentoctl.bash run

Migrating to bentoctl

Key changes versus the Makefile include:

Running all services

Makefile: make run-all

bentoctl: ./bentoctl.bash run

Restarting a specific service, while pulling a new image

Makefile

make stop-drs
docker pull ghcr.io/bento-platform/...
make run-drs

bentoctl

./bentoctl.bash restart --pull drs

Switching a service (e.g., web) to development mode

Makefile

make clean-web
make run-web-dev

bentoctl

Note: that the first time work-on is called, it will clone the service in question in the repos/ directory and run the version of the service that code specifies. This is a change from the old approach, where the repos were located in lib/.

./bentoctl.bash work-on web

This will automatically restart the service in a local development mode, using code in ./repos/web.

Switching a service (e.g., web) to pre-built mode

Makefile

make clean-web-dev
make run-web

bentoctl

./bentoctl.bash prebuilt web

This will start in either production mode (if MODE=prod in local.env) or development mode, but with a pre-built image, if MODE=dev.

Notes on cBioPortal Usage

If you want to use cBioPortal (which is partially integrated into 2.11), you will need to add the cBioPortal URL (with /*) as valid redirect URI and, plain, as a valid web origin:

redirect URIs: [..., https://cbioportal.my-bento-domain/*]  # Note: /*
web origins: [..., https://cbioportal.my-bento-domain]  # Note: no trailing slash

Also, if developing locally, you should regenerate certificates so that a cBioPortal self-signed certificate is generated.