README.md

Continue integration

The CICD makes use of the docker compose armadillo-compose build in build/docker/armadillo-compose together with an R image capable of running release-test.R.

Preparation

From the project root directory run

./gradlew clean build docker

This creates Dockerfile and Armadillo JAR in build/docker.

./docker/bin/prepare.bash ci

This creates armadillo-compose/ and cicd/ trees in build/docker.

• build/docker/armadillo-compose for running Armadillo demo and used by CICD.
• build/docker/cicd for running the release-test.R script.
• Note build/docker/cicd/ which hold an armadillo/ tree needed for release-test.R to run properly.

find ./build/docker
# if available
tree ./build/docker

Changing settings

In this directory docker/ci directory:

• Check ci.env for correct values which are used by release-test.R script.
• Check application.yml for the needed profiles matching those in docker-compose.yml.
• Make sure to run the preparation steps again.

If needed check available images defined in application.yml and docker-compose.yml match.

Run Armadillo and profiles

From within build/docker/armadillo-compos run

# First time build new image
docker compose build
# Use CTRL-C to stop
docker compose up

In same directory you can:

• check running images

docker compose images

should list

• molgenis/molgenis-armadillo (required)

• datashield/rock-base (depends)

• datashield/rock-dolomite-xenon (depends)

• molgenis/r-cicd (required)

• check status

docker container ls

• stop all

docker container down

Run the R CICD image

From with in build/docker/cicd/ run

docker container run \
    --network container:armadillo-compose-armadillo-1 \
    --volume armadillo:/cicd:rw \
    --interactive --tty \
    --entrypoint /bin/bash \
    molgenis/r-cicd -c "ls -l /cicd ; cd /cicd/scripts/release ; ./armadillo-ready.bash"

Debugging

docker run --interactive --tty --entrypoint /bin/bash molgenis/r-cicd