This is a repository for the Dockerfile and file dependencies for the RESTful-PFRED service that is compiled as a .war file (see pfred-rest-service).
If you are cloning this repository and wnat to create the service in a Windows machine, then set git to not change the scripts EOL Unix setting. Do this via the following git command in CLI:
git config --global core.autocrlf false
Then the environment on WIndows should be ready to deploy.
To use this Dockerfile layer, run the following docker command:
docker build -t pfredimg .
Note that this process will setup the pfredservice environment and install all needed dependencies. Process might take up to 10 mins in a regular modern laptop.
Once the pfredimg image has been created, docker should now show the status and running uptime:
docker images
Then, the container can be loaded by the following command:
docker-compose up -d
If run for the first time, this will create a docker volume named dockerfiles-sl_pfred-vol and a docker container
named pfredservice. Note that the -d flag will detach the shell from the running container, the RESTful service will not be ready to use until the command docker-compose logs shows a Tomcat started message.
Once the service is ready, you should be able to access the REST API at https://os.biogen.com/PFREDRestService/api. Keep in mind that the entrypoint will download the scripts and data generated from bowtie, therefore it might take up to 10 mins while the container downloads everything it needs before the pfredservice is ready.
The entrypoint will also create a docker volume named pfred-docker_pfred-vol so that if the pfredservice docker container is killed, it can be reloaded via the command:
docker-compose up -d pfred-service
And the service container should be immediately ready for use since all the data has been stored into pfred-docker_pfred-vol.
Once the service has been used and it is not longer needed, execute:
docker-compose down
This will remove containers, networks, volumes and images created by docker-compose up.
If the pfredimg is not longer needed, it can be removed via the command:
docker rmi pfredimg
Likewise for the docker volume. If it is not longer needed, run the command:
docker volume rm pfred-docker_pfred-vol
Docker provides a single command that will clean up any resources — images, containers, volumes, and networks that are dangling (not associated with a container), and to additionally remove any stopped containers and all unused images (not just dangling images), add the -a flag to the command:
docker system prune -a
Then you should see no images or volumes,
docker images -a
docker volume ls