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INSTALL.md

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Using Docker

Step by step

On Ubuntu, with Git installed and no Docker installed:

# clone DryFHIR repository
git clone https://github.com/DryFHIR/dryfhir.git
cd dryfhir

# Docker setup - add Dockers key
sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D

# add Docker Ubuntu repository
sudo sh -c "echo deb https://apt.dockerproject.org/repo ubuntu-xenial main > /etc/apt/sources.list.d/docker.list"
sudo apt-get update

sudo apt-get install docker-engine linux-image-extra-$(uname -r) linux-image-extra-virtual

# add your user to the Docker group, so you don't need sudo to run docker commands
sudo service docker start
sudo groupadd docker
sudo usermod -aG docker $USER

# log out and log back in, to ensure your user account has new permissions
cd dryfhir

# wait for this to complete as it does the database setup and all
docker-compose up

# CTRL+C after the first-time setup completes

# now run it for real
docker-compose up

Docker setup explanation

For development, the docker-compose up command starts the database server and the web server within the same network and linked, so that they can access each other. The docker-compose.yml and docker-compose.orverride.yml are used automatically. The web server will be reachable at localhost:8080 and it will have the current directory mounted /opt/dryfhir, overriding the original content (the stable, released version). That way, code changes are immediately reflected on the server.

For production, you can use docker-compose as well with docker-compose -f docker-compose.yml -f docker-compose.prod.yml up. This will ignore the override file and use the production file instead, where /opt/dryfhir is not overwritten and the published port is 80 (which you may change editing the prod file).

The last interesting bit is, that docker-compose can be used to create a definition of a release of multiple connected docker-images. By using docker.compose -f docker-compose.yml -f docker-compose.prod.yml bundle, a json file is generated, which contains the exact versions of both images at the time (you want to use docker-compose pull first). With that file, you can use docker deploy and be up and running without installing docker.compose on the prod machine.

The Dockerfile builds an image with all dependencies and the dryFHIR code at /opt/dryfhir and is set to start the lapis server with the dockerdev environment by default. You can use other environments (like dockerprod) with docker run <options> server <environment>.

For the ease of starting the docker machines in a usual state, there are two docker-compose setups available, one for development (the default) and one for production.

Natively

Use the following instructions to get DryFHIR setup and running natively on your Linux machine (these instructions have been tested on 16.04 LTS).

# install postgresql and the plv8 extension
sudo apt-get install postgresql-9.5-plv8

# edit according to https://github.com/leafo/pgmoon/issues/19
sudo nano /etc/postgresql/9.5/main/pg_hba.conf

# enable plv8, see https://github.com/fhirbase/fhirbase-plv8
echo "plv8.start_proc='plv8_init'" | sudo tee --append /etc/postgresql/9.5/main/postgresql.conf

# apply changes
sudo service postgresql restart

# create a default user and database for the user
sudo -u postgres createuser -s $(whoami); createdb $(whoami)

# create a database named fhirbase (for normal use) and fhirbase-test (for running busted tests)
createdb fhirbase && createdb fhirbase-test

# load up the fhirbase data into a database named fhirbase
# check if 1.4.0 is still latest fhirbase release before running this
wget https://github.com/fhirbase/fhirbase-plv8/releases/download/v1.4.0.0/fhirbase-1.4.0.0.sql.zip
unzip fhirbase-1.4.0.0.sql.zip
cat fhirbase-1.4.0.0.sql | psql fhirbase
cat fhirbase-1.4.0.0.sql | psql fhirbase-test