Docker container for PostgresRAW

This project creates a lightweight Docker image for running PostgresRAW.

It has been developed on Ubuntu and not tested on other platforms.

Clone this project

$ git clone https://github.com/HBPMedical/PostgresRAW-docker.git
$ cd PostgresRAW-docker

Clone the PostgresRAW sources

$ git clone https://github.com/HBPMedical/PostgresRAW.git src

Build the PostgresRAW docker image

The image is build and given the name 'hbpmip/postgresraw' with the following command:

$ docker build -t hbpmip/postgresraw \
    --build-arg JOBS=8 \
    --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
    --build-arg VCS_REF=`git -C ./src/ rev-parse --short HEAD` \
    .

Warning: If you update the sources, add --no-cache=true to the command above to take the new version in consideration.

Note: Replace the 8 in JOBS=8 with the number of CPU threads to reduce the build time on your machine.

Use the PostgresRAW docker image

To start PostgresRAW, you will need two folders to store the data, one for the PostgreSQL data, and one for the raw CSV files.

Those two folders need to be owned by the user 999, which is the Postgres user id inside the PostgresRAW container.

You can create those two folders with the following commands:

$ mkdir -p $PWD/../data
$ mkdir -p $PWD/../datasets
$ sudo chown 999 $PWD/../data $PWD/../datasets

You can then start the container with the following command:

$ docker run --rm \
    -e POSTGRES_USER=dbuser \
    -e POSTGRES_PASSWORD=secret \
    -e POSTGRES_DB=db \
    -p 5554:5432 \
    -v $PWD/../data:/data:rw \
    -v $PWD/../datasets:/datasets:ro \
    --name PostgresRAW \
    hbpmip/postgresraw

The only specificity compared to a regular PostgreSQL image, is the extra volume which is mounted read-only on datasets. This volume is the folder which contains the CSV files to register as tables.

For more information on how to register manually CSV files, please refer to the source documentation.

You might want to checkout the web interface, which will also watch the folder and automatically register files: PostgresRAW-UI.

Alternatively, you can use psql as usual, for example, assuming the container was started as above:

psql -U dbuser -d db -h localhost -p 5554

Other than that, this container behaves as the official Postgres container, for more information, please refer to https://hub.docker.com/_/postgres/.