What is Opal?
Opal is OBiBa’s core database
application for epidemiological studies. Participant data, collected by
questionnaires, medical instruments, sensors, administrative databases
etc. can be integrated and stored in a central data repository under a
uniform model. Opal is a web application that can import, process, copy
data and has advanced features for cataloguing the data (fully
described, annotated and searchable data dictionaries) as recommended by
the Maelstrom Research
group at McGill University, Canada. Opal is typically used by a research
centre to analyse the data acquired from assessment centres. Its
ultimate purpose is to achieve seamless data-sharing among
epidemiological studies. Opal is the reference implementation of the DataSHIELD infrastructure. More
information on Opal can be found in the Opal description on
OBiBa.
Source: https://isglobal-brge.github.io/resource_bookdown/opal.html
Deploy Docker containers
Here we will spawn a local instance of DataSHIELD with Docker. We will assume you have
installed and configured Docker on your computer; however, if that’s not
the case, visit their get
started with Docker page.
Set up
The easiest way to deploy DataSHIELD with docker is by cloning the
following repo: OllyButters/datashield_pcr.
Here, you will find a step by step guide, including a very useful docker-compose.yml
file, which you can use out of the box.
If you are running Linux or macOS, you can run the following
commands:
git clone https://github.com/OllyButters/datashield_pcr
cd datashield_pcr/docker
docker compose up -d
Then you can inspect the Docker GUI, where you should see something
like the following:
Open connection
By default, the docker-compose.yml
file in the repo above defines a demo user, demo_user, with
the following password: Demo_password1! (edit the variables
OPAL_DEMO_USER_NAME and
OPAL_DEMO_USER_PASSWORD accordingly). Here, we will open a
connection to our local server using these credentials:
# define global variables
USERNAME <- "demo_user"
USERPASS <- "Demo_password1!"
PROJECT <- "DEMO"
TABLES <- c("CNSIM1")
SERVER <- "https://opal-demo.obiba.org"
PROFILE <- "demo"