The Study Explorer is a tool that helps you to understand the contents of individual studies contributed to the HBGD knowledge base.

The Study Explorer tool, as known as the Data Store Explorer, presents information about the experimental design of the individual studies, such as whether a study is longitudinal or cross-sectional, interventional, or observational, and the ages, calendar years, and countries of study enrollment. The tool enables you to search for the presence of standardized data fields such as anthropometry measures, biomarkers, microbiology tests, and nutrient intake quantities.

The simplest way to evaluate StudyExplorer is to use docker-compose

# download https://raw.githubusercontent.com/HBGDki/study-explorer/master/docker-compose.yml
curl -O https://raw.githubusercontent.com/HBGDki/study-explorer/master/docker-compose.yml
# or, alternatively, wget https://raw.githubusercontent.com/HBGDki/study-explorer/master/docker-compose.yml
# or git clone https://github.com/HBGDki/study-explorer.git && cd study-explorer

Start studyexplorer and a database server with docker-compose up

docker-compose up -d

Initialize various settings including database migrations, usernames, passwords and then populate the data.

# Initialize database
docker-compose exec web /usr/local/bin/python manage.py migrate
docker-compose exec web /usr/local/bin/python manage.py createsuperuser --username admin --email [email protected]
psql -h localhost -U postgres postgres -f hbgd_data_store_server/data/sql/000_reset_db.sql
psql -h localhost -U postgres postgres -f hbgd_data_store_server/data/sql/001_import_studies_domain.sql
docker-compose exec web /usr/local/bin/python manage.py load_studies data/csv/studyinfo.csv
psql -h localhost -U postgres postgres -f hbgd_data_store_server/data/sql/002_update_studies_studyfield.sql
docker-compose exec web /usr/local/bin/python manage.py load_idx data/csv/idx.zip
psql -h localhost -U postgres postgres -f hbgd_data_store_server/data/sql/003_import_studies_filter.sql

Navigate to http://localhost:8000 and you will see the study explorer application running.

Note that this is best for development, testing and demonstrations from a local machine.

Pull from Docker Hub & Run

docker pull prevagroup/studyexplorer.io
docker run -it -p 8000:8000 -e SECRET_KEY=foobar prevagroup/studyexplorer.io

Note that the application is running, but will be unable to connect to a database. If you pass in the following environment vars corresponding to a valid postgres server that the docker container can access, you can connect to a database. However, please note that a Docker container is set up in a private network bridged to the host machine, so you may have to do some digging to find the correct IP address for connections.

• RDS_PORT
• RDS_DB_NAME
• RDS_USERNAME
• RDS_PASSWORD
• RDS_HOSTNAME

To run in a production environment, either consult your cloud hosting provider's documentation for installing an application from a Docker image, or set up a server running docker and mapping the host's port 80 to the docker container's port 8000 (you will need admin/root privileges).

$ conda env create
$ source activate hbgd-data-store-server

If you want to install postgres in your conda environment:

$ conda install postgresql
$ mkdir data
$ initdb -D data
# Launch postgres
$ postgres -D data
# In a new terminal
$ createuser -s hbgd --pwprompt --createdb --no-superuser --no-createrole
# setup a password for the user
$ createdb -U hbgd --locale=en_US.utf-8 -E utf-8 -O hbgd hbgd -T template0

Alternatively, you can use vagrant on your development machine (available via brew cask install vagrant). Then run the command:

$ vagrant up

This creates a development database with the user/password of hbgd/123456. You may change this inside of bootstrap.sh.

Setup your environment variables:

export DEBUG=True
export DB_PASSWORD='your db password'
export MY_SECRET_KEY='your secret key'

Migrate the database:

$ ./manage.py migrate

Load the sample data (optional):

$ ./manage.py loaddata ../sampledata.json

Make a superuser:

$ ./manage.py createsuperuser

• Install compass gem install compass
• Use compass to build css from scss
• Edit scss not stylesheets directory
• Check in built css.

$ ./manage.py runserver

Now go to:

• Home page http://localhost:8000
• Admin page http://localhost:8000/admin
• User & Developer Documentation http://localhost:8000/docs

If you've already been through setup once:

$ postgres -D data
$ cd hbgd_data_store_server; ./manage.py runserver

$ ./manage.py test

If you find anything in this documentation unsatisfactory, please let me know at aelgert [at] prevagroup dot com or by submitting a GitHub issue.