dbhi/redcap-harvest repository overview

⁠REDCap to Harvest

Dockerfile and tools for deriving Harvest applications from REDCap projects.

⁠Requirements

• Docker⁠

⁠Run

The Docker file relies on the REDCap data dictionary and data file to build the Harvest application. These files must be made available by mounting a volume to /input containing these files. By default the file names are metadata.csv and data.csv, however these can be configured by setting the $METADATA_FILE and $DATA_FILE environment variables.

To run an interactive container:

docker run --rm -it -p 8000:8000 -v /path/to/your/input:/input dbhi/redcap-harvest

The startup script will build a SQLite database for Harvest from the metadata and data files and then end with running the Django server on port 8000.

⁠Extending

The intent of this image is to provide an ephemeral, read-only Harvest application representative of a REDCap project, however it may be desirable to persist metadata changes and saved queries over time. This is straightforward to accomplish by providing a custom local_settings.py file. At a minimum the following settings are required.

from global_settings import INSTALLED_APPS

INSTALLED_APPS += (
    'djredcap',
)

MODELTREES = {
    'default': {
        'model': 'Record',
    }
}

SECRET_KEY = 'abc123'

To define a custom database, simply define the Django DATABASES setting. This example assumes a container db will be linked to this one.

# ..[snip]..

DATABASES = {
    'default': {
        'ENGINE': 'django.db.backends.postgresql_psycopg2',
        'HOST': 'db',
        'PORT': 5432,
        'USER': 'postgres',
    },
}

The corresponding Dockerfile would look something like this:

FROM dbhi/redcap-harvest

# Install postgresql bindings
RUN pip install psycopg2

# The current working directory is /usr/src/app/project
ADD local_settings.py ./project/conf/