NOTE: Archived on 11-27-2023. No longer in use.
Exploring the idea of a REDCap record switchboard for the SFS kit unboxing team.
Aggregates minimal data from REDCap into a SQLite database. The SQLite database is served by Datasette to provide a lightweight off-the-shelf data browsing and querying interface. A Datasette custom page uses the Datasette JSON web API to provide a "barcode dialer" that jumps you to the associated REDCap record, regardless of which SFS project it is in.
Requires:
- Python 3.6
- SQLite CLI (
sqlite3)
Install the Python deps with:
make venv
and the SQLite CLI with:
apt install sqlite3 # on Ubuntu/Debian
brew install sqlite3 # on macOS with Homebrew
Activate the virtualenv to run any of the commands below:
source .venv/bin/activate
(Or alternatively, run the commands below via ./bin/venv-run.)
You can build the data/sfs-redcap.sqlite database with:
make
Data will be exported from REDCap the first time make is run. Subsequent
times will rebuild the SQLite database but not re-fetch from REDCap unless you
pass the -B / --always-make option (or delete
data/record-barcodes.csv).
You'll need to provide several environment variables with REDCap API credentials:
REDCAP_API_TOKEN_hct.redcap.rit.uw.edu_148
These are the same variables used in the backoffice/id3c-production/env.d/redcap/ envdir.
You can serve the database with Datasette with:
./bin/serve
and then browse the tables and views at http://localhost:3002.
There's a "canned query" for looking up barcodes at http://localhost:3002/sfs-redcap/lookup-barcode. The corresponding JSON web API is http://localhost:3002/sfs-redcap/lookup-barcode.json?barcode=….
The "barcode dialer" is at http://localhost:3002/dial.
Python dependencies are managed with pip-tools.
Edit requirements.in to modify our top-level Python dependency declarations.
Then, regenerate the fully-specified requirements.txt using pip-compile with:
make requirements.txt
Finally, re-create your virtualenv from scratch with:
make venv
Or alternatively, apply the changes to your virtualenv in-place with:
pip-sync
Once you're satisfied, make sure to commit your changes to both requirements.in and requirements.txt.
./bin/serve: line 6: realpath: command not found
You can install realpath as part of coreutils, using Homebrew:
brew install coreutils
SQLite handles concurrency differently than a client-server database system does.
In SQLite, a write operation can lock the entire database and prevent readers
from accessing it, for example. This is good resource for learning about
locks in SQLite: https://sqlite.org/lockingv3.html