ychen306/FHIR-Genomics

Reference API server of SMART Genomics

Note

URL for assessedCondition in GeneticObservation is http://genomics.smartplatforms.org/dictionary/GeneticObservation#AssessedCondition. If the URL doesn't match this, the server can't index the resource properly and won't be able to respond to search with parameter assesed-condition.

How to use it

1. Install dependency with

   # this might require previledge (e.g. sudo)
   # or use virtualenv instead
   $ pip install -r requirements.txt
   

2. Rename config.py.default as config.py and fill in settings as you desire. See comments in config.py.default for detailed instructions. Currently we use PostgresSQL for development, and our script setup_db.py is written specifically for Postgres, you can switch to SQLite by using the proper SQL connection url in config.py. MySQL is however not supported right now. Contributions to support MySQL are welcomed.

3. Optional: load your version of FHIR spec with the script load_spec.py, which will update fhir/fhir_spec.py.

4. If you haven't created the database you specified in config.py, simply use command below to create it

   $ python setup_db.py
   

5. Load sample data with

   $ python load_example.py
   

6. To run with gunicorn do

   $ python server.py run
   

7. Alternatively you can use flask's debug instance like this

   $ python server.py run --debug
   

8. To wipe out the database (for debugging or whatever reason), do

   $ python server.py clear