gafiore/fhir-genomics-2

Reference API server of SMART Genomics

How to use it

1. Install dependency with

   # python 2.7
   # this might require previledge (e.g. sudo)
   # or use virtualenv instead (recommended)
   $ pip install -r requirements.txt
   

   Install PostgreSQL. Currently we use PostgresSQL for development, and our script setup_db.py is written specifically for Postgre. Contributions to support MySQL are welcomed.

2. Edit config.py. Fill in settings for database, host, etc. as you desire. See comments in config.py for detailed instructions.

3. Optional: load your version of FHIR spec with the script load_spec.py, which will update fhir/fhir_spec.py. Please read comments in load_spec.py carefully before using it. The specification for Connectathon 11 can be downloaded at: http://www.hl7.org/fhir/2016Jan/downloads.html

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
   

If you find this useful, please cite the following paper: Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D, Kohane IS. SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. Journal of the American Medical Informatics Association: JAMIA. 2015;22(6):1173-8. doi: 10.1093/jamia/ocv045. PubMed PMID: 26198304. http://www.ncbi.nlm.nih.gov/pubmed/26198304

For more information (including papers, slides, videos, and tutorials on getting started), please email Gil Alterovitz at [email protected]