The latest version of FHIR Genomics server can be found: https://github.com/bcl-lab/FHIR-Genomics_v2
Reference API server of SMART Genomics
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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. -
Edit
config.py
. Fill in settings for database, host, etc. as you desire. See comments inconfig.py
for detailed instructions. -
Optional: load your version of FHIR spec with the script
load_spec.py
, which will updatefhir/fhir_spec.py
. Please read comments inload_spec.py
carefully before using it. The specification for Connectathon 11 can be downloaded at: http://www.hl7.org/fhir/2016Jan/downloads.html -
If you haven't created the database you specified in
config.py
, simply use command below to create it$ python setup_db.py
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Load sample data with
$ python load_example.py
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To run with
gunicorn
do$ python server.py run
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Alternatively you can use
flask
's debug instance like this$ python server.py run --debug
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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 ga@alum.mit.edu