SMART-on-FHIR Genomics API Sandbox deploy tutorial

This readme will cover basic process on how to deploy this server from a clean-new environment. Although it is tested only in Ubuntu, for linux and Mac OS user, this will be no hard to run this server

For Windows user, unfortunately, some part in this server, especially the pysam package of python, cannot run on Windows environment.

1. The quickest way to install python package in this server is using pip:

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

   However, some part cannot build successfully , in that case , run this command:

   $ sudo apt-get install python-dev libpq-dev libxml2-dev libxslt1-dev
   

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

   • postgresql. If you want to use postgresql, check setup_db.py and install posegresql by yourself. You need to set up PGUSERNAME ,PGPASSWORD , and DBNAME in config.py

   • sqlite (no postgresql). That's the default settings now. Just do not change APP_CONFIG['SQLALCHEMY_DATABASE_URI']

   • Mysql (Not tested)

3. Optional: load your version of FHIR spec.

   • before DSTU2: run 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

   • for STU3: run the script load_spec_STU3.py, which will update fhir/fhir_spec.py. Please read comments in load_spec_STU3.py carefully before using it. The specification for STU3 Ballot version can be downloaded at: http://www.hl7.org/fhir/2016Sep/downloads.html

4. Load sample data with

   $ python load_example.py
   

5. Now you can use flask's debug instance like this to test your sandbox server

   $ python server.py run --debug
   

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

   $ python server.py clear
   

7. Simply deploy by gunicorn , try it with parameter 'run' as follows:

   $ python server.py run
   

To be continued

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