README.md

FHIR2Metadata bridge

Retrieving the data from the INCLUDE FHIR Data via the FHIR_resource.

Quick help:

 python fhir_trisomy_bridge.py --help
usage: fhir_trisomy_bridge.py [-h] --cavatica_token CAVATICA_TOKEN --cavatica_project CAVATICA_PROJECT
                              --include_fhir_authentication_cookie INCLUDE_FHIR_AUTHENTICATION_COOKIE

Retrieve metadata from teh INCLUDE Server and updates the metadata on the Cavatica Project

optional arguments:
  -h, --help            show this help message and exit
  --cavatica_token CAVATICA_TOKEN
                        You can find your developer token at https://cavatica.sbgenomics.com/developer/token
  --cavatica_project CAVATICA_PROJECT
                        The Cavatica project where the files are already imported from the INCLUDE Portal
  --include_fhir_authentication_cookie INCLUDE_FHIR_AUTHENTICATION_COOKIE
                        The Authorization cookie from the INCLUDE FHIR Server (https://include-api-fhir-
                        service.includedcc.org/) To obtain the cookie, open the Chorme or Firefox console, go to the
                        Application tab and copy the value contained in `AWSELBAuthSessionCookie-0`.

How to retrieve the CAVATICA TOKEN

You can find your developer token at https://cavatica.sbgenomics.com/developer/token

How to retrieve the CAVATICA Project

You can find your CAVATICA Project id on the top url

How to retrieve the FHIR cookie

The Authorization cookie from the INCLUDE FHIR Server (https://include-api-fhir-service.includedcc.org/) To obtain the cookie, open the Chorme or Firefox console (right click anywhere on the FHIR page response, and then select inspect), go to the Application tab and copy the value contained in AWSELBAuthSessionCookie-0.