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Import FHIR resources

Usage​

The import command can import FHIR resources in a FHIR server from local JSON files.

It supports "primitive" deduplication based on merger bonFHIR rules.

Source formats​

The --source arguments support multiple sources for data:

  • all sources must ultimately resolve to JSON files of individual resources or FHIR Bundle
  • glob patterns are supported - e.g. **/*.json
  • files can be zip archived; in this case, zip files are unzip in a temporary location prior to being processes
  • this can also be a full URL of a file to download; in this case, the file is downloaded first, unzipped if it is a zip file, and all files are processed individually
  • finally, synthea-sample can be used a shorthand for around a thousands synthetic patients generated by the Synthea / SyntheticMass project

FHIR Server authentication​

Authentication mode supported:

  • no authentication (do not pass any --auth-... flag)
  • a stable value in the Authorization header (use the --auth-header flag) -client credentials flow; use the remaining --auth-... flags

Flags​

  • --source: See above for a discussion on possible sources
  • --fhir: The FHIR version to use; we currently support r4b and r5
  • --base-url: The base URL of the FHIR server
  • --auth-header: The value to use as an Authorization header to authenticate to the server with a token
  • --auth-token-url: The URL to use to obtain an OAuth2 token (client credentials)
  • --auth-client-id: The client ID to use to obtain an OAuth2 token (client credentials)
  • --auth-client-secret: The client secret to use to obtain an OAuth2 token (client credentials)
  • --skip-connectivity-test: Skip the server connectivity test prior to running the command

Example usage​

The following command will launch the synthetic patient data import in a local FHIR server setup by any Project template

npx @bonfhir/cli import --source synthea-sample --fhir r4b --base-url http://localhost:8103/fhir/R4/ --auth-token-url http://localhost:8103/oauth2/token --auth-client-id f54370de-eaf3-4d81-a17e-24860f667912 --auth-client-secret 75d8e7d06bf9283926c51d5f461295ccf0b69128e983b6ecdd5a9c07506895de