Skip to content

Latest commit

 

History

History
127 lines (97 loc) · 5.26 KB

README.md

File metadata and controls

127 lines (97 loc) · 5.26 KB
Raw

FHIR-Facade

Deployment

Environment Variables

Variable Default Function Comment
FACADE_PORT 8082 Port on which the Fhir-Facade is available
FHIR_SERVER_URL http://host.docker.internal:8080/fhir/
PAGE_SIZE 50 Number of entries per result page
PAGE_STORE_TIME 1200 Seconds after which queried pages are discarded
INTERNAL_PAGE_SIZE 2000 Number of loaded resources, before internal paging is used
PAGING_STORE LOCAL Use local storage or MongoDb for paging Valid values: LOCAL / MONGO
MONGO_DB_URL mongodb://host.docker.internal:27017 MongoDB Connection String
LOG_LEVEL INFO Determines the amount of console output Valid values: INFO / DEBUG / BENCHMARK
BA_USER_NAME BasicAuth username if required for the connection to the fhir server
BA_PASSWORD BasicAuth password if required for the connection to the fhir server
RESOURCE_CONFIG Multiline yaml, analogue to the resource config file
PASSTHROUGH_CONFIG Multiline yaml, analogue to the passthrough config file
PROVISION_CONFIG Multiline json, analogue to the provison config file
SSL_CERT Certificate for https
SSL_KEY Key for https
GUNICORN_WORKERS 1 Number of Gunicorn Workers
PROCESSES_PER_WORKER 1 Number of processes spawned per request
MP_CHUNK_SIZE 50 Number of resources handled per sub process
CONSENT_CACHE_TIME 60 Seconds till consents are being refreshed

Standalone Deployment

In order to build and run the standalone facade from the cloned repository simply run the following, replacing the forwarded port in case you altered the configuration.

docker build --tag=fhirfacade ./facade_app/

docker run -p 8082:8082 fhirfacade

Or pull the build image from dockerhub, replacing latest with a specific version if required.

docker pull boehmdo/fhir-facade:latest

docker run -p 8082:8082 -e FACADE_PORT=8082 boehmdo/fhir-facade

Test Deployment

Or run a facade test instance with a blaze fhir server with:

docker compose -f compose-with-blaze.yml up

Use the uploadTestData.sh script to upload testdata to blaze

./uploadTestData.sh

All Data was randomly generated with SyntheaTM and manually modified to include Consent (and its dependent) Resources based on the MII Kerndatensatz.

Both variants expose the facade-endpoint on :8082/fhir/ unless configured otherwise

Configuration

Resource Configuration

All Resources that are supposed to be accessed via the facade have to be configured as a environment variable or in the config/resource_config.yml file. It is required that for every resource there is a path from the base resource to a subject/patient and the relevant date with regards to consent.

Example:

Resources:
  Observation:
    EvaluationStrategy: "date"
    Date: "issued"
    Subject: "subject/reference"
  Encounter:
    EvaluationStrategy: "date"
    Date: "period/start"
    Subject: "subject/reference"
  Procedure:
    EvaluationStrategy: "date"
    Date: "performedPeriod/"
    Subject: "subject/reference"
  Specimen:
    EvaluationStrategy: "date"
    Date: "collection/collectedDateTime"
    Subject: "subject/reference"
  Patient:
    EvaluationStrategy: "simple"
    Date: ""
    Subject: "id"

Provision Configuration

Provisions can be configured either before container startup in the config/general_provison_config.json or during runtime: Pass a List of provision codes in a json format based on the MII Kerndatensatz. Every Patient is required to have ALL provided provisions as a subset of its provisions. This structure is required for the preconfiguration as well as the parameter version.

Example:

{
    "coding":  [
        {
            "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
            "code": "2.16.840.1.113883.3.1937.777.24.5.3.8"
        },
        {
            "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
            "code": "2.16.840.1.113883.3.1937.777.24.5.3.5"
        }
    ]   
}

Passthrough Configuration:

Some Applications might require you to additionally access proprietary endpoints in the underlying FHIR-Server. Similar to the previous configuration this can be achieved through a yaml configuration, that can be provided via environment variable, as well as the passthrough_config.yml file. You only need to provide the URL in a example route "fhir.server.url:portURL". If the url contains the usual /fhir/ base it has to be supplied under Resources, where "fhir.server.url:port/fhir/Resource".

Patient and Consent resources get passed through by default.

Example:

URLs:
  - "/metadata"
  - "/test/echo"
Resources:
  - "metadata"
  - "Patient"
  - "Consent"