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CEML (Clinical Element Modeling Language) Service

This software is an API-only service exposing a REST interface for developers to:

  1. Retrieve foundational Clinical Element Model (CEM) types, and
  2. Compile Clinical Element Model (CEM) definitions into other formats.

The API is written in ruby and the underlying complier in Java.

Usage

A development-only, unauthenticated instance of the latest build is available at https://ceml-transform-service.logicahealth.org. Generated content at this public instance is automatically purged periodically without notice.

Development

To run a pre-built copy using Docker:

  docker run -it --rm -p 4567:4567 --name ceml-transform-service p3000/ceml-transform-service:latest

(FIXME Waiting on licensing for this ->) Or to run locally from source code with a copy of the compiled jar:

  bundle update # requires a recent ruby runtime and `gem install bundler`
  thin --threaded start

REST API

The API only accepts and responds in JSON using the "Content-Type: application/json" MIME TYPE. Requesting a non-existant file will yield a 404 (not found) response code. POST'ing with invalid JSON body contents will return a 406 (unacceptable).

Static Assets

The compiler uses a baked-in library of core models and transform configurations. These are accessible by the following endpoints.

  • GET /cem The complete list of core models. curl -s -X GET 'https://ceml-transform-service.logicahealth.org/cem'
  • GET /cem/HeartRateMeas.cem Get a specific model. The model content will be base64 encoded. curl -s -X GET 'https://ceml-transform-service.logicahealth.org/cem/HeartRateMeas.cem'
  • GET /def The complete list of text definitions used by the model library. curl -s -X GET 'https://ceml-transform-service.logicahealth.org/def'
  • GET /def/HeartRateMeas.def Get a specific model. The file content will be base64 encoded. 'curl -s -X GET https://ceml-transform-service.logicahealth.org/def/HeartRateMeas.def'
  • GET /fhir The complete list of FHIR mapping definitions used by the model library. 'curl -s -X GET https://ceml-transform-service.logicahealth.org/fhir'
  • GET /fhir/Base.resource.map Get a specific model. The file content will be base64 encoded. 'curl -s -X GET https://ceml-transform-service.logicahealth.org/fhir/Base.resource.map'

Compiling Your Own CEM Files

New Clinical Element Models may be compiled by submitting them via POST. Individual outputs are retrievable by REST GET calls.

  • GET /transforms/forms Supported output formats, such as 'fsh' and others. curl -s -X GET 'https://ceml-transform-service.logicahealth.org/transforms/formats'
  • POST /transforms Compile your own model(s) to FHIR Shorthand (FSH) notation, synchronously. May take a few seconds or more. curl -s -X POST 'https://ceml-transform-service.logicahealth.org/transforms/<format>'. The body of the POST request MUST contain an array of file names and their base64-encoded contents, as follows:
[
  {"name" : "FoozleA.cem", "content" : "..base64-encoded file content.."},
  {"name" : "FoozleB.cem", "content" : "..base64-encoded file content.."},
  {..}
]

The service's JSON response is templated as follows:

{
  "uuid" : "40bd776a-ea5f-472d-8b9b-d9e889ae8f6e", # Random assigned UUID
  "gets" : # Array of URLs to GET individual outputs
    ["https://ceml-transform-service.logicahealth.org/transforms/40bd776a-ea5f-472d-8b9b-d9e889ae8f6e/FoozleA.fsh",
    "https://ceml-transform-service.logicahealth.org/transforms/40bd776a-ea5f-472d-8b9b-d9e889ae8f6e/FoozleB.fsh"],
  "delete" : # URL to DELETE the job
    "https://ceml-transform-service.logicahealth.org/transforms/40bd776a-ea5f-472d-8b9b-d9e889ae8f6e",
  "message" : "...raw compiler output for troubleshooting..."
}

The service instance will retain your generated output until either you DELETE the job or it is administratively purged for you.

Administrative Functions

  • POST /reset "Factory reset" clearing all generated compiler outputs. Applies globally. curl -s -X POST https://ceml-transform-service.logicahealth.org/reset

License

Apache 2.0. All rights reserved.

Attribution

Preston Lee https://github.com/preston