Create Execution RFC For E2E Demo

[psbrandt]

PhEMA Workbench End To End Demo Execution RFC

High-Level Overview

The Workbench should allow the user to run a PhEMA phenotype definition against an OMOP database. It should be possible to return a list of cohort members directly (when the OHDSI API is running) or generate the SQL that can be used to generate the cohort (when the API isn't available, e.g. at Cornell).

User Interface

In the tab for the phenotype (still in development), the user should just be able to select the appropriate backend/target and click run. When execution is complete, a window should open up with the list of cohort members. It should be possible to download/export this list.

Stretch Goals

If there's time, we could make it possible to click on a member to fetch some extract data about the member to assist the user in verifying if the cohort definition is accurate.

API

Most of the work will be done in the API in the following repositories:

• https://github.com/PheMA/phema-workbench-api
• https://github.com/PheMA/cql-on-omop
• https://github.com/PheMA/elm-utils (maybe)

We should create an API endpoint here that accepts a PhEMA Phenotype (still in development, but basically a FHIR Bundle with Library and ValueSet resources), possibly wrapped in a Parameters resource just to be a little more FHIR-native and behave like an operation.

A lot of the code can be copied from CohortDefinitionResource.java. We will just need to implement a FHIR ValueSet service (this ticket).

Stretch Goals

We could also consider adding an API endpoint that enables running SQL against the OMOP database directly when the OHDSI API isn't available. This would make the whole e2e demo fully automated at both NW and WC.

[psbrandt]

Let's use this ticket to evolve and RFC for how we expect execution will work for the e2e demo.