IDEA4RC Vantage6 Analytics

This repository is home to all IDEA4RC custom vantage6 code. It contains the following important things:

• The required algorithms. It contains two algorithms:
  • v6-analytics (containing all our standard analytics algorithms)
  • v6-sessions (containing the data extraction algorithm)
• The dev_notebooks/raven-api.ipynb notebook contains the code that the people from IDEA4RC use to integrate the vantage6 API into their RAVEN UI.

Overall Architecture

In IDEA4RC there are two main components:

• The Orchestrator (home to the vantage6 server, RAVEN UI and some other services)
• The Capsule (home to the algorithms and the data)

.. DATA (OMOP - IDEA4RC - FHIR) .. RAVEN UI .. VANTAGE6 UI .. OTHER vantage6 components

Orchestrator

The Orchestrator contains the vantage6 server, store (and later the UI). It is deployed by @Alejandro Alonso López, @Daniele Pavia and me (@Frank Martin). It is setup in a primitive way, and you can some file in the home directory of daniele.

In case you need to access the Orchestrator, you should contact @Alejandro Alonso López.

Capsule

The Capsule contains a lot of services we do not care about. @Daniele Pavia is the one responsible for the Capsule but we need to help with the integrations of the helm charts from vantage6.

@Daniele Pavia has a server with a test capsule, which we are trying to connect to the Orchestrator.

Project Partners

These are the most important technical people involved in the project, from our side:

• Architecture: @Eugenio Gaeta (UPM)
• RAVEN UI: @Itziar Alonso, @Alejandro Alonso López (Implementation) and @Laura Lopez Perez (Design and User stories) (UPM)
• KeyCloak: @Athanasios Patenidis (CERTH)
• Capsule Helm chart: @Daniele Pavia (UPM)

Status of the project

The vantage6 infrastructure has all the required major components (ofc. some smaller changes need to be done). So the deployment is now in progress. I hope I can finish it before leaving on holiday.

Synthetic Data

.. TODO store the synthetic data in the right place. .. TODO how to generate the MockData .. TODO show the IDEA4RC data model.

Algorithms

The algorithms are all copied into this repository, I know horrible. But this way we can keep it flexible, and hopefully we can merge it back to the official vantage6 repository. But for now, we are using it as a local repository. The status of the algorithms:

• v6-analytics/summary.py is working with the mock client
• ...

The status of the session algorithm is:

• v6-sessions/cohort.py:create_cohort is working with the mock client

Note

In order to run the create_cohort function from v6-session locally you need install the OHDSI R packages: SqlRender, DatabaseConnector and FeatureExtraction.

I use the make image PUSH_REG=true to build and push the image to the harbor2.vantage6.ai/idea4rc registry. (So no build pipelines yet).

Use Cases