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Currently, documenter.jl is not integrated yet with this repository! We need to fix this by using https://documenter.juliadocs.org/stable/ and https://github.com/JuliaDocs/DocumenterTools.jl. Should be a relatively straightforward process and the docs folder for omopcdmcohortcreator.jl could be a great skeleton to copy from for this issue: https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/tree/main/docs

This is a really cool initiative https://ohdsi.github.io/GIS/index.html

Would pair very well with the OMOP CDM data assets we have! Not sure the best way to use it within the Julia ecosystem but I would REALLY like to have this!!!

We need to generate a cohort using a cohort definition that can then be used for testing within Eunomia.

Adding a test suite for HealthSampleData may be slightly tricky due to having to check to download data, but this is something we need to add to ensure data downloads do work correctly. One will have to enable this for DataDeps as we build tests so that CI runs correctly: https://www.oxinabox.net/DataDeps.jl/stable/z20-for-pkg-devs/#Installing-Data-Eagerly-1

This depends on #6 but once this is completed, a function will be needed to be added which is very similar to the Eunomia function. A download function and test for this function should be added.

This repository was set-up very quickly and needs TagBot to be set-up for it to better manage future releases. Right now, we can copy TagBot workflows from here: https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/blob/main/.github/workflows/TagBot.yml

This should be straightforward to adapt to HealthSampleData.jl

Currently the CI has not been set-up for this package. We need to set it up and can adapt the following workflow from here: https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/blob/main/.github/workflows/ci.yml

Mostly, renaming and removing the section for documentation deployment should be fine.

We need to create a 5K OMOP CDM patient sample for HealthSampleData. This is a rather complex process but can be accomplished in the following steps:

• Set-up a PostgreSQL DBMS on a server
• Generate Synthetic OMOP CDM Data using Synthea
  • Install Java on a server
  • Install Synthea v3.0.0
  • Enable export to CSV (see this: https://github.com/synthetichealth/synthea/wiki/CSV-File-Data-Dictionary)
  • Run synthea jar like `java -jar synthea -s 12345 -p 10000
  • Extract output/csv to directory for loading process
• Load synthetic OMOP CDM data into DBMS
  • Install R on a server
  • Install this package: https://github.com/NACHC-CAD/ETL-Synthea
  • Download Athena vocabularies (see: https://athena.ohdsi.org/search-terms/start for downloading)
  • Create zipped vocabularies into a directory called vocab in the same directory as output/csv
  • Execute tutorial in https://github.com/NACHC-CAD/ETL-Synthea
• Export PostgreSQL database into SQLite
• Share SQLite export with @TheCedarPrince for hosting

That is the overall process but rather complex. Happy to support each step along the way.