[Agile] β: OHDSI Tools

[ThanePi]

Epic

This development milestones work on early supports to OHDSI Tools, primarily focusing on ATLAS.

In later of development, this feature should spin-off to individual repo.

Story

• ATLAS go through
  • ACHILLES as ATLAS required (used in application level)
• Containerized R Server
• More Infra Containerization
  • WebAPI
  • Atlas
  • ACHILLES
  • DQD (Data Quality Dashboard)
• Workflow Optimization

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Review

OHDSI tools were added as container compose of pre-installed R server and combo pack of WebAPI with DB instance for Atlas, this sprint also complete on workflow optimization by re-modular container script, tested in Podman.

Also a hot fix on Postgres of OMOP CDM about configuration file support and shared memory related config.

Feature

• Add Achilles on/and containerized RServer #36
• Feat: ATLAS Stacks #39
• Add OHDSI DQD to R-Server #46
• Remodule: OHDSI Tools Stack #49

Fix

• Patch: Postgres shared buffer and config file support #43
• Fix: Override connection on postgresql.conf #44

Postponed / Changed

• N/A - No task postponed or changed this sprint

Issue Raised (Won't Fix)

Critical

• N/A - No critical issue raised this sprint

Optional

• Rootless supervisord in Dockerfile #37
• Create transferable concept_hierarchy from Vocab DB to ATLAS DB #41
• Limitation: DHCP-Managed Hosts and SECURITY_ORIGIN Configuration in WebAPI #48
• Enhancement: Secure and Dynamic source_daimon Connection Strings in WebAPI Setup for ATLAS #50