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  Release version 1.1.1 (Feature Release) Stable

  gebhardtt released this 2026-11-12 14:27:27 +01:00 | 0 commits to main since this release

  Release Notes - MeDaX Pipeline v1.1.1 (Feature Release)

  Overview

  This feature release modernizes the build and deployment setup, adds optional authentication and a local FHIR test server, and makes batched imports more reliable for large datasets.

  New Features

  Deployment & Infrastructure

  • Switched from Poetry to uv with a locked dependency set; Docker image now uses Python 3.11
  • Replaced the bundled BioCypher copy with the official biocypher package (>= 0.16)
  • New Docker Compose profiles: blaze (local FHIR server preloaded with POLAR test data), keycloak and proxy (login in front of Neo4j), server (production proxy setup)
  • Optional TLS for the Neo4j Bolt connection (ENABLE_BOLT_TLS)

  Import Options

  • Import a fixed list of patients from a file (SELECTED_PATIENTS_FILE)
  • DISABLE_IMPORT modes: run the full pipeline, only load existing import files, or only start Neo4j
  • Synthea reference handling can now be switched on via IS_SYNTHEA
  • Beta support for ODM/MDM data alongside FHIR (multiple_adapters.py)

  Bug Fixes

  • References to resources in other batches are now kept with the correct edge label
  • The Neo4j import script is generated once after all batches instead of with the last batch only
  • Leftover files from earlier runs are cleared before each import, so data is no longer imported twice
  • The pipeline no longer hangs indefinitely while waiting for Neo4j or the FHIR server

  Documentation & Testing

  • README extended with setup guides for each Compose profile and post-processing queries (patient timelines, shared concept nodes)
  • New unit test suite covering graph creation, batching and import script generation

  Compatibility

  • Not compatible with v1.0.1 setups without changes
  • Update your .env using the new .env.example
  • Python 3.10 or newer is required for local runs
  • Neo4j now uses different mount points, so existing databases from v1.0.1 must be re-imported

  Upgrade Recommendation

  All users are recommended to upgrade, especially those importing large FHIR datasets in batches. Review your .env and docker-compose.yml before the first run.

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  © 2026 MeDaX Project Team | Released under MIT License

  Downloads

  • Source Code (ZIP)
  • Source Code (TAR.GZ)