v4.0.0

Breaking changes

• The vocab study has been removed. The UMLS study provides a superset of its functionality.
• The core study no longer cuts data off at 2016. Studies are expected to set their own start/end dates for the study period.

Deprecation warnings

• Manifest import/export functionality has changed with new sections (more customizable with selecting file order, and more types of exports) - older manifests are still supported, but this support will be disabled in a future version

New Features

• Support for AllergyIntolerance FHIR resource has been added in core and discovery
• --version is more verbose and will report on installed study versions
• A new workflow (formerly called a statistic) for generating valuesets from UMLS/VSAC/keyword lists has been added
• Studies may dynamically generate parts of their prefix, if they need to be configurable at runtime. This should not be required for most clinical studies, but has uses for cases like data validation.

Bugfixes

• study discovery is more robust and requires less adherence to a specific folder structure
• The upload command is more constrained in which specific sets of files it will push to the aggregator
• CTAS parquet queries are now appropriately generated for duckdb