v4.1.3

-Splits out the DatabaseBackend init from the connection, allowing for easier use with --prepare mode.

v4.1.2

This release removes the database connectivity check for the --prepare mode.

v4.1.1

• Removes some debugging checks that snuck into main.

v4.1

This release contains the following updates:

• The core study now supports the DiagnosticReport FHIR resource.
• A new build option, --prepare, primarily intended for automation of study distribution, has been added.

v4.0.1

This release fixes an issue in how the docsite renders some renamed pages.

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

v3.0.0

Breaking changes

• Actions/builders APIs now primarily work from StudyConfig and StudyManifest objects
• Minimum python is now 3.11
• Changed _code_system in tables to just _system
• Replace core__medicationrequest with core__medication, removed previous version
• Removed core__study_period, offloaded study definitions to downstream studies

Deprecation warning

• core__observation is now considered deprecated - use a specific observation profile table, if one exists. Once we have more profile coverage, core__observation will be removed.

Major changes

• Added a generic way to log to a study's transaction table
• Allow studies to specify their own unique schema (intended for independent data sets, like code systems)
• Allow studies to specify their own CLI args with --option

Minor changes/bugfixes

• Several new generic templates & jinja syntax helpers
• Added StudyManifest, StudyConfig, BaseTableBuilder, and CountsBuilder to the package-level API
• Use cumulus-fhir-support for reading ndjson
• Fixed Athena's ability to export "decimal" types
• Updated CLI to use terms like database and schema in the context of a specific database's nomenclature
• Added $expand to the UMLS VSAC API, and paginate results
• clean CLI arg now removes views
• generate-sql now masks S3 paths in output

Full Changelog: v2.3.0...v3.0.0

v2.3.0

• Duckdb support for different JSON folder formats
• Added import command for re-loading previously exported studies
• Improvements to exporting for very large files
• Added option for studies to have an explicit schema under specific conditions

v2.2.0

-Bugfix for some CLI args
-Using manifests, rather than filepaths, for discovering study names
-When tables do not exist, fall back to empty tables so queries dont fail
-updated list of official study CLI targets
-Improvements to partial string matching.

v2.1.0

• Added ability to create study tables from static files
• Updated medication tables generation
  • This includes several fixes to core_medication and core_medication-request
• Added API library for UMLS API endpoints
• Improved handling of missing patient extensions
• Improved handling of observation lab/vital signs
• Handling of FHIR component as a denormalized table
• Improvements to table schema parsing
• Fixed handling of Encounter.type field
• Improved handling of errors in the upload command