-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.
2.1.0
- 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
2.0.1
This hotfix release makes the following changes:
- fixes a typo in the encounter.serviceType_code_* column names - fixes a case where `cnt_subject_ref` was not being appropriately specified
2.0.0
Breaking changes: - Table columns renamed to better match FHIR names - Overhaul of how codings are handled - now dynamically detected and joined as appropriate - All core tables are strictly 2 dimensional; unnesting should not be required if using core as the basis. - Minimum python version is now 3.10
Other major changes: - Core builds :should: now gracefully react to missing nested data from the EHR - magical string `cumulus_none` added to reflect cases where null data was recieved from a downstream system - Added missing required/must support fields from US Core R4 - Overhaul of template infrastructure to better centralize/reuse code - Added duckdb support, which we are now using for unit tests - Propensity score matching added as an available statistical library
Minor changes: - Schema validation is now more robustly case insensitive - Added additional coding fields to the discovery study - Added `--archive` cli command for storing study data outside athena - Added `--generate-sql` cli command for making example output from a study's jinja templates - Added `--generate-md` cli command to create markdown documentation directly from a database - Switched to ruff for linting/security - `id` field is now always the first column in a FHIR resource table
1.4.1
This fixes an issue with quoting for the discovery sql template.
1.4.0
- Updates to code handling to better support I2B2 data exports - Better display handling for US Core race & ethnicity codes - Filtering of FHIR resources by status to for encounters/docrefs/observations when generating counts to exclude cancelled/future/superceded data - Better display handling for Encounter class -Added `discovery` study for validating expected data from remote sites