NEWS.md

In patelm9/setupAthena: Setup or Update a Postgres Instance of the Athena Vocabularies

setupAthena 1.0.0

• Fixed bug that did not replace all special characters in vocabulary_id when creating a depivotted log table by vocabularies

setupAthena 0.8.0

• Changed default target schema to 'omop_athena'

• Added default values for umls_api_key and conn_fun arguments

• Changed prepare_cpt4 because on.exit() was not behaving as expected

• Added conditions that warns the user if the release_version is already logged in the database

setupAthena 0.7.0 (2021-12-09)

• Added steps in prepare_cpt4 where the native CONCEPT.csv file is copied for safekeeping and replaced with the original in case the function exits early. This was added to avoid having to redownload the vocabulary files every time this function does not complete successfully.

• Added vocabulary counts to the log as well as a warning if any of the vocabulary_ids had 0 counts.

• Added a diff report that prints to the console between the newest log entry and the one previous to it.

• Introduced postprocessing steps to the run_setup function to include the creation of downstream lookups and tables such as the ATC classifications for the RxNorm drugs.

setupAthena 0.6.0 (2021-08-28)

• Fixed prettyunits parsing error when running indexes
• Added chariotViz package setup integration

setupAthena 0.5.0 (2021-08-12)

• New fetch_* functions that retrieves version information at the entire vocabulary and vocabulary_id level to a setupAthenaLog class object
• Added vocabulary_version to log
• Added improved console messaging, including processing time to indices()
• Converted log to a safer process where the previous log is only dropped when the new one is successfully written

setupAthena 0.4.0 (2021-06-18)

• Added sa_release_version and sa_schema field to log
• Changed logging to a complete rewrite from an append to preserve existing log data.
• Updated documentation on new release_version argument

setupAthena 0.3.0

• Section headers at each step execution is now center justified
• Disclaimer regarding required user permissions level added to README and package argument descriptions.
• Added Code of Conduct.

setupAthena 0.2.0

• Added a NEWS.md file to track changes to the package.
• Added log feature that logs updates with row counts for each table to a setup_athena_log table in the public schema.
• Added a steps feature to run_setup to be able to customize the steps taken for each setup, but not the order.
• Removed deprecated functions.

patelm9/setupAthena documentation built on June 11, 2024, 4:23 a.m.