Publish a tidy ClinVar evidence export to DuckLake — rclinvarbitration_publish

Registers one tidy Parquet export in a persistent staging table, then replaces the current evidence set by key in one DuckLake transaction. New keys are inserted, absent keys are deleted, changed content is updated, and byte-identical records are left untouched. DuckLake's native data-change feed is the release-delta authority.

Usage

rclinvarbitration_publish_ducklake(
  con,
  export,
  table_name = "clinvar",
  staging_table = "clinvar_incoming",
  ducklake_name = NULL,
  author = "RClinVarbitration",
  commit_message = NULL
)

Arguments

con: A DuckDB DBI connection whose current database is the writable DuckLake catalog.
export: The returned value from rclinvarbitration_export_clinvarbitration_parquet() with schema = "tidy", or the returned value from rclinvarbitration_import_flat() when parquet_path was supplied.
table_name: Persistent current-decision table.
staging_table: Persistent empty staging table.
ducklake_name: Attached DuckLake catalog. NULL uses the current database.
author: Snapshot author.
commit_message: Snapshot message. NULL derives one from the export.

Value

Invisibly returns the publication snapshot, source identity, input row count, and DuckLake change counts.

Details

The staging and target tables are initialized once from the Parquet schema. The staging table is retained because current DuckLake releases cannot create, register, and drop that table safely in the same transaction. It is empty before and after every successful publication.