Stream a ClinVar VCV XML release into relational DuckDB tables — rclinvarbitration_import

The native extension reads .xml and .xml.gz with a libxml2 forward reader. One compact JSON-backed row per selected ClinVar entity is written to a disk-backed staging table in one XML pass, projected into the public ClinVar relations without an EAV pivot, and dropped. No XML DOM, XML blob, generic parser-node graph, or R data-frame materialization is used. Each public relation is committed independently, the release catalogue row marks completion, and failed imports remove partial rows for release_id.

Usage

rclinvarbitration_import_xml(
  con,
  path,
  release_id,
  replace = FALSE,
  source_url = NULL,
  source_md5 = NULL
)

Arguments

con: A DuckDB DBI connection.
path: Path to an official ClinVar VCV XML or XML.GZ release.
release_id: User-supplied release label stored with every row.
replace: Replace rows already stored for release_id?
source_url: Optional source URL for the release catalogue. When path is returned directly by rclinvarbitration_download_clinvar(), its download metadata supplies this value automatically.
source_md5: Optional 32-character source MD5 digest. Download metadata is used automatically when available.

Value

A named numeric vector with imported entity counts.