Rebuild HNAP-aware EDH XML from a reviewed Salmon Data Package — write_edh_xml_from

Reads metadata/dataset.csv from an existing Salmon Data Package and writes a fresh metadata-edh-hnap.xml file using the canonical edh_build_hnap_xml() builder. This is the preferred post-review rebuild path after metadata has been edited manually in Excel or another spreadsheet tool. The helper refuses to rebuild when obvious review-state markers remain, such as REVIEW:-prefixed IRIs anywhere in the package metadata or unresolved MISSING METADATA: / MISSING DESCRIPTION: placeholders in metadata/dataset.csv or metadata/tables.csv.

Usage

write_edh_xml_from_sdp(
  path,
  output_path = NULL,
  overwrite = TRUE,
  language = "eng",
  file_identifier = NULL,
  date_stamp = Sys.Date()
)

Arguments

path: Character path to the Salmon Data Package directory.
output_path: Optional path for the regenerated XML. Defaults to metadata/metadata-edh-hnap.xml inside path. Parent directories are created automatically when needed.
overwrite: Logical; if FALSE, error when output_path already exists. Default is TRUE.
language: ISO 639-2/T language code for the primary metadata language (default: "eng").
file_identifier: Optional metadata file identifier forwarded to edh_build_hnap_xml().
date_stamp: Metadata date stamp forwarded to edh_build_hnap_xml().

Value

Invisibly returns the same list as edh_build_hnap_xml(), with elements xml and path.

Examples

if (FALSE) { # \dontrun{
pkg_path <- create_sdp(
  mtcars,
  dataset_id = "demo-1",
  table_id = "counts",
  overwrite = TRUE
)

# ...edit metadata/dataset.csv in Excel...
write_edh_xml_from_sdp(pkg_path)
} # }