Stage 1: read a file, detect frontmatter, and validate the tag map

Usage

stage_ingest(
  input_path,
  tag_map,
  header_row = NULL,
  reference_lists = NULL,
  reference_list_snapshot = NULL,
  activate_all_references = FALSE,
  site_manifest = NULL,
  site_alias_map = NULL,
  ignored_identifier_cols = character()
)

Arguments

input_path: Character. Path to the input file (CSV, XLSX, or XLS).
tag_map: Named list mapping cleaned column names to tag roles. Keys must match column names after janitor::clean_names() normalization. Values are one of "Name", "CASRN", "Other", "Result", "Numeric", "Unit", "Qualifier", "ReportingLimit", "Uncertainty", "UncertaintyCoverage", etc. Example: list(chemical_name = "Name", cas_number = "CASRN", result = "Result", unit = "Unit").
header_row: Integer or NULL. If NULL (default), frontmatter detection runs automatically. If an integer, that row number is used as the header row (manual override).
reference_lists: Named list of reference data. If NULL (default), the package-bundled reference cache is loaded automatically. If provided, must contain keys: stop_words, functional_categories, block_patterns, strip_terms, isotope_lookup.
reference_list_snapshot: Optional compact replay snapshot generated by generate_concert_script(). When supplied, package defaults are loaded without local user_reference_lists.rds overrides, verified against the snapshot hashes, and merged with snapshot overrides.
activate_all_references: Logical. If TRUE, activates all cleaning reference-list rows for this run only.
site_manifest: Optional curated Dataset Context site manifest to include in the workbook export.
site_alias_map: Optional Dataset Context raw-label alias map to include in the workbook export.
ignored_identifier_cols: Retained identifier columns deliberately treated as metadata. These columns never supply identity evidence.

Value

A curation state list. See curate_headless() for the composed run.