Orchestrate the full curation pipeline: dedup -> search -> map -> consensus -> resolution

Usage

run_curation_pipeline(
  clean_data,
  column_tags,
  progress_callback = NULL,
  dedup_only = FALSE,
  wqx_threshold = 0.85,
  starts_with = FALSE,
  pubchem = FALSE,
  original_data = NULL,
  desalt = FALSE,
  ignored_identifier_cols = character(),
  source_lookup_fn = source_identifier_lookup,
  wqx_cas_lookup_fn = validate_and_lookup_cas
)

Arguments

clean_data: The cleaned data frame (data_store$clean)
column_tags: Named list (col_name -> "Name"|"CASRN"|"Other")
progress_callback: Optional function(stage, message) for reporting progress to Shiny
dedup_only: If TRUE, return after dedup stage with just counts (for preview)
wqx_threshold: Numeric WQX fuzzy matching threshold.
starts_with: Logical. If TRUE, enables CompTox starts-with fallback search for names unresolved by exact, CAS, and WQX matching.
pubchem: Logical. If TRUE, add exact-name PubChem candidates for unresolved rows without assigning DTXSIDs.
original_data: Optional input rows used for the original name lookup.
desalt: Logical. If TRUE, suggest parent names and DTXSIDs for unresolved salt names without assigning them. Independent of pubchem.
ignored_identifier_cols: Deliberately unused identifier metadata columns.
source_lookup_fn: Injectable authoritative source DTXSID details lookup.
wqx_cas_lookup_fn: Injectable CAS lookup for canonical WQX dictionary evidence. Receives deduplicated valid CAS values and returns original_cas (or validated_cas), dtxsid, preferredName, and optional lookup_status. All hits remain review candidates; no candidate is selected or accepted. Statuses distinguish candidate, not_found, unavailable, missing, invalid, and ambiguous dictionary evidence. Independent of pubchem. Mapped wqx_match_distance is lossless 17-digit decimal text for portable evidence fingerprints; the matcher's match_distance remains numeric.

Value

List with results, dedup_summary, search_summary, consensus_summary