Stage 3: run the CompTox curation search and optional candidate postprocessing

Usage

stage_curate(
  state,
  wqx_threshold = 0.85,
  starts_with = FALSE,
  postprocess_candidates = FALSE,
  cache_dir = NULL,
  pubchem = FALSE,
  desalt = FALSE,
  desalt_workflows = c("qsar-ready", "ms-ready")
)

Arguments

state: State list from stage_clean().
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.
postprocess_candidates: Logical. If TRUE, runs the same enrichment, similarity scoring, and auto-resolve pass used by the Shiny app after curation. Default FALSE for backward compatibility.
cache_dir: Optional directory. When set, the CompTox search result is cached by a hash of the cleaned chemical columns and search settings, and the candidate enrichment cache persists across runs. Used by curate_iterate() so re-runs after review edits skip the API.
pubchem: Logical. If TRUE, searches unresolved names in PubChem and exports candidates without assigning DTXSIDs.
desalt: Logical. If TRUE, suggests salt parent candidates without assigning parent DTXSIDs, and adds structure-based parent_dtxsid_, parent_name_, parent_casrn_, and parent_status_<workflow> columns for resolved rows via the chemi standardizer. Independent of pubchem.
desalt_workflows: Standardizer workflows used when desalt = TRUE: "qsar-ready", "ms-ready", or both (default).

Value

The state with resolution_state, consensus_summary, enrichment_cache, enrichment_failed, and script_baseline_state added.