Generate a CONCERT replay script

Usage

generate_concert_script(
  input_path,
  output_path,
  tag_map,
  header_row,
  review_overrides = NULL,
  wqx_threshold = 0.85,
  starts_with = FALSE,
  harmonize = FALSE,
  media = NULL,
  unit_map = NULL,
  corrections = NULL,
  media_map = NULL,
  format = "parquet",
  source_name = NULL,
  reference_lists = NULL,
  activate_all_references = FALSE,
  site_manifest = NULL,
  site_alias_map = NULL,
  value_corrections = NULL,
  cleaning_steps = NULL,
  multi_analyte_resolutions = NULL,
  accept_suggestions = FALSE,
  review_picks = NULL,
  row_flags = NULL,
  pubchem = FALSE,
  desalt = FALSE,
  desalt_workflows = c("qsar-ready", "ms-ready"),
  ignored_identifier_cols = character(),
  review_decision_evidence = NULL,
  identity_decisions = NULL,
  candidate_validation = NULL,
  toxval_identity_mode = "lookup"
)

Arguments

input_path: Character input file path shown at the top of the script.
output_path: Character output XLSX path shown at the top of the script.
tag_map: Named list of chemical, numeric, metadata, and study tags.
header_row: Detected header row to pin for replay.
review_overrides: Optional content-match override spec from build_review_overrides() to embed as generated per-column dplyr::rows_update() override tables.
wqx_threshold: WQX fuzzy match threshold.
starts_with: Logical. Enables CompTox starts-with fallback search.
harmonize: Logical. Re-run harmonization during replay.
media: Optional dataset-wide media fallback.
unit_map: Optional effective unit harmonization map. When harmonize = TRUE it is snapshotted against package defaults so only user deltas (plus a baseline hash) are embedded.
corrections: Optional effective numeric corrections table to embed when harmonize = TRUE.
media_map: Optional effective media harmonization map. When harmonize = TRUE it is snapshotted against package defaults so only user deltas (plus a baseline hash) are embedded.
format: ToxVal output format for harmonized headless runs.
source_name: Optional source name for ToxVal mapping.
reference_lists: Optional current cleaning reference lists to snapshot for portable replay.
activate_all_references: Logical. Replays the preflight setting that activates all cleaning reference-list rows for the run.
site_manifest: Optional curated Dataset Context site manifest to embed in the replay script.
site_alias_map: Optional Dataset Context raw-label alias map to embed in the replay script.
value_corrections: Optional pre-cleaning value correction table to embed. See apply_value_corrections().
cleaning_steps: Optional named list of cleaning step switches to embed.
multi_analyte_resolutions: Optional multi-analyte resolution table to embed.
accept_suggestions: Logical. Embed the bulk-accept switch.
review_picks: Optional content-keyed DTXSID picks table to embed.
row_flags: Optional content-keyed row flag table to embed.
pubchem: Logical. Enables PubChem candidate lookup for unresolved names.
desalt: Logical. Enables salt parent suggestions independently of PubChem.
desalt_workflows: Standardizer workflows used when desalt = TRUE: "qsar-ready", "ms-ready", or both (default).
ignored_identifier_cols: Retained identifier columns deliberately treated as metadata, persisted in the replay call.
review_decision_evidence: Portable immutable review evidence contract.
identity_decisions: Explicit structured source-identity decisions.
candidate_validation: Structured candidate validation outcomes.
toxval_identity_mode: ToxVal policy: lookup (compatibility default) or accepted.

Value

Complete R script as a character scalar.