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Compare one watershed group's persisted mapping_code tokens against a reference

Source: R/lnk_compare_mapping_code.R
lnk_compare_mapping_code.Rd

Segment-level QA counterpart to lnk_compare_rollup(). Reads the per-segment mapping_code_<sp> tokens that lnk_pipeline_run() (with mapping_code = TRUE) persisted to <persist_schema>.streams_mapping_code, diffs them against a reference's tokens for the same segments, and returns a per-species match tibble.

Usage

lnk_compare_mapping_code(
  conn,
  aoi,
  cfg,
  reference = "bcfishpass",
  conn_ref = NULL,
  species = NULL,
  ref_table = "fresh.streams_vw_bcfp"
)

Arguments

conn

DBI connection to the local pipeline database (where <persist_schema> and fresh.streams_vw_bcfp live).

aoi

Watershed group code (e.g. "PARS").

cfg

An lnk_config object (resolves cfg$pipeline$schema).

reference

Character scalar identifying the reference. Only "bcfishpass" is supported.

conn_ref

Optional DBI connection to the bcfp tunnel (localhost:63333). Default NULL → tunnel-free local-snapshot compare.

species

Optional character vector of species codes to restrict to. Default NULL discovers the set from the mapping_code columns.

ref_table

Reference table name for the tunnel-free path. Default "fresh.streams_vw_bcfp" (where snapshot_bcfp.sh loads bcfp's output).

Value

A tibble, one row per species: wsg, species, total_segs, match_pct, n_diffs, top_pattern (most common link | bcfp token mismatch), top_pattern_count.

Details

Reads only — no writes, no working schema.

Tunnel-free by default

The reference is the local snapshot fresh.streams_vw_bcfp (loaded by data-raw/snapshot_bcfp.sh --with-bcfp-views from bcfp's published S3 output — no SSH, no :63333). With conn_ref = NULL (default) the compare is a single local join on conn: no second connection, no PG_PASS_SHARE, no tunnel. Pass conn_ref (a DBI connection to the live bcfp tunnel) to diff against bcfishpass.streams_mapping_code instead — the legacy path, kept for back-compat.

Join

link's streams_mapping_code.id_segment is a local surrogate, distinct from bcfp's segmented_stream_id, so the join is on FWA segment-start position: blue_line_key + downstream_route_measure (rounded to 3 decimals — robust to ULP drift on the PostGIS-computed doubles, deterministic across runs that share the same fwapg segmentation). link's position columns come from <persist_schema>.streams, joined on the full PK (id_segment, watershed_group_code) — id_segment alone is not unique across WSGs. The snapshot view carries the position columns inline.

Species resolution

species = NULL (default) compares every species present as a mapping_code_<sp> column on BOTH sides (link's persisted table and the reference), with rows for the WSG. Pass species to restrict; caller-passed species absent on either side drop out (no error).

See also

lnk_compare_rollup(), lnk_compare_wsg(), lnk_pipeline_run()

Other compare: lnk_access(), lnk_compare_rollup(), lnk_compare_wsg(), lnk_mapping_code(), lnk_parity_annotate()

Examples

if (FALSE) { # \dontrun{
conn <- lnk_db_conn()
cfg <- lnk_config("bcfishpass")

# Tunnel-free: diff persisted tokens vs the local fresh.streams_vw_bcfp snapshot.
lnk_compare_mapping_code(conn, aoi = "PARS", cfg = cfg)

# Legacy tunnel path (requires the bcfp tunnel up):
conn_ref <- DBI::dbConnect(RPostgres::Postgres(),
  host = "localhost", port = 63333, dbname = "bcfishpass",
  user = "newgraph", password = Sys.getenv("PG_PASS_SHARE"))
lnk_compare_mapping_code(conn, "PARS", cfg, conn_ref = conn_ref)
} # }