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Run the link pipeline end-to-end for one watershed group

Source: R/lnk_pipeline_run.R
lnk_pipeline_run.Rd

Modelling-only umbrella: chains the lnk_pipeline_* phases and the persist write-out into a single call. Produces per-WSG segment data in the persistent province-wide tables (<persist_schema>.streams, streams_habitat_<sp> per species, barriers).

Usage

lnk_pipeline_run(
  conn,
  aoi,
  cfg,
  loaded,
  schema = paste0("working_", tolower(aoi)),
  dams = TRUE,
  cleanup_working = TRUE,
  mapping_code = FALSE
)

Arguments

conn

DBI connection to the local pipeline database (typically localhost fwapg).

aoi

Watershed group code (e.g. "ADMS"). Validated against ^[A-Z]{3,5}$.

cfg

An lnk_config object (from lnk_config()).

loaded

Named list from lnk_load_overrides().

schema

Working schema name. Default paste0("working_", tolower(aoi)). Per-WSG staging tables live here; dropped on exit when cleanup_working = TRUE.

dams

Logical. When TRUE (default), pass conn as conn_tunnel to lnk_pipeline_prepare() so the CABD dams step runs from local cabd.dams. Pass FALSE to skip dams entirely.

cleanup_working

Logical. When TRUE (default), drop the <schema> working schema at the end. Pass FALSE for interactive debug / manual inspection.

mapping_code

Logical. Gates only the mapping_code token assembly (phase 10b) — when TRUE, lnk_mapping_code() runs and <persist_schema>.streams_mapping_code is produced for the WSG, consumed downstream by data-raw/build_species_views.R --bcfp (QGIS bcfp-shape symbology). Default FALSE. streams_access is built and persisted regardless of this flag (phase 10a, link#218) — access is foundational, not mapping_code-specific. Methodology shift from pre-#187 compare_wsg: access uses link's own per-species barriers (via blocks_species predicate on <schema>.barriers), not bcfp's tunnel-staged tables.

Value

conn, invisibly. Side effects are the writes into <persist_schema>.streams, streams_habitat_<sp>, and barriers.

Details

This is the modelling boundary — the link package's deliverable. Comparison against bcfishpass (or any future reference) lives in lnk_compare_rollup(), which reads the persisted state. The split lets re-running the pipeline and re-running the comparison happen independently; an orchestrator loop's resume check can probe PG state via link:::.lnk_wsg_persisted() rather than the comparison RDS artifact.

Phase order

  1. lnk_pipeline_setup() — create per-WSG working schema.

  2. lnk_pipeline_load() — crossings + modelled fixes + PSCIS status.

  3. lnk_pipeline_prepare() — falls, definite + control, habitat confirms, gradient barriers, natural barriers, barrier overrides, per-model minimal reduction, base segments. Passes conn as conn_tunnel when dams = TRUE so CABD dams flow through.

  4. lnk_pipeline_crossings() — match PSCIS to modelled crossings.

  5. lnk_pipeline_break() — observations, gradient minimal, definite, habitat endpoints, crossings — in config-defined order.

  6. lnk_pipeline_classify() — assemble streams_breaks and run frs_habitat_classify().

  7. lnk_pipeline_connect() — per-species cluster + connected_waterbody.

  8. lnk_pipeline_species() — resolve the active species set for this AOI (cfg$species ∩ wsg_species_presence). Empty set is an error.

  9. lnk_persist_init() — create persistent target tables if absent.

  10. lnk_barriers_unify() — unify per-source barriers into a single working-schema table (always; promotes the mapping_code-only flag in lnk_compare_wsg() to canonical PG state). 10a. Access phase (always-on, link#218). Runs between barriers_unify and persist: a pre-persist of the current WSG (so the next two steps see cross-WSG barriers), lnk_barriers_views() (tunnel-free, link-canonical per-species views over <persist_schema>.barriers), and lnk_pipeline_access() (writes working streams_access). Access is foundational — mapping_code depends on it — so it builds regardless of mapping_code. See link#187, #196. 10b. Optional mapping_code token assembly — gated by mapping_code = TRUE. lnk_mapping_code() consumes streams_access + streams_habitat and writes working streams_mapping_code.

  11. lnk_pipeline_persist() — copy per-WSG streams + per-species habitat + barriers + streams_access (+ optional streams_mapping_code) into <persist_schema> (idempotent DELETE-WHERE-WSG + INSERT).

See also

lnk_compare_rollup(), lnk_compare_wsg(), lnk_pipeline_setup(), lnk_pipeline_persist()

Other pipeline: lnk_pipeline_access(), lnk_pipeline_break(), lnk_pipeline_classify(), lnk_pipeline_connect(), lnk_pipeline_crossings(), lnk_pipeline_load(), lnk_pipeline_mapping_code(), lnk_pipeline_prepare(), lnk_pipeline_setup(), lnk_pipeline_species(), lnk_presence()

Examples

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

# Model one WSG end-to-end (~70s)
lnk_pipeline_run(conn = conn, aoi = "ADMS",
                 cfg = cfg, loaded = loaded)

# Verify PG state
DBI::dbGetQuery(conn,
  "SELECT count(*) FROM fresh.streams WHERE watershed_group_code = 'ADMS'")
} # }