Derive species presence cols from CSV header#107
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NewGraphEnvironment merged 1 commit intomainfrom May 3, 2026
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`R/lnk_pipeline_species.R` and `R/lnk_pipeline_break.R` hardcoded the species-presence column list to 11 codes (bt, ch, cm, co, ct, dv, pk, rb, sk, st, wct). Adding a new species to dimensions.csv + parameters_fresh.csv was silently dropped at the column-list step because the new column was never read. - Extract `.lnk_wsg_species_present(row)` to R/utils.R. Treats every column except `watershed_group_code` and `notes` as a presence flag. Both call sites use the helper. - Add ko (Kokanee) column to wsg_species_presence.csv in both bundles with `t` for PARS, KOTL, NATR, CARP. Sentinel values for testing end-to-end KO flow — actual presence-by-WSG belongs upstream in bcfp's wsg_species_presence.csv (filed at NewGraphEnvironment/bcfishpass#12). Auto-sync workflow will replace these with the authoritative source once that lands. - Add GR + KO species rows to default/parameters_fresh.csv (already present in default/dimensions.csv and rules.yaml). - New tests: lnk_pipeline_species picks up newly-added GR + KO columns when populated, and ignores the `notes` column. Relates to NewGraphEnvironment/sred-2025-2026#24 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
spp_cols <- c("bt", "ch", ...)vector inR/lnk_pipeline_species.RandR/lnk_pipeline_break.R. Both call sites now share.lnk_wsg_species_present(row)(inR/utils.R) which derives the presence-column list from the CSV header.wsg_species_presence.csvpropagates to every callsite without a code edit.kocolumn to both bundles'wsg_species_presence.csvwith sentineltfor PARS, KOTL, NATR, CARP — interim until upstreambcfishpass.wsg_species_presenceships the authoritative coverage (Add ko (Kokanee) column to wsg_species_presence.csv bcfishpass#12).default/parameters_fresh.csv(already present indefault/dimensions.csvandrules.yaml).Why
R/lnk_pipeline_species.R:63-64andR/lnk_pipeline_break.R:167-168were a footgun: the CSV could carry agrcolumn populatedtfor many WSGs, butlnk_pipeline_species()would silently drop GR for every AOI because the hardcoded vector didn't include it. Surfaced when adding GR + KO to enable Kokanee / Arctic Grayling habitat classification on the default bundle.Test plan
devtools::test(filter = "lnk_pipeline_species|lnk_pipeline_break")— 44 PASS / 0 FAIL, including 2 new tests for GR/KO column propagation +notes-column ignoringstream_orderassertions from Wire frs_order_child as link methodology (default off) #97 schema rename) and are unrelated to this PRkosentinel-WSGs are reasonable for interim testing — actual coverage will come from Add ko (Kokanee) column to wsg_species_presence.csv bcfishpass#12Out of scope
Relates to NewGraphEnvironment/sred-2025-2026#24
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