study_area_run.sh: --schema= override for side-by-side bundle compares (v0.41.1)#209
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…s (v0.41.1) Adds --schema=<persist-schema> flag that overrides cfg$pipeline$schema at runtime via the LNK_SCHEMA env var. Propagates to local Rscript invocations (via export) and to cypher SSH invocations (each remote shell exports it before its WSG loop). All four scripts (wsg_run_one, wsg_recompute_one, study_area_compare, study_area_run) honour LNK_SCHEMA. Without the flag, behaviour is unchanged (YAML default). With it, e.g. `--config=default --schema=fresh_default` keeps a default-config run from clobbering an earlier `--config=bcfishpass` baseline sitting in `fresh`. Empty --schema= value errors loudly (not silent fallthrough). Live-validated: ADMS / default config / fresh_default — 2.2 min, 11 species habitat tables in fresh_default, fresh untouched. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
--schema=<persist-schema>flag todata-raw/study_area_run.shfor side-by-side bundle comparespipeline$schemadefault)LNK_SCHEMA; all per-WSG R scripts (wsg_run_one.R,wsg_recompute_one.R,study_area_compare.R) overridecfg$pipeline$schemaat runtimeLNK_SCHEMAbefore its WSG loop)--schema=value errors loudly rather than silently falling through to the YAML default (caught in/code-check)Use case:
--config=default --schema=fresh_defaultkeeps a default-config run from clobbering an earlier--config=bcfishpassbaseline infresh. Unblocks the default-vs-bcfp config comparison run.Related Issues
Test plan
LNK_SCHEMA=fresh_default Rscript data-raw/wsg_run_one.R ADMS defaultran end-to-end in 2.2 min; 11 species habitat tables landed infresh_default;freshschema untouched (baseline preserved)--schema=value errors with"FATAL: --schema= requires a non-empty value"/code-checkRound 1: 1 MEDIUM (empty-value silent fallthrough) fixed; 3 LOW findings accepted as design tradeoffs (SSH single-quote injection theoretical given schema-name conventions; LNK_SCHEMA env leaks to child processes — intentional propagation contract; future-proof flag for study_area_wsgs.R)Notes
The override threads via env var rather than a script param so the four R scripts share one contract (read
Sys.getenv("LNK_SCHEMA"); if non-empty, mutatecfg$pipeline$schemabefore any pipeline call). Same pattern in all three R scripts — easy to extend to future scripts.🤖 Generated with Claude Code