菜单
Use when writing, running, or fixing SysNDD R/Plumber API tests (testthat) — including database-writing tests, running a single test inside the API container, mocking external providers, or diagnosing SKIP-vs-PASS, helper-loading, or path-resolution issues
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基于 SOC 职业分类
Use when adding or changing an external HTTP provider call in SysNDD (gnomAD, Ensembl, UniProt, AlphaFold, MGI, RGD, PubMed, PubTator, MONDO, JAX/HPO) or touching external-call timeouts, retries, caching, or per-request time budgets
Use when wiring a SysNDD Vue 3 view or component to the backend API, adding a typed API client, handling API errors, or binding backend data into BootstrapVueNext tables and tooltips — especially around Plumber response shapes and BVN table/tooltip quirks
Use when adding or changing a SysNDD DB migration, editing a SQL view (especially ndd_entity_view or the core read views), touching the migration runner or manifest, restoring a database, or diagnosing a startup failure related to migrations
Use when reviewing or writing SysNDD code for security vulnerabilities or correctness bugs — authorization/role gates, SQL/expression injection, credential and secret handling, data exposure through public or MCP surfaces, resource-exhaustion/DoS from external calls, error/info leakage, and the repo's known R/Plumber footguns — especially before merging a diff or PR
Use when changing gene clustering (STRING/Leiden functional axis or phenotype MCA/HCPC), the analysis snapshot builder or validator, the memoised clustering cache, cache coherence, or LLM cluster summaries — or deploying a clustering change so public endpoints and summaries reflect it
Use when adding or changing durable async jobs, worker-executed code, job handlers, queue lanes or priorities in SysNDD — or diagnosing why a submitted job never runs, stays queued, or fails with "No durable async job handler registered"
| name | sysndd-api-testing |
| description | Use when writing, running, or fixing SysNDD R/Plumber API tests (testthat) — including database-writing tests, running a single test inside the API container, mocking external providers, or diagnosing SKIP-vs-PASS, helper-loading, or path-resolution issues |
Use this skill before adding or running R API tests under api/tests/testthat/. The suite is large (200+ files) and has non-obvious container, database, and helper conventions. The authoritative helpers are helper-db.R, helper-paths.R, and setup.R.
make test-api-fast — fast PR gate (also what make pre-commit runs).make test-api — full suite locally.make ci-local — closest local mirror of CI (lint + tests with DB). Prefer before handoff.cd api && Rscript -e "testthat::test_file('tests/testthat/test-unit-foo.R')"docker exec sysndd-api-1 Rscript -e "testthat::test_file('/app/tests/testthat/test-foo.R')"api/tests/ is not bind-mounted (only functions/, services/, endpoints/, core/ are). A new or edited test must be copied in or the image rebuilt:
docker cp api/tests/testthat/test-foo.R sysndd-api-1:/app/tests/testthat/test-foo.R
Inside the container the default sysndd_db_test config points at a host-published port that the container can't reach, so skip_if_no_test_db() SKIPs. get_test_config() prefers MYSQL_* env when MYSQL_HOST is set, so pass DB creds to reach the DB service:
docker exec -e MYSQL_HOST=mysql -e MYSQL_DATABASE=sysndd_db_test \
-e MYSQL_USER=<u> -e MYSQL_PASSWORD=<p> sysndd-api-1 \
Rscript -e "testthat::test_file('/app/tests/testthat/test-foo.R')"
SKIP is not PASS. Read the summary: [ FAIL 0 | SKIP 1 ] means the DB test did not run. Only PASS n with SKIP 0 is a real green.
source_api_file("services/foo-service.R", local = FALSE) — resolves /app in-container via get_api_dir(). helper-*.R auto-load through setup.R.with_test_db_transaction({ conn <- getOption(".test_db_con"); ... }) — always rolls back. It calls skip_if_no_test_db() for you. See AGENTS.md: prefer this or document why rollback is impossible.CREATE TABLE/TRUNCATE are DDL and auto-commit — they break rollback isolation. Create fixtures on a separate connection first (mirror ensure_test_user_table()).DBI::dbBind() with ? placeholders needs unname(params) (named lists fail silently); positional params = list(x) is safe.httr2: PubMed tests stub pubmed_esearch_count() / pubmed_fetch_xml(); see helper-mock-apis.R and dittodb.Behavior changes must not break the guard tests that encode invariants: test-unit-filter-column-allowlist.R, test-unit-endpoint-error-handler.R, test-unit-external-budget-guard.R, test-unit-cheap-route-isolation.R, test-unit-analysis-snapshot-coherence.R, test-unit-llm-model-default-guard.R. If your change makes one fail, the change is likely wrong — not the guard.
Report which lane you ran and paste the real summary line. Never claim green on a run that only SKIPped.