القائمة
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
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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.