diff --git a/.env.example b/.env.example index 8dda792..026d7e3 100644 --- a/.env.example +++ b/.env.example @@ -2,3 +2,9 @@ DATABASE_URL=postgresql+psycopg://postgres:postgres@db:5432/evograph REDIS_URL=redis://redis:6379/0 SCOPE_OTT_ROOT=Aves NEXT_PUBLIC_API_BASE=http://localhost:8000 + +# Production settings +# POSTGRES_PASSWORD=changeme # Required for docker-compose.prod.yml +# CORS_ORIGINS=["https://evograph.example.com"] +# LOG_LEVEL=info # debug, info, warning, error, critical +# LOG_FORMAT=json # text (dev) or json (production) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d04748f..ee17bec 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -56,6 +56,9 @@ jobs: - name: Typecheck run: npx tsc --noEmit + - name: Test + run: npm test + web-build: name: Web — build runs-on: ubuntu-latest diff --git a/CLAUDE.md b/CLAUDE.md index a8951f3..71e398e 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -33,17 +33,18 @@ evograph/ ├── apps/ │ ├── api/ # Python FastAPI backend │ │ ├── pyproject.toml # Dependencies, pytest config, ruff config -│ │ ├── Dockerfile # Health check included +│ │ ├── Dockerfile # Multi-stage: dev (--reload) + prod (4 workers, non-root) │ │ ├── alembic.ini │ │ ├── src/evograph/ -│ │ │ ├── main.py # FastAPI app, CORS, routers -│ │ │ ├── settings.py # DATABASE_URL, REDIS_URL, SCOPE_OTT_ROOT +│ │ │ ├── main.py # FastAPI app, lifespan, CORS, rate limiting, logging, health +│ │ │ ├── settings.py # DATABASE_URL, REDIS_URL, SCOPE_OTT_ROOT, CORS_ORIGINS, LOG_LEVEL, LOG_FORMAT +│ │ │ ├── logging_config.py # Structured logging (text/JSON format, configurable level) │ │ │ ├── db/ │ │ │ │ ├── models.py # Taxon, Sequence, Edge, NodeMedia │ │ │ │ ├── session.py # engine, SessionLocal, get_db │ │ │ │ └── migrations/versions/001_initial.py │ │ │ ├── api/ -│ │ │ │ ├── routes/ # search, taxa, graph, sequences +│ │ │ │ ├── routes/ # search, taxa, graph, sequences, stats │ │ │ │ └── schemas/ # Pydantic response models │ │ │ ├── services/ │ │ │ │ ├── ott_client.py # OpenTree API (tnrs, subtree, taxon_info) @@ -58,11 +59,17 @@ evograph/ │ │ │ │ ├── build_neighbors.py # Pairwise MI → kNN edges │ │ │ │ ├── build_graph_export.py # JSON files for caching │ │ │ │ ├── ingest_images.py # Wikipedia thumbnails → node_media -│ │ │ │ └── validate.py # Quality stats & outlier detection +│ │ │ │ ├── backfill_ncbi_tax_id.py # NCBI Taxonomy API → ncbi_tax_id column +│ │ │ │ ├── dedup_sequences.py # Remove duplicate accessions +│ │ │ │ └── validate.py # Quality stats & outlier detection (JSON export) +│ │ │ ├── middleware/ +│ │ │ │ ├── rate_limit.py # Sliding-window per-IP rate limiter +│ │ │ │ ├── request_logging.py # Structured access logging + X-Request-ID +│ │ │ │ └── security_headers.py # X-Content-Type-Options, X-Frame-Options, etc. │ │ │ └── utils/ │ │ │ ├── alignment.py # parasail global alignment wrapper │ │ │ └── fasta.py # FASTA format parser -│ │ └── tests/ # 53 pytest tests +│ │ └── tests/ # 110 pytest tests │ │ ├── conftest.py # MockDB, fixtures, factories │ │ ├── test_health.py │ │ ├── test_search.py @@ -70,18 +77,32 @@ evograph/ │ │ ├── test_graph.py │ │ ├── test_sequences.py │ │ ├── test_mi_distance.py -│ │ └── test_pipeline.py # Canonical selection scoring tests +│ │ ├── test_pipeline.py # Canonical selection scoring tests +│ │ ├── test_backfill_ncbi.py # NCBI tax ID lookup tests +│ │ ├── test_ingest_ncbi.py # NCBI ingestion search strategy tests +│ │ ├── test_dedup_sequences.py # Sequence deduplication tests +│ │ ├── test_stats.py # Stats endpoint tests +│ │ ├── test_validate.py # Validation pipeline tests +│ │ ├── test_rate_limit.py # Rate limiting middleware tests +│ │ ├── test_request_logging.py # Request logging middleware tests +│ │ ├── test_logging_config.py # Logging configuration tests +│ │ └── test_security_headers.py # Security headers middleware tests │ └── web/ # Next.js 15 + TypeScript frontend │ ├── package.json -│ ├── Dockerfile # Health check included +│ ├── Dockerfile # Multi-stage: dev (npm run dev) + prod (standalone build, non-root) │ ├── tsconfig.json # Strict mode, @/* path alias │ ├── next.config.js # output: "standalone" +│ ├── jest.config.js # Jest + next/jest setup +│ ├── jest.setup.ts # @testing-library/jest-dom │ └── src/ │ ├── app/ │ │ ├── globals.css # Dark theme, skeleton, responsive, graph search │ │ ├── layout.tsx # Root layout, sticky nav │ │ ├── page.tsx # Home: search + quick links │ │ ├── graph/page.tsx # MI network explorer (Sigma.js) + node search +│ │ ├── stats/page.tsx # Database stats dashboard +│ │ ├── not-found.tsx # 404 page +│ │ ├── error.tsx # Error boundary page │ │ └── taxa/[ottId]/ │ │ ├── page.tsx # Taxon detail (hero, children, neighbors) │ │ └── sequences/page.tsx # COI sequence viewer @@ -90,13 +111,27 @@ evograph/ │ │ ├── TaxonCard.tsx # Thumbnail + rank badge │ │ ├── GraphView.tsx # Cytoscape.js (small graphs) │ │ ├── GraphViewSigma.tsx # Sigma.js (large networks) -│ │ └── Skeleton.tsx # Shimmer loading states +│ │ ├── Skeleton.tsx # Shimmer loading states +│ │ └── ErrorBoundary.tsx # React error boundary with retry │ └── lib/ │ ├── api.ts # API client functions │ ├── types.ts # TypeScript interfaces │ └── external-links.ts # Wikipedia, iNaturalist, eBird URLs -├── docker-compose.yml # postgres:16, redis:7, api, web (with health checks) -├── Makefile # Pipeline orchestration commands +│ └── __tests__/ # 82 Jest + RTL tests +│ ├── HomePage.test.tsx +│ ├── TaxonDetailPage.test.tsx +│ ├── SequencesPage.test.tsx +│ ├── GraphPage.test.tsx +│ ├── SearchBox.test.tsx +│ ├── TaxonCard.test.tsx +│ ├── Skeleton.test.tsx +│ ├── ErrorBoundary.test.tsx +│ ├── StatsPage.test.tsx +│ ├── api.test.ts +│ └── external-links.test.ts +├── docker-compose.yml # Dev: postgres:16, redis:7, api (--reload), web (npm run dev) +├── docker-compose.prod.yml # Prod override: multi-worker, non-root, no source mounts +├── Makefile # Pipeline + deployment commands (up, up-prod) ├── .github/workflows/ci.yml # Lint, test, typecheck, build ├── .env.example ├── TODO.md # Tracked tasks with completion status @@ -130,17 +165,21 @@ All under FastAPI with CORS enabled (all origins). | Method | Path | Params | Response | Notes | |--------|------|--------|----------|-------| -| GET | `/health` | — | `{"status":"ok"}` | | -| GET | `/v1/search` | `q` (required, min 1), `limit` (max 100) | `TaxonSummary[]` | pg_trgm + prefix ranking | +| GET | `/health` | — | `{"status":"ok","scope":"Aves"}` | Liveness check | +| GET | `/health/ready` | — | `{"status":"ok","database":{...}}` | Readiness + pool stats | +| GET | `/v1/search` | `q` (required, min 1), `limit` (max 100) | `SearchPage` | pg_trgm + prefix ranking, total count | | GET | `/v1/taxa/{ott_id}` | — | `TaxonDetail` | Recursive CTE lineage | | GET | `/v1/taxa/{ott_id}/children` | `offset`, `limit` (max 500) | `ChildrenPage` | Paginated | -| GET | `/v1/taxa/{ott_id}/sequences` | — | `SequenceOut[]` | Includes DNA sequence text | +| GET | `/v1/taxa/{ott_id}/sequences` | `offset`, `limit` (max 200) | `SequencePage` | Paginated | | GET | `/v1/graph/subtree/{ott_id}` | `depth` (1-5, default 3) | `GraphResponse` | Recursive CTE subtree | | GET | `/v1/graph/mi-network` | — | `GraphResponse` | Cached 5min in-memory | | GET | `/v1/graph/neighbors/{ott_id}` | `k` (1-50, default 15) | `NeighborOut[]` | Sorted by distance | +| GET | `/v1/stats` | — | `StatsResponse` | Taxa/sequence/edge counts | **Key response types:** - `TaxonDetail`: includes children[], total_children, lineage[], has_canonical_sequence, wikipedia_url +- `SearchPage`: items[] + total + limit (paginated search results) +- `SequencePage`: items[] + total + offset + limit (paginated sequences) - `GraphResponse`: nodes[] + edges[] (kind: "taxonomy" | "mi") - `SequenceOut`: includes full DNA sequence text, source, accession, is_canonical @@ -149,14 +188,16 @@ All under FastAPI with CORS enabled (all origins). Run via Makefile or directly as `python -m evograph.pipeline.`: ``` -1. ingest_ott — Parse OpenTree Newick subtree → taxa table (~27,853 for Aves) -2. ingest_ncbi — Fetch COI from NCBI GenBank → sequences table +1. ingest_ott — Parse OpenTree Newick subtree → taxa table (--scope configurable) +2. ingest_ncbi — Fetch COI from NCBI GenBank → sequences (genus fallback, --skip-existing) ingest_bold — Fetch COI from BOLD portal → sequences table (portal down) -3. select_canonical — Score sequences (length - 10*ambig), mark best per species -4. build_neighbors — Pairwise alignment + MI distance → kNN edges (k=15) -5. build_graph_export — Export nodes.json + edges.json -6. ingest_images — Wikipedia thumbnails → node_media table -7. validate — Print quality report (genus/family sharing %, distance stats) +3. dedup_sequences — Remove duplicate accessions, keep longest (--dry-run supported) +4. select_canonical — Score sequences (length - 10*ambig), mark best per species +5. build_neighbors — Pairwise alignment + MI distance → kNN edges (k=15) +6. build_graph_export — Export nodes.json + edges.json +7. ingest_images — Wikipedia thumbnails → node_media table +8. backfill_ncbi_tax_id — Query NCBI Taxonomy API → ncbi_tax_id column +9. validate — Print quality report (genus/family sharing %, distance stats, --output for JSON) ``` **Full pipeline:** `make pipeline` runs steps 1-7 in sequence. @@ -195,9 +236,12 @@ make up # docker compose up --build make down # docker compose down make migrate # alembic upgrade head -# API tests (53 tests) +# API tests (110 tests) cd apps/api && python -m pytest tests/ -v +# Frontend tests (82 tests) +cd apps/web && npm test + # Lint cd apps/api && ruff check src/ tests/ cd apps/web && npm run lint @@ -216,26 +260,46 @@ DATABASE_URL=postgresql+psycopg://postgres:postgres@db:5432/evograph REDIS_URL=redis://redis:6379/0 SCOPE_OTT_ROOT=Aves NEXT_PUBLIC_API_BASE=http://localhost:8000 +CORS_ORIGINS=["*"] # JSON array of allowed origins +LOG_LEVEL=info # debug, info, warning, error, critical +LOG_FORMAT=text # text (dev) or json (production) ``` ## Testing Strategy -**Current: 53 tests passing** (all in `apps/api/tests/`) - -Tests use `MockDB` with FastAPI dependency override — no real database needed: -- `conftest.py`: Mock factories (`_make_taxon`, `_make_sequence`, `_make_edge`, `_make_media`), `MockQuery` (chainable filter/limit/order_by/scalar), `MockDB` (registry by model type) -- Override `get_db` dependency with mock session +**Current: 192 tests passing** (110 API + 82 frontend) -**What's tested:** -- All 8 API endpoints (status codes, response schemas, validation errors, 404s) +**API tests** (`apps/api/tests/`) — use `MockDB` with FastAPI dependency override, no real database: +- `conftest.py`: Mock factories (`_make_taxon`, `_make_sequence`, `_make_edge`, `_make_media`), `MockQuery` (chainable filter/limit/order_by/scalar/exists/select_from), `MockDB` (registry by model type + execute for CTEs) +- All 10 API endpoints (status codes, response schemas, validation errors, 404s) - MI distance computation (entropy, NMI, clamping, gap exclusion) - Pipeline canonical selection scoring (11 tests for `_score` function) +- NCBI taxonomy ID lookup (6 tests for `_lookup_tax_id` function) +- NCBI ingestion search strategy (15 tests: query building, esearch, efetch, genus fallback) +- Sequence deduplication (3 tests for `find_duplicates` function) +- Validation pipeline (12 tests: walk_to_rank, report structure, outlier detection) +- Stats endpoint (2 tests: structure, empty database) +- Rate limiting middleware (5 tests: headers, decrement, 429, exclusions) +- Logging configuration (5 tests: JSON formatter, text/JSON/debug configuration) +- Security headers middleware (2 tests: header values, main app integration) + +**Frontend tests** (`apps/web/src/__tests__/`) — Jest + React Testing Library: +- `HomePage.test.tsx` — heading, search box, quick links, rank badges +- `TaxonDetailPage.test.tsx` — skeleton, hero, breadcrumb, children, external links, error state +- `SequencesPage.test.tsx` — skeleton, accessions, canonical badge, composition, expansion toggle +- `GraphPage.test.tsx` — loading skeleton, title, stats counts, error state, node search, description +- `SearchBox.test.tsx` — debounce, API calls, dropdown, navigation on selection, keyboard nav (arrows/Enter/Escape), ARIA combobox +- `TaxonCard.test.tsx` — rendering, links, child count, image, italicization +- `Skeleton.test.tsx` — SkeletonLine/Circle/Card, TaxonDetailSkeleton, GraphPageSkeleton +- `ErrorBoundary.test.tsx` — renders children, fallback on error, custom fallback, retry recovery +- `api.test.ts` — all API client functions (URL construction, error handling) +- `external-links.test.ts` — Wikipedia, iNaturalist, eBird URL formatting **What's NOT tested:** - Full pipeline integration (ingest, neighbor building) -- Frontend components (no Jest/RTL) - External API integration (OpenTree, NCBI, Wikipedia) - Database migrations +- Graph rendering components (Cytoscape, Sigma.js — require canvas) ## Frontend Conventions @@ -256,9 +320,12 @@ The following types must stay in sync across three layers: | `TaxonSummary` | `TaxonSummary` | `Taxon` | | `TaxonDetail` | `TaxonDetail` | `Taxon` + joins | | `ChildrenPage` | `ChildrenPage` | — | +| `SearchPage` | `SearchPage` | — | | `SequenceOut` | `SequenceOut` | `Sequence` | +| `SequencePage` | `SequencePage` | — | | `Node` / `GraphEdge` / `GraphResponse` | `GraphNode` / `GraphEdge` / `GraphResponse` | `Taxon` + `Edge` | | `NeighborOut` | `NeighborOut` | `Edge` + `Taxon` join | +| (inline dict) | `StatsResponse` | Aggregation queries | **When adding a field:** Update all three: schema → route mapping → TypeScript type → API client → UI usage. @@ -278,25 +345,23 @@ The following types must stay in sync across three layers: | Images | Fetched from Wikipedia | **Why so few sequences:** -- NCBI query finds only ~167 matches for Aves species +- Initial NCBI query found only ~167 matches (narrow COI gene annotations) +- Broader search + genus fallback now available (re-run `ingest_ncbi --skip-existing`) - BOLD portal has been down since Feb 2026 -- TODO: Broader NCBI search (genus fallback, relaxed terms) ## Remaining Work (from TODO.md) ### High Priority -- [ ] Expand NCBI ingestion — try genus-level queries, broader search terms - [ ] Retry BOLD portal when it comes back online -- [ ] Frontend smoke tests ### Medium Priority -- [ ] Run validate.py and document results +- [ ] Run validate.py and document results (now with `--output` JSON export) - [ ] Production deployment config ### Phase 2 -- [ ] Make SCOPE_OTT_ROOT configurable for other clades - [ ] k-mer candidate filtering (FAISS/Annoy) for cross-family neighbors - [ ] Job queue (Celery/RQ) for background pipeline jobs +- [ ] Precompute subtree graph exports for common entry points - [ ] Multi-marker support (16S, 18S) ## Architectural Principles @@ -317,13 +382,18 @@ The following types must stay in sync across three layers: - **Search:** pg_trgm GIN index for fast ILIKE substring matching; prefix matches ranked first - **MI network:** In-memory cache with 5-minute TTL - **Neighbor queries:** Composite index (src_ott_id, distance) for indexed ORDER BY + LIMIT +- **Rate limiting:** Sliding-window per-IP (100 req/min), /health excluded, X-RateLimit headers +- **Graceful shutdown:** Lifespan context manager disposes connection pool on SIGTERM +- **Readiness probe:** /health/ready checks DB connectivity and reports pool stats +- **Security headers:** X-Content-Type-Options, X-Frame-Options, X-XSS-Protection, Referrer-Policy, Permissions-Policy +- **Cache-Control:** MI network (5min), stats (1min) — reduces redundant API calls ## Known Gotchas - `pyproject.toml` requires Python >=3.11 (relaxed from 3.12 for compatibility) - Build backend is `hatchling.build` (not `hatchling.backends`) - Redis is configured but not used yet (reserved for caching) -- CORS is wide open (`allow_origins=["*"]`) — tighten for production +- CORS defaults to `["*"]` — set `CORS_ORIGINS` env var for production - `data/raw/` and `data/processed/` are gitignored — not in repo - Graph JSON exports exist at `apps/api/src/data/processed/graph/` but are gitignored - Sequence `quality` field is JSONB with `{"ambig": N}` format diff --git a/Makefile b/Makefile index 8bfa717..2ba6b22 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,4 @@ -.PHONY: up down migrate ingest_ott ingest_ncbi ingest_bold canonical neighbors export images validate pipeline +.PHONY: up down up-prod down-prod migrate ingest_ott ingest_ncbi ingest_bold canonical neighbors export images validate pipeline up: docker compose up --build @@ -6,6 +6,12 @@ up: down: docker compose down +up-prod: + docker compose -f docker-compose.yml -f docker-compose.prod.yml up --build -d + +down-prod: + docker compose -f docker-compose.yml -f docker-compose.prod.yml down + migrate: docker compose exec api alembic upgrade head diff --git a/TODO.md b/TODO.md index 65c0207..a30c327 100644 --- a/TODO.md +++ b/TODO.md @@ -3,15 +3,15 @@ ## High Priority ### Sequence Coverage -- [ ] Expand NCBI ingestion — current query finds only 167/18,805 species. Try broader search terms, search by genus when species fails, increase `--per-species` limit +- [x] Expand NCBI ingestion — broader COI gene search terms (COI/COX1/COXI/CO1 + title variants), genus-level fallback, `--skip-existing` flag - [ ] Retry BOLD portal — `portal.boldsystems.org` has been down since Feb 2026. Check periodically; when it returns, `ingest_bold.py` is ready -- [ ] Add NCBI taxonomy ID lookup — `ncbi_tax_id` column exists but is never populated. Add pipeline step to query NCBI Taxonomy by name and backfill +- [x] Add NCBI taxonomy ID lookup — `backfill_ncbi_tax_id.py` queries NCBI Taxonomy API by scientific name and updates ncbi_tax_id column ### Testing - [x] API route tests — pytest + httpx TestClient for all endpoints (42 tests) - [x] MI distance unit tests — entropy, MI computation, NMI clamping, distance conversion - [x] Pipeline unit tests — canonical selection scoring logic (11 tests) -- [ ] Frontend smoke tests — basic render tests for key pages +- [x] Frontend smoke tests — Jest + React Testing Library, 58 tests across 8 suites (pages, components, API client, utilities) ### Performance - [x] Cache MI network endpoint — in-memory cache with 5-minute TTL @@ -35,8 +35,8 @@ ### Data Quality - [ ] Run `validate.py` and document results — what % of neighbors share genus/family? -- [ ] Flag taxonomic outliers — species whose MI neighbors are in different families -- [ ] Deduplicate sequences — check for identical accessions from multiple sources +- [x] Flag taxonomic outliers — `validate.py` now returns structured `ValidationReport` with `OutlierRecord` objects (cross-family close, within-genus distant), JSON export via `--output` +- [x] Deduplicate sequences — `dedup_sequences.py` removes duplicate accessions, keeping longest per (ott_id, accession, marker) ### DevOps - [x] Add Dockerfile health checks — API (Python urllib), Web (Node fetch), DB (pg_isready), Redis (redis-cli ping) @@ -47,7 +47,7 @@ ## Phase 2 (from ROADMAP.md) ### Scale Across Animalia -- [ ] Make `SCOPE_OTT_ROOT` configurable — support Mammalia, Chordata, etc. +- [x] Make `SCOPE_OTT_ROOT` configurable — env var in docker-compose, `--scope` CLI arg, exposed in `/health` endpoint - [ ] k-mer candidate filtering — replace family-scoped search with ANN index (FAISS/Annoy) for cross-family neighbor detection - [ ] Job queue — replace one-shot scripts with Celery/RQ for background pipeline jobs - [ ] Precompute subtree graph exports for common entry points diff --git a/apps/api/Dockerfile b/apps/api/Dockerfile index 50215dc..251cd3e 100644 --- a/apps/api/Dockerfile +++ b/apps/api/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim +FROM python:3.12-slim AS base WORKDIR /app @@ -13,4 +13,15 @@ ENV PYTHONPATH=/app/src HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 \ CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" || exit 1 +# ── Development (default for docker-compose) ────────── +FROM base AS dev CMD ["uvicorn", "evograph.main:app", "--host", "0.0.0.0", "--port", "8000", "--reload"] + +# ── Production ───────────────────────────────────────── +FROM base AS prod + +RUN groupadd --gid 1000 appuser && \ + useradd --uid 1000 --gid appuser --no-create-home appuser +USER appuser + +CMD ["uvicorn", "evograph.main:app", "--host", "0.0.0.0", "--port", "8000", "--workers", "4", "--log-level", "warning"] diff --git a/apps/api/src/evograph/api/routes/graph.py b/apps/api/src/evograph/api/routes/graph.py index 6118cb7..67b843f 100644 --- a/apps/api/src/evograph/api/routes/graph.py +++ b/apps/api/src/evograph/api/routes/graph.py @@ -2,7 +2,7 @@ import time -from fastapi import APIRouter, Depends, HTTPException, Query +from fastapi import APIRouter, Depends, HTTPException, Query, Response from sqlalchemy import and_, text from sqlalchemy.orm import Session @@ -115,6 +115,7 @@ def get_subtree_graph( @router.get("/graph/mi-network", response_model=GraphResponse) def get_mi_network( + response: Response, db: Session = Depends(get_db), ) -> GraphResponse: """Get the full MI similarity network: all species with MI edges. @@ -128,6 +129,7 @@ def get_mi_network( global _mi_network_cache, _mi_network_cache_time now = time.monotonic() if _mi_network_cache is not None and (now - _mi_network_cache_time) < _MI_NETWORK_TTL: + response.headers["Cache-Control"] = "public, max-age=300" return _mi_network_cache # Get all MI edges @@ -195,6 +197,8 @@ def get_mi_network( result = GraphResponse(nodes=nodes, edges=mi_edges + taxonomy_edges) _mi_network_cache = result _mi_network_cache_time = time.monotonic() + + response.headers["Cache-Control"] = "public, max-age=300" return result diff --git a/apps/api/src/evograph/api/routes/search.py b/apps/api/src/evograph/api/routes/search.py index 51ae357..ae8d672 100644 --- a/apps/api/src/evograph/api/routes/search.py +++ b/apps/api/src/evograph/api/routes/search.py @@ -9,10 +9,10 @@ """ from fastapi import APIRouter, Depends, Query -from sqlalchemy import case +from sqlalchemy import case, func from sqlalchemy.orm import Session -from evograph.api.schemas.taxa import TaxonSummary +from evograph.api.schemas.taxa import SearchPage, TaxonSummary from evograph.db.models import Taxon from evograph.db.session import get_db @@ -24,19 +24,25 @@ def _escape_like(s: str) -> str: return s.replace("\\", "\\\\").replace("%", "\\%").replace("_", "\\_") -@router.get("/search", response_model=list[TaxonSummary]) +@router.get("/search", response_model=SearchPage) def search_taxa( q: str = Query(..., min_length=1), limit: int = Query(20, le=100), db: Session = Depends(get_db), -) -> list[TaxonSummary]: +) -> SearchPage: """Search taxa by name (case-insensitive substring match). Uses pg_trgm GIN index for fast ILIKE on large tables. Results prioritize prefix matches over substring matches. + Returns paginated response with total count. """ escaped = _escape_like(q) + base_filter = Taxon.name.ilike(f"%{escaped}%") + + # Total matching count (for client to know if there are more results) + total = db.query(func.count(Taxon.ott_id)).filter(base_filter).scalar() or 0 + # Prefix matches rank first (sort_key=0), substring matches second (sort_key=1) prefix_case = case( (Taxon.name.ilike(f"{escaped}%"), 0), @@ -45,11 +51,15 @@ def search_taxa( rows = ( db.query(Taxon) - .filter(Taxon.name.ilike(f"%{escaped}%")) + .filter(base_filter) .order_by(prefix_case, Taxon.name) .limit(limit) .all() ) - return [ - TaxonSummary(ott_id=t.ott_id, name=t.name, rank=t.rank) for t in rows - ] + return SearchPage( + items=[ + TaxonSummary(ott_id=t.ott_id, name=t.name, rank=t.rank) for t in rows + ], + total=total, + limit=limit, + ) diff --git a/apps/api/src/evograph/api/routes/sequences.py b/apps/api/src/evograph/api/routes/sequences.py index 587f902..6fba0ba 100644 --- a/apps/api/src/evograph/api/routes/sequences.py +++ b/apps/api/src/evograph/api/routes/sequences.py @@ -1,42 +1,58 @@ """Sequence endpoints for a taxon.""" -from fastapi import APIRouter, Depends, HTTPException +from fastapi import APIRouter, Depends, HTTPException, Query +from sqlalchemy import func from sqlalchemy.orm import Session -from evograph.api.schemas.sequence import SequenceOut +from evograph.api.schemas.sequence import SequenceOut, SequencePage from evograph.db.models import Sequence, Taxon from evograph.db.session import get_db router = APIRouter(tags=["sequences"]) -@router.get("/taxa/{ott_id}/sequences", response_model=list[SequenceOut]) +@router.get("/taxa/{ott_id}/sequences", response_model=SequencePage) def get_sequences( ott_id: int, + offset: int = Query(0, ge=0), + limit: int = Query(50, ge=1, le=200), db: Session = Depends(get_db), -) -> list[SequenceOut]: - """Get all sequences for a taxon.""" +) -> SequencePage: + """Get paginated sequences for a taxon.""" taxon = db.query(Taxon).filter(Taxon.ott_id == ott_id).first() if taxon is None: raise HTTPException(status_code=404, detail="Taxon not found") + total = ( + db.query(func.count(Sequence.id)) + .filter(Sequence.ott_id == ott_id) + .scalar() + ) or 0 + rows = ( db.query(Sequence) .filter(Sequence.ott_id == ott_id) .order_by(Sequence.is_canonical.desc(), Sequence.retrieved_at.desc()) + .offset(offset) + .limit(limit) .all() ) - return [ - SequenceOut( - id=str(s.id), - ott_id=s.ott_id, - marker=s.marker, - source=s.source, - accession=s.accession, - sequence=s.sequence, - length=s.length, - is_canonical=s.is_canonical, - retrieved_at=s.retrieved_at, - ) - for s in rows - ] + return SequencePage( + items=[ + SequenceOut( + id=str(s.id), + ott_id=s.ott_id, + marker=s.marker, + source=s.source, + accession=s.accession, + sequence=s.sequence, + length=s.length, + is_canonical=s.is_canonical, + retrieved_at=s.retrieved_at, + ) + for s in rows + ], + total=total, + offset=offset, + limit=limit, + ) diff --git a/apps/api/src/evograph/api/routes/stats.py b/apps/api/src/evograph/api/routes/stats.py new file mode 100644 index 0000000..a4870f9 --- /dev/null +++ b/apps/api/src/evograph/api/routes/stats.py @@ -0,0 +1,87 @@ +"""Stats endpoint for observability — database counts and data quality overview.""" + +from fastapi import APIRouter, Depends +from fastapi.responses import JSONResponse +from sqlalchemy import func +from sqlalchemy.orm import Session + +from evograph.db.models import Edge, Sequence, Taxon +from evograph.db.session import get_db + +router = APIRouter(tags=["stats"]) + + +@router.get("/stats") +def get_stats(db: Session = Depends(get_db)): + """Return summary statistics about the database contents. + + Includes: + - Total taxa count and breakdown by rank + - Total sequences and breakdown by source/marker + - Total MI edges with distance summary + - Species with/without sequences + """ + # Taxa by rank + rank_counts = ( + db.query(Taxon.rank, func.count()) + .group_by(Taxon.rank) + .order_by(func.count().desc()) + .all() + ) + + total_taxa = sum(c for _, c in rank_counts) + + # Sequences by source + seq_by_source = ( + db.query(Sequence.source, func.count()) + .group_by(Sequence.source) + .all() + ) + total_sequences = sum(c for _, c in seq_by_source) + + # Species with at least one sequence + species_with_seqs = ( + db.query(func.count(func.distinct(Sequence.ott_id))) + .scalar() + ) or 0 + + total_species = next( + (c for r, c in rank_counts if r == "species"), 0 + ) + + # Edge stats + total_edges = db.query(func.count()).select_from(Edge).scalar() or 0 + distance_stats = None + if total_edges > 0: + row = db.query( + func.min(Edge.distance), + func.max(Edge.distance), + func.avg(Edge.distance), + ).one() + distance_stats = { + "min": round(float(row[0]), 4) if row[0] is not None else None, + "max": round(float(row[1]), 4) if row[1] is not None else None, + "avg": round(float(row[2]), 4) if row[2] is not None else None, + } + + data = { + "taxa": { + "total": total_taxa, + "by_rank": {rank: count for rank, count in rank_counts}, + }, + "sequences": { + "total": total_sequences, + "by_source": {source: count for source, count in seq_by_source}, + "species_with_sequences": species_with_seqs, + "species_total": total_species, + "coverage_pct": ( + round(100.0 * species_with_seqs / total_species, 1) + if total_species > 0 else 0.0 + ), + }, + "edges": { + "total": total_edges, + "distance": distance_stats, + }, + } + return JSONResponse(content=data, headers={"Cache-Control": "public, max-age=60"}) diff --git a/apps/api/src/evograph/api/schemas/sequence.py b/apps/api/src/evograph/api/schemas/sequence.py index 9c0ad50..c09a244 100644 --- a/apps/api/src/evograph/api/schemas/sequence.py +++ b/apps/api/src/evograph/api/schemas/sequence.py @@ -1,6 +1,8 @@ -from pydantic import BaseModel from datetime import datetime +from pydantic import BaseModel + + class SequenceOut(BaseModel): id: str ott_id: int @@ -11,3 +13,10 @@ class SequenceOut(BaseModel): length: int is_canonical: bool retrieved_at: datetime | None = None + + +class SequencePage(BaseModel): + items: list[SequenceOut] + total: int + offset: int + limit: int diff --git a/apps/api/src/evograph/api/schemas/taxa.py b/apps/api/src/evograph/api/schemas/taxa.py index 992391f..cbd53ab 100644 --- a/apps/api/src/evograph/api/schemas/taxa.py +++ b/apps/api/src/evograph/api/schemas/taxa.py @@ -29,3 +29,9 @@ class ChildrenPage(BaseModel): total: int offset: int limit: int + + +class SearchPage(BaseModel): + items: list[TaxonSummary] + total: int + limit: int diff --git a/apps/api/src/evograph/logging_config.py b/apps/api/src/evograph/logging_config.py new file mode 100644 index 0000000..6a53957 --- /dev/null +++ b/apps/api/src/evograph/logging_config.py @@ -0,0 +1,56 @@ +"""Logging configuration for EvoGraph API. + +Supports two output formats: +- text: Human-readable format for development +- json: Structured JSON format for production log aggregators (ELK, Datadog, etc.) + +Configured via LOG_LEVEL and LOG_FORMAT environment variables. +""" + +from __future__ import annotations + +import json +import logging +from datetime import datetime, timezone + +from evograph.settings import settings + + +class JSONFormatter(logging.Formatter): + """Format log records as single-line JSON objects.""" + + def format(self, record: logging.LogRecord) -> str: + log_entry = { + "timestamp": datetime.now(timezone.utc).isoformat(), + "level": record.levelname, + "logger": record.name, + "message": record.getMessage(), + } + if record.exc_info and record.exc_info[0] is not None: + log_entry["exception"] = self.formatException(record.exc_info) + return json.dumps(log_entry) + + +def configure_logging() -> None: + """Set up root logger based on application settings.""" + level = getattr(logging, settings.log_level.upper()) + + if settings.log_format == "json": + handler = logging.StreamHandler() + handler.setFormatter(JSONFormatter()) + else: + handler = logging.StreamHandler() + handler.setFormatter( + logging.Formatter("%(asctime)s %(levelname)-8s %(name)s — %(message)s") + ) + + # Configure root logger + root = logging.getLogger() + root.setLevel(level) + # Remove existing handlers to avoid duplicates on reloads + root.handlers.clear() + root.addHandler(handler) + + # Quiet noisy third-party loggers + logging.getLogger("uvicorn.access").setLevel(logging.WARNING) + logging.getLogger("sqlalchemy.engine").setLevel(logging.WARNING) diff --git a/apps/api/src/evograph/main.py b/apps/api/src/evograph/main.py index 1f37113..d89869d 100644 --- a/apps/api/src/evograph/main.py +++ b/apps/api/src/evograph/main.py @@ -1,17 +1,55 @@ +import logging +from contextlib import asynccontextmanager + from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware from fastapi.middleware.gzip import GZipMiddleware +from sqlalchemy import text + +from evograph.api.routes import graph, search, sequences, stats, taxa +from evograph.db.session import SessionLocal, engine +from evograph.logging_config import configure_logging +from evograph.middleware.rate_limit import RateLimitMiddleware +from evograph.middleware.request_logging import RequestLoggingMiddleware +from evograph.middleware.security_headers import SecurityHeadersMiddleware +from evograph.settings import settings + +configure_logging() +logger = logging.getLogger("evograph") + + +@asynccontextmanager +async def lifespan(app: FastAPI): + """Startup/shutdown lifecycle for the application. + + Ensures database connection pool is properly disposed on shutdown, + preventing connection leaks in orchestrated deployments. + """ + logger.info("EvoGraph API starting up (scope=%s)", settings.scope_ott_root) + yield + logger.info("EvoGraph API shutting down — disposing connection pool") + engine.dispose() + -from evograph.api.routes import graph, search, sequences, taxa +app = FastAPI(title="EvoGraph MVP", version="0.1.0", lifespan=lifespan) -app = FastAPI(title="EvoGraph MVP", version="0.1.0") +# Middleware stack (order matters: outermost runs first) +# 1. Request logging — logs every request with method, path, status, duration +app.add_middleware(RequestLoggingMiddleware) -# GZip responses > 500 bytes — critical for graph endpoints with large JSON payloads +# 2. GZip responses > 500 bytes — critical for graph endpoints with large JSON payloads app.add_middleware(GZipMiddleware, minimum_size=500) +# 3. Rate limiting: 100 requests/minute per IP (excludes /health, /docs) +app.add_middleware(RateLimitMiddleware, max_requests=100, window_seconds=60) + +# 4. Security headers — X-Content-Type-Options, X-Frame-Options, etc. +app.add_middleware(SecurityHeadersMiddleware) + +# 5. CORS — configurable origins (default: allow all for dev) app.add_middleware( CORSMiddleware, - allow_origins=["*"], + allow_origins=settings.cors_origins, allow_credentials=True, allow_methods=["*"], allow_headers=["*"], @@ -21,8 +59,42 @@ app.include_router(taxa.router, prefix="/v1") app.include_router(graph.router, prefix="/v1") app.include_router(sequences.router, prefix="/v1") +app.include_router(stats.router, prefix="/v1") @app.get("/health") def health(): - return {"status": "ok"} + """Basic liveness check.""" + return {"status": "ok", "scope": settings.scope_ott_root} + + +@app.get("/health/ready") +def readiness(): + """Readiness check — verifies database connectivity and reports pool stats. + + Use for Kubernetes readinessProbe or load balancer health checks. + Returns pool size, checked-in/out connections, and overflow count. + """ + # Verify DB is reachable + try: + db = SessionLocal() + db.execute(text("SELECT 1")) + db.close() + db_ok = True + except Exception: + db_ok = False + + pool = engine.pool + status = "ok" if db_ok else "degraded" + + return { + "status": status, + "scope": settings.scope_ott_root, + "database": { + "connected": db_ok, + "pool_size": pool.size(), + "checked_in": pool.checkedin(), + "checked_out": pool.checkedout(), + "overflow": pool.overflow(), + }, + } diff --git a/apps/api/src/evograph/middleware/__init__.py b/apps/api/src/evograph/middleware/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/api/src/evograph/middleware/rate_limit.py b/apps/api/src/evograph/middleware/rate_limit.py new file mode 100644 index 0000000..80250d6 --- /dev/null +++ b/apps/api/src/evograph/middleware/rate_limit.py @@ -0,0 +1,95 @@ +"""Sliding-window rate limiting middleware. + +Simple in-memory rate limiter suitable for single-instance deployment. +For multi-instance, swap to Redis-backed (SCOPE_OTT_ROOT already has Redis URL configured). + +Limits by client IP address. Returns 429 with Retry-After header when exceeded. +""" + +from __future__ import annotations + +import time +from collections import defaultdict + +from starlette.middleware.base import BaseHTTPMiddleware +from starlette.requests import Request +from starlette.responses import JSONResponse + + +class RateLimitMiddleware(BaseHTTPMiddleware): + """Per-IP sliding window rate limiter. + + Args: + app: The ASGI application. + max_requests: Maximum requests per window. + window_seconds: Window duration in seconds. + exclude_paths: Paths to exclude from rate limiting (e.g. health checks). + """ + + def __init__( + self, + app, + max_requests: int = 100, + window_seconds: int = 60, + exclude_paths: tuple[str, ...] = ("/health", "/docs", "/openapi.json"), + ): + super().__init__(app) + self.max_requests = max_requests + self.window_seconds = window_seconds + self.exclude_paths = exclude_paths + # {ip: [timestamp, timestamp, ...]} + self._hits: dict[str, list[float]] = defaultdict(list) + self._last_cleanup = time.monotonic() + self._cleanup_interval = 300.0 # clean up stale entries every 5 min + + def _get_client_ip(self, request: Request) -> str: + """Extract client IP, respecting X-Forwarded-For behind a proxy.""" + forwarded = request.headers.get("x-forwarded-for") + if forwarded: + return forwarded.split(",")[0].strip() + return request.client.host if request.client else "unknown" + + def _cleanup_stale(self, now: float) -> None: + """Remove entries for IPs that haven't been seen recently.""" + if now - self._last_cleanup < self._cleanup_interval: + return + self._last_cleanup = now + cutoff = now - self.window_seconds * 2 + stale_keys = [ip for ip, hits in self._hits.items() if not hits or hits[-1] < cutoff] + for key in stale_keys: + del self._hits[key] + + async def dispatch(self, request: Request, call_next): + # Skip excluded paths + if request.url.path in self.exclude_paths: + return await call_next(request) + + now = time.monotonic() + self._cleanup_stale(now) + + ip = self._get_client_ip(request) + window_start = now - self.window_seconds + + # Trim old hits outside the window + hits = self._hits[ip] + while hits and hits[0] < window_start: + hits.pop(0) + + if len(hits) >= self.max_requests: + retry_after = int(hits[0] - window_start) + 1 + return JSONResponse( + status_code=429, + content={"detail": "Too many requests"}, + headers={ + "Retry-After": str(retry_after), + "X-RateLimit-Limit": str(self.max_requests), + "X-RateLimit-Remaining": "0", + }, + ) + + hits.append(now) + + response = await call_next(request) + response.headers["X-RateLimit-Limit"] = str(self.max_requests) + response.headers["X-RateLimit-Remaining"] = str(self.max_requests - len(hits)) + return response diff --git a/apps/api/src/evograph/middleware/request_logging.py b/apps/api/src/evograph/middleware/request_logging.py new file mode 100644 index 0000000..a98c16f --- /dev/null +++ b/apps/api/src/evograph/middleware/request_logging.py @@ -0,0 +1,46 @@ +"""Structured request logging middleware. + +Logs each request with method, path, status code, duration, and client IP. +Uses Python's standard logging — can be forwarded to any log aggregator. +""" + +from __future__ import annotations + +import logging +import time +import uuid + +from starlette.middleware.base import BaseHTTPMiddleware +from starlette.requests import Request + +logger = logging.getLogger("evograph.access") + + +class RequestLoggingMiddleware(BaseHTTPMiddleware): + """Log every request with structured fields.""" + + async def dispatch(self, request: Request, call_next): + request_id = str(uuid.uuid4())[:8] + start = time.monotonic() + + # Attach request ID to response headers for tracing + response = await call_next(request) + duration_ms = (time.monotonic() - start) * 1000 + + forwarded = request.headers.get("x-forwarded-for") + client_ip = forwarded.split(",")[0].strip() if forwarded else ( + request.client.host if request.client else "unknown" + ) + + logger.info( + "%s %s %d %.1fms client=%s req=%s", + request.method, + request.url.path, + response.status_code, + duration_ms, + client_ip, + request_id, + ) + + response.headers["X-Request-ID"] = request_id + return response diff --git a/apps/api/src/evograph/middleware/security_headers.py b/apps/api/src/evograph/middleware/security_headers.py new file mode 100644 index 0000000..a946de8 --- /dev/null +++ b/apps/api/src/evograph/middleware/security_headers.py @@ -0,0 +1,29 @@ +"""Security headers middleware. + +Adds standard security headers to all responses. These headers protect against +common web vulnerabilities (XSS, clickjacking, MIME-sniffing, etc.). + +References: +- https://owasp.org/www-project-secure-headers/ +- https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers +""" + +from __future__ import annotations + +from starlette.middleware.base import BaseHTTPMiddleware +from starlette.requests import Request + + +class SecurityHeadersMiddleware(BaseHTTPMiddleware): + """Add security headers to all responses.""" + + async def dispatch(self, request: Request, call_next): + response = await call_next(request) + + response.headers["X-Content-Type-Options"] = "nosniff" + response.headers["X-Frame-Options"] = "DENY" + response.headers["X-XSS-Protection"] = "1; mode=block" + response.headers["Referrer-Policy"] = "strict-origin-when-cross-origin" + response.headers["Permissions-Policy"] = "camera=(), microphone=(), geolocation=()" + + return response diff --git a/apps/api/src/evograph/pipeline/backfill_ncbi_tax_id.py b/apps/api/src/evograph/pipeline/backfill_ncbi_tax_id.py new file mode 100644 index 0000000..bb3c4f8 --- /dev/null +++ b/apps/api/src/evograph/pipeline/backfill_ncbi_tax_id.py @@ -0,0 +1,133 @@ +"""Backfill ncbi_tax_id for taxa in the database. + +Queries the NCBI Taxonomy E-utilities API to resolve species/genus names +to NCBI taxonomy IDs and updates the taxa table. + +Run as: python -m evograph.pipeline.backfill_ncbi_tax_id [--limit N] [--batch N] +""" + +from __future__ import annotations + +import argparse +import asyncio +import logging + +import httpx +from sqlalchemy import select, update + +from evograph.db.models import Taxon +from evograph.db.session import SessionLocal + +logger = logging.getLogger(__name__) + +NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" + + +async def _lookup_tax_id( + client: httpx.AsyncClient, name: str +) -> int | None: + """Look up NCBI taxonomy ID for a given taxon name. + + Uses esearch against the NCBI Taxonomy database. + Returns the taxonomy ID if exactly one match is found, else None. + """ + resp = await client.get( + f"{NCBI_BASE}/esearch.fcgi", + params={ + "db": "taxonomy", + "term": f'"{name}"[Scientific Name]', + "retmode": "json", + }, + ) + resp.raise_for_status() + data = resp.json() + id_list = data.get("esearchresult", {}).get("idlist", []) + + if len(id_list) == 1: + return int(id_list[0]) + return None + + +async def backfill(limit: int | None = None, batch_size: int = 50) -> None: + """Look up and backfill ncbi_tax_id for taxa that don't have one.""" + session = SessionLocal() + + try: + # Find taxa without ncbi_tax_id + stmt = ( + select(Taxon) + .where(Taxon.ncbi_tax_id.is_(None)) + .order_by(Taxon.ott_id) + ) + if limit is not None: + stmt = stmt.limit(limit) + + taxa = session.execute(stmt).scalars().all() + logger.info("Found %d taxa without ncbi_tax_id", len(taxa)) + + if not taxa: + return + + resolved = 0 + failed = 0 + + async with httpx.AsyncClient(timeout=30, follow_redirects=True) as client: + for i, taxon in enumerate(taxa): + try: + tax_id = await _lookup_tax_id(client, taxon.name) + + if tax_id is not None: + session.execute( + update(Taxon) + .where(Taxon.ott_id == taxon.ott_id) + .values(ncbi_tax_id=tax_id) + ) + resolved += 1 + + if (i + 1) % batch_size == 0: + session.commit() + logger.info( + " [%d/%d] Resolved %d, failed %d", + i + 1, len(taxa), resolved, failed, + ) + + except Exception: + failed += 1 + logger.exception( + " Error looking up %s (ott_id=%d)", taxon.name, taxon.ott_id + ) + + # NCBI rate limit: max 3 requests/second without API key + await asyncio.sleep(0.4) + + session.commit() + logger.info( + "Backfill complete: %d resolved, %d failed, %d total", + resolved, failed, len(taxa), + ) + + finally: + session.close() + + +def main() -> None: + parser = argparse.ArgumentParser(description="Backfill NCBI taxonomy IDs") + parser.add_argument( + "--limit", type=int, default=None, + help="Max number of taxa to process", + ) + parser.add_argument( + "--batch", type=int, default=50, + help="Commit after every N lookups (default: 50)", + ) + args = parser.parse_args() + + logging.basicConfig( + level=logging.INFO, + format="%(asctime)s %(levelname)s %(name)s: %(message)s", + ) + asyncio.run(backfill(limit=args.limit, batch_size=args.batch)) + + +if __name__ == "__main__": + main() diff --git a/apps/api/src/evograph/pipeline/dedup_sequences.py b/apps/api/src/evograph/pipeline/dedup_sequences.py new file mode 100644 index 0000000..3ecdd7b --- /dev/null +++ b/apps/api/src/evograph/pipeline/dedup_sequences.py @@ -0,0 +1,117 @@ +"""Deduplicate sequences by accession. + +When the same accession appears multiple times (e.g., from multiple ingestion +runs or overlapping genus-level fetches), keep only the longest sequence per +(ott_id, accession, marker) tuple and remove the rest. + +Run as: python -m evograph.pipeline.dedup_sequences [--dry-run] +""" + +from __future__ import annotations + +import argparse +import logging + +from sqlalchemy import delete, func, select + +from evograph.db.models import Sequence +from evograph.db.session import SessionLocal + +logger = logging.getLogger(__name__) + + +def find_duplicates(session) -> list[tuple[int, str, str, int]]: + """Find (ott_id, accession, marker) tuples with duplicate entries. + + Returns list of (ott_id, accession, marker, count) tuples. + """ + stmt = ( + select( + Sequence.ott_id, + Sequence.accession, + Sequence.marker, + func.count().label("cnt"), + ) + .group_by(Sequence.ott_id, Sequence.accession, Sequence.marker) + .having(func.count() > 1) + ) + return session.execute(stmt).all() + + +def dedup_sequences(dry_run: bool = False) -> None: + """Remove duplicate sequences, keeping the longest per (ott_id, accession, marker).""" + session = SessionLocal() + + try: + dupes = find_duplicates(session) + logger.info("Found %d (ott_id, accession, marker) groups with duplicates", len(dupes)) + + if not dupes: + logger.info("No duplicates found. Nothing to do.") + return + + total_removed = 0 + for ott_id, accession, marker, cnt in dupes: + # Get all sequences for this tuple, ordered by length desc + seqs = ( + session.execute( + select(Sequence) + .where( + Sequence.ott_id == ott_id, + Sequence.accession == accession, + Sequence.marker == marker, + ) + .order_by(Sequence.length.desc()) + ) + .scalars() + .all() + ) + + # Keep the first (longest), remove the rest + keep = seqs[0] + to_remove = seqs[1:] + + if dry_run: + logger.info( + " [DRY RUN] ott_id=%d accession=%s: keep id=%s (len=%d), " + "would remove %d duplicates", + ott_id, accession, keep.id, keep.length, len(to_remove), + ) + else: + ids_to_delete = [s.id for s in to_remove] + session.execute( + delete(Sequence).where(Sequence.id.in_(ids_to_delete)) + ) + total_removed += len(to_remove) + + if not dry_run: + session.commit() + + logger.info( + "Deduplication complete. %s %d duplicate sequences from %d groups.", + "Would remove" if dry_run else "Removed", + total_removed if not dry_run else sum(c - 1 for _, _, _, c in dupes), + len(dupes), + ) + + finally: + session.close() + + +def main() -> None: + parser = argparse.ArgumentParser(description="Deduplicate sequences by accession") + parser.add_argument( + "--dry-run", action="store_true", + help="Report duplicates without removing them", + ) + args = parser.parse_args() + + logging.basicConfig( + level=logging.INFO, + format="%(asctime)s %(levelname)s %(name)s: %(message)s", + ) + dedup_sequences(dry_run=args.dry_run) + + +if __name__ == "__main__": + main() diff --git a/apps/api/src/evograph/pipeline/ingest_ncbi.py b/apps/api/src/evograph/pipeline/ingest_ncbi.py index 30311dd..9fbb9a2 100644 --- a/apps/api/src/evograph/pipeline/ingest_ncbi.py +++ b/apps/api/src/evograph/pipeline/ingest_ncbi.py @@ -2,7 +2,11 @@ Uses NCBI E-utilities (esearch + efetch) as a fallback when BOLD is unavailable. -Run as: python -m evograph.pipeline.ingest_ncbi [--limit N] [--per-species N] +Search strategy (tiered fallback): +1. Species-level search with broad COI gene name variants +2. Genus-level search if species-level finds nothing + +Run as: python -m evograph.pipeline.ingest_ncbi [--limit N] [--per-species N] [--skip-existing] """ from __future__ import annotations @@ -27,14 +31,30 @@ MIN_SEQ_LEN = 400 MAX_PER_SPECIES = 5 +# Broader COI gene search terms — many GenBank entries use different annotations +_COI_TERMS = ( + 'COI[Gene] OR COX1[Gene] OR COXI[Gene] OR CO1[Gene] ' + 'OR "cytochrome oxidase subunit I"[Title] ' + 'OR "cytochrome oxidase subunit 1"[Title] ' + 'OR "cytochrome c oxidase subunit I"[Title] ' + 'OR "cytochrome c oxidase subunit 1"[Title] ' + 'OR "COI"[Title]' +) + + +def _build_query(organism: str) -> str: + """Build NCBI esearch query for COI sequences of a given organism.""" + return ( + f'"{organism}"[Organism] AND ({_COI_TERMS}) ' + f'AND 400:2000[Sequence Length]' + ) -async def _fetch_coi_sequences( - client: httpx.AsyncClient, species_name: str, max_seqs: int = MAX_PER_SPECIES -) -> list[dict]: - """Fetch COI sequences for a species from NCBI GenBank.""" - # Search for COI/COX1 sequences - query = f'"{species_name}"[Organism] AND (COI[Gene] OR COX1[Gene] OR "cytochrome oxidase subunit I"[Title]) AND 400:2000[Sequence Length]' - search_resp = await client.get( + +async def _esearch( + client: httpx.AsyncClient, query: str, max_seqs: int +) -> list[str]: + """Run NCBI esearch and return list of GI/accession IDs.""" + resp = await client.get( f"{NCBI_BASE}/esearch.fcgi", params={ "db": "nucleotide", @@ -43,15 +63,16 @@ async def _fetch_coi_sequences( "retmode": "json", }, ) - search_resp.raise_for_status() - search_data = search_resp.json() - id_list = search_data.get("esearchresult", {}).get("idlist", []) + resp.raise_for_status() + data = resp.json() + return data.get("esearchresult", {}).get("idlist", []) - if not id_list: - return [] - # Fetch sequences in FASTA format - fetch_resp = await client.get( +async def _efetch_fasta( + client: httpx.AsyncClient, id_list: list[str] +) -> list[dict]: + """Fetch sequences in FASTA format and parse them.""" + resp = await client.get( f"{NCBI_BASE}/efetch.fcgi", params={ "db": "nucleotide", @@ -60,14 +81,13 @@ async def _fetch_coi_sequences( "retmode": "text", }, ) - fetch_resp.raise_for_status() + resp.raise_for_status() - # Parse FASTA records = [] current_header = None current_seq_parts: list[str] = [] - for line in fetch_resp.text.split("\n"): + for line in resp.text.split("\n"): line = line.strip() if line.startswith(">"): if current_header and current_seq_parts: @@ -83,28 +103,89 @@ async def _fetch_coi_sequences( return records -async def ingest(limit: int | None = None, per_species: int = MAX_PER_SPECIES) -> None: +async def _fetch_coi_sequences( + client: httpx.AsyncClient, + species_name: str, + max_seqs: int = MAX_PER_SPECIES, + genus_fallback: bool = True, +) -> list[dict]: + """Fetch COI sequences with tiered search strategy. + + 1. Search by exact species name + 2. If no results and genus_fallback=True, search by genus name + """ + # Tier 1: species-level search + query = _build_query(species_name) + id_list = await _esearch(client, query, max_seqs) + + # Tier 2: genus-level fallback + if not id_list and genus_fallback: + parts = species_name.split() + if len(parts) >= 2: + genus = parts[0] + # NCBI rate limit pause before second request + await asyncio.sleep(0.4) + query = _build_query(genus) + id_list = await _esearch(client, query, max_seqs) + if id_list: + logger.debug( + " Genus fallback for %s → found %d via genus %s", + species_name, len(id_list), genus, + ) + + if not id_list: + return [] + + # NCBI rate limit pause before fetch + await asyncio.sleep(0.4) + return await _efetch_fasta(client, id_list) + + +async def ingest( + limit: int | None = None, + per_species: int = MAX_PER_SPECIES, + skip_existing: bool = False, + genus_fallback: bool = True, +) -> None: """Run the NCBI COI ingestion pipeline.""" session = SessionLocal() try: stmt = select(Taxon).where(Taxon.rank == "species") + + if skip_existing: + # Subquery: species that already have sequences + has_seqs = ( + select(Sequence.ott_id) + .where(Sequence.source == "NCBI", Sequence.marker == "COI") + .distinct() + .subquery() + ) + stmt = stmt.where(Taxon.ott_id.notin_(select(has_seqs.c.ott_id))) + if limit is not None: stmt = stmt.limit(limit) + taxa = session.execute(stmt).scalars().all() logger.info("Found %d species-rank taxa to process", len(taxa)) total_stored = 0 + species_with_seqs = 0 + async with httpx.AsyncClient(timeout=30, follow_redirects=True) as client: for i, taxon in enumerate(taxa): try: if (i + 1) % 50 == 0 or i == 0: logger.info( - "[%d/%d] Fetching NCBI sequences for %s (ott_id=%d)", + "[%d/%d] Fetching NCBI sequences for %s (ott_id=%d) " + "[stored=%d, species_covered=%d]", i + 1, len(taxa), taxon.name, taxon.ott_id, + total_stored, species_with_seqs, ) - records = await _fetch_coi_sequences(client, taxon.name, per_species) + records = await _fetch_coi_sequences( + client, taxon.name, per_species, genus_fallback + ) count = 0 for rec in records: @@ -134,6 +215,8 @@ async def ingest(limit: int | None = None, per_species: int = MAX_PER_SPECIES) - session.commit() total_stored += count + if count > 0: + species_with_seqs += 1 except Exception: session.rollback() @@ -144,7 +227,10 @@ async def ingest(limit: int | None = None, per_species: int = MAX_PER_SPECIES) - # NCBI rate limit: max 3 requests/second without API key await asyncio.sleep(0.4) - logger.info("NCBI ingestion complete. Total sequences stored: %d", total_stored) + logger.info( + "NCBI ingestion complete. Sequences stored: %d, species covered: %d/%d", + total_stored, species_with_seqs, len(taxa), + ) finally: session.close() @@ -152,15 +238,34 @@ async def ingest(limit: int | None = None, per_species: int = MAX_PER_SPECIES) - def main() -> None: parser = argparse.ArgumentParser(description="Ingest NCBI COI sequences") - parser.add_argument("--limit", type=int, default=None, help="Max number of taxa to process") - parser.add_argument("--per-species", type=int, default=MAX_PER_SPECIES, help="Max sequences per species") + parser.add_argument( + "--limit", type=int, default=None, + help="Max number of taxa to process", + ) + parser.add_argument( + "--per-species", type=int, default=MAX_PER_SPECIES, + help="Max sequences per species (default: 5)", + ) + parser.add_argument( + "--skip-existing", action="store_true", + help="Skip species that already have NCBI COI sequences", + ) + parser.add_argument( + "--no-genus-fallback", action="store_true", + help="Disable genus-level fallback when species search fails", + ) args = parser.parse_args() logging.basicConfig( level=logging.INFO, format="%(asctime)s %(levelname)s %(name)s: %(message)s", ) - asyncio.run(ingest(limit=args.limit, per_species=args.per_species)) + asyncio.run(ingest( + limit=args.limit, + per_species=args.per_species, + skip_existing=args.skip_existing, + genus_fallback=not args.no_genus_fallback, + )) if __name__ == "__main__": diff --git a/apps/api/src/evograph/pipeline/ingest_ott.py b/apps/api/src/evograph/pipeline/ingest_ott.py index 6aa5fae..237f679 100644 --- a/apps/api/src/evograph/pipeline/ingest_ott.py +++ b/apps/api/src/evograph/pipeline/ingest_ott.py @@ -1,10 +1,11 @@ """Ingest OpenTree taxonomy for a configurable scope (default: Aves). -Run as: python -m evograph.pipeline.ingest_ott +Run as: python -m evograph.pipeline.ingest_ott [--scope Mammalia] """ from __future__ import annotations +import argparse import asyncio import logging import re @@ -249,9 +250,20 @@ async def ingest(scope: str | None = None) -> None: logger.info("Ingested %d taxa for scope '%s'", count, scope) -if __name__ == "__main__": +def main() -> None: + parser = argparse.ArgumentParser(description="Ingest OpenTree taxonomy") + parser.add_argument( + "--scope", type=str, default=None, + help="Root taxon name (default: from SCOPE_OTT_ROOT env or 'Aves')", + ) + args = parser.parse_args() + logging.basicConfig( level=logging.INFO, format="%(asctime)s %(levelname)s %(name)s: %(message)s", ) - asyncio.run(ingest()) + asyncio.run(ingest(scope=args.scope)) + + +if __name__ == "__main__": + main() diff --git a/apps/api/src/evograph/pipeline/validate.py b/apps/api/src/evograph/pipeline/validate.py index def1d10..d7efa34 100644 --- a/apps/api/src/evograph/pipeline/validate.py +++ b/apps/api/src/evograph/pipeline/validate.py @@ -3,15 +3,18 @@ - % of MI-neighbors sharing genus - % sharing family - Distance distribution stats -- Outlier flagging +- Outlier flagging (cross-family close neighbors, within-genus distant pairs) -Run as: python -m evograph.pipeline.validate +Run as: python -m evograph.pipeline.validate [--output report.json] """ from __future__ import annotations +import argparse +import json import logging import statistics +from dataclasses import dataclass, field from sqlalchemy import select @@ -21,6 +24,77 @@ logger = logging.getLogger(__name__) +@dataclass +class OutlierRecord: + """A single outlier edge with context.""" + + src_ott_id: int + src_name: str + dst_ott_id: int + dst_name: str + distance: float + reason: str # "cross_family_close" or "within_genus_distant" + + +@dataclass +class ValidationReport: + """Structured validation results.""" + + total_edges: int = 0 + same_genus_count: int = 0 + same_family_count: int = 0 + same_genus_pct: float = 0.0 + same_family_pct: float = 0.0 + distance_min: float = 0.0 + distance_max: float = 0.0 + distance_mean: float = 0.0 + distance_median: float = 0.0 + distance_stdev: float | None = None + outliers: list[OutlierRecord] = field(default_factory=list) + + def to_dict(self) -> dict: + return { + "total_edges": self.total_edges, + "taxonomy_coherence": { + "same_genus": self.same_genus_count, + "same_family": self.same_family_count, + "same_genus_pct": round(self.same_genus_pct, 2), + "same_family_pct": round(self.same_family_pct, 2), + }, + "distance_distribution": { + "min": round(self.distance_min, 4), + "max": round(self.distance_max, 4), + "mean": round(self.distance_mean, 4), + "median": round(self.distance_median, 4), + "stdev": round(self.distance_stdev, 4) if self.distance_stdev is not None else None, + }, + "outliers": { + "cross_family_close": [ + { + "src_ott_id": o.src_ott_id, + "src_name": o.src_name, + "dst_ott_id": o.dst_ott_id, + "dst_name": o.dst_name, + "distance": round(o.distance, 4), + } + for o in self.outliers + if o.reason == "cross_family_close" + ], + "within_genus_distant": [ + { + "src_ott_id": o.src_ott_id, + "src_name": o.src_name, + "dst_ott_id": o.dst_ott_id, + "dst_name": o.dst_name, + "distance": round(o.distance, 4), + } + for o in self.outliers + if o.reason == "within_genus_distant" + ], + }, + } + + def _walk_to_rank( ott_id: int, target_rank: str, taxa_by_id: dict[int, Taxon] ) -> int | None: @@ -43,131 +117,177 @@ def _walk_to_rank( return None -def validate() -> None: - """Run all validation checks and print results.""" +def compute_validation_report(session) -> ValidationReport | None: + """Compute validation report from the database. + + Returns a ValidationReport, or None if no edges exist. + """ + all_taxa = session.execute(select(Taxon)).scalars().all() + taxa_by_id = {t.ott_id: t for t in all_taxa} + logger.info("Loaded %d taxa", len(taxa_by_id)) + + edges = session.execute(select(Edge)).scalars().all() + logger.info("Loaded %d edges", len(edges)) + + if not edges: + return None + + # Build genus/family lookup for each species + genus_of: dict[int, int | None] = {} + family_of: dict[int, int | None] = {} + + relevant_ids = set() + for e in edges: + relevant_ids.add(e.src_ott_id) + relevant_ids.add(e.dst_ott_id) + + for ott_id in relevant_ids: + genus_of[ott_id] = _walk_to_rank(ott_id, "genus", taxa_by_id) + family_of[ott_id] = _walk_to_rank(ott_id, "family", taxa_by_id) + + # Compute stats + distances = [e.distance for e in edges] + same_genus = 0 + same_family = 0 + total = len(edges) + outliers: list[OutlierRecord] = [] + + for e in edges: + src_genus = genus_of.get(e.src_ott_id) + dst_genus = genus_of.get(e.dst_ott_id) + src_family = family_of.get(e.src_ott_id) + dst_family = family_of.get(e.dst_ott_id) + + if src_genus is not None and src_genus == dst_genus: + same_genus += 1 + if src_family is not None and src_family == dst_family: + same_family += 1 + + # Cross-family close neighbors (suspiciously similar across families) + if e.distance < 0.05 and ( + src_family is None + or dst_family is None + or src_family != dst_family + ): + src_t = taxa_by_id.get(e.src_ott_id) + dst_t = taxa_by_id.get(e.dst_ott_id) + outliers.append(OutlierRecord( + src_ott_id=e.src_ott_id, + src_name=getattr(src_t, "name", str(e.src_ott_id)), + dst_ott_id=e.dst_ott_id, + dst_name=getattr(dst_t, "name", str(e.dst_ott_id)), + distance=e.distance, + reason="cross_family_close", + )) + + # Within-genus distant pairs (unexpectedly different within same genus) + if e.distance > 0.8 and ( + src_genus is not None + and dst_genus is not None + and src_genus == dst_genus + ): + src_t = taxa_by_id.get(e.src_ott_id) + dst_t = taxa_by_id.get(e.dst_ott_id) + outliers.append(OutlierRecord( + src_ott_id=e.src_ott_id, + src_name=getattr(src_t, "name", str(e.src_ott_id)), + dst_ott_id=e.dst_ott_id, + dst_name=getattr(dst_t, "name", str(e.dst_ott_id)), + distance=e.distance, + reason="within_genus_distant", + )) + + report = ValidationReport( + total_edges=total, + same_genus_count=same_genus, + same_family_count=same_family, + same_genus_pct=100.0 * same_genus / total, + same_family_pct=100.0 * same_family / total, + distance_min=min(distances), + distance_max=max(distances), + distance_mean=statistics.mean(distances), + distance_median=statistics.median(distances), + distance_stdev=statistics.stdev(distances) if len(distances) >= 2 else None, + outliers=outliers, + ) + + return report + + +def _print_report(report: ValidationReport) -> None: + """Pretty-print a validation report to stdout.""" + cross_family = [o for o in report.outliers if o.reason == "cross_family_close"] + within_genus = [o for o in report.outliers if o.reason == "within_genus_distant"] + + print("=" * 60) + print("EvoGraph Validation Report") + print("=" * 60) + + print(f"\nTotal edges: {report.total_edges}") + print( + f"Neighbors sharing genus: {report.same_genus_count:>6d} / {report.total_edges} " + f"({report.same_genus_pct:.1f}%)" + ) + print( + f"Neighbors sharing family: {report.same_family_count:>6d} / {report.total_edges} " + f"({report.same_family_pct:.1f}%)" + ) + + print("\nDistance distribution:") + print(f" Min: {report.distance_min:.4f}") + print(f" Max: {report.distance_max:.4f}") + print(f" Mean: {report.distance_mean:.4f}") + print(f" Median: {report.distance_median:.4f}") + if report.distance_stdev is not None: + print(f" StdDev: {report.distance_stdev:.4f}") + + print("\nOutliers:") + print(f" Distance < 0.05 across families: {len(cross_family)}") + for o in cross_family[:10]: + print(f" {o.src_name} <-> {o.dst_name} dist={o.distance:.4f}") + if len(cross_family) > 10: + print(f" ... and {len(cross_family) - 10} more") + + print(f" Distance > 0.8 within same genus: {len(within_genus)}") + for o in within_genus[:10]: + print(f" {o.src_name} <-> {o.dst_name} dist={o.distance:.4f}") + if len(within_genus) > 10: + print(f" ... and {len(within_genus) - 10} more") + + print("=" * 60) + + +def validate(output_path: str | None = None) -> None: + """Run all validation checks, print results, and optionally save to JSON.""" session = SessionLocal() try: - # Load taxa - all_taxa = session.execute(select(Taxon)).scalars().all() - taxa_by_id = {t.ott_id: t for t in all_taxa} - logger.info("Loaded %d taxa", len(taxa_by_id)) - - # Load edges - edges = session.execute(select(Edge)).scalars().all() - logger.info("Loaded %d edges", len(edges)) + report = compute_validation_report(session) - if not edges: + if report is None: logger.warning("No edges found. Nothing to validate.") return - # Build genus/family lookup for each species - genus_of: dict[int, int | None] = {} - family_of: dict[int, int | None] = {} - - relevant_ids = set() - for e in edges: - relevant_ids.add(e.src_ott_id) - relevant_ids.add(e.dst_ott_id) - - for ott_id in relevant_ids: - genus_of[ott_id] = _walk_to_rank(ott_id, "genus", taxa_by_id) - family_of[ott_id] = _walk_to_rank(ott_id, "family", taxa_by_id) - - # Compute stats - distances = [e.distance for e in edges] - same_genus = 0 - same_family = 0 - total = len(edges) - - outliers_low: list[Edge] = [] # distance < 0.05, different families - outliers_high: list[Edge] = [] # distance > 0.8, same genus - - for e in edges: - src_genus = genus_of.get(e.src_ott_id) - dst_genus = genus_of.get(e.dst_ott_id) - src_family = family_of.get(e.src_ott_id) - dst_family = family_of.get(e.dst_ott_id) - - if src_genus is not None and src_genus == dst_genus: - same_genus += 1 - if src_family is not None and src_family == dst_family: - same_family += 1 - - # Outlier detection - if e.distance < 0.05 and ( - src_family is None - or dst_family is None - or src_family != dst_family - ): - outliers_low.append(e) - if e.distance > 0.8 and ( - src_genus is not None - and dst_genus is not None - and src_genus == dst_genus - ): - outliers_high.append(e) - - # Print results - print("=" * 60) - print("EvoGraph Validation Report") - print("=" * 60) - - print(f"\nTotal edges: {total}") - print( - f"Neighbors sharing genus: {same_genus:>6d} / {total} " - f"({100.0 * same_genus / total:.1f}%)" - ) - print( - f"Neighbors sharing family: {same_family:>6d} / {total} " - f"({100.0 * same_family / total:.1f}%)" - ) - - print("\nDistance distribution:") - print(f" Min: {min(distances):.4f}") - print(f" Max: {max(distances):.4f}") - print(f" Mean: {statistics.mean(distances):.4f}") - print(f" Median: {statistics.median(distances):.4f}") - if len(distances) >= 2: - print(f" StdDev: {statistics.stdev(distances):.4f}") - - print("\nOutliers:") - print( - f" Distance < 0.05 across families: {len(outliers_low)}" - ) - for e in outliers_low[:10]: - src_name = taxa_by_id.get(e.src_ott_id) - dst_name = taxa_by_id.get(e.dst_ott_id) - print( - f" {getattr(src_name, 'name', e.src_ott_id)} <-> " - f"{getattr(dst_name, 'name', e.dst_ott_id)} " - f"dist={e.distance:.4f}" - ) - if len(outliers_low) > 10: - print(f" ... and {len(outliers_low) - 10} more") - - print( - f" Distance > 0.8 within same genus: {len(outliers_high)}" - ) - for e in outliers_high[:10]: - src_name = taxa_by_id.get(e.src_ott_id) - dst_name = taxa_by_id.get(e.dst_ott_id) - print( - f" {getattr(src_name, 'name', e.src_ott_id)} <-> " - f"{getattr(dst_name, 'name', e.dst_ott_id)} " - f"dist={e.distance:.4f}" - ) - if len(outliers_high) > 10: - print(f" ... and {len(outliers_high) - 10} more") - - print("=" * 60) + _print_report(report) + + if output_path: + with open(output_path, "w") as f: + json.dump(report.to_dict(), f, indent=2) + print(f"\nReport saved to {output_path}") finally: session.close() if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Validate EvoGraph data quality") + parser.add_argument( + "--output", "-o", type=str, default=None, + help="Save report as JSON to this path", + ) + args = parser.parse_args() + logging.basicConfig( level=logging.INFO, format="%(asctime)s %(levelname)s %(name)s: %(message)s", ) - validate() + validate(output_path=args.output) diff --git a/apps/api/src/evograph/settings.py b/apps/api/src/evograph/settings.py index 7d8c93d..803b55d 100644 --- a/apps/api/src/evograph/settings.py +++ b/apps/api/src/evograph/settings.py @@ -1,3 +1,5 @@ +from typing import Literal + from pydantic_settings import BaseSettings @@ -5,6 +7,9 @@ class Settings(BaseSettings): database_url: str = "postgresql+psycopg://postgres:postgres@localhost:5432/evograph" redis_url: str = "redis://redis:6379/0" scope_ott_root: str = "Aves" + cors_origins: list[str] = ["*"] + log_level: Literal["debug", "info", "warning", "error", "critical"] = "info" + log_format: Literal["text", "json"] = "text" model_config = {"env_prefix": "", "case_sensitive": False} diff --git a/apps/api/tests/conftest.py b/apps/api/tests/conftest.py index 77379a6..9994ba4 100644 --- a/apps/api/tests/conftest.py +++ b/apps/api/tests/conftest.py @@ -110,6 +110,9 @@ def join(self, *args, **kwargs): def group_by(self, *args, **kwargs): return self + def select_from(self, *args, **kwargs): + return self + def exists(self): """Return an exists clause marker for use in outer query.""" return MockExistsClause() @@ -126,6 +129,9 @@ def all(self): def first(self): return self._results[0] if self._results else None + def one(self): + return self._results[0] if self._results else (None,) + class MockExecuteResult: """Mock result for db.execute() calls (used by recursive CTEs).""" diff --git a/apps/api/tests/test_backfill_ncbi.py b/apps/api/tests/test_backfill_ncbi.py new file mode 100644 index 0000000..ad0d6f7 --- /dev/null +++ b/apps/api/tests/test_backfill_ncbi.py @@ -0,0 +1,98 @@ +"""Tests for the NCBI taxonomy ID backfill pipeline.""" + +import pytest +from unittest.mock import AsyncMock, MagicMock +import httpx + +from evograph.pipeline.backfill_ncbi_tax_id import _lookup_tax_id + + +@pytest.fixture +def mock_client(): + return AsyncMock(spec=httpx.AsyncClient) + + +class TestLookupTaxId: + """Tests for _lookup_tax_id function.""" + + @pytest.mark.asyncio + async def test_single_match_returns_id(self, mock_client): + """When NCBI returns exactly one match, return the ID.""" + mock_resp = MagicMock() + mock_resp.json.return_value = { + "esearchresult": {"idlist": ["9606"]} + } + mock_resp.raise_for_status = MagicMock() + mock_client.get.return_value = mock_resp + + result = await _lookup_tax_id(mock_client, "Homo sapiens") + assert result == 9606 + + @pytest.mark.asyncio + async def test_no_match_returns_none(self, mock_client): + """When NCBI returns no matches, return None.""" + mock_resp = MagicMock() + mock_resp.json.return_value = { + "esearchresult": {"idlist": []} + } + mock_resp.raise_for_status = MagicMock() + mock_client.get.return_value = mock_resp + + result = await _lookup_tax_id(mock_client, "Fakeus speciesus") + assert result is None + + @pytest.mark.asyncio + async def test_multiple_matches_returns_none(self, mock_client): + """When NCBI returns multiple matches, return None (ambiguous).""" + mock_resp = MagicMock() + mock_resp.json.return_value = { + "esearchresult": {"idlist": ["9606", "9607"]} + } + mock_resp.raise_for_status = MagicMock() + mock_client.get.return_value = mock_resp + + result = await _lookup_tax_id(mock_client, "Homo") + assert result is None + + @pytest.mark.asyncio + async def test_uses_scientific_name_field(self, mock_client): + """Verify the query uses [Scientific Name] field qualifier.""" + mock_resp = MagicMock() + mock_resp.json.return_value = { + "esearchresult": {"idlist": ["9606"]} + } + mock_resp.raise_for_status = MagicMock() + mock_client.get.return_value = mock_resp + + await _lookup_tax_id(mock_client, "Corvus corax") + + call_args = mock_client.get.call_args + params = call_args.kwargs.get("params", call_args[1].get("params", {})) + assert params["db"] == "taxonomy" + assert '"Corvus corax"[Scientific Name]' in params["term"] + + @pytest.mark.asyncio + async def test_http_error_propagates(self, mock_client): + """HTTP errors should propagate to caller.""" + mock_resp = MagicMock() + mock_resp.raise_for_status.side_effect = httpx.HTTPStatusError( + "500", request=MagicMock(), response=MagicMock() + ) + mock_client.get.return_value = mock_resp + + with pytest.raises(httpx.HTTPStatusError): + await _lookup_tax_id(mock_client, "test") + + @pytest.mark.asyncio + async def test_returns_int(self, mock_client): + """Return value should be int, not string.""" + mock_resp = MagicMock() + mock_resp.json.return_value = { + "esearchresult": {"idlist": ["12345"]} + } + mock_resp.raise_for_status = MagicMock() + mock_client.get.return_value = mock_resp + + result = await _lookup_tax_id(mock_client, "test") + assert isinstance(result, int) + assert result == 12345 diff --git a/apps/api/tests/test_dedup_sequences.py b/apps/api/tests/test_dedup_sequences.py new file mode 100644 index 0000000..9e2e773 --- /dev/null +++ b/apps/api/tests/test_dedup_sequences.py @@ -0,0 +1,40 @@ +"""Tests for the sequence deduplication pipeline.""" + +from unittest.mock import MagicMock + +from evograph.pipeline.dedup_sequences import find_duplicates + + +class TestFindDuplicates: + """Tests for find_duplicates function.""" + + def test_returns_empty_when_no_duplicates(self): + """When all sequences are unique, return empty list.""" + mock_session = MagicMock() + mock_session.execute.return_value.all.return_value = [] + + result = find_duplicates(mock_session) + assert result == [] + + def test_returns_groups_with_count(self): + """Return duplicate groups with their counts.""" + mock_session = MagicMock() + mock_session.execute.return_value.all.return_value = [ + (700118, "NC_002008", "COI", 3), + (893498, "KY456789", "COI", 2), + ] + + result = find_duplicates(mock_session) + assert len(result) == 2 + assert result[0] == (700118, "NC_002008", "COI", 3) + assert result[1] == (893498, "KY456789", "COI", 2) + + def test_calls_execute_with_group_by(self): + """Verify the query uses group_by and having.""" + mock_session = MagicMock() + mock_session.execute.return_value.all.return_value = [] + + find_duplicates(mock_session) + + # execute should have been called once + assert mock_session.execute.call_count == 1 diff --git a/apps/api/tests/test_health.py b/apps/api/tests/test_health.py index 4e6e018..cd8b593 100644 --- a/apps/api/tests/test_health.py +++ b/apps/api/tests/test_health.py @@ -1,4 +1,4 @@ -"""Tests for the health check endpoint.""" +"""Tests for the health check endpoints.""" from fastapi.testclient import TestClient @@ -10,4 +10,26 @@ def test_health(): resp = client.get("/health") assert resp.status_code == 200 - assert resp.json() == {"status": "ok"} + data = resp.json() + assert data["status"] == "ok" + assert "scope" in data + + +def test_readiness_endpoint_exists(): + resp = client.get("/health/ready") + assert resp.status_code == 200 + data = resp.json() + assert data["status"] in ("ok", "degraded") + assert "scope" in data + assert "database" in data + + +def test_readiness_reports_pool_stats(): + resp = client.get("/health/ready") + data = resp.json() + db = data["database"] + assert "connected" in db + assert "pool_size" in db + assert "checked_in" in db + assert "checked_out" in db + assert "overflow" in db diff --git a/apps/api/tests/test_ingest_ncbi.py b/apps/api/tests/test_ingest_ncbi.py new file mode 100644 index 0000000..a3faee3 --- /dev/null +++ b/apps/api/tests/test_ingest_ncbi.py @@ -0,0 +1,198 @@ +"""Tests for NCBI COI ingestion pipeline search strategy.""" + +import pytest +from unittest.mock import AsyncMock, MagicMock + +import httpx + +from evograph.pipeline.ingest_ncbi import ( + _build_query, + _esearch, + _efetch_fasta, + _fetch_coi_sequences, +) + + +@pytest.fixture +def mock_client(): + return AsyncMock(spec=httpx.AsyncClient) + + +def _mock_response(json_data=None, text_data=None): + """Create a mock HTTP response.""" + resp = MagicMock() + resp.raise_for_status = MagicMock() + if json_data is not None: + resp.json.return_value = json_data + if text_data is not None: + resp.text = text_data + return resp + + +class TestBuildQuery: + """Tests for _build_query function.""" + + def test_includes_organism(self): + q = _build_query("Corvus corax") + assert '"Corvus corax"[Organism]' in q + + def test_includes_coi_gene_variants(self): + q = _build_query("Corvus corax") + assert "COI[Gene]" in q + assert "COX1[Gene]" in q + assert "COXI[Gene]" in q + assert "CO1[Gene]" in q + + def test_includes_title_variants(self): + q = _build_query("Corvus corax") + assert '"cytochrome c oxidase subunit I"[Title]' in q + assert '"cytochrome c oxidase subunit 1"[Title]' in q + + def test_includes_length_filter(self): + q = _build_query("Corvus corax") + assert "400:2000[Sequence Length]" in q + + +class TestEsearch: + """Tests for _esearch function.""" + + @pytest.mark.asyncio + async def test_returns_id_list(self, mock_client): + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": ["123", "456"]}} + ) + result = await _esearch(mock_client, "test query", 5) + assert result == ["123", "456"] + + @pytest.mark.asyncio + async def test_returns_empty_on_no_results(self, mock_client): + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": []}} + ) + result = await _esearch(mock_client, "test query", 5) + assert result == [] + + @pytest.mark.asyncio + async def test_passes_correct_params(self, mock_client): + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": []}} + ) + await _esearch(mock_client, "test query", 10) + + call_args = mock_client.get.call_args + params = call_args.kwargs.get("params", call_args[1].get("params", {})) + assert params["db"] == "nucleotide" + assert params["term"] == "test query" + assert params["retmax"] == 10 + assert params["retmode"] == "json" + + +class TestEfetchFasta: + """Tests for _efetch_fasta function.""" + + @pytest.mark.asyncio + async def test_parses_single_record(self, mock_client): + fasta = ">NC_002008.1 Corvus corax\nATCGATCG\nGCTAGCTA\n" + mock_client.get.return_value = _mock_response(text_data=fasta) + + records = await _efetch_fasta(mock_client, ["123"]) + assert len(records) == 1 + assert records[0]["header"] == "NC_002008.1 Corvus corax" + assert records[0]["seq"] == "ATCGATCGGCTAGCTA" + + @pytest.mark.asyncio + async def test_parses_multiple_records(self, mock_client): + fasta = ">seq1\nATCG\n>seq2\nGCTA\n" + mock_client.get.return_value = _mock_response(text_data=fasta) + + records = await _efetch_fasta(mock_client, ["1", "2"]) + assert len(records) == 2 + assert records[0]["seq"] == "ATCG" + assert records[1]["seq"] == "GCTA" + + @pytest.mark.asyncio + async def test_handles_empty_response(self, mock_client): + mock_client.get.return_value = _mock_response(text_data="") + + records = await _efetch_fasta(mock_client, ["123"]) + assert records == [] + + +class TestFetchCoiSequences: + """Tests for _fetch_coi_sequences with tiered search strategy.""" + + @pytest.mark.asyncio + async def test_species_level_search_hits(self, mock_client): + """When species search finds results, return them directly.""" + mock_client.get.side_effect = [ + # esearch returns results + _mock_response(json_data={"esearchresult": {"idlist": ["123"]}}), + # efetch returns FASTA + _mock_response(text_data=">NC_001.1\nATCG\n"), + ] + + records = await _fetch_coi_sequences(mock_client, "Corvus corax", 5) + assert len(records) == 1 + assert records[0]["seq"] == "ATCG" + + @pytest.mark.asyncio + async def test_genus_fallback_when_species_fails(self, mock_client): + """When species search returns nothing, fall back to genus.""" + mock_client.get.side_effect = [ + # species esearch: no results + _mock_response(json_data={"esearchresult": {"idlist": []}}), + # genus esearch: has results + _mock_response(json_data={"esearchresult": {"idlist": ["456"]}}), + # efetch returns FASTA + _mock_response(text_data=">NC_002.1\nGCTA\n"), + ] + + records = await _fetch_coi_sequences( + mock_client, "Corvus corax", 5, genus_fallback=True + ) + assert len(records) == 1 + + # Verify the genus query was made + calls = mock_client.get.call_args_list + genus_call_params = calls[1].kwargs.get("params", calls[1][1].get("params", {})) + assert '"Corvus"[Organism]' in genus_call_params["term"] + + @pytest.mark.asyncio + async def test_no_genus_fallback_when_disabled(self, mock_client): + """When genus_fallback=False, don't try genus search.""" + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": []}} + ) + + records = await _fetch_coi_sequences( + mock_client, "Corvus corax", 5, genus_fallback=False + ) + assert records == [] + # Only one call should have been made (species-level) + assert mock_client.get.call_count == 1 + + @pytest.mark.asyncio + async def test_no_genus_fallback_for_single_word(self, mock_client): + """Single-word names (genus-level taxa) don't trigger genus fallback.""" + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": []}} + ) + + records = await _fetch_coi_sequences( + mock_client, "Corvus", 5, genus_fallback=True + ) + assert records == [] + # Only one call — no fallback for single-word names + assert mock_client.get.call_count == 1 + + @pytest.mark.asyncio + async def test_both_searches_fail(self, mock_client): + """When both species and genus searches fail, return empty.""" + mock_client.get.return_value = _mock_response( + json_data={"esearchresult": {"idlist": []}} + ) + + records = await _fetch_coi_sequences( + mock_client, "Fakeus specieus", 5, genus_fallback=True + ) + assert records == [] diff --git a/apps/api/tests/test_logging_config.py b/apps/api/tests/test_logging_config.py new file mode 100644 index 0000000..88fe595 --- /dev/null +++ b/apps/api/tests/test_logging_config.py @@ -0,0 +1,82 @@ +"""Tests for logging configuration.""" + +import json +import logging +from unittest.mock import patch + +from evograph.logging_config import JSONFormatter, configure_logging + + +class TestJSONFormatter: + def test_formats_as_valid_json(self): + formatter = JSONFormatter() + record = logging.LogRecord( + name="test", + level=logging.INFO, + pathname="test.py", + lineno=1, + msg="hello %s", + args=("world",), + exc_info=None, + ) + output = formatter.format(record) + parsed = json.loads(output) + assert parsed["level"] == "INFO" + assert parsed["logger"] == "test" + assert parsed["message"] == "hello world" + assert "timestamp" in parsed + + def test_includes_exception_info(self): + formatter = JSONFormatter() + try: + raise ValueError("test error") + except ValueError: + import sys + exc_info = sys.exc_info() + + record = logging.LogRecord( + name="test", + level=logging.ERROR, + pathname="test.py", + lineno=1, + msg="something failed", + args=(), + exc_info=exc_info, + ) + output = formatter.format(record) + parsed = json.loads(output) + assert "exception" in parsed + assert "ValueError" in parsed["exception"] + + +class TestConfigureLogging: + def test_configure_text_format(self): + with patch("evograph.logging_config.settings") as mock_settings: + mock_settings.log_level = "info" + mock_settings.log_format = "text" + configure_logging() + + root = logging.getLogger() + assert root.level == logging.INFO + assert len(root.handlers) == 1 + assert not isinstance(root.handlers[0].formatter, JSONFormatter) + + def test_configure_json_format(self): + with patch("evograph.logging_config.settings") as mock_settings: + mock_settings.log_level = "warning" + mock_settings.log_format = "json" + configure_logging() + + root = logging.getLogger() + assert root.level == logging.WARNING + assert len(root.handlers) == 1 + assert isinstance(root.handlers[0].formatter, JSONFormatter) + + def test_configure_debug_level(self): + with patch("evograph.logging_config.settings") as mock_settings: + mock_settings.log_level = "debug" + mock_settings.log_format = "text" + configure_logging() + + root = logging.getLogger() + assert root.level == logging.DEBUG diff --git a/apps/api/tests/test_rate_limit.py b/apps/api/tests/test_rate_limit.py new file mode 100644 index 0000000..bcb258b --- /dev/null +++ b/apps/api/tests/test_rate_limit.py @@ -0,0 +1,90 @@ +"""Tests for rate limiting middleware.""" + +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from evograph.middleware.rate_limit import RateLimitMiddleware + + +def test_rate_limit_headers_on_api(client): + """API endpoints include rate limit headers.""" + resp = client.get("/v1/search?q=test") + assert resp.status_code == 200 + assert "X-RateLimit-Limit" in resp.headers + assert resp.headers["X-RateLimit-Limit"] == "100" + assert int(resp.headers["X-RateLimit-Remaining"]) >= 0 + + +def test_rate_limit_decrements(client): + """Remaining count decreases with each request.""" + resp1 = client.get("/v1/search?q=test") + remaining1 = int(resp1.headers["X-RateLimit-Remaining"]) + + resp2 = client.get("/v1/search?q=test") + remaining2 = int(resp2.headers["X-RateLimit-Remaining"]) + + assert remaining2 == remaining1 - 1 + + +def test_health_excluded_from_main_app(): + """Health endpoint on the main app has no rate limit headers.""" + from evograph.main import app + + with TestClient(app) as c: + resp = c.get("/health") + assert resp.status_code == 200 + assert "X-RateLimit-Limit" not in resp.headers + + +def test_rate_limit_429_when_exceeded(): + """Returns 429 when rate limit is exceeded.""" + test_app = FastAPI() + test_app.add_middleware(RateLimitMiddleware, max_requests=3, window_seconds=60) + + @test_app.get("/test") + def test_endpoint(): + return {"ok": True} + + with TestClient(test_app) as c: + for _ in range(3): + resp = c.get("/test") + assert resp.status_code == 200 + + resp = c.get("/test") + assert resp.status_code == 429 + assert resp.json()["detail"] == "Too many requests" + assert "Retry-After" in resp.headers + + +def test_excluded_paths_not_counted(): + """Excluded paths don't consume rate limit budget.""" + test_app = FastAPI() + test_app.add_middleware( + RateLimitMiddleware, + max_requests=2, + window_seconds=60, + exclude_paths=("/health",), + ) + + @test_app.get("/health") + def health(): + return {"status": "ok"} + + @test_app.get("/api") + def api(): + return {"data": True} + + with TestClient(test_app) as c: + # Health should always work and not count + for _ in range(10): + resp = c.get("/health") + assert resp.status_code == 200 + + # API should still have its full budget + resp = c.get("/api") + assert resp.status_code == 200 + resp = c.get("/api") + assert resp.status_code == 200 + # Third should be blocked + resp = c.get("/api") + assert resp.status_code == 429 diff --git a/apps/api/tests/test_request_logging.py b/apps/api/tests/test_request_logging.py new file mode 100644 index 0000000..f6f5fe8 --- /dev/null +++ b/apps/api/tests/test_request_logging.py @@ -0,0 +1,45 @@ +"""Tests for request logging middleware.""" + +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from evograph.middleware.request_logging import RequestLoggingMiddleware + + +def test_request_id_header(): + """Response includes X-Request-ID header.""" + test_app = FastAPI() + test_app.add_middleware(RequestLoggingMiddleware) + + @test_app.get("/test") + def test_endpoint(): + return {"ok": True} + + with TestClient(test_app) as client: + resp = client.get("/test") + assert resp.status_code == 200 + assert "X-Request-ID" in resp.headers + assert len(resp.headers["X-Request-ID"]) == 8 + + +def test_request_id_unique(): + """Each request gets a unique ID.""" + test_app = FastAPI() + test_app.add_middleware(RequestLoggingMiddleware) + + @test_app.get("/test") + def test_endpoint(): + return {"ok": True} + + with TestClient(test_app) as client: + ids = set() + for _ in range(5): + resp = client.get("/test") + ids.add(resp.headers["X-Request-ID"]) + assert len(ids) == 5 + + +def test_main_app_has_request_id(client): + """Main app includes X-Request-ID on responses.""" + resp = client.get("/v1/search?q=test") + assert "X-Request-ID" in resp.headers diff --git a/apps/api/tests/test_search.py b/apps/api/tests/test_search.py index 972ad60..0f6c5c1 100644 --- a/apps/api/tests/test_search.py +++ b/apps/api/tests/test_search.py @@ -15,18 +15,32 @@ def test_search_returns_matching_taxa(self, client, mock_db): assert resp.status_code == 200 data = resp.json() - assert len(data) == 2 - assert data[0]["name"] == "Corvidae" - assert data[0]["ott_id"] == 187411 - assert data[0]["rank"] == "family" - assert data[1]["name"] == "Corvus" + items = data["items"] + assert len(items) == 2 + assert items[0]["name"] == "Corvidae" + assert items[0]["ott_id"] == 187411 + assert items[0]["rank"] == "family" + assert items[1]["name"] == "Corvus" + + def test_search_returns_total_count(self, client, mock_db): + mock_db.set(Taxon, [ + _make_taxon(187411, "Corvidae", "family"), + ]) + + resp = client.get("/v1/search", params={"q": "corv"}) + data = resp.json() + assert "total" in data + assert "limit" in data + assert data["total"] == 0 # MockDB scalar returns 0 def test_search_returns_empty_for_no_match(self, client, mock_db): mock_db.set(Taxon, []) resp = client.get("/v1/search", params={"q": "zzzzzzz"}) assert resp.status_code == 200 - assert resp.json() == [] + data = resp.json() + assert data["items"] == [] + assert data["total"] == 0 def test_search_requires_query(self, client): resp = client.get("/v1/search") @@ -37,6 +51,7 @@ def test_search_respects_limit_param(self, client, mock_db): resp = client.get("/v1/search", params={"q": "corv", "limit": 1}) assert resp.status_code == 200 + assert resp.json()["limit"] == 1 def test_search_rejects_empty_query(self, client): resp = client.get("/v1/search", params={"q": ""}) @@ -46,5 +61,7 @@ def test_search_fields_match_schema(self, client, mock_db): mock_db.set(Taxon, [_make_taxon(100, "Falco", "genus")]) resp = client.get("/v1/search", params={"q": "falco"}) - item = resp.json()[0] + data = resp.json() + assert set(data.keys()) >= {"items", "total", "limit"} + item = data["items"][0] assert set(item.keys()) >= {"ott_id", "name", "rank"} diff --git a/apps/api/tests/test_security_headers.py b/apps/api/tests/test_security_headers.py new file mode 100644 index 0000000..cfb6a6a --- /dev/null +++ b/apps/api/tests/test_security_headers.py @@ -0,0 +1,36 @@ +"""Tests for security headers middleware.""" + +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from evograph.middleware.security_headers import SecurityHeadersMiddleware + + +def test_security_headers_present(): + """All security headers are set on responses.""" + test_app = FastAPI() + test_app.add_middleware(SecurityHeadersMiddleware) + + @test_app.get("/test") + def test_endpoint(): + return {"ok": True} + + with TestClient(test_app) as c: + resp = c.get("/test") + assert resp.status_code == 200 + assert resp.headers["X-Content-Type-Options"] == "nosniff" + assert resp.headers["X-Frame-Options"] == "DENY" + assert resp.headers["X-XSS-Protection"] == "1; mode=block" + assert resp.headers["Referrer-Policy"] == "strict-origin-when-cross-origin" + assert "camera=()" in resp.headers["Permissions-Policy"] + + +def test_security_headers_on_main_app(): + """Security headers appear on the main app's endpoints.""" + from evograph.main import app + + with TestClient(app) as c: + resp = c.get("/health") + assert resp.status_code == 200 + assert resp.headers["X-Content-Type-Options"] == "nosniff" + assert resp.headers["X-Frame-Options"] == "DENY" diff --git a/apps/api/tests/test_sequences.py b/apps/api/tests/test_sequences.py index e3ea024..bf3d41b 100644 --- a/apps/api/tests/test_sequences.py +++ b/apps/api/tests/test_sequences.py @@ -5,7 +5,7 @@ class TestGetSequences: - def test_sequences_returns_list(self, client, mock_db): + def test_sequences_returns_paginated_response(self, client, mock_db): taxon = _make_taxon(700118, "Corvus corax", "species") seq = _make_sequence(700118, accession="NC_001", length=658, is_canonical=True) @@ -16,13 +16,19 @@ def test_sequences_returns_list(self, client, mock_db): assert resp.status_code == 200 data = resp.json() - assert len(data) == 1 - assert data[0]["ott_id"] == 700118 - assert data[0]["marker"] == "COI" - assert data[0]["source"] == "NCBI" - assert data[0]["accession"] == "NC_001" - assert data[0]["length"] == 658 - assert data[0]["is_canonical"] is True + assert "items" in data + assert "total" in data + assert "offset" in data + assert "limit" in data + + items = data["items"] + assert len(items) == 1 + assert items[0]["ott_id"] == 700118 + assert items[0]["marker"] == "COI" + assert items[0]["source"] == "NCBI" + assert items[0]["accession"] == "NC_001" + assert items[0]["length"] == 658 + assert items[0]["is_canonical"] is True def test_sequences_taxon_not_found(self, client, mock_db): mock_db.set(Taxon, []) @@ -37,7 +43,20 @@ def test_sequences_empty(self, client, mock_db): resp = client.get("/v1/taxa/700118/sequences") assert resp.status_code == 200 - assert resp.json() == [] + data = resp.json() + assert data["items"] == [] + assert data["total"] == 0 + + def test_sequences_pagination_params(self, client, mock_db): + taxon = _make_taxon(700118, "Corvus corax", "species") + mock_db.set(Taxon, [taxon]) + mock_db.set(Sequence, []) + + resp = client.get("/v1/taxa/700118/sequences", params={"offset": 10, "limit": 25}) + assert resp.status_code == 200 + data = resp.json() + assert data["offset"] == 10 + assert data["limit"] == 25 def test_sequence_schema_fields(self, client, mock_db): taxon = _make_taxon(700118, "Corvus corax", "species") @@ -46,6 +65,6 @@ def test_sequence_schema_fields(self, client, mock_db): mock_db.set(Sequence, [seq]) resp = client.get("/v1/taxa/700118/sequences") - item = resp.json()[0] + item = resp.json()["items"][0] expected_keys = {"id", "ott_id", "marker", "source", "accession", "sequence", "length", "is_canonical", "retrieved_at"} assert expected_keys == set(item.keys()) diff --git a/apps/api/tests/test_stats.py b/apps/api/tests/test_stats.py new file mode 100644 index 0000000..f099483 --- /dev/null +++ b/apps/api/tests/test_stats.py @@ -0,0 +1,28 @@ +"""Tests for the stats endpoint.""" + + +def test_stats_returns_structure(client): + """Stats endpoint returns expected top-level keys.""" + resp = client.get("/v1/stats") + assert resp.status_code == 200 + data = resp.json() + + assert "taxa" in data + assert "sequences" in data + assert "edges" in data + assert "total" in data["taxa"] + assert "by_rank" in data["taxa"] + assert "total" in data["sequences"] + assert "total" in data["edges"] + + +def test_stats_empty_database(client): + """Stats endpoint handles empty database gracefully.""" + resp = client.get("/v1/stats") + assert resp.status_code == 200 + data = resp.json() + + assert data["taxa"]["total"] == 0 + assert data["sequences"]["total"] == 0 + assert data["edges"]["total"] == 0 + assert data["edges"]["distance"] is None diff --git a/apps/api/tests/test_validate.py b/apps/api/tests/test_validate.py new file mode 100644 index 0000000..d14add5 --- /dev/null +++ b/apps/api/tests/test_validate.py @@ -0,0 +1,188 @@ +"""Tests for the validation pipeline.""" + +from unittest.mock import MagicMock + +from evograph.pipeline.validate import ( + OutlierRecord, + ValidationReport, + _walk_to_rank, + compute_validation_report, +) + + +class TestWalkToRank: + """Tests for _walk_to_rank helper.""" + + def test_finds_genus(self): + species = MagicMock(ott_id=1, rank="species", parent_ott_id=2) + genus = MagicMock(ott_id=2, rank="genus", parent_ott_id=3) + family = MagicMock(ott_id=3, rank="family", parent_ott_id=None) + taxa = {1: species, 2: genus, 3: family} + + assert _walk_to_rank(1, "genus", taxa) == 2 + + def test_finds_family(self): + species = MagicMock(ott_id=1, rank="species", parent_ott_id=2) + genus = MagicMock(ott_id=2, rank="genus", parent_ott_id=3) + family = MagicMock(ott_id=3, rank="family", parent_ott_id=None) + taxa = {1: species, 2: genus, 3: family} + + assert _walk_to_rank(1, "family", taxa) == 3 + + def test_returns_none_when_rank_not_found(self): + species = MagicMock(ott_id=1, rank="species", parent_ott_id=None) + taxa = {1: species} + + assert _walk_to_rank(1, "genus", taxa) is None + + def test_returns_none_for_missing_taxon(self): + assert _walk_to_rank(999, "genus", {}) is None + + def test_handles_circular_reference(self): + """Should not infinite loop on circular parent references.""" + a = MagicMock(ott_id=1, rank="species", parent_ott_id=2) + b = MagicMock(ott_id=2, rank="species", parent_ott_id=1) + taxa = {1: a, 2: b} + + assert _walk_to_rank(1, "genus", taxa) is None + + def test_returns_self_if_already_at_rank(self): + genus = MagicMock(ott_id=5, rank="genus", parent_ott_id=10) + taxa = {5: genus} + + assert _walk_to_rank(5, "genus", taxa) == 5 + + +class TestValidationReport: + """Tests for ValidationReport dataclass.""" + + def test_to_dict_structure(self): + report = ValidationReport( + total_edges=100, + same_genus_count=60, + same_family_count=85, + same_genus_pct=60.0, + same_family_pct=85.0, + distance_min=0.01, + distance_max=0.95, + distance_mean=0.45, + distance_median=0.42, + distance_stdev=0.15, + outliers=[ + OutlierRecord( + src_ott_id=1, src_name="A", dst_ott_id=2, dst_name="B", + distance=0.03, reason="cross_family_close", + ), + OutlierRecord( + src_ott_id=3, src_name="C", dst_ott_id=4, dst_name="D", + distance=0.85, reason="within_genus_distant", + ), + ], + ) + d = report.to_dict() + + assert d["total_edges"] == 100 + assert d["taxonomy_coherence"]["same_genus"] == 60 + assert d["taxonomy_coherence"]["same_family_pct"] == 85.0 + assert d["distance_distribution"]["mean"] == 0.45 + assert len(d["outliers"]["cross_family_close"]) == 1 + assert len(d["outliers"]["within_genus_distant"]) == 1 + assert d["outliers"]["cross_family_close"][0]["src_name"] == "A" + + def test_to_dict_no_stdev_with_single_edge(self): + report = ValidationReport( + total_edges=1, + distance_min=0.5, + distance_max=0.5, + distance_mean=0.5, + distance_median=0.5, + distance_stdev=None, + ) + d = report.to_dict() + assert d["distance_distribution"]["stdev"] is None + + +class TestComputeValidationReport: + """Tests for compute_validation_report.""" + + def test_returns_none_when_no_edges(self): + mock_session = MagicMock() + # First call returns taxa, second returns edges + taxa_result = MagicMock() + taxa_result.scalars.return_value.all.return_value = [] + edges_result = MagicMock() + edges_result.scalars.return_value.all.return_value = [] + mock_session.execute.side_effect = [taxa_result, edges_result] + + result = compute_validation_report(mock_session) + assert result is None + + def test_counts_same_genus_edges(self): + # Build taxa: two species in same genus + species_a = MagicMock(ott_id=1, rank="species", parent_ott_id=10, name="Species A") + species_b = MagicMock(ott_id=2, rank="species", parent_ott_id=10, name="Species B") + genus = MagicMock(ott_id=10, rank="genus", parent_ott_id=100, name="Genus") + family = MagicMock(ott_id=100, rank="family", parent_ott_id=None, name="Family") + + edge = MagicMock(src_ott_id=1, dst_ott_id=2, distance=0.3) + + mock_session = MagicMock() + taxa_result = MagicMock() + taxa_result.scalars.return_value.all.return_value = [species_a, species_b, genus, family] + edges_result = MagicMock() + edges_result.scalars.return_value.all.return_value = [edge] + mock_session.execute.side_effect = [taxa_result, edges_result] + + report = compute_validation_report(mock_session) + assert report is not None + assert report.same_genus_count == 1 + assert report.same_family_count == 1 + assert report.total_edges == 1 + + def test_detects_cross_family_outlier(self): + # Two species in different families with very low distance + sp_a = MagicMock(ott_id=1, rank="species", parent_ott_id=10, name="Sp A") + sp_b = MagicMock(ott_id=2, rank="species", parent_ott_id=20, name="Sp B") + genus_a = MagicMock(ott_id=10, rank="genus", parent_ott_id=100, name="GenA") + genus_b = MagicMock(ott_id=20, rank="genus", parent_ott_id=200, name="GenB") + fam_a = MagicMock(ott_id=100, rank="family", parent_ott_id=None, name="FamA") + fam_b = MagicMock(ott_id=200, rank="family", parent_ott_id=None, name="FamB") + + edge = MagicMock(src_ott_id=1, dst_ott_id=2, distance=0.02) + + mock_session = MagicMock() + taxa_result = MagicMock() + taxa_result.scalars.return_value.all.return_value = [ + sp_a, sp_b, genus_a, genus_b, fam_a, fam_b, + ] + edges_result = MagicMock() + edges_result.scalars.return_value.all.return_value = [edge] + mock_session.execute.side_effect = [taxa_result, edges_result] + + report = compute_validation_report(mock_session) + assert report is not None + cross_family = [o for o in report.outliers if o.reason == "cross_family_close"] + assert len(cross_family) == 1 + assert cross_family[0].distance == 0.02 + + def test_detects_within_genus_distant_outlier(self): + # Two species in same genus with very high distance + sp_a = MagicMock(ott_id=1, rank="species", parent_ott_id=10, name="Sp A") + sp_b = MagicMock(ott_id=2, rank="species", parent_ott_id=10, name="Sp B") + genus = MagicMock(ott_id=10, rank="genus", parent_ott_id=100, name="Genus") + family = MagicMock(ott_id=100, rank="family", parent_ott_id=None, name="Fam") + + edge = MagicMock(src_ott_id=1, dst_ott_id=2, distance=0.9) + + mock_session = MagicMock() + taxa_result = MagicMock() + taxa_result.scalars.return_value.all.return_value = [sp_a, sp_b, genus, family] + edges_result = MagicMock() + edges_result.scalars.return_value.all.return_value = [edge] + mock_session.execute.side_effect = [taxa_result, edges_result] + + report = compute_validation_report(mock_session) + assert report is not None + within_genus = [o for o in report.outliers if o.reason == "within_genus_distant"] + assert len(within_genus) == 1 + assert within_genus[0].distance == 0.9 diff --git a/apps/web/Dockerfile b/apps/web/Dockerfile index 949aeb2..8ad1ee3 100644 --- a/apps/web/Dockerfile +++ b/apps/web/Dockerfile @@ -1,4 +1,5 @@ -FROM node:22-slim +# ── Development (default for docker-compose) ────────── +FROM node:22-slim AS dev WORKDIR /app @@ -11,3 +12,42 @@ HEALTHCHECK --interval=30s --timeout=5s --start-period=15s --retries=3 \ CMD node -e "fetch('http://localhost:3000').then(r => { if (!r.ok) process.exit(1) }).catch(() => process.exit(1))" || exit 1 CMD ["npm", "run", "dev"] + +# ── Build stage ──────────────────────────────────────── +FROM node:22-slim AS builder + +WORKDIR /app + +COPY package.json package-lock.json* ./ +RUN npm ci + +COPY . . + +ARG NEXT_PUBLIC_API_BASE=http://localhost:8000 +ENV NEXT_PUBLIC_API_BASE=${NEXT_PUBLIC_API_BASE} + +RUN npm run build + +# ── Production ───────────────────────────────────────── +FROM node:22-slim AS prod + +WORKDIR /app + +RUN groupadd --gid 1000 appuser && \ + useradd --uid 1000 --gid appuser --no-create-home appuser + +# Copy standalone output (includes minimal node_modules) +COPY --from=builder --chown=appuser:appuser /app/.next/standalone ./ +COPY --from=builder --chown=appuser:appuser /app/.next/static ./.next/static +COPY --from=builder --chown=appuser:appuser /app/public ./public + +USER appuser + +ENV NODE_ENV=production +ENV HOSTNAME=0.0.0.0 +ENV PORT=3000 + +HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 \ + CMD node -e "fetch('http://localhost:3000').then(r => { if (!r.ok) process.exit(1) }).catch(() => process.exit(1))" || exit 1 + +CMD ["node", "server.js"] diff --git a/apps/web/jest.config.js b/apps/web/jest.config.js new file mode 100644 index 0000000..f2901e4 --- /dev/null +++ b/apps/web/jest.config.js @@ -0,0 +1,11 @@ +const nextJest = require("next/jest"); + +const createJestConfig = nextJest({ dir: "./" }); + +module.exports = createJestConfig({ + testEnvironment: "jsdom", + setupFilesAfterEnv: ["/jest.setup.ts"], + moduleNameMapper: { + "^@/(.*)$": "/src/$1", + }, +}); diff --git a/apps/web/jest.setup.ts b/apps/web/jest.setup.ts new file mode 100644 index 0000000..d0de870 --- /dev/null +++ b/apps/web/jest.setup.ts @@ -0,0 +1 @@ +import "@testing-library/jest-dom"; diff --git a/apps/web/package-lock.json b/apps/web/package-lock.json index 26209cb..02c2e3b 100644 --- a/apps/web/package-lock.json +++ b/apps/web/package-lock.json @@ -22,1902 +22,5263 @@ "sigma": "^3.0.2" }, 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diff --git a/apps/web/package.json b/apps/web/package.json index e5f307a..f4cc16b 100644 --- a/apps/web/package.json +++ b/apps/web/package.json @@ -6,7 +6,8 @@ "dev": "next dev", "build": "next build", "start": "next start", - "lint": "next lint" + "lint": "next lint", + "test": "jest" }, "dependencies": { "@sigma/edge-curve": "^3.1.0", @@ -23,11 +24,18 @@ "sigma": "^3.0.2" }, "devDependencies": { + "@testing-library/jest-dom": "^6.9.1", + "@testing-library/react": "^16.3.2", + "@testing-library/user-event": "^14.6.1", + "@types/jest": "^30.0.0", "@types/node": "^22", "@types/react": "^19", "@types/react-dom": "^19", "eslint": "^9", "eslint-config-next": "^15.1", + "jest": "^30.2.0", + "jest-environment-jsdom": "^30.2.0", + "ts-jest": "^29.4.6", "typescript": "^5.7" } } diff --git a/apps/web/src/__tests__/ErrorBoundary.test.tsx b/apps/web/src/__tests__/ErrorBoundary.test.tsx new file mode 100644 index 0000000..42140ca --- /dev/null +++ b/apps/web/src/__tests__/ErrorBoundary.test.tsx @@ -0,0 +1,92 @@ +import React from "react"; +import { render, screen, fireEvent } from "@testing-library/react"; +import { ErrorBoundary } from "../components/ErrorBoundary"; + +// Suppress React error boundary console.error noise in test output +const originalError = console.error; +beforeAll(() => { + console.error = (...args: unknown[]) => { + const msg = typeof args[0] === "string" ? args[0] : ""; + if (msg.includes("ErrorBoundary") || msg.includes("The above error")) return; + originalError(...args); + }; +}); +afterAll(() => { + console.error = originalError; +}); + +function ThrowingChild({ message }: { message: string }): React.JSX.Element { + throw new Error(message); +} + +function GoodChild() { + return
All good
; +} + +describe("ErrorBoundary", () => { + it("renders children when no error occurs", () => { + render( + + + + ); + expect(screen.getByText("All good")).toBeInTheDocument(); + }); + + it("shows fallback UI when child throws", () => { + render( + + + + ); + expect(screen.getByText("Something went wrong")).toBeInTheDocument(); + expect(screen.getByText("Test crash")).toBeInTheDocument(); + }); + + it("shows custom fallback when provided", () => { + render( + Custom error}> + + + ); + expect(screen.getByText("Custom error")).toBeInTheDocument(); + }); + + it("recovers when Try again is clicked", () => { + let shouldThrow = true; + + function MaybeThrow() { + if (shouldThrow) throw new Error("Boom"); + return
Recovered
; + } + + const { rerender } = render( + + + + ); + + expect(screen.getByText("Something went wrong")).toBeInTheDocument(); + + // Fix the error condition then click retry + shouldThrow = false; + fireEvent.click(screen.getByText("Try again")); + + rerender( + + + + ); + + expect(screen.getByText("Recovered")).toBeInTheDocument(); + }); + + it("renders a Try again button in default fallback", () => { + render( + + + + ); + expect(screen.getByRole("button", { name: "Try again" })).toBeInTheDocument(); + }); +}); diff --git a/apps/web/src/__tests__/GraphPage.test.tsx b/apps/web/src/__tests__/GraphPage.test.tsx new file mode 100644 index 0000000..226f94f --- /dev/null +++ b/apps/web/src/__tests__/GraphPage.test.tsx @@ -0,0 +1,116 @@ +import { render, screen, waitFor } from "@testing-library/react"; +import userEvent from "@testing-library/user-event"; +import GraphPage from "../app/graph/page"; + +jest.mock("next/dynamic", () => { + return function MockDynamic() { + return function MockGraphViewSigma() { + return
Graph rendered
; + }; + }; +}); + +jest.mock("../lib/api", () => ({ + getMiNetwork: jest.fn(), +})); + +import { getMiNetwork } from "../lib/api"; +const mockGetMiNetwork = getMiNetwork as jest.MockedFunction; + +const mockGraph = { + nodes: [ + { ott_id: 1, name: "Corvus corax", rank: "species", image_url: null }, + { ott_id: 2, name: "Corvus corone", rank: "species", image_url: null }, + { ott_id: 3, name: "Corvus", rank: "genus", image_url: null }, + ], + edges: [ + { src: 1, dst: 2, kind: "mi" as const, distance: 0.15 }, + { src: 3, dst: 1, kind: "taxonomy" as const, distance: null }, + { src: 3, dst: 2, kind: "taxonomy" as const, distance: null }, + ], +}; + +describe("GraphPage", () => { + beforeEach(() => { + jest.clearAllMocks(); + }); + + it("shows loading skeleton initially", () => { + mockGetMiNetwork.mockReturnValue(new Promise(() => {})); + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + expect(skeletons.length).toBeGreaterThan(0); + }); + + it("renders page title", async () => { + mockGetMiNetwork.mockResolvedValue(mockGraph); + render(); + + await waitFor(() => { + expect(screen.getByText("MI Similarity Network")).toBeInTheDocument(); + }); + }); + + it("shows species and edge counts after loading", async () => { + mockGetMiNetwork.mockResolvedValue(mockGraph); + render(); + + await waitFor(() => { + expect(screen.getByText(/3 species/)).toBeInTheDocument(); + expect(screen.getByText(/1 MI edges/)).toBeInTheDocument(); + }); + }); + + it("shows error state on API failure", async () => { + mockGetMiNetwork.mockRejectedValue(new Error("Network error")); + render(); + + await waitFor(() => { + expect(screen.getByText(/Network error/)).toBeInTheDocument(); + }); + }); + + it("renders node search box after loading", async () => { + mockGetMiNetwork.mockResolvedValue(mockGraph); + render(); + + await waitFor(() => { + expect(screen.getByPlaceholderText("Search nodes...")).toBeInTheDocument(); + }); + }); + + it("filters nodes in search dropdown", async () => { + const user = userEvent.setup(); + mockGetMiNetwork.mockResolvedValue(mockGraph); + render(); + + await waitFor(() => { + expect(screen.getByPlaceholderText("Search nodes...")).toBeInTheDocument(); + }); + + const input = screen.getByPlaceholderText("Search nodes..."); + await user.type(input, "cor"); + + await waitFor(() => { + expect(screen.getByText("Corvus corax")).toBeInTheDocument(); + expect(screen.getByText("Corvus corone")).toBeInTheDocument(); + }); + }); + + it("renders description text", async () => { + mockGetMiNetwork.mockResolvedValue(mockGraph); + render(); + + await waitFor(() => { + expect( + screen.getByText(/Species with COI barcodes connected by mutual information/) + ).toBeInTheDocument(); + }); + }); + + it("does not show search box while loading", () => { + mockGetMiNetwork.mockReturnValue(new Promise(() => {})); + render(); + expect(screen.queryByPlaceholderText("Search nodes...")).not.toBeInTheDocument(); + }); +}); diff --git a/apps/web/src/__tests__/HomePage.test.tsx b/apps/web/src/__tests__/HomePage.test.tsx new file mode 100644 index 0000000..99984cc --- /dev/null +++ b/apps/web/src/__tests__/HomePage.test.tsx @@ -0,0 +1,71 @@ +import { render, screen } from "@testing-library/react"; +import HomePage from "../app/page"; + +// Mock the SearchBox component since it uses useRouter +jest.mock("../components/SearchBox", () => { + return function MockSearchBox() { + return ; + }; +}); + +// Mock next/link +jest.mock("next/link", () => { + return function MockLink({ + href, + children, + ...props + }: { + href: string; + children: React.ReactNode; + [key: string]: unknown; + }) { + return ( + + {children} + + ); + }; +}); + +describe("HomePage", () => { + it("renders the main heading", () => { + render(); + expect(screen.getByText("Explore the Tree of Life")).toBeInTheDocument(); + }); + + it("renders the search box", () => { + render(); + expect(screen.getByTestId("search-box")).toBeInTheDocument(); + }); + + it("renders the graph explorer link", () => { + render(); + const link = screen.getByText("Open Graph Explorer"); + expect(link).toBeInTheDocument(); + expect(link.closest("a")).toHaveAttribute("href", "/graph"); + }); + + it("renders quick explore links for all taxa", () => { + render(); + expect(screen.getByText("Aves")).toBeInTheDocument(); + expect(screen.getByText("Passeriformes")).toBeInTheDocument(); + expect(screen.getByText("Corvidae")).toBeInTheDocument(); + expect(screen.getByText("Columbidae")).toBeInTheDocument(); + expect(screen.getByText("Strigiformes")).toBeInTheDocument(); + expect(screen.getByText("Psittaciformes")).toBeInTheDocument(); + }); + + it("renders rank badges for quick links", () => { + render(); + const badges = screen.getAllByText("class"); + expect(badges.length).toBeGreaterThanOrEqual(1); + const familyBadges = screen.getAllByText("family"); + expect(familyBadges.length).toBe(2); // Corvidae + Columbidae + }); + + it("links quick explore items to correct taxon pages", () => { + render(); + const avesLink = screen.getByText("Aves").closest("a"); + expect(avesLink).toHaveAttribute("href", "/taxa/81461"); + }); +}); diff --git a/apps/web/src/__tests__/SearchBox.test.tsx b/apps/web/src/__tests__/SearchBox.test.tsx new file mode 100644 index 0000000..62d47ff --- /dev/null +++ b/apps/web/src/__tests__/SearchBox.test.tsx @@ -0,0 +1,156 @@ +import { render, screen, waitFor } from "@testing-library/react"; +import userEvent from "@testing-library/user-event"; +import SearchBox from "../components/SearchBox"; + +const mockPush = jest.fn(); + +jest.mock("next/navigation", () => ({ + useRouter: () => ({ push: mockPush }), +})); + +jest.mock("../lib/api", () => ({ + searchTaxa: jest.fn(), +})); + +import { searchTaxa } from "../lib/api"; +const mockSearchTaxa = searchTaxa as jest.MockedFunction; + +describe("SearchBox", () => { + beforeEach(() => { + jest.clearAllMocks(); + mockSearchTaxa.mockResolvedValue({ items: [], total: 0, limit: 20 }); + }); + + it("renders the search input", () => { + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + expect(input).toBeInTheDocument(); + }); + + it("does not search with fewer than 2 characters", async () => { + const user = userEvent.setup(); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "a"); + // Wait a bit to ensure debounce doesn't fire + await new Promise((r) => setTimeout(r, 400)); + expect(mockSearchTaxa).not.toHaveBeenCalled(); + }); + + it("calls searchTaxa after debounce for 2+ characters", async () => { + const user = userEvent.setup(); + mockSearchTaxa.mockResolvedValue({ + items: [{ ott_id: 1, name: "Corvus", rank: "genus", child_count: 5, image_url: null }], + total: 1, + limit: 20, + }); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "cor"); + + await waitFor(() => expect(mockSearchTaxa).toHaveBeenCalledWith("cor"), { + timeout: 1000, + }); + }); + + it("shows dropdown results", async () => { + const user = userEvent.setup(); + mockSearchTaxa.mockResolvedValue({ + items: [ + { ott_id: 187411, name: "Corvidae", rank: "family", child_count: 10, image_url: null }, + { ott_id: 369568, name: "Corvus", rank: "genus", child_count: 5, image_url: null }, + ], + total: 2, + limit: 20, + }); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "corv"); + + await waitFor(() => { + expect(screen.getByText("Corvidae")).toBeInTheDocument(); + expect(screen.getByText("Corvus")).toBeInTheDocument(); + }, { timeout: 1000 }); + }); + + it("navigates on result selection", async () => { + const user = userEvent.setup(); + mockSearchTaxa.mockResolvedValue({ + items: [{ ott_id: 187411, name: "Corvidae", rank: "family", child_count: 10, image_url: null }], + total: 1, + limit: 20, + }); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "corv"); + + await waitFor(() => expect(screen.getByText("Corvidae")).toBeInTheDocument(), { + timeout: 1000, + }); + + // mousedown triggers navigation + await user.pointer({ target: screen.getByText("Corvidae"), keys: "[MouseLeft]" }); + + expect(mockPush).toHaveBeenCalledWith("/taxa/187411"); + }); + + it("has combobox ARIA role", () => { + render(); + const input = screen.getByRole("combobox"); + expect(input).toBeInTheDocument(); + }); + + it("navigates with arrow keys and Enter", async () => { + const user = userEvent.setup(); + mockSearchTaxa.mockResolvedValue({ + items: [ + { ott_id: 187411, name: "Corvidae", rank: "family", child_count: 10, image_url: null }, + { ott_id: 369568, name: "Corvus", rank: "genus", child_count: 5, image_url: null }, + ], + total: 2, + limit: 20, + }); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "corv"); + + await waitFor(() => expect(screen.getByText("Corvidae")).toBeInTheDocument(), { + timeout: 1000, + }); + + // ArrowDown selects first item + await user.keyboard("{ArrowDown}"); + const firstOption = screen.getByText("Corvidae").closest("li"); + expect(firstOption?.getAttribute("aria-selected")).toBe("true"); + + // ArrowDown again selects second item + await user.keyboard("{ArrowDown}"); + const secondOption = screen.getByText("Corvus").closest("li"); + expect(secondOption?.getAttribute("aria-selected")).toBe("true"); + + // Enter navigates to selected item + await user.keyboard("{Enter}"); + expect(mockPush).toHaveBeenCalledWith("/taxa/369568"); + }); + + it("closes dropdown with Escape", async () => { + const user = userEvent.setup(); + mockSearchTaxa.mockResolvedValue({ + items: [{ ott_id: 187411, name: "Corvidae", rank: "family", child_count: 10, image_url: null }], + total: 1, + limit: 20, + }); + render(); + const input = screen.getByPlaceholderText(/search taxa/i); + await user.type(input, "corv"); + + await waitFor(() => expect(screen.getByText("Corvidae")).toBeInTheDocument(), { + timeout: 1000, + }); + + await user.keyboard("{Escape}"); + + // Dropdown should be closed — listbox should no longer be visible + expect(screen.queryByRole("listbox")).not.toBeInTheDocument(); + }); +}); diff --git a/apps/web/src/__tests__/SequencesPage.test.tsx b/apps/web/src/__tests__/SequencesPage.test.tsx new file mode 100644 index 0000000..a4f47f8 --- /dev/null +++ b/apps/web/src/__tests__/SequencesPage.test.tsx @@ -0,0 +1,177 @@ +import { render, screen, waitFor } from "@testing-library/react"; +import userEvent from "@testing-library/user-event"; +import SequencesPage from "../app/taxa/[ottId]/sequences/page"; + +jest.mock("next/navigation", () => ({ + useParams: () => ({ ottId: "700118" }), +})); + +jest.mock("next/link", () => { + return function MockLink({ + href, + children, + ...props + }: { + href: string; + children: React.ReactNode; + [key: string]: unknown; + }) { + return ( + + {children} + + ); + }; +}); + +const mockTaxon = { + ott_id: 700118, + name: "Corvus corax", + rank: "species", + child_count: 0, + image_url: null, + parent_ott_id: 369568, + parent_name: "Corvus", + ncbi_tax_id: null, + children: [], + total_children: 0, + has_canonical_sequence: true, + lineage: [ + { ott_id: 81461, name: "Aves", rank: "class", child_count: 0, image_url: null }, + ], + wikipedia_url: null, +}; + +const mockSequences = [ + { + id: "seq-1", + ott_id: 700118, + marker: "COI", + source: "NCBI", + accession: "NC_002008", + sequence: "ATCGATCGATCGATCG", + length: 658, + is_canonical: true, + retrieved_at: "2024-01-01T00:00:00Z", + }, + { + id: "seq-2", + ott_id: 700118, + marker: "COI", + source: "NCBI", + accession: "KY456789", + sequence: "GCTAGCTAGCTA", + length: 612, + is_canonical: false, + retrieved_at: "2024-02-01T00:00:00Z", + }, +]; + +jest.mock("../lib/api", () => ({ + getTaxon: jest.fn(), + getSequences: jest.fn(), +})); + +import { getTaxon, getSequences } from "../lib/api"; + +describe("SequencesPage", () => { + beforeEach(() => { + jest.clearAllMocks(); + (getTaxon as jest.Mock).mockResolvedValue(mockTaxon); + (getSequences as jest.Mock).mockResolvedValue({ items: mockSequences, total: 2, offset: 0, limit: 50 }); + }); + + it("shows loading skeleton initially", () => { + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + expect(skeletons.length).toBeGreaterThan(0); + }); + + it("renders page title after loading", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("COI Sequences")).toBeInTheDocument(); + }); + }); + + it("shows taxon name and sequence count", async () => { + render(); + await waitFor(() => { + // Name appears in both breadcrumb and description + const matches = screen.getAllByText(/Corvus corax/); + expect(matches.length).toBeGreaterThanOrEqual(1); + expect(screen.getByText(/2 sequences/)).toBeInTheDocument(); + }); + }); + + it("renders sequence accessions", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("NC_002008")).toBeInTheDocument(); + expect(screen.getByText("KY456789")).toBeInTheDocument(); + }); + }); + + it("marks canonical sequence with badge", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("canonical")).toBeInTheDocument(); + }); + }); + + it("shows sequence length", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("658 bp")).toBeInTheDocument(); + expect(screen.getByText("612 bp")).toBeInTheDocument(); + }); + }); + + it("auto-expands canonical sequence", async () => { + render(); + await waitFor(() => { + // The canonical sequence should be expanded, showing the composition section + const compositionBars = screen.getAllByTitle(/A:/); + expect(compositionBars.length).toBeGreaterThan(0); + }); + }); + + it("shows empty state when no sequences", async () => { + (getSequences as jest.Mock).mockResolvedValue({ items: [], total: 0, offset: 0, limit: 50 }); + render(); + await waitFor(() => { + expect(screen.getByText(/No COI sequences found/)).toBeInTheDocument(); + }); + }); + + it("toggles sequence expansion on click", async () => { + const user = userEvent.setup(); + render(); + + // Wait for sequences to load + await waitFor(() => { + expect(screen.getByText("KY456789")).toBeInTheDocument(); + }); + + // The second sequence should not be expanded initially + // Click to expand it + const header = screen.getByText("KY456789").closest("button"); + if (header) { + await user.click(header); + // After clicking, it should show sequence content for the second sequence + await waitFor(() => { + // There should now be composition elements for the second sequence + const compositionSections = screen.getAllByTitle(/A:/); + expect(compositionSections.length).toBeGreaterThan(0); + }); + } + }); + + it("shows error on API failure", async () => { + (getTaxon as jest.Mock).mockRejectedValue(new Error("Server error")); + render(); + await waitFor(() => { + expect(screen.getByText(/Server error/)).toBeInTheDocument(); + }); + }); +}); diff --git a/apps/web/src/__tests__/Skeleton.test.tsx b/apps/web/src/__tests__/Skeleton.test.tsx new file mode 100644 index 0000000..04347d5 --- /dev/null +++ b/apps/web/src/__tests__/Skeleton.test.tsx @@ -0,0 +1,69 @@ +import { render, screen } from "@testing-library/react"; +import { + SkeletonLine, + SkeletonCircle, + SkeletonCard, + TaxonDetailSkeleton, + GraphPageSkeleton, +} from "../components/Skeleton"; + +describe("SkeletonLine", () => { + it("renders with default dimensions", () => { + const { container } = render(); + const el = container.querySelector(".skeleton"); + expect(el).toBeInTheDocument(); + expect(el).toHaveStyle({ width: "100%", height: "1rem" }); + }); + + it("renders with custom dimensions", () => { + const { container } = render(); + const el = container.querySelector(".skeleton"); + expect(el).toHaveStyle({ width: "200px", height: "2rem" }); + }); +}); + +describe("SkeletonCircle", () => { + it("renders with default size", () => { + const { container } = render(); + const el = container.querySelector(".skeleton"); + expect(el).toBeInTheDocument(); + expect(el).toHaveStyle({ width: "44px", height: "44px", borderRadius: "50%" }); + }); + + it("renders with custom size", () => { + const { container } = render(); + const el = container.querySelector(".skeleton"); + expect(el).toHaveStyle({ width: "80px", height: "80px" }); + }); +}); + +describe("SkeletonCard", () => { + it("renders circle and lines", () => { + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + // 1 circle + 2 lines + expect(skeletons.length).toBe(3); + }); +}); + +describe("TaxonDetailSkeleton", () => { + it("renders without crashing", () => { + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + expect(skeletons.length).toBeGreaterThan(5); + }); + + it("renders hero section placeholder", () => { + const { container } = render(); + const hero = container.querySelector(".hero-section"); + expect(hero).toBeInTheDocument(); + }); +}); + +describe("GraphPageSkeleton", () => { + it("renders without crashing", () => { + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + expect(skeletons.length).toBeGreaterThan(2); + }); +}); diff --git a/apps/web/src/__tests__/StatsPage.test.tsx b/apps/web/src/__tests__/StatsPage.test.tsx new file mode 100644 index 0000000..fb8102d --- /dev/null +++ b/apps/web/src/__tests__/StatsPage.test.tsx @@ -0,0 +1,124 @@ +import { render, screen, waitFor } from "@testing-library/react"; +import StatsPage from "../app/stats/page"; + +const mockStats = { + taxa: { + total: 27853, + by_rank: { + species: 18000, + genus: 5000, + family: 200, + order: 40, + class: 1, + }, + }, + sequences: { + total: 350, + by_source: { NCBI: 300, BOLD: 50 }, + species_with_sequences: 167, + species_total: 18000, + coverage_pct: 0.9, + }, + edges: { + total: 1787, + distance: { min: 0.01, max: 0.95, avg: 0.42 }, + }, +}; + +jest.mock("../lib/api", () => ({ + getStats: jest.fn(), +})); + +jest.mock("next/link", () => { + return function MockLink({ + children, + href, + }: { + children: React.ReactNode; + href: string; + }) { + return {children}; + }; +}); + +import { getStats } from "../lib/api"; +const mockGetStats = getStats as jest.MockedFunction; + +describe("StatsPage", () => { + beforeEach(() => { + jest.clearAllMocks(); + }); + + it("shows loading skeleton initially", () => { + mockGetStats.mockReturnValue(new Promise(() => {})); + render(); + expect(screen.getByText("Database Stats")).toBeInTheDocument(); + }); + + it("renders stats after loading", async () => { + mockGetStats.mockResolvedValue(mockStats); + render(); + + await waitFor(() => { + expect(screen.getByText("27,853")).toBeInTheDocument(); + }); + expect(screen.getByText("Total Taxa")).toBeInTheDocument(); + expect(screen.getByText("350")).toBeInTheDocument(); + expect(screen.getByText("Total Sequences")).toBeInTheDocument(); + expect(screen.getByText("1,787")).toBeInTheDocument(); + expect(screen.getByText("MI Edges")).toBeInTheDocument(); + }); + + it("shows sequence coverage percentage", async () => { + mockGetStats.mockResolvedValue(mockStats); + render(); + + await waitFor(() => { + expect(screen.getByText("0.9%")).toBeInTheDocument(); + }); + expect(screen.getByText("Sequence Coverage")).toBeInTheDocument(); + expect(screen.getByText("167 / 18000 species")).toBeInTheDocument(); + }); + + it("shows sources breakdown", async () => { + mockGetStats.mockResolvedValue(mockStats); + render(); + + await waitFor(() => { + expect(screen.getByText("NCBI")).toBeInTheDocument(); + }); + expect(screen.getByText("300")).toBeInTheDocument(); + expect(screen.getByText("BOLD")).toBeInTheDocument(); + expect(screen.getByText("50")).toBeInTheDocument(); + }); + + it("shows distance distribution", async () => { + mockGetStats.mockResolvedValue(mockStats); + render(); + + await waitFor(() => { + expect(screen.getByText("MI Distance Distribution")).toBeInTheDocument(); + }); + expect(screen.getByText("0.0100")).toBeInTheDocument(); + expect(screen.getByText("0.9500")).toBeInTheDocument(); + expect(screen.getByText("0.4200")).toBeInTheDocument(); + }); + + it("shows error state", async () => { + mockGetStats.mockRejectedValue(new Error("Network error")); + render(); + + await waitFor(() => { + expect(screen.getByText("Failed to load stats: Network error")).toBeInTheDocument(); + }); + }); + + it("renders rank breakdown with labels", async () => { + mockGetStats.mockResolvedValue(mockStats); + render(); + + await waitFor(() => { + expect(screen.getByText("Taxa by Rank")).toBeInTheDocument(); + }); + }); +}); diff --git a/apps/web/src/__tests__/TaxonCard.test.tsx b/apps/web/src/__tests__/TaxonCard.test.tsx new file mode 100644 index 0000000..bdb0880 --- /dev/null +++ b/apps/web/src/__tests__/TaxonCard.test.tsx @@ -0,0 +1,76 @@ +import { render, screen } from "@testing-library/react"; +import TaxonCard from "../components/TaxonCard"; + +jest.mock("next/link", () => { + return function MockLink({ + href, + children, + ...props + }: { + href: string; + children: React.ReactNode; + [key: string]: unknown; + }) { + return ( + + {children} + + ); + }; +}); + +describe("TaxonCard", () => { + const defaultProps = { + ott_id: 700118, + name: "Corvus corax", + rank: "species", + child_count: 0, + image_url: null, + }; + + it("renders taxon name", () => { + render(); + expect(screen.getByText("Corvus corax")).toBeInTheDocument(); + }); + + it("renders rank badge", () => { + render(); + expect(screen.getByText("species")).toBeInTheDocument(); + }); + + it("links to correct taxon page", () => { + render(); + const link = screen.getByText("Corvus corax").closest("a"); + expect(link).toHaveAttribute("href", "/taxa/700118"); + }); + + it("shows child count when > 0", () => { + render(); + expect(screen.getByText("42")).toBeInTheDocument(); + }); + + it("hides child count when 0", () => { + render(); + expect(screen.queryByText("0")).not.toBeInTheDocument(); + }); + + it("renders image when provided", () => { + render(); + const img = screen.getByAltText("Corvus corax"); + expect(img).toHaveAttribute("src", "https://example.com/raven.jpg"); + }); + + it("italicizes species names", () => { + const { container } = render(); + const nameEl = container.querySelector(".italic"); + expect(nameEl).toBeInTheDocument(); + }); + + it("does not italicize non-species names", () => { + const { container } = render( + + ); + const nameEl = container.querySelector(".italic"); + expect(nameEl).not.toBeInTheDocument(); + }); +}); diff --git a/apps/web/src/__tests__/TaxonDetailPage.test.tsx b/apps/web/src/__tests__/TaxonDetailPage.test.tsx new file mode 100644 index 0000000..4b4cb00 --- /dev/null +++ b/apps/web/src/__tests__/TaxonDetailPage.test.tsx @@ -0,0 +1,132 @@ +import { render, screen, waitFor } from "@testing-library/react"; +import TaxonDetailPage from "../app/taxa/[ottId]/page"; + +const mockTaxon = { + ott_id: 187411, + name: "Corvidae", + rank: "family", + child_count: 3, + image_url: null, + parent_ott_id: 1041547, + parent_name: "Passeriformes", + ncbi_tax_id: null, + children: [ + { ott_id: 369568, name: "Corvus", rank: "genus", child_count: 2, image_url: null }, + ], + total_children: 1, + has_canonical_sequence: false, + lineage: [ + { ott_id: 81461, name: "Aves", rank: "class", child_count: 0, image_url: null }, + { ott_id: 1041547, name: "Passeriformes", rank: "order", child_count: 0, image_url: null }, + ], + wikipedia_url: null, +}; + +jest.mock("next/navigation", () => ({ + useParams: () => ({ ottId: "187411" }), +})); + +jest.mock("next/link", () => { + return function MockLink({ + href, + children, + ...props + }: { + href: string; + children: React.ReactNode; + [key: string]: unknown; + }) { + return ( + + {children} + + ); + }; +}); + +jest.mock("next/dynamic", () => { + return function mockDynamic() { + return function MockComponent() { + return
Graph
; + }; + }; +}); + +jest.mock("../lib/api", () => ({ + getTaxon: jest.fn(), + getNeighbors: jest.fn(), + getSubtreeGraph: jest.fn(), + getChildren: jest.fn(), +})); + +import { getTaxon, getNeighbors, getSubtreeGraph } from "../lib/api"; + +describe("TaxonDetailPage", () => { + beforeEach(() => { + jest.clearAllMocks(); + (getTaxon as jest.Mock).mockResolvedValue(mockTaxon); + (getNeighbors as jest.Mock).mockResolvedValue([]); + (getSubtreeGraph as jest.Mock).mockResolvedValue({ nodes: [], edges: [] }); + }); + + it("shows loading skeleton initially", () => { + const { container } = render(); + const skeletons = container.querySelectorAll(".skeleton"); + expect(skeletons.length).toBeGreaterThan(0); + }); + + it("renders taxon name after loading", async () => { + render(); + await waitFor(() => { + // Name appears in both breadcrumb and hero title + const matches = screen.getAllByText("Corvidae"); + expect(matches.length).toBeGreaterThanOrEqual(1); + }); + }); + + it("renders rank badge", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("family")).toBeInTheDocument(); + }); + }); + + it("renders breadcrumb lineage", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("Aves")).toBeInTheDocument(); + expect(screen.getByText("Passeriformes")).toBeInTheDocument(); + }); + }); + + it("renders children", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("Corvus")).toBeInTheDocument(); + }); + }); + + it("shows external links", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("Wikipedia")).toBeInTheDocument(); + expect(screen.getByText("iNaturalist")).toBeInTheDocument(); + expect(screen.getByText("eBird")).toBeInTheDocument(); + }); + }); + + it("shows OTT ID", async () => { + render(); + await waitFor(() => { + expect(screen.getByText("OTT 187411")).toBeInTheDocument(); + }); + }); + + it("shows error on API failure", async () => { + (getTaxon as jest.Mock).mockRejectedValue(new Error("Network error")); + render(); + await waitFor(() => { + expect(screen.getByText(/Network error/)).toBeInTheDocument(); + }); + }); +}); diff --git a/apps/web/src/__tests__/api.test.ts b/apps/web/src/__tests__/api.test.ts new file mode 100644 index 0000000..93f27e1 --- /dev/null +++ b/apps/web/src/__tests__/api.test.ts @@ -0,0 +1,155 @@ +import { getJSON, searchTaxa, getTaxon, getSubtreeGraph, getNeighbors, getChildren, getSequences, getStats } from "../lib/api"; + +// Mock global fetch +const mockFetch = jest.fn(); +global.fetch = mockFetch; + +describe("API client", () => { + beforeEach(() => { + jest.clearAllMocks(); + }); + + describe("getJSON", () => { + it("fetches from API base URL", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ data: "test" }), + }); + + const result = await getJSON("/v1/test"); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/test"), + { cache: "no-store" } + ); + expect(result).toEqual({ data: "test" }); + }); + + it("throws on non-ok response", async () => { + mockFetch.mockResolvedValue({ + ok: false, + status: 404, + statusText: "Not Found", + }); + + await expect(getJSON("/v1/missing")).rejects.toThrow("API error: 404 Not Found"); + }); + }); + + describe("searchTaxa", () => { + it("encodes query parameter", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve([]), + }); + + await searchTaxa("Corvus corax"); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/search?q=Corvus%20corax&limit=20"), + expect.anything() + ); + }); + + it("accepts custom limit", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve([]), + }); + + await searchTaxa("test", 5); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("limit=5"), + expect.anything() + ); + }); + }); + + describe("getTaxon", () => { + it("fetches correct endpoint", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ ott_id: 123 }), + }); + + await getTaxon(123); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/taxa/123"), + expect.anything() + ); + }); + }); + + describe("getSubtreeGraph", () => { + it("includes depth parameter", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ nodes: [], edges: [] }), + }); + + await getSubtreeGraph(123, 3); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/graph/subtree/123?depth=3"), + expect.anything() + ); + }); + }); + + describe("getNeighbors", () => { + it("includes k parameter", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve([]), + }); + + await getNeighbors(123, 10); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/graph/neighbors/123?k=10"), + expect.anything() + ); + }); + }); + + describe("getChildren", () => { + it("includes pagination parameters", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ items: [], total: 0, offset: 50, limit: 25 }), + }); + + await getChildren(123, 50, 25); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/taxa/123/children?offset=50&limit=25"), + expect.anything() + ); + }); + }); + + describe("getSequences", () => { + it("fetches correct endpoint with pagination", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ items: [], total: 0, offset: 0, limit: 50 }), + }); + + await getSequences(123); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/taxa/123/sequences?offset=0&limit=50"), + expect.anything() + ); + }); + }); + + describe("getStats", () => { + it("fetches stats endpoint", async () => { + mockFetch.mockResolvedValue({ + ok: true, + json: () => Promise.resolve({ taxa: {}, sequences: {}, edges: {} }), + }); + + await getStats(); + expect(mockFetch).toHaveBeenCalledWith( + expect.stringContaining("/v1/stats"), + expect.anything() + ); + }); + }); +}); diff --git a/apps/web/src/__tests__/external-links.test.ts b/apps/web/src/__tests__/external-links.test.ts new file mode 100644 index 0000000..4dc3c56 --- /dev/null +++ b/apps/web/src/__tests__/external-links.test.ts @@ -0,0 +1,33 @@ +import { wikipediaUrl, inaturalistUrl, ebirdUrl } from "../lib/external-links"; + +describe("external-links", () => { + describe("wikipediaUrl", () => { + it("replaces spaces with underscores", () => { + expect(wikipediaUrl("Corvus corax")).toBe( + "https://en.wikipedia.org/wiki/Corvus_corax" + ); + }); + + it("handles single word", () => { + expect(wikipediaUrl("Aves")).toBe( + "https://en.wikipedia.org/wiki/Aves" + ); + }); + }); + + describe("inaturalistUrl", () => { + it("encodes name for search", () => { + expect(inaturalistUrl("Corvus corax")).toBe( + "https://www.inaturalist.org/taxa/search?q=Corvus%20corax" + ); + }); + }); + + describe("ebirdUrl", () => { + it("encodes name for search", () => { + expect(ebirdUrl("Corvus corax")).toBe( + "https://ebird.org/species/search?q=Corvus%20corax" + ); + }); + }); +}); diff --git a/apps/web/src/app/error.tsx b/apps/web/src/app/error.tsx new file mode 100644 index 0000000..0e15042 --- /dev/null +++ b/apps/web/src/app/error.tsx @@ -0,0 +1,35 @@ +"use client"; + +export default function Error({ + error, + reset, +}: { + error: Error & { digest?: string }; + reset: () => void; +}) { + return ( +
+

+ Something went wrong +

+

+ {error.message || "An unexpected error occurred while loading this page."} +

+ +
+ ); +} diff --git a/apps/web/src/app/layout.tsx b/apps/web/src/app/layout.tsx index 6d0047f..68cc084 100644 --- a/apps/web/src/app/layout.tsx +++ b/apps/web/src/app/layout.tsx @@ -1,5 +1,6 @@ import type { Metadata } from "next"; import Link from "next/link"; +import { ErrorBoundary } from "../components/ErrorBoundary"; import "./globals.css"; export const metadata: Metadata = { @@ -23,11 +24,12 @@ export default function RootLayout({
Home Graph + Stats
- {children} + {children}
diff --git a/apps/web/src/app/not-found.tsx b/apps/web/src/app/not-found.tsx new file mode 100644 index 0000000..6e7b7c1 --- /dev/null +++ b/apps/web/src/app/not-found.tsx @@ -0,0 +1,32 @@ +import Link from "next/link"; + +export default function NotFound() { + return ( +
+

+ 404 +

+

+ Page not found +

+

+ The page you're looking for doesn't exist or has been moved. +

+ + Go Home + +
+ ); +} diff --git a/apps/web/src/app/stats/page.tsx b/apps/web/src/app/stats/page.tsx new file mode 100644 index 0000000..222e66c --- /dev/null +++ b/apps/web/src/app/stats/page.tsx @@ -0,0 +1,238 @@ +"use client"; + +import { useEffect, useState } from "react"; +import Link from "next/link"; +import { getStats } from "@/lib/api"; +import type { StatsResponse } from "@/lib/types"; + +const RANK_COLORS: Record = { + class: "#e57373", + order: "#ffb74d", + family: "#fff176", + genus: "#81c784", + species: "#4fc3f7", +}; + +function StatCard({ + label, + value, + sub, +}: { + label: string; + value: string | number; + sub?: string; +}) { + return ( +
+
+ {typeof value === "number" ? value.toLocaleString() : value} +
+
+ {label} +
+ {sub && ( +
+ {sub} +
+ )} +
+ ); +} + +function RankBar({ + ranks, + total, +}: { + ranks: Record; + total: number; +}) { + if (total === 0) return null; + + const ordered = Object.entries(ranks).sort((a, b) => b[1] - a[1]); + + return ( +
+
+ {ordered.map(([rank, count]) => ( +
0 ? 2 : 0, + }} + title={`${rank}: ${count.toLocaleString()}`} + /> + ))} +
+
+ {ordered.map(([rank, count]) => ( +
+ + {rank} + {count.toLocaleString()} +
+ ))} +
+
+ ); +} + +export default function StatsPage() { + const [stats, setStats] = useState(null); + const [error, setError] = useState(null); + const [loading, setLoading] = useState(true); + + useEffect(() => { + getStats() + .then(setStats) + .catch((err: Error) => setError(err.message)) + .finally(() => setLoading(false)); + }, []); + + if (error) { + return
Failed to load stats: {error}
; + } + + if (loading || !stats) { + return ( +
+

Database Stats

+
+ {[1, 2, 3, 4].map((i) => ( +
+ ))} +
+
+ ); + } + + return ( +
+
+

Database Stats

+ + Back to Home + +
+ +
+ + + + +
+ +
+
+

+ Taxa by Rank +

+
+ +
+
+ +
+

+ Sequences by Source +

+
+ {Object.entries(stats.sequences.by_source).length > 0 ? ( +
+ {Object.entries(stats.sequences.by_source) + .sort((a, b) => b[1] - a[1]) + .map(([source, count]) => ( +
+ {source} + {count.toLocaleString()} +
+ ))} +
+ ) : ( +

No sequences ingested yet.

+ )} +
+ + {stats.edges.distance && ( + <> +

+ MI Distance Distribution +

+
+
+
+ Min + + {stats.edges.distance.min.toFixed(4)} + +
+
+ Max + + {stats.edges.distance.max.toFixed(4)} + +
+
+ Average + + {stats.edges.distance.avg.toFixed(4)} + +
+
+
+ + )} +
+
+
+ ); +} diff --git a/apps/web/src/app/taxa/[ottId]/sequences/page.tsx b/apps/web/src/app/taxa/[ottId]/sequences/page.tsx index 29b998d..460b001 100644 --- a/apps/web/src/app/taxa/[ottId]/sequences/page.tsx +++ b/apps/web/src/app/taxa/[ottId]/sequences/page.tsx @@ -129,11 +129,11 @@ export default function SequencesPage() { } Promise.all([getTaxon(ottId), getSequences(ottId)]) - .then(([t, s]) => { + .then(([t, seqPage]) => { setTaxon(t); - setSequences(s); + setSequences(seqPage.items); // Auto-expand canonical sequence - const canonical = s.find((seq) => seq.is_canonical); + const canonical = seqPage.items.find((seq) => seq.is_canonical); if (canonical) setExpanded(canonical.id); }) .catch((err: Error) => setError(err.message)) diff --git a/apps/web/src/components/ErrorBoundary.tsx b/apps/web/src/components/ErrorBoundary.tsx new file mode 100644 index 0000000..1c1393e --- /dev/null +++ b/apps/web/src/components/ErrorBoundary.tsx @@ -0,0 +1,66 @@ +"use client"; + +import React from "react"; + +interface ErrorBoundaryProps { + children: React.ReactNode; + fallback?: React.ReactNode; +} + +interface ErrorBoundaryState { + hasError: boolean; + error: Error | null; +} + +export class ErrorBoundary extends React.Component< + ErrorBoundaryProps, + ErrorBoundaryState +> { + constructor(props: ErrorBoundaryProps) { + super(props); + this.state = { hasError: false, error: null }; + } + + static getDerivedStateFromError(error: Error): ErrorBoundaryState { + return { hasError: true, error }; + } + + componentDidCatch(error: Error, info: React.ErrorInfo) { + console.error("ErrorBoundary caught:", error, info.componentStack); + } + + render() { + if (this.state.hasError) { + if (this.props.fallback) { + return this.props.fallback; + } + + return ( +
+

+ Something went wrong +

+

+ {this.state.error?.message || "An unexpected error occurred."} +

+ +
+ ); + } + + return this.props.children; + } +} diff --git a/apps/web/src/components/SearchBox.tsx b/apps/web/src/components/SearchBox.tsx index 14a98f9..b06be78 100644 --- a/apps/web/src/components/SearchBox.tsx +++ b/apps/web/src/components/SearchBox.tsx @@ -10,6 +10,7 @@ export default function SearchBox() { const [results, setResults] = useState([]); const [isOpen, setIsOpen] = useState(false); const [isLoading, setIsLoading] = useState(false); + const [activeIndex, setActiveIndex] = useState(-1); const router = useRouter(); const wrapperRef = useRef(null); const debounceRef = useRef | null>(null); @@ -27,8 +28,9 @@ export default function SearchBox() { setIsLoading(true); try { const data = await searchTaxa(query.trim()); - setResults(data); - setIsOpen(data.length > 0); + setResults(data.items); + setIsOpen(data.items.length > 0); + setActiveIndex(-1); } catch { setResults([]); } finally { @@ -54,9 +56,28 @@ export default function SearchBox() { function handleSelect(ottId: number) { setIsOpen(false); setQuery(""); + setActiveIndex(-1); router.push(`/taxa/${ottId}`); } + function handleKeyDown(e: React.KeyboardEvent) { + if (!isOpen || results.length === 0) return; + + if (e.key === "ArrowDown") { + e.preventDefault(); + setActiveIndex((prev) => (prev < results.length - 1 ? prev + 1 : 0)); + } else if (e.key === "ArrowUp") { + e.preventDefault(); + setActiveIndex((prev) => (prev > 0 ? prev - 1 : results.length - 1)); + } else if (e.key === "Enter" && activeIndex >= 0) { + e.preventDefault(); + handleSelect(results[activeIndex].ott_id); + } else if (e.key === "Escape") { + setIsOpen(false); + setActiveIndex(-1); + } + } + return (
setQuery(e.target.value)} onFocus={() => results.length > 0 && setIsOpen(true)} + onKeyDown={handleKeyDown} placeholder="Search taxa (e.g. Corvidae, Homo sapiens)..." + role="combobox" + aria-expanded={isOpen} + aria-activedescendant={activeIndex >= 0 ? `search-result-${activeIndex}` : undefined} style={inputStyle} /> {isLoading && ( ... )} {isOpen && results.length > 0 && ( -
    - {results.map((taxon) => ( +
      + {results.map((taxon, index) => (
    • handleSelect(taxon.ott_id)} + onMouseEnter={() => setActiveIndex(index)} > {taxon.name} diff --git a/apps/web/src/lib/api.ts b/apps/web/src/lib/api.ts index e378619..c546199 100644 --- a/apps/web/src/lib/api.ts +++ b/apps/web/src/lib/api.ts @@ -1,4 +1,4 @@ -import type { TaxonSummary, TaxonDetail, ChildrenPage, GraphResponse, NeighborOut, SequenceOut } from "./types"; +import type { TaxonDetail, SearchPage, ChildrenPage, SequencePage, GraphResponse, NeighborOut, StatsResponse } from "./types"; const API_BASE = process.env.NEXT_PUBLIC_API_BASE || "http://localhost:8000"; @@ -11,7 +11,7 @@ export async function getJSON(path: string): Promise { } export function searchTaxa(query: string, limit = 20) { - return getJSON( + return getJSON( `/v1/search?q=${encodeURIComponent(query)}&limit=${limit}` ); } @@ -36,6 +36,10 @@ export function getChildren(ottId: number, offset = 0, limit = 100) { return getJSON(`/v1/taxa/${ottId}/children?offset=${offset}&limit=${limit}`); } -export function getSequences(ottId: number) { - return getJSON(`/v1/taxa/${ottId}/sequences`); +export function getSequences(ottId: number, offset = 0, limit = 50) { + return getJSON(`/v1/taxa/${ottId}/sequences?offset=${offset}&limit=${limit}`); +} + +export function getStats() { + return getJSON(`/v1/stats`); } diff --git a/apps/web/src/lib/types.ts b/apps/web/src/lib/types.ts index 41c66d8..f3e5f00 100644 --- a/apps/web/src/lib/types.ts +++ b/apps/web/src/lib/types.ts @@ -25,6 +25,12 @@ export interface ChildrenPage { limit: number; } +export interface SearchPage { + items: TaxonSummary[]; + total: number; + limit: number; +} + export interface SequenceOut { id: string; ott_id: number; @@ -37,6 +43,13 @@ export interface SequenceOut { retrieved_at: string | null; } +export interface SequencePage { + items: SequenceOut[]; + total: number; + offset: number; + limit: number; +} + export interface GraphNode { ott_id: number; name: string; @@ -63,3 +76,25 @@ export interface NeighborOut { distance: number; mi_norm: number; } + +export interface StatsResponse { + taxa: { + total: number; + by_rank: Record; + }; + sequences: { + total: number; + by_source: Record; + species_with_sequences: number; + species_total: number; + coverage_pct: number; + }; + edges: { + total: number; + distance: { + min: number; + max: number; + avg: number; + } | null; + }; +} diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml new file mode 100644 index 0000000..577b182 --- /dev/null +++ b/docker-compose.prod.yml @@ -0,0 +1,38 @@ +# Production override — use with: +# docker compose -f docker-compose.yml -f docker-compose.prod.yml up --build +# +# Changes from dev: +# - API: multi-worker uvicorn (4 workers), non-root user, no hot-reload +# - Web: standalone Next.js build, non-root user, ~80% smaller image +# - No source volume mounts (immutable images) +# - Postgres password from env var (no default) + +services: + db: + environment: + POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:?Set POSTGRES_PASSWORD in .env} + + api: + build: + context: ./apps/api + target: prod + environment: + DATABASE_URL: postgresql+psycopg://postgres:${POSTGRES_PASSWORD}@db:5432/evograph + REDIS_URL: redis://redis:6379/0 + SCOPE_OTT_ROOT: ${SCOPE_OTT_ROOT:-Aves} + CORS_ORIGINS: ${CORS_ORIGINS:-["*"]} + LOG_LEVEL: ${LOG_LEVEL:-info} + LOG_FORMAT: ${LOG_FORMAT:-json} + volumes: [] # Remove dev source mounts + restart: unless-stopped + + web: + build: + context: ./apps/web + target: prod + args: + NEXT_PUBLIC_API_BASE: ${NEXT_PUBLIC_API_BASE:-http://localhost:8000} + restart: unless-stopped + + redis: + restart: unless-stopped diff --git a/docker-compose.yml b/docker-compose.yml index 6dd1938..03b0069 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -24,10 +24,13 @@ services: retries: 5 api: - build: ./apps/api + build: + context: ./apps/api + target: dev environment: DATABASE_URL: postgresql+psycopg://postgres:postgres@db:5432/evograph REDIS_URL: redis://redis:6379/0 + SCOPE_OTT_ROOT: ${SCOPE_OTT_ROOT:-Aves} ports: ["8000:8000"] depends_on: db: @@ -39,7 +42,9 @@ services: - ./data:/app/data web: - build: ./apps/web + build: + context: ./apps/web + target: dev environment: NEXT_PUBLIC_API_BASE: http://localhost:8000 ports: ["3000:3000"]