diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..8a88ba8 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,39 @@ +name: Deploy to GitHub Pages + +on: + # New releases will cause the gh-pages branch to be updated. + release: + # TODO: Remove the pull_request trigger below before merging this PR + pull_request: + +permissions: + contents: write + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - uses: actions/setup-node@v4 + with: + node-version: '22' + cache: npm + cache-dependency-path: web/package-lock.json + + - name: Install dependencies + run: npm ci + working-directory: web + + - name: Build + run: npm run build + working-directory: web + + - name: Deploy to gh-pages + uses: peaceiris/actions-gh-pages@v4 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: web/dist + # force_orphan replaces the entire gh-pages branch on every deploy, + # ensuring no previously-deployed files are left behind. + force_orphan: true diff --git a/.gitignore b/.gitignore index 55c6b2a..53b4f8c 100644 --- a/.gitignore +++ b/.gitignore @@ -192,6 +192,10 @@ cython_debug/ # you could uncomment the following to ignore the entire vscode folder # .vscode/ +# Node.js (web/ frontend) +node_modules/ +web/dist/ + # Ruff stuff: .ruff_cache/ diff --git a/CLAUDE.md b/CLAUDE.md index 8ecea72..23d6a57 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -8,17 +8,15 @@ babel-explorer is a tool for querying and exploring Babel intermediate files. It ## Development Setup -This project uses **uv** for package management: +This project has two package managers — **uv** for Python and **npm** for the Astro/Vue frontend: ```bash -# Install dependencies -uv sync - -# Install with dev dependencies +# Python (CLI + server frontend) uv sync --group dev - -# Run the CLI uv run babel-explorer --help + +# Astro/Vue frontend (GitHub Pages) +cd web && npm install && npm run dev ``` ## Commands @@ -43,6 +41,12 @@ uv run babel-explorer test-concord MONDO:0004979 HP:0000001 # Use custom Babel server or local directory uv run babel-explorer xrefs MONDO:0004979 --local-dir data/2025nov19 --babel-url https://stars.renci.org:443/var/babel_outputs/2025nov19/ + +# Start the web server +uv run babel-explorer web + +# Start with custom options +uv run babel-explorer web --host 0.0.0.0 --port 9000 --reload ``` ### Development Commands @@ -65,6 +69,12 @@ uv run ruff check # Format code uv run ruff format + +# Astro/Vue frontend (from web/ directory) +cd web && npm run dev # Dev server at localhost:4321 +cd web && npm run build # Build to web/dist/ +cd web && npm test # Run Vitest unit + component tests +cd web && npm run test:watch # Watch mode ``` ## Architecture @@ -87,11 +97,36 @@ uv run ruff format - Integration with NodeNormalization API (https://nodenormalization-sri.renci.org/) - Fetches labels, biolink types, and equivalent identifiers for CURIEs - Uses `@functools.lru_cache` for performance + - `NodeNorm.URLs` loaded from `config/translator-endpoints.json` (shared with the Astro frontend) - Optional component for label enrichment 4. **CLI** (`src/babel_explorer/cli.py`): - Click-based command-line interface - - Three main commands: `xrefs`, `ids`, `test-concord` + - Four main commands: `xrefs`, `ids`, `test-concord`, `web` + +5. **Python Web Frontend** (`src/babel_explorer/web/`): + - FastAPI + Jinja2 + htmx + Bootstrap 5 (CDN) web interface + - App factory in `web/__init__.py` — `create_app(local_dir, babel_url, nodenorm_url)` + - All routes in `web/routes.py` — HTML pages, htmx partials, JSON API, CSV downloads + - Templates in `web/templates/` with `_partials/` for htmx fragments + - Sync route handlers (core code is synchronous; FastAPI runs them in a threadpool) + - Four tools exposed: NodeNorm, XRefs, IDs, Test Concordance + - Deployed to Kubernetes (hosts DB-dependent tools) + +6. **Astro/Vue Web Frontend** (`web/`): + - Astro + Vue 3 static site for browser-only tools (no backend required) + - npm package name: `babel-explorer` (directory stays `web/`) + - Deployed to GitHub Pages + - Currently hosts: NodeNorm lookup (unified instance selection via checkboxes, expandable result table, shareable URLs) + - Calls NodeNorm API directly from the browser via `fetch()` (CORS-enabled) + - Uses Bootstrap 5 (CDN) with the same dark-navbar styling as the Python frontend + - CURIE link-outs via [biolink-model prefix map](https://github.com/biolink/biolink-model) (v4.3.7, fetched at runtime) + - Tested with Vitest + @vue/test-utils + happy-dom (99 tests); see `web/tests/README.md` + - See `web/README.md` for development instructions and `web/FUTURE.md` for deferred features + +7. **Shared Configuration** (`config/`): + - `config/translator-endpoints.json` — single source of truth for NodeNorm and NameRes deployment URLs across all environments (dev, exp, ci, test, prod) + - Consumed by Python CLI/frontend (`nodenorm.py`) and Astro frontend (`NodeNormApp.vue`) ### Data Flow @@ -100,6 +135,57 @@ uv run ruff format 3. BabelXRefs queries files using DuckDB 4. If `--labels` or `--recurse` flags are set, NodeNorm is queried for additional metadata 5. Results are printed to stdout +1. User provides CURIEs via CLI, Python web UI, or Astro web UI +2. For DB-dependent tools (XRefs, IDs): BabelDownloader ensures required Parquet files are downloaded, BabelXRefs queries files using DuckDB +3. For API-only tools (NodeNorm): the Astro frontend calls the NodeNorm API directly from the browser; the Python frontend proxies through the server +4. If `--labels` or `--expand` flags are set, NodeNorm is queried for additional metadata +5. Results are printed to stdout (CLI), rendered as HTML tables / JSON / CSV (Python web), or rendered as Vue components (Astro web) + +### Astro/Vue Frontend Structure (`web/`) + +``` +web/src/ + layouts/BaseLayout.astro # Bootstrap 5 CDN + dark navbar + components/ + Navbar.astro # Dark navbar matching Python frontend + nodenorm/ + NodeNormApp.vue # Root Vue island (client:only="vue") + NodeNormForm.vue # Form: textarea, checkboxes + custom URL, API toggles + ComparisonView.vue # Results table (rows=CURIEs, cols=instances) with expandable rows + CurieDetailPanel.vue # Expandable detail body: description, types, IC, equiv IDs + CurieResultCard.vue # Accordion card wrapping CurieDetailPanel (single-instance use) + ResultsSummary.vue # Unified stat tiles: normalized count, disagreements, types + EquivalentIdTable.vue # Striped table with togglable columns + ColumnVisibility.vue # Page-wide column show/hide controls + shared/ + CurieLink.vue # CURIE → external URL link using biolink prefix map + lib/ + nodenorm-api.ts # fetch() wrapper for NodeNorm get_normalized_nodes (AbortSignal support) + curie-links.ts # Biolink prefix map loader + URL builder + url-state.ts # Encode/decode query state in URL params (readQueryState, buildQueryUrl) + types.ts # TypeScript interfaces + DEFAULT_API_OPTIONS + pages/ + index.astro # Landing page with tool cards + nodenorm.astro # NodeNorm tool page +``` + +Key patterns: +- Each tool page hosts one Vue island via `client:only="vue"` (no SSR — all client-side) +- Shared config imported from `config/translator-endpoints.json` at build time +- Bootstrap via CDN (not npm) to match the Python frontend exactly + +### Python Web Route Structure + +| Route | Method | Returns | Purpose | +|-------|--------|---------|---------| +| `/` | GET | HTML | Landing page | +| `/nodenorm`, `/xrefs`, `/ids`, `/test-concord` | GET | HTML | Tool form pages | +| `/htmx/nodenorm`, `/htmx/xrefs`, `/htmx/ids`, `/htmx/test-concord` | POST | HTML partial | htmx result fragments | +| `/api/nodenorm`, `/api/xrefs`, `/api/ids`, `/api/test-concord` | GET | JSON | REST API (`?curie=X&curie=Y`) | +| `/api/*/csv` | GET | CSV file | CSV download for each tool | +| `/docs` | GET | HTML | Swagger UI (auto-generated by FastAPI) | + +The NodeNorm and Test Concordance pages include a dropdown to select from predefined `NodeNorm.URLs` instances or enter a custom URL. ### Key Design Patterns @@ -107,6 +193,8 @@ uv run ruff format - **LRU caching**: Heavy use of `@functools.lru_cache` to avoid redundant downloads and API calls - **Recursive expansion**: The `--recurse` flag recursively follows all cross-references to build complete graphs - **DuckDB for querying**: In-memory SQL queries against Parquet files for fast lookups +- **Dual frontend**: DB-dependent tools on a server (FastAPI + htmx), API-only tools in the browser (Astro + Vue). Split follows data dependencies. +- **Shared config**: `config/translator-endpoints.json` is the single source of truth for deployment URLs, consumed by both frontends and the CLI ## Testing @@ -123,12 +211,14 @@ Tests live in `tests/` and are split into fast **unit tests** (mocked, no networ | `tests/test_babel_xrefs.py` | 23 | 20 | 3 | 46 | | `tests/test_nodenorm.py` | 20 | 13 | 0 | 33 | | `tests/test_cli.py` | 24 | 0 | 0 | 24 | +| `tests/test_web.py` | 25 | 0 | 0 | 25 | ### Test Infrastructure - **`tests/conftest.py`** — Session-scoped fixtures that download Parquet files once and share them across all integration tests. Teardown removes the `data/test/` directory so the next run starts fresh. - **`tests/constants.py`** — Shared constants (URLs, file paths) and `load_curies()` helper. - **`tests/data/valid_curies.txt`** — One CURIE per line (`#` comments allowed). Integration tests are parametrized over this list — adding a new line automatically expands test coverage. +- **`tests/fixtures/`** — JSON snapshots of real NodeNorm API responses, shared by both Python and TypeScript test suites. Includes single-CURIE responses, batch (multi-CURIE) responses, conflated vs. non-conflated variants, and a biolink prefix map subset. See `web/tests/README.md` for the full fixture list and how to regenerate them. ### Key Dataclasses @@ -144,8 +234,17 @@ Tests live in `tests/` and are split into fast **unit tests** (mocked, no networ ## File Locations -- Source code: `src/babel_explorer/` +- Python source code: `src/babel_explorer/` - Tests: `tests/` - Test CURIEs: `tests/data/valid_curies.txt` - Downloaded Babel files: `data//duckdb/*.parquet` +- Generated DuckDB databases: `data//output/duckdbs/` +- Python web frontend: `src/babel_explorer/web/` +- Python web templates: `src/babel_explorer/web/templates/` +- Astro/Vue web frontend: `web/` +- Astro/Vue components: `web/src/components/` +- Astro/Vue pages: `web/src/pages/` +- Astro/Vue tests: `web/src/**/__tests__/` (co-located) + `web/tests/README.md` +- Shared config: `config/translator-endpoints.json` +- Shared test fixtures (Python + TS): `tests/fixtures/` - Entry point: `src/babel_explorer/cli.py` diff --git a/README.md b/README.md index 00fff8c..48ab742 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,92 @@ uv run babel-explorer ids MONDO:0004979 uv run babel-explorer test-concord MONDO:0004979 HP:0000001 ``` +## Web Frontends + +babel-explorer has **two** web frontends that share the same Bootstrap 5 dark-navbar styling. See [Architecture: Frontend Deployment](#architecture-frontend-deployment) for the rationale behind the split. + +### Astro/Vue Frontend (GitHub Pages) + +Static site built with Astro + Vue 3. Hosts API-only tools that run entirely in the browser. + +```bash +cd web +npm install +npm run dev # Dev server at http://localhost:4321 +npm run build # Build to web/dist/ +``` + +**Currently available:** NodeNorm lookup (single-instance and multi-instance comparison). + +### Python Frontend (Kubernetes) + +FastAPI + htmx server. Hosts database-dependent tools that need DuckDB and multi-GB Parquet files. + +```bash +# Start the web server (default: http://127.0.0.1:8000) +uv run babel-explorer web + +# Custom host/port +uv run babel-explorer web --host 0.0.0.0 --port 9000 + +# Auto-reload for development +uv run babel-explorer web --reload +``` + +Once running, open http://127.0.0.1:8000 in a browser. The navbar links to each tool page, the Swagger API docs (`/docs`), and this GitHub repository. + +### REST API + +The JSON API accepts CURIEs as repeated query parameters: + +```bash +# NodeNorm lookup +curl "http://127.0.0.1:8000/api/nodenorm?curie=MONDO:0004979" + +# Cross-references with expansion +curl "http://127.0.0.1:8000/api/xrefs?curie=MONDO:0004979&expand=true" + +# Identifier records +curl "http://127.0.0.1:8000/api/ids?curie=MONDO:0004979" + +# Test concordance +curl "http://127.0.0.1:8000/api/test-concord?curie=MONDO:0004979" +``` + +CSV downloads are available at `/api/nodenorm/csv`, `/api/xrefs/csv`, `/api/ids/csv`, and `/api/test-concord/csv` with the same query parameters. + +## Architecture: Frontend Deployment + +babel-explorer's four web tools have fundamentally different infrastructure needs: + +| Tool | Data dependency | Needs a server? | +|------|----------------|-----------------| +| **XRefs** | Concord.parquet (~626 MB) + DuckDB | Yes | +| **IDs** | Identifiers.parquet (~2 GB+) + DuckDB | Yes | +| **NodeNorm** | External API only (CORS-enabled) | No | +| **Test Concordance** | External API only (CORS-enabled) | No | + +XRefs and IDs query multi-GB Parquet files via DuckDB — they genuinely need a server with those files on disk. NodeNorm and Test Concordance are pure API proxies: the server adds latency and a failure point for zero value, since the NodeNorm API supports CORS and can be called directly from the browser. + +The frontend is therefore split along this natural dependency boundary: + +### Server (Kubernetes) — `src/babel_explorer/web/` + +The FastAPI + htmx server hosts **XRefs** and **IDs**. It downloads and caches Parquet files, runs DuckDB queries, and renders HTML server-side. It also exposes the JSON REST API (`/api/xrefs`, `/api/ids`) and CSV downloads for programmatic access. + +### GitHub Pages (static) — `web/` + +**NodeNorm** (and eventually **Test Concordance**) are built as an Astro + Vue 3 static site in the `web/` directory. These pages call the NodeNorm API directly from the browser using `fetch()` — no server required. + +Deployment URLs for NodeNorm and NameRes are defined once in `config/translator-endpoints.json`, shared by both frontends and the CLI. CURIE link-outs use the [biolink-model prefix map](https://github.com/biolink/biolink-model) (fetched at runtime). Both sites share Bootstrap 5 dark-navbar styling for a consistent look. + +### Why this split? + +- **Preserves htmx where it matters.** XRefs/IDs benefit from server-side rendering because the data is already on the server. No need to rewrite them in client-side JS. +- **Minimal new code.** The JS for calling NodeNorm directly is trivial (~200 lines). A fully headless API approach would require replicating htmx partial rendering for XRefs/IDs dynamic columns in JS — more code for no gain. +- **Resilience.** If the Kubernetes pod is down or a Parquet download stalls, the API-only tools still work on GitHub Pages. +- **Reusable pattern.** Any CORS-enabled Translator API (NameRes, Node Annotator, etc.) can get a GitHub Pages demo the same way. This demonstrates to the [translator_sdk](https://github.com/NCATSTranslator/Translator_sdk) team that web UIs for API tools are easy and free to host, without complicating that repo's PyPI package. translator_sdk stays as a Python SDK (pipx-runnable CLI); web demos can live in `docs/` here or in a shared repo if the pattern scales. + ## Testing Tests are split into fast **unit tests** (mocked, no network) and slower **integration tests** (real file downloads and API calls), controlled by pytest markers. diff --git a/config/translator-endpoints.json b/config/translator-endpoints.json new file mode 100644 index 0000000..acb974d --- /dev/null +++ b/config/translator-endpoints.json @@ -0,0 +1,16 @@ +{ + "nodenorm": { + "dev": "https://nodenormalization-sri.renci.org/", + "exp": "https://nodenormalization-exp.apps.renci.org/", + "ci": "https://nodenorm.ci.transltr.io/", + "test": "https://nodenorm.test.transltr.io/", + "prod": "https://nodenorm.transltr.io/" + }, + "nameres": { + "dev": "https://name-resolution-sri.renci.org/", + "exp": "https://name-resolution-exp.apps.renci.org/", + "ci": "https://name-lookup.ci.transltr.io/", + "test": "https://name-lookup.test.transltr.io/", + "prod": "https://name-lookup.transltr.io/" + } +} diff --git a/pyproject.toml b/pyproject.toml index 59c1b68..d0db919 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,8 +7,12 @@ requires-python = ">=3.11" dependencies = [ "click>=8.3.1", "duckdb>=1.4.2", + "fastapi>=0.115.0", + "jinja2>=3.1.0", + "python-multipart>=0.0.9", "requests>=2.32.5", "tqdm>=4.67.0", + "uvicorn[standard]>=0.30.0", ] [build-system] @@ -17,6 +21,7 @@ build-backend = "hatchling.build" [dependency-groups] dev = [ + "httpx>=0.27.0", "filelock>=3.16", "pytest>=8.3.5", "pytest-xdist[psutil]>=3.6", diff --git a/src/babel_explorer/cli.py b/src/babel_explorer/cli.py index bcd8787..05a069e 100644 --- a/src/babel_explorer/cli.py +++ b/src/babel_explorer/cli.py @@ -189,5 +189,50 @@ def test_concord(curies, nodenorm_url): print(f"{curie}\t{identifier.curie}\t\t{biolink}") +@cli.command("web") +@click.option("--host", type=str, default="127.0.0.1", help="Host to bind to") +@click.option("--port", type=int, default=8000, help="Port to bind to") +@click.option( + "--local-dir", + type=str, + default="data/2025nov19", + help="Local location to save Babel download files to", +) +@click.option( + "--babel-url", + type=str, + default="https://stars.renci.org:443/var/babel_outputs/2025nov19/", + help="Base URL of the Babel server", +) +@click.option( + "--nodenorm-url", + type=str, + default="https://nodenormalization-sri.renci.org/", + help="NodeNorm URL", +) +@click.option("--reload", is_flag=True, help="Enable auto-reload for development") +def web(host, port, local_dir, babel_url, nodenorm_url, reload): + """Start the web server.""" + import os + import uvicorn + + os.environ["BABEL_LOCAL_DIR"] = local_dir + os.environ["BABEL_URL"] = babel_url + os.environ["BABEL_NODENORM_URL"] = nodenorm_url + + if reload: + uvicorn.run( + "babel_explorer.web:create_app", + host=host, + port=port, + reload=True, + factory=True, + ) + else: + from babel_explorer.web import create_app + + uvicorn.run(create_app(), host=host, port=port) + + if __name__ == "__main__": cli() diff --git a/src/babel_explorer/core/babel_xrefs.py b/src/babel_explorer/core/babel_xrefs.py index 0c94074..c2d1f2c 100644 --- a/src/babel_explorer/core/babel_xrefs.py +++ b/src/babel_explorer/core/babel_xrefs.py @@ -228,9 +228,14 @@ def get_curie_xrefs( if recurse: return self._get_curie_xrefs_recursive(curies, label_curies) - xrefs = set() + seen = set() + xrefs = [] for curie in curies: logging.info(f"Searching for cross-references for {curie}") - xrefs.update(self.get_curie_xref(curie, label_curies)) + for xref in self.get_curie_xref(curie, label_curies): + key = (xref.filename, xref.subj, xref.pred, xref.obj) + if key not in seen: + seen.add(key) + xrefs.append(xref) return sorted(xrefs) diff --git a/src/babel_explorer/core/downloader.py b/src/babel_explorer/core/downloader.py index 4d2f9a2..702891f 100644 --- a/src/babel_explorer/core/downloader.py +++ b/src/babel_explorer/core/downloader.py @@ -48,15 +48,17 @@ def __init__( local_path = tempfile.gettempdir() # Make sure the local path is an existing directory or that we can create it. - if not os.path.exists(local_path): + try: os.makedirs(local_path, exist_ok=True) - self.local_path = local_path - elif os.path.exists(local_path) and os.path.isdir(local_path): - self.local_path = local_path - else: + except (FileExistsError, NotADirectoryError) as exc: + raise ValueError( + f"Invalid local_path (must be an existing directory): '{local_path}'" + ) from exc + if not os.path.isdir(local_path): raise ValueError( f"Invalid local_path (must be an existing directory): '{local_path}'" ) + self.local_path = local_path @functools.lru_cache(maxsize=None) def get_output_file(self, filename): @@ -264,9 +266,10 @@ def _download_with_retry(self, url, local_path, chunk_size): "Server doesn't support resume, restarting from beginning" ) resume_byte_pos = 0 - # Remove partial file - if os.path.exists(local_path): + try: os.remove(local_path) + except FileNotFoundError: + pass else: response.raise_for_status() @@ -356,8 +359,10 @@ def get_downloaded_file(self, dirpath: str, chunk_size: int = 1024 * 1024): ) os.replace(tmp_path, local_path_to_download_to) except Exception: - if os.path.exists(tmp_path): + try: os.remove(tmp_path) + except FileNotFoundError: + pass raise # Save sidecar metadata diff --git a/src/babel_explorer/core/nodenorm.py b/src/babel_explorer/core/nodenorm.py index 9ce916d..0bd6682 100644 --- a/src/babel_explorer/core/nodenorm.py +++ b/src/babel_explorer/core/nodenorm.py @@ -2,10 +2,37 @@ import dataclasses import functools +import json +import pathlib import requests import logging +def _load_nodenorm_urls() -> dict[str, str]: + """Load NodeNorm deployment URLs from shared config file.""" + config_path = ( + pathlib.Path(__file__).parents[3] / "config" / "translator-endpoints.json" + ) + try: + endpoints = json.loads(config_path.read_text()) + env_labels = { + "dev": "Dev", + "exp": "Exp", + "ci": "CI", + "test": "Test", + "prod": "Production", + } + return { + f"NodeNorm {env_labels.get(env, env)}": url + for env, url in endpoints["nodenorm"].items() + } + except (FileNotFoundError, KeyError, json.JSONDecodeError) as exc: + logging.warning(f"Could not load config/translator-endpoints.json: {exc}") + return { + "NodeNorm Dev": "https://nodenormalization-sri.renci.org/", + } + + @dataclasses.dataclass(frozen=True) class Identifier: """Normalised identifier record returned by the NodeNorm API.""" diff --git a/src/babel_explorer/web/__init__.py b/src/babel_explorer/web/__init__.py new file mode 100644 index 0000000..0a94162 --- /dev/null +++ b/src/babel_explorer/web/__init__.py @@ -0,0 +1,39 @@ +from pathlib import Path + +from fastapi import FastAPI +from fastapi.templating import Jinja2Templates + +from babel_explorer.core.downloader import BabelDownloader +from babel_explorer.core.babel_xrefs import BabelXRefs +from babel_explorer.core.nodenorm import NodeNorm + +TEMPLATES_DIR = Path(__file__).parent / "templates" + + +def create_app( + local_dir: str | None = None, + babel_url: str | None = None, + nodenorm_url: str | None = None, +) -> FastAPI: + import os + + local_dir = local_dir or os.environ.get("BABEL_LOCAL_DIR", "data/2025nov19") + babel_url = babel_url or os.environ.get( + "BABEL_URL", "https://stars.renci.org:443/var/babel_outputs/2025nov19/" + ) + nodenorm_url = nodenorm_url or os.environ.get( + "BABEL_NODENORM_URL", "https://nodenormalization-sri.renci.org/" + ) + app = FastAPI(title="Babel Explorer") + + app.state.templates = Jinja2Templates(directory=str(TEMPLATES_DIR)) + app.state.nodenorm_url = nodenorm_url + app.state.nodenorm_cache = {} + app.state.downloader = BabelDownloader(babel_url, local_path=local_dir) + app.state.nodenorm = NodeNorm(nodenorm_url) + app.state.bxref = BabelXRefs(app.state.downloader, app.state.nodenorm) + + from babel_explorer.web.routes import router + + app.include_router(router) + return app diff --git a/src/babel_explorer/web/routes.py b/src/babel_explorer/web/routes.py new file mode 100644 index 0000000..ff93c5d --- /dev/null +++ b/src/babel_explorer/web/routes.py @@ -0,0 +1,409 @@ +import csv +import io +import logging + +from fastapi import APIRouter, Form, Query, Request +from fastapi.responses import JSONResponse, StreamingResponse + +from babel_explorer.core.babel_xrefs import LabeledCrossReference +from babel_explorer.core.nodenorm import NodeNorm + +router = APIRouter() +logger = logging.getLogger(__name__) + + +def _parse_curies(raw: str) -> list[str]: + """Split a textarea string into a deduplicated list of CURIEs.""" + curies = [] + seen = set() + for line in raw.splitlines(): + c = line.strip() + if c and not c.startswith("#") and c not in seen: + curies.append(c) + seen.add(c) + return curies + + +def _csv_response(rows: list[list[str]], headers: list[str], filename: str): + buf = io.StringIO() + writer = csv.writer(buf) + writer.writerow(headers) + writer.writerows(rows) + buf.seek(0) + return StreamingResponse( + iter([buf.getvalue()]), + media_type="text/csv", + headers={"Content-Disposition": f"attachment; filename={filename}"}, + ) + + +def _render(request: Request, template: str, context: dict | None = None): + ctx = context or {} + return request.app.state.templates.TemplateResponse(request, template, ctx) + + +def _get_nodenorm(request: Request, nodenorm_url: str) -> NodeNorm: + if not nodenorm_url: + return request.app.state.nodenorm + cache: dict = request.app.state.nodenorm_cache + if nodenorm_url not in cache: + cache[nodenorm_url] = NodeNorm(nodenorm_url) + return cache[nodenorm_url] + + +def _extract_extra_field_names(records) -> list[str]: + names = [] + seen = set() + for rec in records: + for name, _ in rec.extra_fields: + if name not in seen: + names.append(name) + seen.add(name) + return names + + +# --------------------------------------------------------------------------- +# HTML pages +# --------------------------------------------------------------------------- + + +@router.get("/") +def index(request: Request): + return _render(request, "index.html") + + +@router.get("/nodenorm") +def nodenorm_page(request: Request): + return _render( + request, + "nodenorm.html", + { + "default_url": request.app.state.nodenorm_url, + "nodenorm_urls": NodeNorm.URLs, + }, + ) + + +@router.get("/xrefs") +def xrefs_page(request: Request): + return _render(request, "xrefs.html") + + +@router.get("/ids") +def ids_page(request: Request): + return _render(request, "ids.html") + + +@router.get("/test-concord") +def test_concord_page(request: Request): + return _render( + request, + "test_concord.html", + { + "default_url": request.app.state.nodenorm_url, + "nodenorm_urls": NodeNorm.URLs, + }, + ) + + +# --------------------------------------------------------------------------- +# htmx partials +# --------------------------------------------------------------------------- + + +@router.post("/htmx/nodenorm") +def htmx_nodenorm( + request: Request, curies: str = Form(""), nodenorm_url: str = Form("") +): + parsed = _parse_curies(curies) + if not parsed: + return _render( + request, "_partials/error.html", {"message": "No CURIEs provided."} + ) + try: + nn = _get_nodenorm(request, nodenorm_url) + rows = [] + for curie in parsed: + ident = nn.get_identifier(curie) + rows.append( + { + "input_curie": curie, + "normalized_curie": ident.curie, + "label": ident.label, + "biolink_type": ident.biolink_type, + "taxa": ", ".join(ident.taxa) if ident.taxa else "", + "description": ident.description if ident.description else "", + } + ) + return _render(request, "_partials/nodenorm_results.html", {"rows": rows}) + except Exception as exc: + logger.exception("NodeNorm lookup failed") + return _render(request, "_partials/error.html", {"message": str(exc)}) + + +@router.post("/htmx/xrefs") +def htmx_xrefs( + request: Request, + curies: str = Form(""), + expand: bool = Form(False), + labels: bool = Form(False), +): + parsed = _parse_curies(curies) + if not parsed: + return _render( + request, "_partials/error.html", {"message": "No CURIEs provided."} + ) + try: + bxref = request.app.state.bxref + xrefs = bxref.get_curie_xrefs(parsed, recurse=expand, label_curies=labels) + has_labels = labels and xrefs and isinstance(xrefs[0], LabeledCrossReference) + return _render( + request, + "_partials/xrefs_results.html", + {"xrefs": xrefs, "has_labels": has_labels}, + ) + except Exception as exc: + logger.exception("XRefs lookup failed") + return _render(request, "_partials/error.html", {"message": str(exc)}) + + +@router.post("/htmx/ids") +def htmx_ids(request: Request, curies: str = Form("")): + parsed = _parse_curies(curies) + if not parsed: + return _render( + request, "_partials/error.html", {"message": "No CURIEs provided."} + ) + try: + bxref = request.app.state.bxref + records = bxref.get_curie_ids(parsed) + extra_names = _extract_extra_field_names(records) + return _render( + request, + "_partials/ids_results.html", + {"records": records, "extra_names": extra_names}, + ) + except Exception as exc: + logger.exception("IDs lookup failed") + return _render(request, "_partials/error.html", {"message": str(exc)}) + + +@router.post("/htmx/test-concord") +def htmx_test_concord( + request: Request, curies: str = Form(""), nodenorm_url: str = Form("") +): + parsed = _parse_curies(curies) + if not parsed: + return _render( + request, "_partials/error.html", {"message": "No CURIEs provided."} + ) + try: + nn = _get_nodenorm(request, nodenorm_url) + rows = [] + for curie in parsed: + identifiers = nn.get_clique_identifiers(curie) + if identifiers: + for ident in identifiers: + rows.append( + { + "source_curie": curie, + "identifier": ident.curie, + "label": ident.label, + "biolink_type": ident.biolink_type, + } + ) + return _render(request, "_partials/test_concord_results.html", {"rows": rows}) + except Exception as exc: + logger.exception("Test Concordance lookup failed") + return _render(request, "_partials/error.html", {"message": str(exc)}) + + +# --------------------------------------------------------------------------- +# JSON API +# --------------------------------------------------------------------------- + + +@router.get("/api/nodenorm") +def api_nodenorm( + request: Request, curie: list[str] = Query(...), nodenorm_url: str = Query("") +): + nn = _get_nodenorm(request, nodenorm_url) + results = [] + for c in curie: + ident = nn.get_identifier(c) + results.append( + { + "input_curie": c, + "normalized_curie": ident.curie, + "label": ident.label, + "biolink_type": ident.biolink_type, + "taxa": ident.taxa, + "description": ident.description, + } + ) + return JSONResponse(results) + + +@router.get("/api/xrefs") +def api_xrefs( + request: Request, + curie: list[str] = Query(...), + expand: bool = Query(False), + labels: bool = Query(False), +): + bxref = request.app.state.bxref + xrefs = bxref.get_curie_xrefs(list(curie), recurse=expand, label_curies=labels) + results = [] + for xref in xrefs: + row = { + "filename": xref.filename, + "subj": xref.subj, + "pred": xref.pred, + "obj": xref.obj, + } + if isinstance(xref, LabeledCrossReference): + row.update( + { + "subj_label": xref.subj_label, + "subj_biolink_type": xref.subj_biolink_type, + "obj_label": xref.obj_label, + "obj_biolink_type": xref.obj_biolink_type, + } + ) + results.append(row) + return JSONResponse(results) + + +@router.get("/api/ids") +def api_ids(request: Request, curie: list[str] = Query(...)): + bxref = request.app.state.bxref + records = bxref.get_curie_ids(list(curie)) + results = [] + for rec in records: + row = {"curie": rec.curie} + for name, value in rec.extra_fields: + row[name] = value + results.append(row) + return JSONResponse(results) + + +@router.get("/api/test-concord") +def api_test_concord( + request: Request, curie: list[str] = Query(...), nodenorm_url: str = Query("") +): + nn = _get_nodenorm(request, nodenorm_url) + results = [] + for c in curie: + identifiers = nn.get_clique_identifiers(c) + if identifiers: + for ident in identifiers: + results.append( + { + "source_curie": c, + "identifier": ident.curie, + "label": ident.label, + "biolink_type": ident.biolink_type, + } + ) + return JSONResponse(results) + + +# --------------------------------------------------------------------------- +# CSV downloads +# --------------------------------------------------------------------------- + + +@router.get("/api/nodenorm/csv") +def api_nodenorm_csv( + request: Request, curie: list[str] = Query(...), nodenorm_url: str = Query("") +): + nn = _get_nodenorm(request, nodenorm_url) + headers = [ + "Input CURIE", + "Normalized CURIE", + "Label", + "Biolink Type", + "Taxa", + "Description", + ] + rows = [] + for c in curie: + ident = nn.get_identifier(c) + rows.append( + [ + c, + ident.curie, + ident.label, + ident.biolink_type, + ", ".join(ident.taxa) if ident.taxa else "", + "; ".join(ident.description) if ident.description else "", + ] + ) + return _csv_response(rows, headers, "nodenorm.csv") + + +@router.get("/api/xrefs/csv") +def api_xrefs_csv( + request: Request, + curie: list[str] = Query(...), + expand: bool = Query(False), + labels: bool = Query(False), +): + bxref = request.app.state.bxref + xrefs = bxref.get_curie_xrefs(list(curie), recurse=expand, label_curies=labels) + if labels and xrefs and isinstance(xrefs[0], LabeledCrossReference): + headers = [ + "Filename", + "Subject", + "Subject Label", + "Subject Type", + "Predicate", + "Object", + "Object Label", + "Object Type", + ] + rows = [ + [ + x.filename, + x.subj, + x.subj_label, + x.subj_biolink_type, + x.pred, + x.obj, + x.obj_label, + x.obj_biolink_type, + ] + for x in xrefs + ] + else: + headers = ["Filename", "Subject", "Predicate", "Object"] + rows = [[x.filename, x.subj, x.pred, x.obj] for x in xrefs] + return _csv_response(rows, headers, "xrefs.csv") + + +@router.get("/api/ids/csv") +def api_ids_csv(request: Request, curie: list[str] = Query(...)): + bxref = request.app.state.bxref + records = bxref.get_curie_ids(list(curie)) + extra_names = _extract_extra_field_names(records) + headers = ["CURIE"] + extra_names + rows = [] + for rec in records: + extras = dict(rec.extra_fields) + rows.append([rec.curie] + [extras.get(n, "") for n in extra_names]) + return _csv_response(rows, headers, "ids.csv") + + +@router.get("/api/test-concord/csv") +def api_test_concord_csv( + request: Request, curie: list[str] = Query(...), nodenorm_url: str = Query("") +): + nn = _get_nodenorm(request, nodenorm_url) + headers = ["Source CURIE", "Identifier", "Label", "Biolink Type"] + rows = [] + for c in curie: + identifiers = nn.get_clique_identifiers(c) + if identifiers: + for ident in identifiers: + rows.append([c, ident.curie, ident.label, ident.biolink_type]) + return _csv_response(rows, headers, "test_concord.csv") diff --git a/src/babel_explorer/web/templates/_partials/error.html b/src/babel_explorer/web/templates/_partials/error.html new file mode 100644 index 0000000..abf994a --- /dev/null +++ b/src/babel_explorer/web/templates/_partials/error.html @@ -0,0 +1,3 @@ + diff --git a/src/babel_explorer/web/templates/_partials/ids_results.html b/src/babel_explorer/web/templates/_partials/ids_results.html new file mode 100644 index 0000000..2e0a37b --- /dev/null +++ b/src/babel_explorer/web/templates/_partials/ids_results.html @@ -0,0 +1,37 @@ +

{{ records|length }} result{{ "s" if records|length != 1 else "" }} found.

+ +
+ + Download CSV +
+ +
+ + + + + {% for name in extra_names %} + + {% endfor %} + + + + {% for rec in records %} + + + {% for name in extra_names %} + + {% endfor %} + + {% endfor %} + +
CURIE{{ name }}
{{ rec.curie }}{{ dict(rec.extra_fields).get(name, '') }}
+
+ + diff --git a/src/babel_explorer/web/templates/_partials/nodenorm_results.html b/src/babel_explorer/web/templates/_partials/nodenorm_results.html new file mode 100644 index 0000000..651884a --- /dev/null +++ b/src/babel_explorer/web/templates/_partials/nodenorm_results.html @@ -0,0 +1,44 @@ +

{{ rows|length }} result{{ "s" if rows|length != 1 else "" }} found.

+ +
+ + Download CSV +
+ +
+ + + + + + + + + + + + + {% for row in rows %} + + + + + + + + + {% endfor %} + +
Input CURIENormalized CURIELabelBiolink TypeTaxaDescription
{{ row.input_curie }}{{ row.normalized_curie }}{{ row.label }}{{ row.biolink_type }}{{ row.taxa }}{{ row.description }}
+
+ + diff --git a/src/babel_explorer/web/templates/_partials/test_concord_results.html b/src/babel_explorer/web/templates/_partials/test_concord_results.html new file mode 100644 index 0000000..46af66d --- /dev/null +++ b/src/babel_explorer/web/templates/_partials/test_concord_results.html @@ -0,0 +1,40 @@ +

{{ rows|length }} result{{ "s" if rows|length != 1 else "" }} found.

+ +
+ + Download CSV +
+ +
+ + + + + + + + + + + {% for row in rows %} + + + + + + + {% endfor %} + +
Source CURIEIdentifierLabelBiolink Type
{{ row.source_curie }}{{ row.identifier }}{{ row.label }}{{ row.biolink_type }}
+
+ + diff --git a/src/babel_explorer/web/templates/_partials/xrefs_results.html b/src/babel_explorer/web/templates/_partials/xrefs_results.html new file mode 100644 index 0000000..ce55f95 --- /dev/null +++ b/src/babel_explorer/web/templates/_partials/xrefs_results.html @@ -0,0 +1,45 @@ +

{{ xrefs|length }} result{{ "s" if xrefs|length != 1 else "" }} found.

+ +
+ + Download CSV +
+ +
+ + + + + + {% if has_labels %}{% endif %} + + + {% if has_labels %}{% endif %} + + + + {% for xref in xrefs %} + + + + {% if has_labels %}{% endif %} + + + {% if has_labels %}{% endif %} + + {% endfor %} + +
FilenameSubjectSubject LabelSubject TypePredicateObjectObject LabelObject Type
{{ xref.filename }}{{ xref.subj }}{{ xref.subj_label }}{{ xref.subj_biolink_type }}{{ xref.pred }}{{ xref.obj }}{{ xref.obj_label }}{{ xref.obj_biolink_type }}
+
+ + diff --git a/src/babel_explorer/web/templates/base.html b/src/babel_explorer/web/templates/base.html new file mode 100644 index 0000000..8fefe8b --- /dev/null +++ b/src/babel_explorer/web/templates/base.html @@ -0,0 +1,55 @@ + + + + + + {% block title %}Babel Explorer{% endblock %} + + + + + + + +
+ {% block content %}{% endblock %} +
+ + + + + diff --git a/src/babel_explorer/web/templates/ids.html b/src/babel_explorer/web/templates/ids.html new file mode 100644 index 0000000..4f50720 --- /dev/null +++ b/src/babel_explorer/web/templates/ids.html @@ -0,0 +1,24 @@ +{% extends "base.html" %} +{% block title %}IDs - Babel Explorer{% endblock %} +{% block content %} +

Identifier Records (IDs)

+

Look up identifier records from the Babel Identifiers file.

+
+ Note: The first query may trigger an Identifiers.parquet download (2 GB+). This may take a while. +
+ +
+
+ + +
+ + +
+ Loading... +
+
+
+ +
+{% endblock %} diff --git a/src/babel_explorer/web/templates/index.html b/src/babel_explorer/web/templates/index.html new file mode 100644 index 0000000..214de42 --- /dev/null +++ b/src/babel_explorer/web/templates/index.html @@ -0,0 +1,45 @@ +{% extends "base.html" %} +{% block title %}Babel Explorer{% endblock %} +{% block content %} +

Babel Explorer

+

Explore Babel intermediate files and discover why two identifiers are considered identical.

+ +
+
+
+
+
NodeNorm
+

Look up normalized identifiers, labels, and biolink types from NodeNormalization.

+ Open +
+
+
+
+
+
+
XRefs
+

Query cross-references from Babel Concord files with optional expansion and labels.

+ Open +
+
+
+
+
+
+
IDs
+

Look up identifier records from the Babel Identifiers file.

+ Open +
+
+
+
+
+
+
Test Concordance
+

See all equivalent identifiers (clique members) for CURIEs via NodeNorm.

+ Open +
+
+
+
+{% endblock %} diff --git a/src/babel_explorer/web/templates/nodenorm.html b/src/babel_explorer/web/templates/nodenorm.html new file mode 100644 index 0000000..f563d3d --- /dev/null +++ b/src/babel_explorer/web/templates/nodenorm.html @@ -0,0 +1,52 @@ +{% extends "base.html" %} +{% block title %}NodeNorm - Babel Explorer{% endblock %} +{% block content %} +

NodeNorm Lookup

+

Look up normalized identifiers, labels, and biolink types for CURIEs.

+ +
+
+ + +
+
+ + +
+ + + + +
+ Loading... +
+
+
+ +
+ + +{% endblock %} diff --git a/src/babel_explorer/web/templates/test_concord.html b/src/babel_explorer/web/templates/test_concord.html new file mode 100644 index 0000000..ccb2ae8 --- /dev/null +++ b/src/babel_explorer/web/templates/test_concord.html @@ -0,0 +1,52 @@ +{% extends "base.html" %} +{% block title %}Test Concordance - Babel Explorer{% endblock %} +{% block content %} +

Test Concordance

+

See all equivalent identifiers (clique members) for CURIEs via NodeNorm.

+ +
+
+ + +
+
+ + +
+ + + + +
+ Loading... +
+
+
+ +
+ + +{% endblock %} diff --git a/src/babel_explorer/web/templates/xrefs.html b/src/babel_explorer/web/templates/xrefs.html new file mode 100644 index 0000000..fc82661 --- /dev/null +++ b/src/babel_explorer/web/templates/xrefs.html @@ -0,0 +1,32 @@ +{% extends "base.html" %} +{% block title %}XRefs - Babel Explorer{% endblock %} +{% block content %} +

Cross-References (XRefs)

+

Query cross-references from Babel Concord files.

+
+ Note: The first query triggers a Parquet file download (~626 MB). This may take a while. +
+ +
+
+ + +
+
+ + +
+
+ + +
+ + +
+ Loading... +
+
+
+ +
+{% endblock %} diff --git a/tests/fixtures/nodenorm_responses/batch_mixed.json b/tests/fixtures/nodenorm_responses/batch_mixed.json new file mode 100644 index 0000000..b86f649 --- /dev/null +++ b/tests/fixtures/nodenorm_responses/batch_mixed.json @@ -0,0 +1,181 @@ +{ + "MONDO:0004979": { + "id": { + "identifier": "MONDO:0004979", + "label": "asthma", + "description": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety." + }, + "equivalent_identifiers": [ + { + "identifier": "MONDO:0004979", + "label": "asthma", + "description": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", + "type": "biolink:Disease" + }, + { + "identifier": "DOID:2841", + "label": "asthma", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0004096", + "label": "Asthma", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0085129", + "label": "Bronchial Hyperreactivity", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0340062", + "label": "Hyperreactive airway disease", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C3714497", + "label": "Reactive airway disease", + "type": "biolink:Disease" + }, + { + "identifier": "MESH:D001249", + "label": "Asthma", + "type": "biolink:Disease" + }, + { + "identifier": "MESH:D016535", + "label": "Bronchial Hyperreactivity", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003553", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003555", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003560", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003561", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003565", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10006450", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10037993", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10056285", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10066091", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10066863", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10082852", + "type": "biolink:Disease" + }, + { + "identifier": "NCIT:C28397", + "label": "Asthma", + "description": "A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways.", + "type": "biolink:Disease" + }, + { + "identifier": "SNOMEDCT:195967001", + "type": "biolink:Disease" + }, + { + "identifier": "SNOMEDCT:991000119106", + "type": "biolink:Disease" + }, + { + "identifier": "medgen:2109", + "type": "biolink:Disease" + }, + { + "identifier": "icd11.foundation:1656445230", + "type": "biolink:Disease" + }, + { + "identifier": "ICD10:J45", + "type": "biolink:Disease" + }, + { + "identifier": "ICD9:493", + "type": "biolink:Disease" + }, + { + "identifier": "KEGG.DISEASE:05310", + "type": "biolink:Disease" + }, + { + "identifier": "HP:0002099", + "label": "Asthma", + "description": "Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.", + "type": "biolink:Disease" + } + ], + "descriptions": [ + "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", + "A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways.", + "Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing." + ], + "type": [ + "biolink:Disease", + "biolink:DiseaseOrPhenotypicFeature", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing" + ], + "information_content": 77.3 + }, + "NCIT:C55060": { + "id": { + "identifier": "NCIT:C55060", + "label": "Hypertension, CTCAE", + "description": "A disorder characterized by a pathological increase in blood pressure." + }, + "equivalent_identifiers": [ + { + "identifier": "NCIT:C55060", + "label": "Hypertension, CTCAE", + "description": "A disorder characterized by a pathological increase in blood pressure.", + "type": "biolink:PhenotypicFeature" + }, + { + "identifier": "UMLS:C1963138", + "label": "Hypertension, CTCAE", + "type": "biolink:PhenotypicFeature" + } + ], + "descriptions": [ + "A disorder characterized by a pathological increase in blood pressure." + ], + "type": [ + "biolink:PhenotypicFeature", + "biolink:DiseaseOrPhenotypicFeature", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing" + ], + "information_content": 88.2 + }, + "FAKE:9999999": null +} diff --git a/tests/fixtures/nodenorm_responses/chebi_48947.json b/tests/fixtures/nodenorm_responses/chebi_48947.json new file mode 100644 index 0000000..57c28fc --- /dev/null +++ b/tests/fixtures/nodenorm_responses/chebi_48947.json @@ -0,0 +1,408 @@ +{ + "CHEBI:48947": { + "id": { + "identifier": "CHEBI:48947", + "label": "Clavulanic acid", + "description": "Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes." + }, + "equivalent_identifiers": [ + { + "identifier": "CHEBI:48947", + "label": "clavulanic acid", + "description": "Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes.", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:43442", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:3736", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:23521W1S24", + "label": "CLAVULANIC ACID", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:5280980", + "label": "Clavulanic Acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL777", + "label": "CLAVULANIC ACID", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DRUGBANK:DB00766", + "label": "Clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D019818", + "label": "Clavulanic Acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:1365254-41-6", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:261-069-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:58001-44-8", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DrugCentral:669", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "GTOPDB:11128", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "HMDB:HMDB0014904", + "label": "Clavulanate", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "KEGG.COMPOUND:C06662", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:HZZVJAQRINQKSD-PBFISZAISA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C0055860", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "RXCUI:21216", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:48947", + "label": "clavulanic acid", + "description": "Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes.", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:43442", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:3736", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:23521W1S24", + "label": "CLAVULANIC ACID", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:5280980", + "label": "Clavulanic Acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL777", + "label": "CLAVULANIC ACID", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DRUGBANK:DB00766", + "label": "Clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D019818", + "label": "Clavulanic Acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:1365254-41-6", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:261-069-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:58001-44-8", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DrugCentral:669", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "GTOPDB:11128", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "HMDB:HMDB0014904", + "label": "Clavulanate", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "KEGG.COMPOUND:C06662", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:HZZVJAQRINQKSD-PBFISZAISA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C0055860", + "label": "clavulanic acid", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "RXCUI:21216", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:85264", + "label": "potassium clavulanate", + "description": "A potassium salt having clavulanate as the counterion. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes and has only weak anitbiotic activity when administered alone. However it can be used in combination with amoxicillin trihydrate (under the trade name Augmentin) for treatment of a variety of bacterial infections, where it prevents antibiotic inactivation by microbial lactamases.", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "UNII:Q42OMW3AT8", + "label": "CLAVULANATE POTASSIUM", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "PUBCHEM.COMPOUND:23665591", + "label": "Potassium Clavulanate", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL1003", + "label": "CLAVULANATE POTASSIUM", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "CAS:61177-45-5", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "INCHIKEY:ABVRVIZBZKUTMK-JSYANWSFSA-M", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "CHEBI:85264", + "label": "potassium clavulanate", + "description": "A potassium salt having clavulanate as the counterion. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes and has only weak anitbiotic activity when administered alone. However it can be used in combination with amoxicillin trihydrate (under the trade name Augmentin) for treatment of a variety of bacterial infections, where it prevents antibiotic inactivation by microbial lactamases.", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "UNII:Q42OMW3AT8", + "label": "CLAVULANATE POTASSIUM", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "PUBCHEM.COMPOUND:23665591", + "label": "Potassium Clavulanate", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL1003", + "label": "CLAVULANATE POTASSIUM", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "CAS:61177-45-5", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "INCHIKEY:ABVRVIZBZKUTMK-JSYANWSFSA-M", + "type": "biolink:MolecularMixture" + }, + { + "identifier": "UMLS:C0110038", + "label": "clavulanate", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:48203", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "UMLS:C0137997", + "label": "clavulanate potassium", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:831418", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:345821", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1126575", + "label": "clavulanate 125 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:345822", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1178616", + "label": "clavulanate 31.2 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:346380", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1161326", + "label": "clavulanate 10 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617300", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1126105", + "label": "clavulanate 6.25 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617303", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1123175", + "label": "clavulanate 62.5 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617308", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1124803", + "label": "clavulanate 28.5 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617315", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1130127", + "label": "clavulanate 57 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617321", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1123169", + "label": "clavulanate 12.5 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617422", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1124804", + "label": "clavulanate 5.7 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617429", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1124182", + "label": "clavulanate 11.4 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:617992", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1171095", + "label": "clavulanate 8.58 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1810267", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4283615", + "label": "clavulanate 12.5 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1810269", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4283617", + "label": "clavulanate 50 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1810272", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4283620", + "label": "clavulanate 75 MG", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2105775", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4741294", + "label": "clavulanate 25 MG", + "type": "biolink:Drug" + } + ], + "descriptions": [ + "Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes.", + "A potassium salt having clavulanate as the counterion. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes and has only weak anitbiotic activity when administered alone. However it can be used in combination with amoxicillin trihydrate (under the trade name Augmentin) for treatment of a variety of bacterial infections, where it prevents antibiotic inactivation by microbial lactamases." + ], + "type": [ + "biolink:SmallMolecule", + "biolink:MolecularEntity", + "biolink:ChemicalEntity", + "biolink:PhysicalEssence", + "biolink:ChemicalOrDrugOrTreatment", + "biolink:ChemicalEntityOrGeneOrGeneProduct", + "biolink:ChemicalEntityOrProteinOrPolypeptide", + "biolink:NamedThing", + "biolink:PhysicalEssenceOrOccurrent", + "biolink:MolecularMixture", + "biolink:ChemicalMixture", + "biolink:Drug", + "biolink:OntologyClass" + ], + "information_content": 95.4 + } +} diff --git a/tests/fixtures/nodenorm_responses/mesh_d014867_conflated.json b/tests/fixtures/nodenorm_responses/mesh_d014867_conflated.json new file mode 100644 index 0000000..28d8809 --- /dev/null +++ b/tests/fixtures/nodenorm_responses/mesh_d014867_conflated.json @@ -0,0 +1,954 @@ +{ + "MESH:D014867": { + "id": { + "identifier": "CHEBI:15377", + "label": "Water", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms" + }, + "equivalent_identifiers": [ + { + "identifier": "CHEBI:15377", + "label": "water", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44701", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:27313", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:10743", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44819", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44292", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:43228", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42043", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42857", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:13352", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:5585", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:059QF0KO0R", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:962", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL1098659", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DRUGBANK:DB09145", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D014867", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D060766", + "label": "Drinking Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-49-3", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-50-6", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:158061-35-9", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-61-0", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-63-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:231-791-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:686-299-4", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:7732-18-5", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "HMDB:HMDB0002111", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "KEGG.COMPOUND:C00001", + "label": "H2O", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C0043047", + "label": "water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "RXCUI:11295", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:15377", + "label": "water", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44701", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:27313", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:10743", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44819", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44292", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:43228", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42043", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42857", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:13352", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:5585", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:059QF0KO0R", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:962", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL1098659", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DRUGBANK:DB09145", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D014867", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D060766", + "label": "Drinking Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-49-3", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-50-6", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:158061-35-9", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-61-0", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-63-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:231-791-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:686-299-4", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:7732-18-5", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "HMDB:HMDB0002111", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "KEGG.COMPOUND:C00001", + "label": "H2O", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C0043047", + "label": "water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "RXCUI:11295", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:33813", + "label": "((18)O)water", + "description": "A form of water consisting of two hydrogen atoms covalently bonded to an oxygen-18 atom.", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:7QV8F8BYNJ", + "label": "WATER O-18", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:105142", + "label": "Water-18O", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:14314-42-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-NJFSPNSNSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:33813", + "label": "((18)O)water", + "description": "A form of water consisting of two hydrogen atoms covalently bonded to an oxygen-18 atom.", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:7QV8F8BYNJ", + "label": "WATER O-18", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:105142", + "label": "Water-18O", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:14314-42-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-NJFSPNSNSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:63M8RYN44N", + "label": "WATER O-15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:10129877", + "label": "Water O-15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL2106489", + "label": "WATER O 15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:24286-21-3", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-BJUDXGSMSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:63M8RYN44N", + "label": "WATER O-15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:10129877", + "label": "Water O-15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL2106489", + "label": "WATER O 15", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:24286-21-3", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-BJUDXGSMSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C3857954", + "label": "water, O-18", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:1551628", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "UMLS:C1883551", + "label": "water, O-15", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:1427071", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "UMLS:C0359299", + "label": "sterile water", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:107129", + "type": "biolink:ChemicalEntity" + }, + { + "identifier": "RXCUI:150985", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C0590256", + "label": "water 1000 MG/ML Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:204918", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C0705005", + "label": "water 1000 MG/ML Inhalation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:340584", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1141499", + "label": "water 1000 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:379002", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1253380", + "label": "water Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1043588", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2948223", + "label": "water Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1045437", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2948996", + "label": "OcuFresh", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1045439", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2948997", + "label": "water Ophthalmic Irrigation Solution [OcuFresh]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053147", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961554", + "label": "water 980 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053148", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961555", + "label": "water 980 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053153", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961560", + "label": "water 951 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053154", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961561", + "label": "water 951 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053172", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961577", + "label": "water 986 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053173", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2949578", + "label": "water 986 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053428", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2961756", + "label": "water 991 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1053429", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C2948224", + "label": "water 991 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1151100", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3205651", + "label": "water 983 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1151101", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3205652", + "label": "water 983 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1161792", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3216125", + "label": "water Inhalant Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1161794", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3216127", + "label": "water Irrigation Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1161795", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3216128", + "label": "water Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1180556", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3234408", + "label": "OcuFresh Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235498", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254839", + "label": "water 984 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235499", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254840", + "label": "water 984 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235500", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254841", + "label": "Dorama-Neo", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235501", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254842", + "label": "water 984 MG/ML [Dorama-Neo]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235502", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254843", + "label": "water Ophthalmic Irrigation Solution [Dorama-Neo]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235503", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3254844", + "label": "Dorama-Neo Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1235504", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C1584203", + "label": "water 984 MG/ML Ophthalmic Irrigation Solution [Dorama-Neo]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1423320", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644056", + "label": "water 985 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1423321", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644010", + "label": "water 985 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1424601", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644310", + "label": "Pur-Wash", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1424602", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644311", + "label": "water 983 MG/ML [Pur-Wash]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1424603", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644312", + "label": "water Ophthalmic Irrigation Solution [Pur-Wash]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1424604", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644313", + "label": "Pur-Wash Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1424605", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3542472", + "label": "water 983 MG/ML Ophthalmic Irrigation Solution [Pur-Wash]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1425974", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644850", + "label": "Opticlear", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1425975", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644851", + "label": "water 985 MG/ML [Opticlear]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1425976", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644852", + "label": "water Ophthalmic Irrigation Solution [Opticlear]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1425977", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644853", + "label": "Opticlear Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1425978", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3644854", + "label": "water 985 MG/ML Ophthalmic Irrigation Solution [Opticlear]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1489375", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3820231", + "label": "water 988 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1489376", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3820105", + "label": "water 988 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1489377", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3819654", + "label": "water 988 MG/ML [OcuFresh]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1489378", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3818671", + "label": "water 988 MG/ML Ophthalmic Irrigation Solution [OcuFresh]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1539535", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3832760", + "label": "water 1000 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1549851", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C0720356", + "label": "Eye Stream", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1549852", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3856248", + "label": "water 986 MG/ML [Eye Stream]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1549853", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3856249", + "label": "water Ophthalmic Irrigation Solution [Eye Stream]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1549854", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C3856250", + "label": "Eye Stream Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1549855", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C0976847", + "label": "water 986 MG/ML Ophthalmic Irrigation Solution [Eye Stream]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1923419", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4476407", + "label": "water 987 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:1923420", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C4476408", + "label": "water 987 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2108561", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C0770156", + "label": "water Inhalation Solution", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2360606", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5244464", + "label": "Firstflush", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2360607", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5244465", + "label": "water 983 MG/ML [Firstflush]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2360608", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5244466", + "label": "water Ophthalmic Irrigation Solution [Firstflush]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2360609", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5244467", + "label": "Firstflush Ophthalmic Product", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2360610", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5244468", + "label": "water 983 MG/ML Ophthalmic Irrigation Solution [Firstflush]", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2704855", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5979196", + "label": "water 921 MG/ML", + "type": "biolink:Drug" + }, + { + "identifier": "RXCUI:2704856", + "type": "biolink:Drug" + }, + { + "identifier": "UMLS:C5979197", + "label": "water 921 MG/ML Ophthalmic Irrigation Solution", + "type": "biolink:Drug" + } + ], + "descriptions": [ + "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms", + "A form of water consisting of two hydrogen atoms covalently bonded to an oxygen-18 atom." + ], + "type": [ + "biolink:SmallMolecule", + "biolink:MolecularEntity", + "biolink:ChemicalEntity", + "biolink:PhysicalEssence", + "biolink:ChemicalOrDrugOrTreatment", + "biolink:ChemicalEntityOrGeneOrGeneProduct", + "biolink:ChemicalEntityOrProteinOrPolypeptide", + "biolink:NamedThing", + "biolink:PhysicalEssenceOrOccurrent", + "biolink:Drug", + "biolink:OntologyClass", + "biolink:MolecularMixture", + "biolink:ChemicalMixture" + ], + "information_content": 47.5 + } +} diff --git a/tests/fixtures/nodenorm_responses/mesh_d014867_no_conflate.json b/tests/fixtures/nodenorm_responses/mesh_d014867_no_conflate.json new file mode 100644 index 0000000..41c841f --- /dev/null +++ b/tests/fixtures/nodenorm_responses/mesh_d014867_no_conflate.json @@ -0,0 +1,157 @@ +{ + "MESH:D014867": { + "id": { + "identifier": "CHEBI:15377", + "label": "Water", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms" + }, + "equivalent_identifiers": [ + { + "identifier": "CHEBI:15377", + "label": "water", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44701", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:27313", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:10743", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44819", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:44292", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:43228", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42043", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:42857", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:13352", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEBI:5585", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UNII:059QF0KO0R", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "PUBCHEM.COMPOUND:962", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CHEMBL.COMPOUND:CHEMBL1098659", + "label": "WATER", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "DRUGBANK:DB09145", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D014867", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "MESH:D060766", + "label": "Drinking Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-49-3", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:146915-50-6", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:158061-35-9", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-61-0", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:191612-63-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:231-791-2", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:686-299-4", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "CAS:7732-18-5", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "HMDB:HMDB0002111", + "label": "Water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "KEGG.COMPOUND:C00001", + "label": "H2O", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "UMLS:C0043047", + "label": "water", + "type": "biolink:SmallMolecule" + }, + { + "identifier": "RXCUI:11295", + "type": "biolink:SmallMolecule" + } + ], + "descriptions": [ + "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms" + ], + "type": [ + "biolink:SmallMolecule", + "biolink:MolecularEntity", + "biolink:ChemicalEntity", + "biolink:PhysicalEssence", + "biolink:ChemicalOrDrugOrTreatment", + "biolink:ChemicalEntityOrGeneOrGeneProduct", + "biolink:ChemicalEntityOrProteinOrPolypeptide", + "biolink:NamedThing", + "biolink:PhysicalEssenceOrOccurrent" + ], + "information_content": 47.5 + } +} diff --git a/tests/fixtures/nodenorm_responses/mondo_0004979.json b/tests/fixtures/nodenorm_responses/mondo_0004979.json new file mode 100644 index 0000000..cff2c95 --- /dev/null +++ b/tests/fixtures/nodenorm_responses/mondo_0004979.json @@ -0,0 +1,149 @@ +{ + "MONDO:0004979": { + "id": { + "identifier": "MONDO:0004979", + "label": "asthma", + "description": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety." + }, + "equivalent_identifiers": [ + { + "identifier": "MONDO:0004979", + "label": "asthma", + "description": "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", + "type": "biolink:Disease" + }, + { + "identifier": "DOID:2841", + "label": "asthma", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0004096", + "label": "Asthma", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0085129", + "label": "Bronchial Hyperreactivity", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0340062", + "label": "Hyperreactive airway disease", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C3714497", + "label": "Reactive airway disease", + "type": "biolink:Disease" + }, + { + "identifier": "MESH:D001249", + "label": "Asthma", + "type": "biolink:Disease" + }, + { + "identifier": "MESH:D016535", + "label": "Bronchial Hyperreactivity", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003553", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003555", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003560", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003561", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10003565", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10006450", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10037993", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10056285", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10066091", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10066863", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10082852", + "type": "biolink:Disease" + }, + { + "identifier": "NCIT:C28397", + "label": "Asthma", + "description": "A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways.", + "type": "biolink:Disease" + }, + { + "identifier": "SNOMEDCT:195967001", + "type": "biolink:Disease" + }, + { + "identifier": "SNOMEDCT:991000119106", + "type": "biolink:Disease" + }, + { + "identifier": "medgen:2109", + "type": "biolink:Disease" + }, + { + "identifier": "icd11.foundation:1656445230", + "type": "biolink:Disease" + }, + { + "identifier": "ICD10:J45", + "type": "biolink:Disease" + }, + { + "identifier": "ICD9:493", + "type": "biolink:Disease" + }, + { + "identifier": "KEGG.DISEASE:05310", + "type": "biolink:Disease" + }, + { + "identifier": "HP:0002099", + "label": "Asthma", + "description": "Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.", + "type": "biolink:Disease" + } + ], + "descriptions": [ + "A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors resulting in recurring periods of wheezing (a whistling sound while breathing), chest tightness, shortness of breath, mucus production and coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety.", + "A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways.", + "Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing." + ], + "type": [ + "biolink:Disease", + "biolink:DiseaseOrPhenotypicFeature", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing" + ], + "information_content": 77.3 + } +} diff --git a/tests/fixtures/nodenorm_responses/ncbigene_1756.json b/tests/fixtures/nodenorm_responses/ncbigene_1756.json new file mode 100644 index 0000000..b324240 --- /dev/null +++ b/tests/fixtures/nodenorm_responses/ncbigene_1756.json @@ -0,0 +1,183 @@ +{ + "NCBIGene:1756": { + "id": { + "identifier": "NCBIGene:1756", + "label": "DMD", + "description": "dystrophin" + }, + "equivalent_identifiers": [ + { + "identifier": "NCBIGene:1756", + "label": "DMD", + "description": "dystrophin", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Gene" + }, + { + "identifier": "ENSEMBL:ENSG00000198947", + "type": "biolink:Gene" + }, + { + "identifier": "HGNC:2928", + "label": "DMD", + "type": "biolink:Gene" + }, + { + "identifier": "OMIM:300377", + "type": "biolink:Gene" + }, + { + "identifier": "UMLS:C1414083", + "label": "DMD gene", + "type": "biolink:Gene" + }, + { + "identifier": "UniProtKB:A0A087WV90", + "label": "A0A087WV90_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A0S2Z3B5", + "label": "A0A0S2Z3B5_HUMAN Dystrophin isoform 2 (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A0S2Z3J7", + "label": "A0A0S2Z3J7_HUMAN Dystrophin isoform 1 (Fragment) (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A5H1ZRP9", + "label": "A0A5H1ZRP9_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A5H1ZRQ1", + "label": "A0A5H1ZRQ1_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A5H1ZRQ8", + "label": "A0A5H1ZRQ8_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A5H1ZRR9", + "label": "A0A5H1ZRR9_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A0A804HKY9", + "label": "A0A804HKY9_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:A7E212", + "label": "A7E212_HUMAN Dystrophin (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:P11532", + "label": "DMD_HUMAN Dystrophin (sprot)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "PR:P11532", + "label": "dystrophin (human)", + "description": "A dystrophin that is encoded in the genome of human.", + "type": "biolink:Protein" + }, + { + "identifier": "UMLS:C1437024", + "label": "DMD protein, human", + "type": "biolink:Protein" + }, + { + "identifier": "MESH:C484258", + "label": "DMD protein, human", + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:Q16484", + "label": "Q16484_HUMAN DMD protein (Fragment) (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "UniProtKB:Q4G0X0", + "label": "Q4G0X0_HUMAN DMD protein (trembl)", + "taxa": [ + "NCBITaxon:9606" + ], + "type": "biolink:Protein" + }, + { + "identifier": "ENSEMBL:ENSP00000288447", + "type": "biolink:Protein" + }, + { + "identifier": "ENSEMBL:ENSP00000288447.4", + "type": "biolink:Protein" + } + ], + "descriptions": [ + "dystrophin", + "A dystrophin that is encoded in the genome of human." + ], + "taxa": [ + "NCBITaxon:9606" + ], + "type": [ + "biolink:Gene", + "biolink:GeneOrGeneProduct", + "biolink:GenomicEntity", + "biolink:ChemicalEntityOrGeneOrGeneProduct", + "biolink:PhysicalEssence", + "biolink:OntologyClass", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing", + "biolink:PhysicalEssenceOrOccurrent", + "biolink:MacromolecularMachineMixin", + "biolink:Protein", + "biolink:GeneProductMixin", + "biolink:Polypeptide", + "biolink:ChemicalEntityOrProteinOrPolypeptide" + ], + "information_content": 79.9 + } +} diff --git a/tests/fixtures/nodenorm_responses/ncit_c34373.json b/tests/fixtures/nodenorm_responses/ncit_c34373.json new file mode 100644 index 0000000..3e2b1df --- /dev/null +++ b/tests/fixtures/nodenorm_responses/ncit_c34373.json @@ -0,0 +1,95 @@ +{ + "NCIT:C34373": { + "id": { + "identifier": "MONDO:0004976", + "label": "amyotrophic lateral sclerosis", + "description": "Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord." + }, + "equivalent_identifiers": [ + { + "identifier": "MONDO:0004976", + "label": "amyotrophic lateral sclerosis", + "description": "Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.", + "type": "biolink:Disease" + }, + { + "identifier": "DOID:332", + "label": "amyotrophic lateral sclerosis", + "type": "biolink:Disease" + }, + { + "identifier": "orphanet:803", + "type": "biolink:Disease" + }, + { + "identifier": "UMLS:C0002736", + "label": "Amyotrophic Lateral Sclerosis", + "type": "biolink:Disease" + }, + { + "identifier": "MESH:D000690", + "label": "Amyotrophic Lateral Sclerosis", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10002026", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10052889", + "type": "biolink:Disease" + }, + { + "identifier": "MEDDRA:10090869", + "type": "biolink:Disease" + }, + { + "identifier": "NCIT:C34373", + "label": "Amyotrophic Lateral Sclerosis", + "description": "A neurodegenerative disorder characterized by progressive degeneration of the motor neurons of the central nervous system. It results in weakness and atrophy of the muscles which leads to an inability to initiate and control voluntary movements.", + "type": "biolink:Disease" + }, + { + "identifier": "SNOMEDCT:86044005", + "type": "biolink:Disease" + }, + { + "identifier": "medgen:274", + "type": "biolink:Disease" + }, + { + "identifier": "icd11.foundation:1982355687", + "type": "biolink:Disease" + }, + { + "identifier": "ICD10:G12.21", + "type": "biolink:Disease" + }, + { + "identifier": "ICD9:335.20", + "type": "biolink:Disease" + }, + { + "identifier": "KEGG.DISEASE:05014", + "type": "biolink:Disease" + }, + { + "identifier": "HP:0007354", + "label": "Amyotrophic lateral sclerosis", + "type": "biolink:Disease" + } + ], + "descriptions": [ + "Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.", + "A neurodegenerative disorder characterized by progressive degeneration of the motor neurons of the central nervous system. It results in weakness and atrophy of the muscles which leads to an inability to initiate and control voluntary movements." + ], + "type": [ + "biolink:Disease", + "biolink:DiseaseOrPhenotypicFeature", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing" + ], + "information_content": 74.9 + } +} diff --git a/tests/fixtures/nodenorm_responses/ncit_c55060.json b/tests/fixtures/nodenorm_responses/ncit_c55060.json new file mode 100644 index 0000000..58e77bc --- /dev/null +++ b/tests/fixtures/nodenorm_responses/ncit_c55060.json @@ -0,0 +1,33 @@ +{ + "NCIT:C55060": { + "id": { + "identifier": "NCIT:C55060", + "label": "Hypertension, CTCAE", + "description": "A disorder characterized by a pathological increase in blood pressure." + }, + "equivalent_identifiers": [ + { + "identifier": "NCIT:C55060", + "label": "Hypertension, CTCAE", + "description": "A disorder characterized by a pathological increase in blood pressure.", + "type": "biolink:PhenotypicFeature" + }, + { + "identifier": "UMLS:C1963138", + "label": "Hypertension, CTCAE", + "type": "biolink:PhenotypicFeature" + } + ], + "descriptions": [ + "A disorder characterized by a pathological increase in blood pressure." + ], + "type": [ + "biolink:PhenotypicFeature", + "biolink:DiseaseOrPhenotypicFeature", + "biolink:BiologicalEntity", + "biolink:ThingWithTaxon", + "biolink:NamedThing" + ], + "information_content": 88.2 + } +} diff --git a/tests/fixtures/nodenorm_responses/not_found.json b/tests/fixtures/nodenorm_responses/not_found.json new file mode 100644 index 0000000..c6443d9 --- /dev/null +++ b/tests/fixtures/nodenorm_responses/not_found.json @@ -0,0 +1,3 @@ +{ + "FAKE:9999999": null +} diff --git a/tests/fixtures/prefix_map_subset.json b/tests/fixtures/prefix_map_subset.json new file mode 100644 index 0000000..dd1ced7 --- /dev/null +++ b/tests/fixtures/prefix_map_subset.json @@ -0,0 +1,12 @@ +{ + "MONDO": "http://purl.obolibrary.org/obo/MONDO_", + "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", + "HP": "http://purl.obolibrary.org/obo/HP_", + "HGNC": "http://identifiers.org/hgnc/", + "NCIT": "http://purl.obolibrary.org/obo/NCIT_", + "UMLS": "http://identifiers.org/umls/", + "DOID": "http://purl.obolibrary.org/obo/DOID_", + "MESH": "http://id.nlm.nih.gov/mesh/", + "GO": "http://purl.obolibrary.org/obo/GO_", + "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_" +} diff --git a/tests/test_web.py b/tests/test_web.py new file mode 100644 index 0000000..6921f7c --- /dev/null +++ b/tests/test_web.py @@ -0,0 +1,237 @@ +"""Unit tests for the web frontend. All core objects are mocked — no network or Parquet files needed.""" + +import pytest +from unittest.mock import MagicMock + +from fastapi.testclient import TestClient + +from babel_explorer.core.nodenorm import Identifier +from babel_explorer.core.babel_xrefs import CrossReference, IdentifierRecord +from babel_explorer.web import create_app + + +@pytest.fixture() +def mock_nodenorm(): + nn = MagicMock() + nn.get_identifier.return_value = Identifier( + curie="MONDO:0004979", + label="asthma", + biolink_type="biolink:Disease", + taxa=[], + description=["A chronic respiratory disease"], + ) + nn.get_clique_identifiers.return_value = [ + Identifier( + curie="MONDO:0004979", label="asthma", biolink_type="biolink:Disease" + ), + Identifier(curie="DOID:2841", label="asthma", biolink_type="biolink:Disease"), + ] + return nn + + +@pytest.fixture() +def mock_bxref(): + bx = MagicMock() + bx.get_curie_xrefs.return_value = [ + CrossReference( + filename="compendia/diseases.txt", + subj="MONDO:0004979", + pred="skos:exactMatch", + obj="DOID:2841", + ), + ] + bx.get_curie_ids.return_value = [ + IdentifierRecord( + curie="MONDO:0004979", + extra_fields=(("label", "asthma"), ("type", "biolink:Disease")), + ), + ] + return bx + + +@pytest.fixture() +def client(mock_nodenorm, mock_bxref): + app = create_app() + # Replace real core objects with mocks + app.state.nodenorm = mock_nodenorm + app.state.bxref = mock_bxref + return TestClient(app) + + +# --------------------------------------------------------------------------- +# HTML pages load +# --------------------------------------------------------------------------- + + +class TestHTMLPages: + def test_index(self, client): + r = client.get("/") + assert r.status_code == 200 + assert "Babel Explorer" in r.text + + def test_nodenorm_page(self, client): + r = client.get("/nodenorm") + assert r.status_code == 200 + assert "NodeNorm" in r.text + + def test_xrefs_page(self, client): + r = client.get("/xrefs") + assert r.status_code == 200 + assert "XRefs" in r.text + + def test_ids_page(self, client): + r = client.get("/ids") + assert r.status_code == 200 + assert "IDs" in r.text + + def test_test_concord_page(self, client): + r = client.get("/test-concord") + assert r.status_code == 200 + assert "Test Concordance" in r.text + + +# --------------------------------------------------------------------------- +# htmx partials +# --------------------------------------------------------------------------- + + +class TestHtmxPartials: + def test_nodenorm(self, client, mock_nodenorm): + r = client.post( + "/htmx/nodenorm", data={"curies": "MONDO:0004979", "nodenorm_url": ""} + ) + assert r.status_code == 200 + assert "asthma" in r.text + mock_nodenorm.get_identifier.assert_called_once_with("MONDO:0004979") + + def test_nodenorm_empty(self, client): + r = client.post("/htmx/nodenorm", data={"curies": "", "nodenorm_url": ""}) + assert r.status_code == 200 + assert "No CURIEs provided" in r.text + + def test_xrefs(self, client, mock_bxref): + r = client.post("/htmx/xrefs", data={"curies": "MONDO:0004979"}) + assert r.status_code == 200 + assert "DOID:2841" in r.text + mock_bxref.get_curie_xrefs.assert_called_once() + + def test_xrefs_empty(self, client): + r = client.post("/htmx/xrefs", data={"curies": ""}) + assert r.status_code == 200 + assert "No CURIEs provided" in r.text + + def test_ids(self, client, mock_bxref): + r = client.post("/htmx/ids", data={"curies": "MONDO:0004979"}) + assert r.status_code == 200 + assert "MONDO:0004979" in r.text + mock_bxref.get_curie_ids.assert_called_once() + + def test_ids_empty(self, client): + r = client.post("/htmx/ids", data={"curies": ""}) + assert r.status_code == 200 + assert "No CURIEs provided" in r.text + + def test_test_concord(self, client, mock_nodenorm): + r = client.post( + "/htmx/test-concord", data={"curies": "MONDO:0004979", "nodenorm_url": ""} + ) + assert r.status_code == 200 + assert "DOID:2841" in r.text + mock_nodenorm.get_clique_identifiers.assert_called_once_with("MONDO:0004979") + + def test_test_concord_empty(self, client): + r = client.post("/htmx/test-concord", data={"curies": "", "nodenorm_url": ""}) + assert r.status_code == 200 + assert "No CURIEs provided" in r.text + + +# --------------------------------------------------------------------------- +# JSON API +# --------------------------------------------------------------------------- + + +class TestAPI: + def test_nodenorm(self, client, mock_nodenorm): + r = client.get("/api/nodenorm", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + data = r.json() + assert len(data) == 1 + assert data[0]["label"] == "asthma" + + def test_xrefs(self, client, mock_bxref): + r = client.get("/api/xrefs", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + data = r.json() + assert len(data) == 1 + assert data[0]["obj"] == "DOID:2841" + + def test_ids(self, client, mock_bxref): + r = client.get("/api/ids", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + data = r.json() + assert len(data) == 1 + assert data[0]["curie"] == "MONDO:0004979" + + def test_test_concord(self, client, mock_nodenorm): + r = client.get("/api/test-concord", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + data = r.json() + assert len(data) == 2 + + +# --------------------------------------------------------------------------- +# CSV downloads +# --------------------------------------------------------------------------- + + +class TestCSV: + def test_nodenorm_csv(self, client): + r = client.get("/api/nodenorm/csv", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + assert r.headers["content-type"].startswith("text/csv") + assert "asthma" in r.text + + def test_xrefs_csv(self, client): + r = client.get("/api/xrefs/csv", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + assert r.headers["content-type"].startswith("text/csv") + assert "DOID:2841" in r.text + + def test_ids_csv(self, client): + r = client.get("/api/ids/csv", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + assert r.headers["content-type"].startswith("text/csv") + assert "MONDO:0004979" in r.text + + def test_test_concord_csv(self, client): + r = client.get("/api/test-concord/csv", params={"curie": "MONDO:0004979"}) + assert r.status_code == 200 + assert r.headers["content-type"].startswith("text/csv") + assert "DOID:2841" in r.text + + +# --------------------------------------------------------------------------- +# _parse_curies helper +# --------------------------------------------------------------------------- + + +class TestParseCuries: + def test_basic(self): + from babel_explorer.web.routes import _parse_curies + + assert _parse_curies("A\nB\nC") == ["A", "B", "C"] + + def test_dedup(self): + from babel_explorer.web.routes import _parse_curies + + assert _parse_curies("A\nA\nB") == ["A", "B"] + + def test_comments_and_blanks(self): + from babel_explorer.web.routes import _parse_curies + + assert _parse_curies("# comment\n\nA\n \nB") == ["A", "B"] + + def test_strips_whitespace(self): + from babel_explorer.web.routes import _parse_curies + + assert _parse_curies(" A \n B ") == ["A", "B"] diff --git a/uv.lock b/uv.lock index b8496b5..6ae147f 100644 --- a/uv.lock +++ b/uv.lock @@ -2,6 +2,37 @@ version = 1 revision = 3 requires-python = ">=3.11" +[[package]] +name = "annotated-doc" +version = "0.0.4" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/57/ba/046ceea27344560984e26a590f90bc7f4a75b06701f653222458922b558c/annotated_doc-0.0.4.tar.gz", hash = "sha256:fbcda96e87e9c92ad167c2e53839e57503ecfda18804ea28102353485033faa4", size = 7288, upload-time = "2025-11-10T22:07:42.062Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/1e/d3/26bf1008eb3d2daa8ef4cacc7f3bfdc11818d111f7e2d0201bc6e3b49d45/annotated_doc-0.0.4-py3-none-any.whl", hash = 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A deeper diff would show: +- Which equivalent identifiers were added/removed between instances +- Label changes for the same identifier +- Type reclassifications +- Side-by-side diff view with expandable details per CURIE + +### URL State Persistence +Encode form state (CURIEs, selected instance, API options) in URL query parameters so results are shareable and bookmarkable. This would also enable linking directly to a comparison. + +### CSV/TSV Export +Add download buttons for results, matching the CSV export pattern from the Python frontend. Use Blob URLs for client-side file generation. + +### Keyboard Navigation +- Arrow keys to navigate between accordion cards +- Enter to expand/collapse +- Ctrl+A to expand all / collapse all + +### Batch Size Limits +For very large CURIE lists (100+), consider: +- Chunked API calls to avoid URL length limits +- Progress indicator showing how many chunks have completed +- Streaming results as they arrive + +## General + +### Additional Tools +- **Test Concordance**: Compare equivalence cliques across NodeNorm instances +- **NameRes Lookup**: Name resolution using the NameRes API (also CORS-enabled) +- **Node Annotator**: Annotation lookup via the Node Annotator API + +### Pinia Store +If multiple tool pages need shared state (e.g. a shared CURIE list across tools), migrate from component-local `ref()`/`reactive()` to a Pinia store. + +### Testing +Vitest unit and component tests are implemented (see `web/tests/README.md`). Future testing work: +- **Playwright E2E tests** for full-page interaction (form submission, accordion, Bootstrap JS) +- **Integration tests** calling live NodeNorm API to verify response parsing end-to-end +- **Coverage thresholds** via `vitest --coverage` +- **CI integration** — run `npm test` in GitHub Actions alongside Python tests +- **NodeNormForm / NodeNormApp tests** — form validation, orchestration logic, error states + +### GitHub Actions Deployment +CI workflow that builds the Astro site and deploys to the `gh-pages` branch on push to `main` or on new releases. + +### CORS Proxy Fallback +If any NodeNorm instance blocks browser requests, add an optional lightweight CORS proxy mode (configurable in the UI). + +### Dark Mode +Full dark theme beyond just the navbar, using Bootstrap's `data-bs-theme="dark"`. + +### Shared CSS Between Frontends +Extract common Bootstrap customizations (if any) into a shared CSS file that both the Python and Astro frontends can reference. diff --git a/web/README.md b/web/README.md new file mode 100644 index 0000000..be63d53 --- /dev/null +++ b/web/README.md @@ -0,0 +1,107 @@ +# Babel Explorer Web Frontend (GitHub Pages) + +This is the **static frontend** for Babel Explorer, built with [Astro](https://astro.build/) and [Vue 3](https://vuejs.org/). It hosts browser-only tools that call public APIs directly — no backend server required. + +## Dual-Frontend Architecture + +babel-explorer has **two** web frontends: + +| Frontend | Stack | Deployment | Tools | Directory | +|----------|-------|------------|-------|-----------| +| **This one** | Astro + Vue 3 | GitHub Pages | NodeNorm (more planned) | `web/` | +| **Python frontend** | FastAPI + htmx | Kubernetes | XRefs, IDs, Test Concordance, NodeNorm | `src/babel_explorer/web/` | + +The split follows data dependencies: tools that only call external APIs (NodeNorm, NameRes) can run entirely in the browser. Tools that query multi-GB Parquet files via DuckDB need a server. + +Both frontends share the same Bootstrap 5 dark-navbar styling for visual consistency. The long-term vision is a unified navigation bar with tabs that seamlessly link between the two sites — some tools on GitHub Pages, others on the Kubernetes server. + +## Current Features + +### NodeNorm Lookup (`/nodenorm`) + +- **Bulk normalization**: Enter multiple CURIEs, toggle API options (conflation, descriptions, individual types, taxa) +- **Unified instance selection**: Checkboxes for known NodeNorm deployments (Dev, Exp, CI, Test, Prod) plus a custom URL input; any combination of instances can be queried together +- **Comparison table**: Results shown as a table — rows = CURIEs, columns = selected instances; rows highlighted amber when instances disagree on preferred ID +- **Expandable row detail**: Click any CURIE row to reveal per-instance panels showing description, biolink types, IC score, and equivalent identifiers (prefix summary + expand/collapse for large cliques) +- **Column visibility**: Toggle biolink type, taxa, description columns page-wide +- **Unified summary**: Stat tiles above the table — normalized count (with partial/not-found detail), disagreement count across instances, and biolink type frequency badges +- **Shareable URLs**: Query state encoded in URL params (`?curie=`, `?target=`, non-default options); Share button copies link to clipboard; auto-submits on page load when URL contains CURIEs +- **CURIE link-outs**: Identifiers link to external resources via [biolink-model prefix map](https://github.com/biolink/biolink-model) (v4.3.7) + +## Development + +```bash +cd web +npm install +npm run dev +``` + +This starts a local dev server at `http://localhost:4321/babel-explorer/`. + +## Testing + +```bash +npm test # Run all 99 Vitest unit + component tests +npm run test:watch # Watch mode +``` + +Tests are co-located with source in `__tests__/` directories. See [`web/tests/README.md`](tests/README.md) for the full test plan, fixture catalogue, and future improvements. + +## Building + +```bash +npm run build +``` + +Output goes to `web/dist/`. This is a fully static site that can be served from any web server or GitHub Pages. + +## Deployment + +The built site will be deployed to the `gh-pages` branch via GitHub Actions (triggered on new releases). GitHub Pages will serve it at `https://TranslatorSRI.github.io/babel-explorer/`. See `web/FUTURE.md` for the GitHub Actions workflow (not yet implemented). + +## Shared Configuration + +Deployment URLs for NodeNorm and NameRes are defined once in `config/translator-endpoints.json` at the repo root, shared by both frontends and the CLI. The Python frontend's `NodeNorm.URLs` dict is loaded from this file at startup. The Astro frontend imports it at build time. + +CURIE link-outs use the [biolink-model prefix map](https://github.com/biolink/biolink-model), fetched at runtime from GitHub and cached. The biolink model version is configurable in `src/lib/curie-links.ts` (currently v4.3.7). + +## Architecture + +Each tool is an Astro page that hosts a Vue 3 island via `client:only="vue"`. This means: +- Astro handles page routing and the shared layout (navbar, Bootstrap CDN) +- Vue handles all interactivity within a tool (form state, API calls, result rendering) +- No server-side rendering of Vue components (everything is client-side) + +``` +src/ + layouts/BaseLayout.astro # Bootstrap CDN + dark navbar + pages/ + index.astro # Landing page with tool cards + nodenorm.astro # Hosts NodeNormApp Vue island + components/ + Navbar.astro # Shared navbar (Astro component) + nodenorm/ # NodeNorm Vue components + NodeNormApp.vue # Root island: orchestrates form + results + NodeNormForm.vue # CURIE input, checkbox instance selection, custom URL, API options + ComparisonView.vue # Results table with expandable per-CURIE rows + CurieDetailPanel.vue # Detail body: description, types, IC, equiv IDs table + CurieResultCard.vue # Accordion card wrapping CurieDetailPanel + ResultsSummary.vue # Stat tiles: normalized count, disagreements, type badges + EquivalentIdTable.vue # Equiv ID table with togglable columns + ColumnVisibility.vue # Column show/hide controls + shared/ + CurieLink.vue # CURIE → external URL link + lib/ + nodenorm-api.ts # NodeNorm API fetch wrapper (supports AbortSignal) + curie-links.ts # Biolink prefix map loader + url-state.ts # Encode/decode query state in URL params + types.ts # TypeScript interfaces +``` + +## Adding a New Tool + +1. Create a new Astro page in `src/pages/` (e.g. `test-concord.astro`) +2. Create a root Vue island component in `src/components//` +3. Add a nav link in `src/components/Navbar.astro` +4. Add a card on the landing page in `src/pages/index.astro` +5. 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b/web/public/favicon.svg @@ -0,0 +1,9 @@ + + + + diff --git a/web/src/components/Navbar.astro b/web/src/components/Navbar.astro new file mode 100644 index 0000000..5828c5c --- /dev/null +++ b/web/src/components/Navbar.astro @@ -0,0 +1,31 @@ +--- +interface Props { + activePage?: string; +} +const { activePage = '' } = Astro.props; +const rawBase = import.meta.env.BASE_URL; +const base = rawBase.endsWith('/') ? rawBase : rawBase + '/'; +--- + + diff --git a/web/src/components/nodenorm/ColumnVisibility.vue b/web/src/components/nodenorm/ColumnVisibility.vue new file mode 100644 index 0000000..d323911 --- /dev/null +++ b/web/src/components/nodenorm/ColumnVisibility.vue @@ -0,0 +1,32 @@ + + + diff --git a/web/src/components/nodenorm/ComparisonView.vue b/web/src/components/nodenorm/ComparisonView.vue new file mode 100644 index 0000000..6ccbd46 --- /dev/null +++ b/web/src/components/nodenorm/ComparisonView.vue @@ -0,0 +1,172 @@ + + + diff --git a/web/src/components/nodenorm/CurieDetailPanel.vue b/web/src/components/nodenorm/CurieDetailPanel.vue new file mode 100644 index 0000000..e37ccc6 --- /dev/null +++ b/web/src/components/nodenorm/CurieDetailPanel.vue @@ -0,0 +1,84 @@ + + + diff --git a/web/src/components/nodenorm/CurieResultCard.vue b/web/src/components/nodenorm/CurieResultCard.vue new file mode 100644 index 0000000..86b3570 --- /dev/null +++ b/web/src/components/nodenorm/CurieResultCard.vue @@ -0,0 +1,69 @@ + + + diff --git a/web/src/components/nodenorm/EquivalentIdTable.vue b/web/src/components/nodenorm/EquivalentIdTable.vue new file mode 100644 index 0000000..09d5d63 --- /dev/null +++ b/web/src/components/nodenorm/EquivalentIdTable.vue @@ -0,0 +1,50 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormApp.vue b/web/src/components/nodenorm/NodeNormApp.vue new file mode 100644 index 0000000..18929d5 --- /dev/null +++ b/web/src/components/nodenorm/NodeNormApp.vue @@ -0,0 +1,252 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormForm.vue b/web/src/components/nodenorm/NodeNormForm.vue new file mode 100644 index 0000000..9ce689c --- /dev/null +++ b/web/src/components/nodenorm/NodeNormForm.vue @@ -0,0 +1,223 @@ + + + diff --git a/web/src/components/nodenorm/ResultsSummary.vue b/web/src/components/nodenorm/ResultsSummary.vue new file mode 100644 index 0000000..72ed3c4 --- /dev/null +++ b/web/src/components/nodenorm/ResultsSummary.vue @@ -0,0 +1,162 @@ + + + diff --git a/web/src/components/nodenorm/__tests__/ColumnVisibility.test.ts b/web/src/components/nodenorm/__tests__/ColumnVisibility.test.ts new file mode 100644 index 0000000..78d7f5e --- /dev/null +++ b/web/src/components/nodenorm/__tests__/ColumnVisibility.test.ts @@ -0,0 +1,151 @@ +import { describe, it, expect } from 'vitest'; +import { defineComponent, ref } from 'vue'; +import { mount } from '@vue/test-utils'; +import ColumnVisibility from '../ColumnVisibility.vue'; + +// ── Rendering ───────────────────────────────────────────────────────────────── + +describe('ColumnVisibility — rendering', () => { + it('renders three toggle buttons with correct labels', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + const buttons = wrapper.findAll('button'); + expect(buttons.length).toBe(3); + expect(buttons[0].text()).toBe('Biolink Type'); + expect(buttons[1].text()).toBe('Taxa'); + expect(buttons[2].text()).toBe('Description'); + }); + + it('active column button has btn-secondary class', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + const buttons = wrapper.findAll('button'); + expect(buttons[0].classes()).toContain('btn-secondary'); + expect(buttons[0].classes()).not.toContain('btn-outline-secondary'); + }); + + it('inactive column button has btn-outline-secondary class', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + const buttons = wrapper.findAll('button'); + expect(buttons[1].classes()).toContain('btn-outline-secondary'); + expect(buttons[1].classes()).not.toContain('btn-secondary'); + expect(buttons[2].classes()).toContain('btn-outline-secondary'); + expect(buttons[2].classes()).not.toContain('btn-secondary'); + }); + + it('highlights multiple active columns correctly', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['taxa', 'description']) }, + }); + const buttons = wrapper.findAll('button'); + expect(buttons[0].classes()).toContain('btn-outline-secondary'); // type hidden + expect(buttons[1].classes()).toContain('btn-secondary'); // taxa visible + expect(buttons[2].classes()).toContain('btn-secondary'); // description visible + }); + + it('shows all buttons as inactive when visibleColumns is empty', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set() }, + }); + for (const btn of wrapper.findAll('button')) { + expect(btn.classes()).toContain('btn-outline-secondary'); + expect(btn.classes()).not.toContain('btn-secondary'); + } + }); + + it('shows all buttons as active when all columns are visible', () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type', 'taxa', 'description']) }, + }); + for (const btn of wrapper.findAll('button')) { + expect(btn.classes()).toContain('btn-secondary'); + expect(btn.classes()).not.toContain('btn-outline-secondary'); + } + }); +}); + +// ── Emits ───────────────────────────────────────────────────────────────────── + +describe('ColumnVisibility — emits', () => { + it('emits toggle with "type" when Biolink Type button clicked', async () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + await wrapper.findAll('button')[0].trigger('click'); + expect(wrapper.emitted('toggle')).toEqual([['type']]); + }); + + it('emits toggle with "taxa" when Taxa button clicked', async () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + await wrapper.findAll('button')[1].trigger('click'); + expect(wrapper.emitted('toggle')).toEqual([['taxa']]); + }); + + it('emits toggle with "description" when Description button clicked', async () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + await wrapper.findAll('button')[2].trigger('click'); + expect(wrapper.emitted('toggle')).toEqual([['description']]); + }); +}); + +// ── Reactivity ──────────────────────────────────────────────────────────────── + +describe('ColumnVisibility — reactivity', () => { + it('button classes update when visibleColumns prop is replaced with a new Set', async () => { + const wrapper = mount(ColumnVisibility, { + props: { visibleColumns: new Set(['type']) }, + }); + expect(wrapper.findAll('button')[0].classes()).toContain('btn-secondary'); + + await wrapper.setProps({ visibleColumns: new Set() }); + + expect(wrapper.findAll('button')[0].classes()).toContain('btn-outline-secondary'); + expect(wrapper.findAll('button')[0].classes()).not.toContain('btn-secondary'); + }); + + it('button classes update when a column is added via parent ref replacement', async () => { + // This test exercises the correct fix: parent uses ref + replace-on-toggle. + // It fails if the parent uses reactive(new Set()) + mutate-in-place, because + // child props only update when the parent re-renders with a new prop value. + const Parent = defineComponent({ + components: { ColumnVisibility }, + setup() { + const visibleColumns = ref(new Set(['type'])); + function toggle(col: string) { + const next = new Set(visibleColumns.value); + if (next.has(col)) next.delete(col); + else next.add(col); + visibleColumns.value = next; + } + return { visibleColumns, toggle }; + }, + template: '', + }); + + const wrapper = mount(Parent); + const buttons = () => wrapper.findAll('button'); + + // Initially: type active, taxa inactive + expect(buttons()[0].classes()).toContain('btn-secondary'); + expect(buttons()[1].classes()).toContain('btn-outline-secondary'); + + // Click "Biolink Type" — should deactivate it + await buttons()[0].trigger('click'); + expect(buttons()[0].classes()).toContain('btn-outline-secondary'); + expect(buttons()[0].classes()).not.toContain('btn-secondary'); + + // Click "Taxa" — should activate it + await buttons()[1].trigger('click'); + expect(buttons()[1].classes()).toContain('btn-secondary'); + expect(buttons()[1].classes()).not.toContain('btn-outline-secondary'); + }); + +}); diff --git a/web/src/components/nodenorm/__tests__/ComparisonView.test.ts b/web/src/components/nodenorm/__tests__/ComparisonView.test.ts new file mode 100644 index 0000000..04be3a3 --- /dev/null +++ b/web/src/components/nodenorm/__tests__/ComparisonView.test.ts @@ -0,0 +1,243 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import ComparisonView from '../ComparisonView.vue'; +import type { NodeNormResponse, NodeNormInstance } from '../../../lib/types'; +import { DEFAULT_API_OPTIONS } from '../../../lib/types'; +import mondoFixture from '../../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import prefixMapSubset from '../../../../../tests/fixtures/prefix_map_subset.json'; + +const devInstance: NodeNormInstance = { name: 'Dev', env: 'dev', url: 'https://dev.example.com/' }; +const prodInstance: NodeNormInstance = { name: 'Prod', env: 'prod', url: 'https://prod.example.com/' }; + +// Both instances agree on MONDO:0004979 +const agreeResults = new Map([ + [devInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], + [prodInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], +]); + +// Instances disagree: dev normalizes, prod returns null +const disagreeResults = new Map([ + [devInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], + [prodInstance.url, { 'MONDO:0004979': null }], +]); + +const defaultProps = { + curies: ['MONDO:0004979'], + queriedInstances: [devInstance, prodInstance], + prefixMap: prefixMapSubset, + visibleColumns: new Set(['type']), + typeFilter: new Set(), + apiOptions: DEFAULT_API_OPTIONS, +}; + +describe('ComparisonView', () => { + it('renders instance names as column headers', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + expect(wrapper.text()).toContain('Dev'); + expect(wrapper.text()).toContain('Prod'); + }); + + it('shows preferred ID and label when instances agree', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const text = wrapper.text(); + expect(text).toContain('MONDO:0004979'); + expect(text).toContain('asthma'); + }); + + it('does not highlight row when all instances agree', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + // Summary row is the first tr in the first tbody + const summaryRow = wrapper.findAll('tbody')[0].find('tr'); + expect(summaryRow.classes()).not.toContain('table-warning'); + }); + + it('highlights row with table-warning when instances disagree', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: disagreeResults }, + }); + const summaryRow = wrapper.findAll('tbody')[0].find('tr'); + expect(summaryRow.classes()).toContain('table-warning'); + }); + + it('shows "Not found" for instances that return null', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: disagreeResults }, + }); + expect(wrapper.text()).toContain('Not found'); + }); + + it('shows equiv ID count for found results', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const equivCount = mondoFixture['MONDO:0004979'].equivalent_identifiers.length; + expect(wrapper.text()).toContain(`${equivCount} equivalent IDs`); + }); + + it('does not highlight row when only one instance queried', () => { + const singleInstance = new Map([ + [devInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], + ]); + const wrapper = mount(ComparisonView, { + props: { + ...defaultProps, + queriedInstances: [devInstance], + resultsByInstance: singleInstance, + typeFilter: new Set(), + }, + }); + const summaryRow = wrapper.findAll('tbody')[0].find('tr'); + expect(summaryRow.classes()).not.toContain('table-warning'); + }); + + it('summary row has cursor:pointer style', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const summaryRow = wrapper.findAll('tbody')[0].find('tr'); + expect(summaryRow.attributes('style')).toContain('cursor: pointer'); + }); + + it('detail row is not rendered before clicking the summary row', () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const rows = wrapper.findAll('tbody')[0].findAll('tr'); + expect(rows.length).toBe(1); + }); + + it('renders detail row after clicking the summary row', async () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const tbody = wrapper.findAll('tbody')[0]; + await tbody.find('tr').trigger('click'); + expect(tbody.findAll('tr').length).toBe(2); + }); + + it('detail row contains instance name in expanded panel', async () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + await wrapper.findAll('tbody')[0].find('tr').trigger('click'); + expect(wrapper.text()).toContain('Dev'); + expect(wrapper.text()).toContain('Prod'); + }); + +// ── Column visibility in main row ───────────────────────────────────────────── + +describe('ComparisonView — column visibility', () => { + const singleInstance = new Map([ + [devInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], + ]); + const singleInstanceProps = { + curies: ['MONDO:0004979'], + queriedInstances: [devInstance], + prefixMap: prefixMapSubset, + resultsByInstance: singleInstance, + typeFilter: new Set(), + apiOptions: DEFAULT_API_OPTIONS, + }; + + it('shows type badges in main row when "type" is visible', () => { + const wrapper = mount(ComparisonView, { + props: { ...singleInstanceProps, visibleColumns: new Set(['type']) }, + }); + expect(wrapper.find('.badge').exists()).toBe(true); + }); + + it('hides type badges in main row when "type" is not visible', () => { + const wrapper = mount(ComparisonView, { + props: { ...singleInstanceProps, visibleColumns: new Set() }, + }); + expect(wrapper.find('.badge').exists()).toBe(false); + }); + + it('updates type badge visibility when visibleColumns prop changes', async () => { + const wrapper = mount(ComparisonView, { + props: { ...singleInstanceProps, visibleColumns: new Set(['type']) }, + }); + expect(wrapper.find('.badge').exists()).toBe(true); + + await wrapper.setProps({ visibleColumns: new Set() }); + expect(wrapper.find('.badge').exists()).toBe(false); + + await wrapper.setProps({ visibleColumns: new Set(['type']) }); + expect(wrapper.find('.badge').exists()).toBe(true); + }); +}); + + it('collapses detail row on second click', async () => { + const wrapper = mount(ComparisonView, { + props: { ...defaultProps, resultsByInstance: agreeResults }, + }); + const tbody = wrapper.findAll('tbody')[0]; + const summaryRow = tbody.find('tr'); + await summaryRow.trigger('click'); + await summaryRow.trigger('click'); + expect(tbody.findAll('tr').length).toBe(1); + }); +}); + +// ── Type filtering ──────────────────────────────────────────────────────────── + +describe('ComparisonView — type filtering', () => { + const results = new Map([ + [devInstance.url, { 'MONDO:0004979': mondoFixture['MONDO:0004979'] }], + ]); + const baseProps = { + curies: ['MONDO:0004979'], + queriedInstances: [devInstance], + prefixMap: prefixMapSubset, + visibleColumns: new Set(), + resultsByInstance: results, + apiOptions: DEFAULT_API_OPTIONS, + }; + + it('shows all CURIEs when typeFilter is empty', () => { + const wrapper = mount(ComparisonView, { + props: { ...baseProps, typeFilter: new Set() }, + }); + expect(wrapper.text()).toContain('MONDO:0004979'); + }); + + it('shows CURIE when its type matches the active filter', () => { + const wrapper = mount(ComparisonView, { + props: { ...baseProps, typeFilter: new Set(['Disease']) }, + }); + expect(wrapper.text()).toContain('MONDO:0004979'); + }); + + it('hides CURIE when its type does not match the active filter', () => { + const wrapper = mount(ComparisonView, { + props: { ...baseProps, typeFilter: new Set(['Gene']) }, + }); + expect(wrapper.text()).not.toContain('MONDO:0004979'); + }); + + it('shows empty-state message when filter excludes all CURIEs', () => { + const wrapper = mount(ComparisonView, { + props: { ...baseProps, typeFilter: new Set(['Gene']) }, + }); + expect(wrapper.text()).toContain('No CURIEs match the selected type filter'); + }); + + it('updates visible rows reactively when typeFilter prop changes', async () => { + const wrapper = mount(ComparisonView, { + props: { ...baseProps, typeFilter: new Set() }, + }); + expect(wrapper.text()).toContain('MONDO:0004979'); + + await wrapper.setProps({ typeFilter: new Set(['Gene']) }); + expect(wrapper.text()).not.toContain('MONDO:0004979'); + + await wrapper.setProps({ typeFilter: new Set() }); + expect(wrapper.text()).toContain('MONDO:0004979'); + }); +}); diff --git a/web/src/components/nodenorm/__tests__/CurieDetailPanel.test.ts b/web/src/components/nodenorm/__tests__/CurieDetailPanel.test.ts new file mode 100644 index 0000000..c893275 --- /dev/null +++ b/web/src/components/nodenorm/__tests__/CurieDetailPanel.test.ts @@ -0,0 +1,106 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import CurieDetailPanel from '../CurieDetailPanel.vue'; +import type { NormalizedNode } from '../../../lib/types'; +import ncitFixture from '../../../../../tests/fixtures/nodenorm_responses/ncit_c55060.json'; +import mondoFixture from '../../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import prefixMapSubset from '../../../../../tests/fixtures/prefix_map_subset.json'; + +// NCIT:C55060 has 2 equiv IDs (≤10, small clique) +const smallCliqueNode = ncitFixture['NCIT:C55060'] as NormalizedNode; +// MONDO:0004979 has 28 equiv IDs (>10, large clique) +const largeCliqueNode = mondoFixture['MONDO:0004979'] as NormalizedNode; + +const defaultProps = { + visibleColumns: new Set(['type', 'taxa', 'description']), + prefixMap: prefixMapSubset, +}; + +describe('CurieDetailPanel', () => { + it('shows "not found" message when node is null', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: null, ...defaultProps }, + }); + expect(wrapper.text()).toContain('not found in NodeNorm'); + }); + + it('shows description when available', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: smallCliqueNode, ...defaultProps }, + }); + // NCIT:C55060 has descriptions + expect(wrapper.text()).toContain('Description:'); + }); + + it('shows biolink type badges', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: smallCliqueNode, ...defaultProps }, + }); + expect(wrapper.text()).toContain('PhenotypicFeature'); + }); + + it('shows information content when available', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: smallCliqueNode, ...defaultProps }, + }); + if (smallCliqueNode.information_content) { + expect(wrapper.text()).toContain('Information Content:'); + } + }); + + it('shows equiv ID count heading', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: smallCliqueNode, ...defaultProps }, + }); + expect(wrapper.text()).toContain(`Equivalent Identifiers (${smallCliqueNode.equivalent_identifiers.length})`); + }); + + it('shows full equiv ID table immediately for small clique (≤10 IDs)', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: smallCliqueNode, ...defaultProps }, + }); + // Should not show "Show all" button for small clique + expect(wrapper.text()).not.toContain('Show all'); + // Table should be present + expect(wrapper.find('table').exists()).toBe(true); + }); + + it('shows prefix summary and "Show all" button for large clique (>10 IDs)', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: largeCliqueNode, ...defaultProps }, + }); + expect(wrapper.text()).toContain('Show all'); + expect(wrapper.text()).toContain(`${largeCliqueNode.equivalent_identifiers.length} identifiers`); + // Prefix summary shows prefix: count entries + expect(wrapper.text()).toContain('MONDO:'); + }); + + it('does not show full table before expanding large clique', () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: largeCliqueNode, ...defaultProps }, + }); + expect(wrapper.find('table').exists()).toBe(false); + }); + + it('reveals equiv ID table after clicking "Show all"', async () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: largeCliqueNode, ...defaultProps }, + }); + await wrapper.find('button').trigger('click'); + expect(wrapper.find('table').exists()).toBe(true); + expect(wrapper.text()).toContain('Collapse'); + }); + + it('collapses table after clicking "Collapse"', async () => { + const wrapper = mount(CurieDetailPanel, { + props: { node: largeCliqueNode, ...defaultProps }, + }); + // Expand + await wrapper.find('button').trigger('click'); + // Collapse + const collapseBtn = wrapper.findAll('button').find((b) => b.text() === 'Collapse'); + await collapseBtn!.trigger('click'); + expect(wrapper.find('table').exists()).toBe(false); + expect(wrapper.text()).toContain('Show all'); + }); +}); diff --git a/web/src/components/nodenorm/__tests__/CurieResultCard.test.ts b/web/src/components/nodenorm/__tests__/CurieResultCard.test.ts new file mode 100644 index 0000000..e2a55e7 --- /dev/null +++ b/web/src/components/nodenorm/__tests__/CurieResultCard.test.ts @@ -0,0 +1,69 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import CurieResultCard from '../CurieResultCard.vue'; +import type { NormalizedNode } from '../../../lib/types'; +import ncitFixture from '../../../../../tests/fixtures/nodenorm_responses/ncit_c55060.json'; +import mondoFixture from '../../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import prefixMapSubset from '../../../../../tests/fixtures/prefix_map_subset.json'; + +// NCIT:C55060 has 2 equiv IDs (≤10, small clique) +const smallCliqueNode = ncitFixture['NCIT:C55060'] as NormalizedNode; +// MONDO:0004979 has 28 equiv IDs (>10, large clique) +const largeCliqueNode = mondoFixture['MONDO:0004979'] as NormalizedNode; + +const defaultProps = { + index: 0, + visibleColumns: new Set(['type', 'taxa', 'description']), + prefixMap: prefixMapSubset, +}; + +describe('CurieResultCard', () => { + it('shows preferred ID and label for a found CURIE', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'NCIT:C55060', node: smallCliqueNode, ...defaultProps }, + }); + expect(wrapper.text()).toContain('NCIT:C55060'); + expect(wrapper.text()).toContain('Hypertension, CTCAE'); + }); + + it('shows "not found" for a null node', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'FAKE:9999', node: null, ...defaultProps }, + }); + expect(wrapper.text()).toContain('FAKE:9999'); + expect(wrapper.text()).toContain('not found'); + }); + + it('shows equiv ID count in header', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'NCIT:C55060', node: smallCliqueNode, ...defaultProps }, + }); + expect(wrapper.text()).toContain('2 equivalent IDs'); + }); + + it('does not show expand button for small clique (≤10 equiv IDs)', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'NCIT:C55060', node: smallCliqueNode, ...defaultProps }, + }); + // Small clique should NOT have "Show all" button + expect(wrapper.text()).not.toContain('Show all'); + }); + + it('shows prefix summary and expand button for large clique (>10 equiv IDs)', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'MONDO:0004979', node: largeCliqueNode, ...defaultProps }, + }); + // Large clique should show prefix summary (e.g. "MONDO: 1, DOID: 1, UMLS: ...") + expect(wrapper.text()).toContain('MONDO:'); + expect(wrapper.text()).toContain('Show all'); + expect(wrapper.text()).toContain(`${largeCliqueNode.equivalent_identifiers.length} identifiers`); + }); + + it('displays biolink type badges in header', () => { + const wrapper = mount(CurieResultCard, { + props: { inputCurie: 'NCIT:C55060', node: smallCliqueNode, ...defaultProps }, + }); + // First type should be shown as badge (without biolink: prefix) + expect(wrapper.text()).toContain('PhenotypicFeature'); + }); +}); diff --git a/web/src/components/nodenorm/__tests__/EquivalentIdTable.test.ts b/web/src/components/nodenorm/__tests__/EquivalentIdTable.test.ts new file mode 100644 index 0000000..3367a8f --- /dev/null +++ b/web/src/components/nodenorm/__tests__/EquivalentIdTable.test.ts @@ -0,0 +1,131 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import EquivalentIdTable from '../EquivalentIdTable.vue'; +import mondoFixture from '../../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import prefixMapSubset from '../../../../../tests/fixtures/prefix_map_subset.json'; + +const identifiers = mondoFixture['MONDO:0004979'].equivalent_identifiers; + +function headers(wrapper: ReturnType) { + return wrapper.findAll('th').map((th) => th.text()); +} + +// ── Column presence ─────────────────────────────────────────────────────────── + +describe('EquivalentIdTable — column visibility', () => { + it('always renders Identifier and Label columns', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).toContain('Identifier'); + expect(headers(wrapper)).toContain('Label'); + }); + + it('shows Biolink Type column when "type" is visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).toContain('Biolink Type'); + }); + + it('hides Biolink Type column when "type" is not visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).not.toContain('Biolink Type'); + }); + + it('shows Taxa column when "taxa" is visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['taxa']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).toContain('Taxa'); + }); + + it('hides Taxa column when "taxa" is not visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).not.toContain('Taxa'); + }); + + it('shows Description column when "description" is visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['description']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).toContain('Description'); + }); + + it('hides Description column when "description" is not visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).not.toContain('Description'); + }); + + it('shows all three extra columns when all are visible', () => { + const wrapper = mount(EquivalentIdTable, { + props: { + identifiers, + visibleColumns: new Set(['type', 'taxa', 'description']), + prefixMap: prefixMapSubset, + }, + }); + const h = headers(wrapper); + expect(h).toContain('Biolink Type'); + expect(h).toContain('Taxa'); + expect(h).toContain('Description'); + }); + + it('shows only Identifier and Label when visibleColumns is empty', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(), prefixMap: prefixMapSubset }, + }); + const h = headers(wrapper); + expect(h).toEqual(['Identifier', 'Label']); + }); +}); + +// ── Data rows ──────────────────────────────────────────────────────────────── + +describe('EquivalentIdTable — data rows', () => { + it('renders one row per identifier', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(wrapper.findAll('tbody tr').length).toBe(identifiers.length); + }); + + it('renders no rows for empty identifier list', () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers: [], visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(wrapper.findAll('tbody tr').length).toBe(0); + }); +}); + +// ── Reactivity ─────────────────────────────────────────────────────────────── + +describe('EquivalentIdTable — reactivity', () => { + it('adds column header when visibleColumns prop gains a key', async () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).not.toContain('Biolink Type'); + + await wrapper.setProps({ visibleColumns: new Set(['type']) }); + + expect(headers(wrapper)).toContain('Biolink Type'); + }); + + it('removes column header when visibleColumns prop loses a key', async () => { + const wrapper = mount(EquivalentIdTable, { + props: { identifiers, visibleColumns: new Set(['type']), prefixMap: prefixMapSubset }, + }); + expect(headers(wrapper)).toContain('Biolink Type'); + + await wrapper.setProps({ visibleColumns: new Set() }); + + expect(headers(wrapper)).not.toContain('Biolink Type'); + }); +}); diff --git a/web/src/components/nodenorm/__tests__/ResultsSummary.test.ts b/web/src/components/nodenorm/__tests__/ResultsSummary.test.ts new file mode 100644 index 0000000..634b3f7 --- /dev/null +++ b/web/src/components/nodenorm/__tests__/ResultsSummary.test.ts @@ -0,0 +1,283 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import ResultsSummary from '../ResultsSummary.vue'; +import type { NodeNormResponse, NodeNormInstance } from '../../../lib/types'; +import mondoFixture from '../../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import ncitFixture from '../../../../../tests/fixtures/nodenorm_responses/ncit_c55060.json'; + +const devInstance: NodeNormInstance = { name: 'Dev', env: 'dev', url: 'https://dev.example.com/' }; +const prodInstance: NodeNormInstance = { name: 'Prod', env: 'prod', url: 'https://prod.example.com/' }; + +const mondoNode = mondoFixture['MONDO:0004979']; +const ncitNode = ncitFixture['NCIT:C55060']; + +// ── Fixture helpers ─────────────────────────────────────────────────────────── + +function singleInstanceResults(resp: NodeNormResponse) { + return { + resultsByInstance: new Map([[devInstance.url, resp]]), + queriedInstances: [devInstance], + selectedTypes: new Set(), + }; +} + +function twoInstanceResults(devResp: NodeNormResponse, prodResp: NodeNormResponse) { + return { + resultsByInstance: new Map([ + [devInstance.url, devResp], + [prodInstance.url, prodResp], + ]), + queriedInstances: [devInstance, prodInstance], + selectedTypes: new Set(), + }; +} + +// ── Normalized tile ─────────────────────────────────────────────────────────── + +describe('ResultsSummary — normalized tile', () => { + it('shows correct count when all CURIEs are found', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).toContain('1'); + expect(wrapper.text()).toContain('/ 1'); + }); + + it('shows "not found" detail when a CURIE is missing from all instances', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode, 'FAKE:999': null }), + curies: ['MONDO:0004979', 'FAKE:999'], + }, + }); + expect(wrapper.text()).toContain('not found'); + expect(wrapper.text()).toContain('FAKE:999'); + }); + + it('does not show "not found" when all CURIEs are found', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).not.toContain('not found'); + }); + + it('shows "partial" when a CURIE is found by some instances but not all', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...twoInstanceResults( + { 'MONDO:0004979': mondoNode }, + { 'MONDO:0004979': null }, // prod doesn't find it + ), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).toContain('partial'); + expect(wrapper.text()).toContain('MONDO:0004979'); + }); + + it('truncates long not-found list with "+N more"', () => { + const resp: NodeNormResponse = { + 'FAKE:1': null, 'FAKE:2': null, 'FAKE:3': null, 'FAKE:4': null, + }; + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults(resp), + curies: ['FAKE:1', 'FAKE:2', 'FAKE:3', 'FAKE:4'], + }, + }); + expect(wrapper.text()).toContain('+1 more'); + }); +}); + +// ── Disagreements tile ──────────────────────────────────────────────────────── + +describe('ResultsSummary — disagreements tile', () => { + it('is not rendered for a single instance', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).not.toContain('Disagreements'); + }); + + it('shows 0 disagreements and "All instances agree" when both agree', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...twoInstanceResults( + { 'MONDO:0004979': mondoNode }, + { 'MONDO:0004979': mondoNode }, + ), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).toContain('Disagreements'); + expect(wrapper.text()).toContain('0'); + expect(wrapper.text()).toContain('All instances agree'); + }); + + it('counts a disagreement when one instance returns null and another does not', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...twoInstanceResults( + { 'MONDO:0004979': mondoNode }, + { 'MONDO:0004979': null }, + ), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).toContain('1'); + expect(wrapper.text()).toContain('MONDO:0004979'); + }); + + it('counts a disagreement when instances return different preferred IDs', () => { + // Simulate dev returning MONDO:0004979 and prod returning NCIT:C55060 + // as the preferred ID for the same input + const modifiedProdNode = { ...mondoNode, id: { ...mondoNode.id, identifier: 'NCIT:C55060' } }; + const wrapper = mount(ResultsSummary, { + props: { + ...twoInstanceResults( + { 'MONDO:0004979': mondoNode }, + { 'MONDO:0004979': modifiedProdNode }, + ), + curies: ['MONDO:0004979'], + }, + }); + expect(wrapper.text()).toContain('1'); + }); +}); + +// ── Types tile ──────────────────────────────────────────────────────────────── + +describe('ResultsSummary — types tile', () => { + it('shows most-specific type as a button', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'NCIT:C55060': ncitNode }), + curies: ['NCIT:C55060'], + }, + }); + const buttons = wrapper.findAll('button'); + expect(buttons.some((b) => b.text().includes('PhenotypicFeature'))).toBe(true); + }); + + it('uses only the most-specific type per CURIE — no ancestor types', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ + 'MONDO:0004979': mondoNode, + 'NCIT:C55060': ncitNode, + }), + curies: ['MONDO:0004979', 'NCIT:C55060'], + }, + }); + expect(wrapper.text()).toContain('Disease'); + expect(wrapper.text()).toContain('PhenotypicFeature'); + expect(wrapper.text()).not.toContain('NamedThing'); + }); + + it('counts each CURIE once even when queried on multiple instances', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...twoInstanceResults( + { 'MONDO:0004979': mondoNode }, + { 'MONDO:0004979': mondoNode }, + ), + curies: ['MONDO:0004979'], + }, + }); + // Same CURIE on 2 instances should still count as 1 distinct CURIE + expect(wrapper.text()).toContain('Disease'); + expect(wrapper.text()).not.toContain('Disease 2'); + }); + + it('does not render types tile when no results are found', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'FAKE:999': null }), + curies: ['FAKE:999'], + }, + }); + expect(wrapper.text()).not.toContain('Types'); + }); + + it('inactive type button has btn-outline-secondary class', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + selectedTypes: new Set(), + }, + }); + const typeBtn = wrapper.findAll('button').find((b) => b.text().includes('Disease'))!; + expect(typeBtn.classes()).toContain('btn-outline-secondary'); + expect(typeBtn.classes()).not.toContain('btn-secondary'); + }); + + it('active type button has btn-secondary class', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + selectedTypes: new Set(['Disease']), + }, + }); + const typeBtn = wrapper.findAll('button').find((b) => b.text().includes('Disease'))!; + expect(typeBtn.classes()).toContain('btn-secondary'); + expect(typeBtn.classes()).not.toContain('btn-outline-secondary'); + }); + + it('emits toggle-type-filter with the type name when a button is clicked', async () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + }, + }); + const typeBtn = wrapper.findAll('button').find((b) => b.text().includes('Disease'))!; + await typeBtn.trigger('click'); + expect(wrapper.emitted('toggle-type-filter')).toEqual([['Disease']]); + }); + + it('"clear" button is absent when no types are selected', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + selectedTypes: new Set(), + }, + }); + expect(wrapper.text()).not.toContain('clear'); + }); + + it('"clear" button appears when selectedTypes is non-empty', () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + selectedTypes: new Set(['Disease']), + }, + }); + expect(wrapper.text()).toContain('clear'); + }); + + it('emits clear-type-filter when "clear" button is clicked', async () => { + const wrapper = mount(ResultsSummary, { + props: { + ...singleInstanceResults({ 'MONDO:0004979': mondoNode }), + curies: ['MONDO:0004979'], + selectedTypes: new Set(['Disease']), + }, + }); + const clearBtn = wrapper.findAll('button').find((b) => b.text() === 'clear')!; + await clearBtn.trigger('click'); + expect(wrapper.emitted('clear-type-filter')).toBeTruthy(); + }); +}); diff --git a/web/src/components/shared/BiolinkTypeLink.vue b/web/src/components/shared/BiolinkTypeLink.vue new file mode 100644 index 0000000..fed06cd --- /dev/null +++ b/web/src/components/shared/BiolinkTypeLink.vue @@ -0,0 +1,10 @@ + + + diff --git a/web/src/components/shared/CurieLink.vue b/web/src/components/shared/CurieLink.vue new file mode 100644 index 0000000..56a5f07 --- /dev/null +++ b/web/src/components/shared/CurieLink.vue @@ -0,0 +1,16 @@ + + + diff --git a/web/src/components/shared/__tests__/CurieLink.test.ts b/web/src/components/shared/__tests__/CurieLink.test.ts new file mode 100644 index 0000000..f9aa2d9 --- /dev/null +++ b/web/src/components/shared/__tests__/CurieLink.test.ts @@ -0,0 +1,39 @@ +import { describe, it, expect } from 'vitest'; +import { mount } from '@vue/test-utils'; +import CurieLink from '../CurieLink.vue'; +import prefixMapSubset from '../../../../../tests/fixtures/prefix_map_subset.json'; + +describe('CurieLink', () => { + it('renders with correct href when prefix is in map', () => { + const wrapper = mount(CurieLink, { + props: { curie: 'MONDO:0004979', prefixMap: prefixMapSubset }, + }); + const link = wrapper.find('a'); + expect(link.exists()).toBe(true); + expect(link.attributes('href')).toBe('http://purl.obolibrary.org/obo/MONDO_0004979'); + expect(link.attributes('target')).toBe('_blank'); + expect(link.text()).toBe('MONDO:0004979'); + }); + + it('renders when prefix is not in map', () => { + const wrapper = mount(CurieLink, { + props: { curie: 'FAKE:9999', prefixMap: prefixMapSubset }, + }); + expect(wrapper.find('a').exists()).toBe(false); + const span = wrapper.find('span'); + expect(span.exists()).toBe(true); + expect(span.text()).toBe('FAKE:9999'); + }); + + it('displays CURIE text in both linked and unlinked cases', () => { + const linked = mount(CurieLink, { + props: { curie: 'CHEBI:48947', prefixMap: prefixMapSubset }, + }); + expect(linked.text()).toBe('CHEBI:48947'); + + const unlinked = mount(CurieLink, { + props: { curie: 'UNKNOWN:123', prefixMap: prefixMapSubset }, + }); + expect(unlinked.text()).toBe('UNKNOWN:123'); + }); +}); diff --git a/web/src/layouts/BaseLayout.astro b/web/src/layouts/BaseLayout.astro new file mode 100644 index 0000000..2e9a1e3 --- /dev/null +++ b/web/src/layouts/BaseLayout.astro @@ -0,0 +1,28 @@ +--- +import Navbar from '../components/Navbar.astro'; + +interface Props { + title?: string; + activePage?: string; +} +const { title = 'Babel Explorer', activePage = '' } = Astro.props; +--- + + + + + + + {title} + + + + + +
+ +
+ + + + diff --git a/web/src/lib/__tests__/curie-links.test.ts b/web/src/lib/__tests__/curie-links.test.ts new file mode 100644 index 0000000..1129e01 --- /dev/null +++ b/web/src/lib/__tests__/curie-links.test.ts @@ -0,0 +1,141 @@ +import { describe, it, expect, vi, beforeEach } from 'vitest'; +import prefixMapSubset from '../../../../tests/fixtures/prefix_map_subset.json'; + +// Module-level cache in curie-links.ts requires re-importing after reset. +// Each describe block that tests loadPrefixMap uses vi.resetModules(). + +// --------------------------------------------------------------------------- +// parseCurie (pure function — no module cache issues) +// --------------------------------------------------------------------------- + +describe('parseCurie', () => { + // Import once since parseCurie is pure. + let parseCurie: typeof import('../curie-links').parseCurie; + + beforeEach(async () => { + const mod = await import('../curie-links'); + parseCurie = mod.parseCurie; + }); + + it('parses a standard CURIE', () => { + expect(parseCurie('MONDO:0004979')).toEqual({ + prefix: 'MONDO', + localId: '0004979', + }); + }); + + it('splits only on first colon (multi-colon local ID)', () => { + expect(parseCurie('GO:0008150')).toEqual({ + prefix: 'GO', + localId: '0008150', + }); + }); + + it('returns null for string without colon', () => { + expect(parseCurie('MONDO0004979')).toBeNull(); + }); + + it('returns null for string starting with colon', () => { + expect(parseCurie(':0004979')).toBeNull(); + }); + + it('handles prefix with dots', () => { + expect(parseCurie('biolink:Disease')).toEqual({ + prefix: 'biolink', + localId: 'Disease', + }); + }); +}); + +// --------------------------------------------------------------------------- +// getCurieUrl (pure function given a map) +// --------------------------------------------------------------------------- + +describe('getCurieUrl', () => { + let getCurieUrl: typeof import('../curie-links').getCurieUrl; + + beforeEach(async () => { + const mod = await import('../curie-links'); + getCurieUrl = mod.getCurieUrl; + }); + + it('returns IRI URL for a known prefix', () => { + expect(getCurieUrl('MONDO:0004979', prefixMapSubset)).toBe( + 'http://purl.obolibrary.org/obo/MONDO_0004979', + ); + }); + + it('returns IRI URL for CHEBI prefix', () => { + expect(getCurieUrl('CHEBI:48947', prefixMapSubset)).toBe( + 'http://purl.obolibrary.org/obo/CHEBI_48947', + ); + }); + + it('returns IRI URL for HGNC (identifiers.org base)', () => { + expect(getCurieUrl('HGNC:1234', prefixMapSubset)).toBe( + 'http://identifiers.org/hgnc/1234', + ); + }); + + it('returns null for unknown prefix', () => { + expect(getCurieUrl('FAKE:9999', prefixMapSubset)).toBeNull(); + }); + + it('returns null for unparseable CURIE', () => { + expect(getCurieUrl('nocolon', prefixMapSubset)).toBeNull(); + }); +}); + +// --------------------------------------------------------------------------- +// loadPrefixMap (has module-level cache, needs vi.resetModules) +// --------------------------------------------------------------------------- + +describe('loadPrefixMap', () => { + beforeEach(() => { + vi.resetModules(); + vi.restoreAllMocks(); + }); + + it('returns map on successful fetch', async () => { + vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(prefixMapSubset), + })); + + const { loadPrefixMap } = await import('../curie-links'); + const map = await loadPrefixMap(); + expect(map).toEqual(prefixMapSubset); + }); + + it('returns empty map on fetch failure', async () => { + vi.stubGlobal('fetch', vi.fn().mockRejectedValue(new Error('Network error'))); + + const { loadPrefixMap } = await import('../curie-links'); + const map = await loadPrefixMap(); + expect(map).toEqual({}); + }); + + it('returns empty map on non-OK response', async () => { + vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: false, + status: 404, + })); + + const { loadPrefixMap } = await import('../curie-links'); + const map = await loadPrefixMap(); + expect(map).toEqual({}); + }); + + it('caches result — second call does not re-fetch', async () => { + const mockFetch = vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(prefixMapSubset), + }); + vi.stubGlobal('fetch', mockFetch); + + const { loadPrefixMap } = await import('../curie-links'); + await loadPrefixMap(); + await loadPrefixMap(); + expect(mockFetch).toHaveBeenCalledOnce(); + }); +}); diff --git a/web/src/lib/__tests__/nodenorm-api.test.ts b/web/src/lib/__tests__/nodenorm-api.test.ts new file mode 100644 index 0000000..25e2058 --- /dev/null +++ b/web/src/lib/__tests__/nodenorm-api.test.ts @@ -0,0 +1,295 @@ +import { describe, it, expect, vi, beforeEach } from 'vitest'; +import { parseCuries, fetchNormalizedNodes } from '../nodenorm-api'; +import { DEFAULT_API_OPTIONS } from '../types'; +import type { ApiOptions, NormalizedNode } from '../types'; +import mondoFixture from '../../../../tests/fixtures/nodenorm_responses/mondo_0004979.json'; +import ncitFixture from '../../../../tests/fixtures/nodenorm_responses/ncit_c55060.json'; +import batchFixture from '../../../../tests/fixtures/nodenorm_responses/batch_mixed.json'; +import meshConflatedFixture from '../../../../tests/fixtures/nodenorm_responses/mesh_d014867_conflated.json'; +import meshNoConflateFixture from '../../../../tests/fixtures/nodenorm_responses/mesh_d014867_no_conflate.json'; +import ncbigeneFixture from '../../../../tests/fixtures/nodenorm_responses/ncbigene_1756.json'; + +// --------------------------------------------------------------------------- +// parseCuries +// --------------------------------------------------------------------------- + +describe('parseCuries', () => { + it('splits multi-line input into array', () => { + expect(parseCuries('MONDO:0004979\nCHEBI:48947')).toEqual([ + 'MONDO:0004979', + 'CHEBI:48947', + ]); + }); + + it('skips blank lines', () => { + expect(parseCuries('MONDO:0004979\n\n\nCHEBI:48947')).toEqual([ + 'MONDO:0004979', + 'CHEBI:48947', + ]); + }); + + it('skips # comment lines', () => { + expect(parseCuries('# This is a comment\nMONDO:0004979\n# Another\nCHEBI:48947')).toEqual([ + 'MONDO:0004979', + 'CHEBI:48947', + ]); + }); + + it('deduplicates CURIEs preserving first occurrence', () => { + expect(parseCuries('MONDO:0004979\nCHEBI:48947\nMONDO:0004979')).toEqual([ + 'MONDO:0004979', + 'CHEBI:48947', + ]); + }); + + it('trims whitespace from each line', () => { + expect(parseCuries(' MONDO:0004979 \n CHEBI:48947 ')).toEqual([ + 'MONDO:0004979', + 'CHEBI:48947', + ]); + }); + + it('returns empty array for empty input', () => { + expect(parseCuries('')).toEqual([]); + }); + + it('returns empty array for whitespace-only input', () => { + expect(parseCuries(' \n \n ')).toEqual([]); + }); + + it('handles the same format as Python tests/data/valid_curies.txt', () => { + const raw = '# Valid CURIEs for integration tests.\nMONDO:0004979\nMONDO:0005044\nNCIT:C55060'; + expect(parseCuries(raw)).toEqual(['MONDO:0004979', 'MONDO:0005044', 'NCIT:C55060']); + }); +}); + +// --------------------------------------------------------------------------- +// fetchNormalizedNodes +// --------------------------------------------------------------------------- + +describe('fetchNormalizedNodes', () => { + beforeEach(() => { + vi.restoreAllMocks(); + }); + + it('constructs correct URL with query params', async () => { + const mockFetch = vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(mondoFixture), + }); + vi.stubGlobal('fetch', mockFetch); + + await fetchNormalizedNodes( + 'https://nodenormalization-sri.renci.org/', + ['MONDO:0004979'], + DEFAULT_API_OPTIONS, + ); + + expect(mockFetch).toHaveBeenCalledOnce(); + const calledUrl = new URL(mockFetch.mock.calls[0][0]); + expect(calledUrl.pathname).toBe('/get_normalized_nodes'); + expect(calledUrl.searchParams.getAll('curie')).toEqual(['MONDO:0004979']); + expect(calledUrl.searchParams.get('conflate')).toBe('true'); + expect(calledUrl.searchParams.get('drug_chemical_conflate')).toBe('true'); + expect(calledUrl.searchParams.get('description')).toBe('true'); + expect(calledUrl.searchParams.get('individual_types')).toBe('true'); + expect(calledUrl.searchParams.get('include_taxa')).toBe('true'); + }); + + it('sends multiple curie= params for a multi-CURIE request', async () => { + const mockFetch = vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(batchFixture), + }); + vi.stubGlobal('fetch', mockFetch); + + const result = await fetchNormalizedNodes( + 'https://nodenormalization-sri.renci.org/', + ['MONDO:0004979', 'NCIT:C55060', 'FAKE:9999999'], + DEFAULT_API_OPTIONS, + ); + + const calledUrl = new URL(mockFetch.mock.calls[0][0]); + expect(calledUrl.searchParams.getAll('curie')).toEqual([ + 'MONDO:0004979', + 'NCIT:C55060', + 'FAKE:9999999', + ]); + // Response contains all three keys + expect(Object.keys(result)).toEqual(expect.arrayContaining([ + 'MONDO:0004979', 'NCIT:C55060', 'FAKE:9999999', + ])); + // Not-found CURIE is null + expect(result['FAKE:9999999']).toBeNull(); + // Found CURIEs are non-null + expect(result['MONDO:0004979']).not.toBeNull(); + expect(result['NCIT:C55060']).not.toBeNull(); + }); + + it('sets boolean options as string values', async () => { + const mockFetch = vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve({}), + }); + vi.stubGlobal('fetch', mockFetch); + + const opts: ApiOptions = { + conflate: false, + drug_chemical_conflate: false, + description: true, + individual_types: false, + include_taxa: true, + }; + await fetchNormalizedNodes('https://example.com/', ['X:1'], opts); + + const calledUrl = new URL(mockFetch.mock.calls[0][0]); + expect(calledUrl.searchParams.get('conflate')).toBe('false'); + expect(calledUrl.searchParams.get('drug_chemical_conflate')).toBe('false'); + expect(calledUrl.searchParams.get('description')).toBe('true'); + expect(calledUrl.searchParams.get('individual_types')).toBe('false'); + expect(calledUrl.searchParams.get('include_taxa')).toBe('true'); + }); + + it('returns parsed JSON on success', async () => { + vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(mondoFixture), + })); + + const result = await fetchNormalizedNodes( + 'https://example.com/', + ['MONDO:0004979'], + DEFAULT_API_OPTIONS, + ); + expect(result).toEqual(mondoFixture); + }); + + it('throws on non-OK HTTP response', async () => { + vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: false, + status: 500, + statusText: 'Internal Server Error', + })); + + await expect( + fetchNormalizedNodes('https://example.com/', ['X:1'], DEFAULT_API_OPTIONS), + ).rejects.toThrow('NodeNorm returned HTTP 500'); + }); + + it('throws AbortError when called with an already-aborted signal', async () => { + const controller = new AbortController(); + controller.abort(); + + vi.stubGlobal('fetch', vi.fn().mockRejectedValue( + Object.assign(new Error('The operation was aborted.'), { name: 'AbortError' }), + )); + + const err = await fetchNormalizedNodes( + 'https://example.com/', ['X:1'], DEFAULT_API_OPTIONS, controller.signal, + ).catch((e) => e); + + expect(err.name).toBe('AbortError'); + }); +}); + +// --------------------------------------------------------------------------- +// NodeNorm response shape (documented via fixture assertions) +// +// These tests serve as executable documentation of the API contract. +// They verify the exact field types returned by NodeNorm, catching any +// future API changes that break our type assumptions. +// --------------------------------------------------------------------------- + +describe('NodeNorm API response shape', () => { + it('id.description is a plain string (not an array)', () => { + const node = ncitFixture['NCIT:C55060'] as NormalizedNode; + expect(typeof node.id.description).toBe('string'); + expect(node.id.description).toBe('A disorder characterized by a pathological increase in blood pressure.'); + }); + + it('top-level descriptions is an array of strings', () => { + const node = mondoFixture['MONDO:0004979'] as NormalizedNode; + expect(Array.isArray(node.descriptions)).toBe(true); + expect(node.descriptions!.length).toBeGreaterThan(1); + node.descriptions!.forEach(d => expect(typeof d).toBe('string')); + }); + + it('equivalent_identifiers[].description is a plain string when present', () => { + const node = ncitFixture['NCIT:C55060'] as NormalizedNode; + const withDesc = node.equivalent_identifiers.filter(ei => ei.description != null); + expect(withDesc.length).toBeGreaterThan(0); + withDesc.forEach(ei => expect(typeof ei.description).toBe('string')); + }); + + it('id.description matches the first (longest) entry in top-level descriptions', () => { + // NodeNorm sets id.description to the best/longest description + const node = mondoFixture['MONDO:0004979'] as NormalizedNode; + expect(node.id.description).toBe(node.descriptions![0]); + }); + + it('not-found CURIE returns null (not a missing key)', () => { + expect('FAKE:9999999' in batchFixture).toBe(true); + expect(batchFixture['FAKE:9999999']).toBeNull(); + }); + + it('gene node (NCBIGene:1756) has taxa on its identifiers', () => { + const node = ncbigeneFixture['NCBIGene:1756'] as NormalizedNode; + const withTaxa = node.equivalent_identifiers.filter(ei => ei.taxa && ei.taxa.length > 0); + expect(withTaxa.length).toBeGreaterThan(0); + withTaxa.forEach(ei => { + expect(Array.isArray(ei.taxa)).toBe(true); + ei.taxa!.forEach(t => expect(typeof t).toBe('string')); + }); + }); +}); + +// --------------------------------------------------------------------------- +// Conflation effects +// +// conflate=true merges Chemical/SmallMolecule cliques and Drug cliques. +// MESH:D014867 (water) is a good test case: conflated produces a much larger +// clique (206 equiv IDs) than non-conflated (30 equiv IDs). +// --------------------------------------------------------------------------- + +describe('conflation', () => { + it('conflated MESH:D014867 has more equivalent identifiers than non-conflated', () => { + const conflated = meshConflatedFixture['MESH:D014867'] as NormalizedNode; + const noConflate = meshNoConflateFixture['MESH:D014867'] as NormalizedNode; + expect(conflated.equivalent_identifiers.length).toBeGreaterThan( + noConflate.equivalent_identifiers.length, + ); + }); + + it('conflated MESH:D014867 has more descriptions than non-conflated', () => { + const conflated = meshConflatedFixture['MESH:D014867'] as NormalizedNode; + const noConflate = meshNoConflateFixture['MESH:D014867'] as NormalizedNode; + expect(conflated.descriptions!.length).toBeGreaterThan(noConflate.descriptions!.length); + }); + + it('conflated and non-conflated share the same preferred ID', () => { + // Conflation may change which clique "wins" in other cases, but for water + // both resolve to the same canonical CHEBI ID + const conflated = meshConflatedFixture['MESH:D014867'] as NormalizedNode; + const noConflate = meshNoConflateFixture['MESH:D014867'] as NormalizedNode; + expect(conflated.id.identifier).toBe(noConflate.id.identifier); + }); + + it('fetchNormalizedNodes sends conflate=false correctly', async () => { + vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(meshNoConflateFixture), + })); + + await fetchNormalizedNodes( + 'https://example.com/', + ['MESH:D014867'], + { ...DEFAULT_API_OPTIONS, conflate: false, drug_chemical_conflate: false }, + ); + + const calledUrl = new URL((vi.mocked(fetch) as ReturnType).mock.calls[0][0]); + expect(calledUrl.searchParams.get('conflate')).toBe('false'); + expect(calledUrl.searchParams.get('drug_chemical_conflate')).toBe('false'); + + vi.restoreAllMocks(); + }); +}); diff --git a/web/src/lib/__tests__/types.test.ts b/web/src/lib/__tests__/types.test.ts new file mode 100644 index 0000000..3ed76f7 --- /dev/null +++ b/web/src/lib/__tests__/types.test.ts @@ -0,0 +1,14 @@ +import { describe, it, expect } from 'vitest'; +import { DEFAULT_API_OPTIONS } from '../types'; + +describe('DEFAULT_API_OPTIONS', () => { + it('has all five boolean fields set to true', () => { + expect(DEFAULT_API_OPTIONS).toEqual({ + conflate: true, + drug_chemical_conflate: true, + description: true, + individual_types: true, + include_taxa: true, + }); + }); +}); diff --git a/web/src/lib/__tests__/url-state.test.ts b/web/src/lib/__tests__/url-state.test.ts new file mode 100644 index 0000000..5581411 --- /dev/null +++ b/web/src/lib/__tests__/url-state.test.ts @@ -0,0 +1,203 @@ +import { describe, it, expect, beforeEach } from 'vitest'; +import { DEFAULT_API_OPTIONS } from '../types'; +import type { ApiOptions } from '../types'; + +// We need to stub window.location before importing, so we use dynamic imports +// inside each test group after setting up the stub. + +// Helper: set window.location.search + pathname via stub +function setLocation(search: string, pathname = '/nodenorm') { + Object.defineProperty(window, 'location', { + value: { search, pathname, href: `http://localhost${pathname}${search}` }, + writable: true, + configurable: true, + }); +} + +// --------------------------------------------------------------------------- +// readQueryState +// --------------------------------------------------------------------------- + +describe('readQueryState', () => { + beforeEach(() => { + setLocation(''); + }); + + it('returns empty arrays and no options when there are no params', async () => { + setLocation(''); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.curies).toEqual([]); + expect(state.targets).toEqual([]); + expect(state.options).toEqual({}); + }); + + it('parses repeated curie= params', async () => { + setLocation('?curie=MONDO%3A0004979&curie=CHEBI%3A48947'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.curies).toEqual(['MONDO:0004979', 'CHEBI:48947']); + }); + + it('parses a single target= param', async () => { + setLocation('?curie=MONDO%3A0004979&target=dev'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.targets).toEqual(['dev']); + }); + + it('parses multiple target= params (compare mode)', async () => { + setLocation('?curie=MONDO%3A0004979&target=dev&target=prod'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.targets.length).toBe(2); + expect(state.targets).toContain('dev'); + expect(state.targets).toContain('prod'); + }); + + it('parses conflate=false into options.conflate === false', async () => { + setLocation('?curie=MONDO%3A0004979&target=dev&conflate=false'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.options.conflate).toBe(false); + }); + + it('parses conflate=true into options.conflate === true', async () => { + setLocation('?conflate=true'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.options.conflate).toBe(true); + }); + + it('omits option keys that are absent from the URL', async () => { + setLocation('?conflate=false'); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect('drug_chemical_conflate' in state.options).toBe(false); + expect('description' in state.options).toBe(false); + expect('individual_types' in state.options).toBe(false); + expect('include_taxa' in state.options).toBe(false); + }); + + it('parses all option keys when present', async () => { + setLocation( + '?conflate=false&drug_chemical_conflate=false&description=false&individual_types=false&include_taxa=false', + ); + const { readQueryState } = await import('../url-state'); + const state = readQueryState(); + expect(state.options).toEqual({ + conflate: false, + drug_chemical_conflate: false, + description: false, + individual_types: false, + include_taxa: false, + }); + }); +}); + +// --------------------------------------------------------------------------- +// buildQueryUrl +// --------------------------------------------------------------------------- + +describe('buildQueryUrl', () => { + beforeEach(() => { + setLocation('', '/nodenorm'); + }); + + it('produces curie= and target= params', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const url = buildQueryUrl(['MONDO:0004979', 'CHEBI:48947'], ['dev'], DEFAULT_API_OPTIONS); + const params = new URLSearchParams(url.split('?')[1]); + expect(params.getAll('curie')).toEqual(['MONDO:0004979', 'CHEBI:48947']); + expect(params.getAll('target')).toEqual(['dev']); + }); + + it('omits all API option params when using defaults', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const url = buildQueryUrl(['MONDO:0004979'], ['dev'], DEFAULT_API_OPTIONS); + const params = new URLSearchParams(url.split('?')[1] ?? ''); + for (const key of ['conflate', 'drug_chemical_conflate', 'description', 'individual_types', 'include_taxa']) { + expect(params.has(key)).toBe(false); + } + }); + + it('includes conflate=false when it differs from default', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const opts: ApiOptions = { ...DEFAULT_API_OPTIONS, conflate: false }; + const url = buildQueryUrl(['MONDO:0004979'], ['dev'], opts); + const params = new URLSearchParams(url.split('?')[1]); + expect(params.get('conflate')).toBe('false'); + // Other options are still default, so not included + expect(params.has('drug_chemical_conflate')).toBe(false); + }); + + it('includes multiple target= params for compare mode', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const url = buildQueryUrl(['MONDO:0004979'], ['dev', 'prod'], DEFAULT_API_OPTIONS); + const params = new URLSearchParams(url.split('?')[1]); + expect(params.getAll('target')).toEqual(['dev', 'prod']); + }); + + it('uses current pathname as the base path', async () => { + setLocation('', '/babel-explorer/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const url = buildQueryUrl(['MONDO:0004979'], ['dev'], DEFAULT_API_OPTIONS); + expect(url.startsWith('/babel-explorer/nodenorm?')).toBe(true); + }); + + it('returns just the pathname when curies and targets are empty', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl } = await import('../url-state'); + const url = buildQueryUrl([], [], DEFAULT_API_OPTIONS); + expect(url).toBe('/nodenorm'); + }); +}); + +// --------------------------------------------------------------------------- +// Round-trip: buildQueryUrl → readQueryState +// --------------------------------------------------------------------------- + +describe('round-trip', () => { + it('recovers curies, targets, and non-default options through a URL round-trip', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl, readQueryState } = await import('../url-state'); + + const curies = ['MONDO:0004979', 'CHEBI:48947']; + const targets = ['dev', 'prod']; + const opts: ApiOptions = { ...DEFAULT_API_OPTIONS, conflate: false }; + + const url = buildQueryUrl(curies, targets, opts); + + // Simulate opening the URL + const qs = url.includes('?') ? url.slice(url.indexOf('?')) : ''; + setLocation(qs, '/nodenorm'); + + const state = readQueryState(); + expect(state.curies).toEqual(curies); + expect(state.targets).toEqual(targets); + expect(state.options.conflate).toBe(false); + // Options that match defaults are not encoded and therefore not present + expect('drug_chemical_conflate' in state.options).toBe(false); + }); + + it('round-trips correctly with all-default options (no option params in URL)', async () => { + setLocation('', '/nodenorm'); + const { buildQueryUrl, readQueryState } = await import('../url-state'); + + const url = buildQueryUrl(['MONDO:0004979'], ['dev'], DEFAULT_API_OPTIONS); + const qs = url.includes('?') ? url.slice(url.indexOf('?')) : ''; + setLocation(qs, '/nodenorm'); + + const state = readQueryState(); + expect(state.curies).toEqual(['MONDO:0004979']); + expect(state.targets).toEqual(['dev']); + expect(state.options).toEqual({}); + // Merging with defaults recovers full options + const merged = { ...DEFAULT_API_OPTIONS, ...state.options }; + expect(merged).toEqual(DEFAULT_API_OPTIONS); + }); +}); diff --git a/web/src/lib/curie-links.ts b/web/src/lib/curie-links.ts new file mode 100644 index 0000000..46d6137 --- /dev/null +++ b/web/src/lib/curie-links.ts @@ -0,0 +1,64 @@ +/** + * CURIE link-out support using the biolink-model prefix map. + * + * The prefix map is fetched from GitHub at build time and bundled. + * It maps CURIE prefixes to IRI bases (e.g. MONDO → http://purl.obolibrary.org/obo/MONDO_). + * These IRIs generally resolve via 303/302 redirects to useful browseable pages + * (OLS, identifiers.org, GenNames, etc.). + * + * Biolink model version is configurable — update BIOLINK_VERSION below. + */ + +const BIOLINK_VERSION = 'v4.3.7'; + +const PREFIX_MAP_URL = + `https://raw.githubusercontent.com/biolink/biolink-model/${BIOLINK_VERSION}/src/biolink_model/prefixmaps/biolink-model-prefix-map.json`; + +/** Cached prefix map: prefix → IRI base URL. */ +let prefixMap: Record | null = null; + +/** + * Load the biolink prefix map. Fetches from GitHub on first call, + * then returns the cached copy. Falls back to an empty map on error. + */ +export async function loadPrefixMap(): Promise> { + if (prefixMap) return prefixMap; + + try { + const resp = await fetch(PREFIX_MAP_URL); + if (!resp.ok) throw new Error(`HTTP ${resp.status}`); + prefixMap = await resp.json(); + return prefixMap!; + } catch (err) { + console.warn('Failed to load biolink prefix map:', err); + prefixMap = {}; + return prefixMap; + } +} + +/** + * Parse a CURIE into prefix and local ID. + * e.g. "MONDO:0004979" → { prefix: "MONDO", localId: "0004979" } + */ +export function parseCurie(curie: string): { prefix: string; localId: string } | null { + const idx = curie.indexOf(':'); + if (idx < 1) return null; + return { prefix: curie.substring(0, idx), localId: curie.substring(idx + 1) }; +} + +/** + * Construct a browseable URL for a CURIE using the biolink prefix map. + * Returns null if the prefix is unknown. + * + * The IRI base typically ends with _ or / — we append the local ID directly. + * e.g. MONDO:0004979 → http://purl.obolibrary.org/obo/MONDO_0004979 + */ +export function getCurieUrl(curie: string, map: Record): string | null { + const parsed = parseCurie(curie); + if (!parsed) return null; + + const iriBase = map[parsed.prefix]; + if (!iriBase) return null; + + return iriBase + parsed.localId; +} diff --git a/web/src/lib/nodenorm-api.ts b/web/src/lib/nodenorm-api.ts new file mode 100644 index 0000000..e7c5a15 --- /dev/null +++ b/web/src/lib/nodenorm-api.ts @@ -0,0 +1,100 @@ +import type { ApiOptions, NormalizedNode, NodeNormResponse } from './types'; + +/** + * Call the NodeNorm get_normalized_nodes endpoint. + * + * @param baseUrl NodeNorm instance URL (must end with /) + * @param curies List of CURIEs to normalize + * @param options API query options (conflation, descriptions, etc.) + * @returns Raw NodeNorm response keyed by input CURIE + */ +export async function fetchNormalizedNodes( + baseUrl: string, + curies: string[], + options: ApiOptions, + signal?: AbortSignal, +): Promise { + const url = new URL('get_normalized_nodes', baseUrl); + + for (const curie of curies) { + url.searchParams.append('curie', curie); + } + url.searchParams.set('conflate', String(options.conflate)); + url.searchParams.set('drug_chemical_conflate', String(options.drug_chemical_conflate)); + url.searchParams.set('description', String(options.description)); + url.searchParams.set('individual_types', String(options.individual_types)); + url.searchParams.set('include_taxa', String(options.include_taxa)); + + const resp = await fetch(url.toString(), { signal }); + if (!resp.ok) { + throw new Error(`NodeNorm returned HTTP ${resp.status}: ${resp.statusText}`); + } + return resp.json(); +} + +/** + * Build the NodeNorm GET URL for a single CURIE with the given options. + * Useful for linking directly to the raw API response. + */ +export function buildNodeNormUrl(baseUrl: string, curie: string, options: ApiOptions): string { + const url = new URL('get_normalized_nodes', baseUrl); + url.searchParams.append('curie', curie); + url.searchParams.set('conflate', String(options.conflate)); + url.searchParams.set('drug_chemical_conflate', String(options.drug_chemical_conflate)); + url.searchParams.set('description', String(options.description)); + url.searchParams.set('individual_types', String(options.individual_types)); + url.searchParams.set('include_taxa', String(options.include_taxa)); + return url.toString(); +} + +/** + * Compute the "direct types" for a normalized node. + * + * NodeNorm returns two distinct type structures: + * + * node.type — The full biolink type *hierarchy* for the clique, from most-specific + * (type[0]) to root (NamedThing). Example: ["biolink:Gene", "biolink:BiologicalEntity", + * "biolink:NamedThing"]. This is the lineage, not just the direct type, so it is + * not useful for display on its own. + * + * identifier.type — The *direct* biolink type for one specific identifier within the + * clique. Only present when individual_types=true is passed to the API (always + * enabled in this app). Example: "biolink:Gene" for NCBIGene entries, + * "biolink:Protein" for UniProtKB entries in a conflated gene+protein result. + * + * This function collects unique type values from equivalent_identifiers[*].type, + * preserving first-appearance order. For most non-conflated results this returns a + * single type (e.g. ["biolink:Gene"]). For conflated results (e.g. a gene/protein + * conflation) it returns 2–5 types in the order they first appear among the identifiers. + * + * Falls back to [node.type[0]] if no individual types are present (e.g. if the API + * was called without individual_types=true). + */ +export function getDirectTypes(node: NormalizedNode): string[] { + const seen = new Set(); + const result: string[] = []; + for (const id of node.equivalent_identifiers) { + if (id.type && !seen.has(id.type)) { + seen.add(id.type); + result.push(id.type); + } + } + return result.length > 0 ? result : node.type.slice(0, 1); +} + +/** + * Parse a textarea value into a deduplicated list of CURIEs. + * Skips blank lines and lines starting with #. + */ +export function parseCuries(raw: string): string[] { + const seen = new Set(); + const result: string[] = []; + for (const line of raw.split('\n')) { + const trimmed = line.trim(); + if (trimmed && !trimmed.startsWith('#') && !seen.has(trimmed)) { + seen.add(trimmed); + result.push(trimmed); + } + } + return result; +} diff --git a/web/src/lib/types.ts b/web/src/lib/types.ts new file mode 100644 index 0000000..e356b41 --- /dev/null +++ b/web/src/lib/types.ts @@ -0,0 +1,56 @@ +/** A single identifier within a NodeNorm equivalence clique. */ +export interface NormalizedIdentifier { + identifier: string; + label?: string; + /** Individual biolink type (only present when individual_types=true). */ + type?: string; + taxa?: string[]; + /** Plain string description for this identifier (only present when description=true). */ + description?: string; +} + +/** A normalized node returned by the NodeNorm API for one input CURIE. */ +export interface NormalizedNode { + /** + * The preferred (canonical) identifier for this clique. + * description is the single best description string (longest, when description=true). + */ + id: { identifier: string; label?: string; description?: string }; + equivalent_identifiers: NormalizedIdentifier[]; + /** Top-level biolink type hierarchy. */ + type: string[]; + information_content?: number; + /** + * All descriptions collected across the clique, sorted longest-to-shortest. + * Only present when description=true. Each entry is a plain string. + */ + descriptions?: string[]; +} + +/** Raw API response: keys are the input CURIEs. */ +export type NodeNormResponse = Record; + +/** A named NodeNorm deployment endpoint. */ +export interface NodeNormInstance { + name: string; + env: string; + url: string; +} + +/** API query options matching NodeNorm get_normalized_nodes parameters. */ +export interface ApiOptions { + conflate: boolean; + drug_chemical_conflate: boolean; + description: boolean; + individual_types: boolean; + include_taxa: boolean; +} + +/** Default API options — all enabled. */ +export const DEFAULT_API_OPTIONS: ApiOptions = { + conflate: true, + drug_chemical_conflate: true, + description: true, + individual_types: true, + include_taxa: true, +}; diff --git a/web/src/lib/url-state.ts b/web/src/lib/url-state.ts new file mode 100644 index 0000000..db943ea --- /dev/null +++ b/web/src/lib/url-state.ts @@ -0,0 +1,80 @@ +import type { ApiOptions } from './types'; +import { DEFAULT_API_OPTIONS } from './types'; + +/** Parsed state from URL query parameters. */ +export interface QueryState { + /** CURIEs from repeated ?curie= params. */ + curies: string[]; + /** + * NodeNorm target identifiers from repeated ?target= params. + * Each value is either an env key (dev, exp, ci, test, prod) + * or a full URL for custom instances. + */ + targets: string[]; + /** + * API options that differ from defaults. + * Absent keys should fall back to DEFAULT_API_OPTIONS. + */ + options: Partial; +} + +const OPTION_KEYS: (keyof ApiOptions)[] = [ + 'conflate', + 'drug_chemical_conflate', + 'description', + 'individual_types', + 'include_taxa', +]; + +/** + * Read the current URL's query params and return the encoded query state. + * Returns empty arrays and no options if no relevant params are present. + */ +export function readQueryState(): QueryState { + const params = new URLSearchParams(window.location.search); + + const curies = params.getAll('curie'); + const targets = params.getAll('target'); + + const options: Partial = {}; + for (const key of OPTION_KEYS) { + const val = params.get(key); + if (val !== null) { + options[key] = val !== 'false'; + } + } + + return { curies, targets, options }; +} + +/** + * Build a shareable relative URL for the current query. + * + * Uses the current page path (window.location.pathname) so the URL is + * relative to the deployment base — works both locally and on GitHub Pages. + * + * Only API options that differ from DEFAULT_API_OPTIONS are included, + * keeping shared URLs short when using standard settings. + */ +export function buildQueryUrl( + curies: string[], + targets: string[], + options: ApiOptions, +): string { + const params = new URLSearchParams(); + + for (const curie of curies) { + params.append('curie', curie); + } + for (const target of targets) { + params.append('target', target); + } + for (const key of OPTION_KEYS) { + if (options[key] !== DEFAULT_API_OPTIONS[key]) { + params.set(key, String(options[key])); + } + } + + const qs = params.toString(); + return qs ? `${window.location.pathname}?${qs}` : window.location.pathname; +} diff --git a/web/src/pages/index.astro b/web/src/pages/index.astro new file mode 100644 index 0000000..b77653d --- /dev/null +++ b/web/src/pages/index.astro @@ -0,0 +1,31 @@ +--- +import BaseLayout from '../layouts/BaseLayout.astro'; +const rawBase = import.meta.env.BASE_URL; +const base = rawBase.endsWith('/') ? rawBase : rawBase + '/'; +--- + + +

Babel Explorer Tools

+

+ Browser-based tools for exploring + Babel + cross-references and + NodeNormalization + results. +

+ +
+
+
+
+
NodeNorm
+

+ Normalize CURIEs, inspect equivalent identifiers, compare results + across NodeNorm deployments. +

+ Open NodeNorm +
+
+
+
+ diff --git a/web/src/pages/nodenorm.astro b/web/src/pages/nodenorm.astro new file mode 100644 index 0000000..2ea0b38 --- /dev/null +++ b/web/src/pages/nodenorm.astro @@ -0,0 +1,15 @@ +--- +import BaseLayout from '../layouts/BaseLayout.astro'; +import NodeNormApp from '../components/nodenorm/NodeNormApp.vue'; +--- + + +

NodeNorm Lookup

+

+ Normalize CURIEs using the + NodeNormalization API. + Inspect equivalent identifiers, labels, biolink types, and more. +

+ + +
diff --git a/web/tests/README.md b/web/tests/README.md new file mode 100644 index 0000000..6daa5c2 --- /dev/null +++ b/web/tests/README.md @@ -0,0 +1,166 @@ +# Web Frontend Tests + +Tests for the Astro + Vue 3 static frontend (`web/`). + +## Test Stack + +| Tool | Purpose | +|------|---------| +| [Vitest](https://vitest.dev/) | Test runner — native ESM, fast, Vite-compatible | +| [@vue/test-utils](https://test-utils.vuejs.org/) | Vue component mounting and assertions | +| [happy-dom](https://github.com/nicedayjs/happy-dom) | Lightweight DOM environment (no browser needed) | + +Vitest's built-in `vi.fn()`, `vi.spyOn()`, and `vi.stubGlobal()` handle all mocking — no additional libraries needed. + +## Running Tests + +```bash +cd web +npm test # Run all tests once +npm run test:watch # Watch mode (re-runs on file changes) +``` + +## Test Organization + +Tests are **co-located** with source using `__tests__/` directories: + +``` +web/src/ + lib/ + __tests__/ + nodenorm-api.test.ts # parseCuries + fetchNormalizedNodes + AbortSignal + fixture shape + url-state.test.ts # readQueryState + buildQueryUrl + round-trip + curie-links.test.ts # parseCurie + getCurieUrl + loadPrefixMap + types.test.ts # DEFAULT_API_OPTIONS smoke test + components/ + nodenorm/ + __tests__/ + ResultsSummary.test.ts + CurieDetailPanel.test.ts + CurieResultCard.test.ts + ComparisonView.test.ts + shared/ + __tests__/ + CurieLink.test.ts +``` + +### Library tests (highest priority) + +Pure function tests with mocked `fetch()`. These cover: +- **`nodenorm-api.ts`**: CURIE parsing (blank lines, comments, deduplication), API request construction, AbortSignal pass-through, and NodeNorm response shape assertions (executed as documentation of the API contract) +- **`url-state.ts`**: `readQueryState` (no params, curie/target/option parsing), `buildQueryUrl` (default option omission, multi-target), and round-trip fidelity +- **`curie-links.ts`**: CURIE parsing, URL construction from biolink prefix map, cache behavior +- **`types.ts`**: Default options constant + +### Component tests + +Mount Vue components with `@vue/test-utils` and assert on rendered output and computed logic: +- **`ResultsSummary`**: normalized/partial/not-found counts, disagreement detection across instances, type badge aggregation; disagreements tile hidden for single instance +- **`CurieDetailPanel`**: description, types, IC score display; adaptive threshold (≤10 full table vs >10 prefix summary + expand); "Show all" / "Collapse" toggle +- **`CurieResultCard`**: accordion header (preferred ID, label, type badges, equiv count); delegates body to CurieDetailPanel +- **`ComparisonView`**: agreement detection, row highlighting, expandable rows (click → detail sub-row appears; click again → collapses) +- **`CurieLink`**: conditional `` vs `` rendering + +## Shared Fixtures + +Test fixtures live at the repo root so both Python and TypeScript tests can use them: + +``` +tests/fixtures/ + nodenorm_responses/ + mondo_0004979.json # Asthma — 28 equiv IDs (large clique), 3 descriptions + chebi_48947.json # Metformin — 82 equiv IDs (very large clique) + ncit_c55060.json # Hypertension CTCAE — 2 equiv IDs (small clique) + ncit_c34373.json # ALS — multiple descriptions + ncbigene_1756.json # DMD gene — has taxa on equiv IDs + mesh_d014867_conflated.json # Water — 206 equiv IDs (conflate=true) + mesh_d014867_no_conflate.json # Water — 30 equiv IDs (conflate=false, drug_chemical_conflate=false) + batch_mixed.json # Multi-CURIE GET: MONDO:0004979 + NCIT:C55060 + FAKE:9999999 + not_found.json # FAKE:9999999 → null (key present, value null) + prefix_map_subset.json # 10 entries from biolink-model prefix map (MONDO, CHEBI, …) +``` + +### NodeNorm API response shape (key facts for test authors) + +These facts are verified by tests in `nodenorm-api.test.ts` and should be kept in sync if the API changes: + +- **`id.description`** — plain `string` (the best/longest description). Same as `descriptions[0]`. Only present when `description=true`. +- **`descriptions`** — `string[]` collecting all descriptions found across the clique. `descriptions[0]` is the best description. Only present when `description=true`. +- **`equivalent_identifiers[i].description`** — plain `string` when present (not an array). Not every identifier has one. +- **Not-found CURIEs** — the key is present in the response with a `null` value (not a missing key). +- **Conflation** — `conflate=true` merges Chemical/SmallMolecule/Drug cliques, significantly expanding the equivalent identifier set. MESH:D014867 (water): 206 equiv IDs conflated vs. 30 without. +- **Multi-CURIE requests** — send repeated `curie=` params in GET, or send a JSON body `{"curies": [...]}` via POST to the same endpoint. All options (`conflate`, `description`, etc.) apply to the whole batch. + +### Regenerating fixtures + +Fixtures are snapshots of real NodeNorm Dev responses. To regenerate a single CURIE: + +```bash +curl -s 'https://nodenormalization-sri.renci.org/get_normalized_nodes?curie=MONDO:0004979&conflate=true&drug_chemical_conflate=true&description=true&individual_types=true&include_taxa=true' \ + | python3 -m json.tool > tests/fixtures/nodenorm_responses/mondo_0004979.json +``` + +For a multi-CURIE batch (GET with repeated params): + +```bash +curl -s 'https://nodenormalization-sri.renci.org/get_normalized_nodes?curie=MONDO:0004979&curie=NCIT:C55060&curie=FAKE:9999999&conflate=true&drug_chemical_conflate=true&description=true&individual_types=true&include_taxa=true' \ + | python3 -m json.tool > tests/fixtures/nodenorm_responses/batch_mixed.json +``` + +Or equivalently via POST: + +```bash +curl -s -X POST \ + 'https://nodenormalization-sri.renci.org/get_normalized_nodes?conflate=true&drug_chemical_conflate=true&description=true&individual_types=true&include_taxa=true' \ + -H 'Content-Type: application/json' \ + -d '{"curies": ["MONDO:0004979", "NCIT:C55060", "FAKE:9999999"]}' \ + | python3 -m json.tool > tests/fixtures/nodenorm_responses/batch_mixed.json +``` + +For the prefix map subset: + +```bash +curl -s 'https://raw.githubusercontent.com/biolink/biolink-model/v4.3.7/src/biolink_model/prefixmaps/biolink-model-prefix-map.json' | python3 -c " +import json, sys +full = json.load(sys.stdin) +keep = ['MONDO', 'CHEBI', 'HP', 'HGNC', 'NCIT', 'UMLS', 'DOID', 'MESH', 'GO', 'NCBITaxon'] +print(json.dumps({k: full[k] for k in keep if k in full}, indent=2)) +" > tests/fixtures/prefix_map_subset.json +``` + +## Key Testing Patterns + +### Mocking `fetch()` + +```typescript +vi.stubGlobal('fetch', vi.fn().mockResolvedValue({ + ok: true, + json: () => Promise.resolve(fixtureData), +})); +``` + +### Module cache isolation (`curie-links.ts`) + +`curie-links.ts` caches the prefix map in a module-level variable. Tests that exercise `loadPrefixMap()` must reset the module between tests: + +```typescript +beforeEach(() => { + vi.resetModules(); + vi.restoreAllMocks(); +}); + +it('test case', async () => { + const { loadPrefixMap } = await import('../curie-links'); + // ... +}); +``` + +## Future Improvements + +- **Playwright e2e tests** — test the full page in a real browser (form submission, accordion interaction, Bootstrap JS) +- **Integration tests** — call live NodeNorm API and verify response parsing end-to-end +- **Coverage thresholds** — enforce minimum coverage via `vitest --coverage` +- **CI integration** — run `npm test` in GitHub Actions alongside Python tests +- **Snapshot tests** — if component markup stabilizes, add snapshots for regression detection +- **NodeNormForm tests** — test checkbox selection, custom URL add/remove, submit payload, initial-value prop wiring from URL params +- **NodeNormApp tests** — test orchestration logic (loading state, error handling, parallel fetch across instances, URL auto-submit on mount) diff --git a/web/tsconfig.json b/web/tsconfig.json new file mode 100644 index 0000000..0649e42 --- /dev/null +++ b/web/tsconfig.json @@ -0,0 +1,13 @@ +{ + "extends": "astro/tsconfigs/strict", + "include": [ + ".astro/types.d.ts", + "**/*" + ], + "exclude": [ + "dist" + ], + "compilerOptions": { + "jsx": "preserve" + } +} \ No newline at end of file diff --git a/web/vitest.config.ts b/web/vitest.config.ts new file mode 100644 index 0000000..df7c740 --- /dev/null +++ b/web/vitest.config.ts @@ -0,0 +1,17 @@ +import { defineConfig } from 'vitest/config'; +import vue from '@vitejs/plugin-vue'; +import path from 'path'; + +export default defineConfig({ + plugins: [vue()], + test: { + environment: 'happy-dom', + globals: true, + include: ['src/**/*.test.ts'], + }, + resolve: { + alias: { + '@': path.resolve(__dirname, './src'), + }, + }, +});