From 4e6dd33180c8d9d4fdf72c0f67fdb1d1be8bcec2 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 16 Feb 2026 17:22:55 -0500 Subject: [PATCH 01/41] Add FastAPI + htmx web frontend for all tools Adds a web UI (FastAPI + Jinja2 + htmx + Bootstrap 5) exposing NodeNorm, XRefs, IDs, and Test Concordance via browser forms, a JSON REST API, and CSV downloads. Launched with `babel-explorer web`. Co-Authored-By: Claude Opus 4.6 --- CLAUDE.md | 19 +- pyproject.toml | 5 + src/babel_explorer/cli.py | 16 + src/babel_explorer/web/__init__.py | 29 + src/babel_explorer/web/routes.py | 306 ++++++ .../web/templates/_partials/error.html | 3 + .../web/templates/_partials/ids_results.html | 37 + .../templates/_partials/nodenorm_results.html | 44 + .../_partials/test_concord_results.html | 40 + .../templates/_partials/xrefs_results.html | 45 + src/babel_explorer/web/templates/base.html | 51 + src/babel_explorer/web/templates/ids.html | 24 + src/babel_explorer/web/templates/index.html | 45 + .../web/templates/nodenorm.html | 25 + .../web/templates/test_concord.html | 25 + src/babel_explorer/web/templates/xrefs.html | 32 + tests/test_web.py | 213 ++++ uv.lock | 939 ++++++++++++++++++ 18 files changed, 1897 insertions(+), 1 deletion(-) create mode 100644 src/babel_explorer/web/__init__.py create mode 100644 src/babel_explorer/web/routes.py create mode 100644 src/babel_explorer/web/templates/_partials/error.html create mode 100644 src/babel_explorer/web/templates/_partials/ids_results.html create mode 100644 src/babel_explorer/web/templates/_partials/nodenorm_results.html create mode 100644 src/babel_explorer/web/templates/_partials/test_concord_results.html create mode 100644 src/babel_explorer/web/templates/_partials/xrefs_results.html create mode 100644 src/babel_explorer/web/templates/base.html create mode 100644 src/babel_explorer/web/templates/ids.html create mode 100644 src/babel_explorer/web/templates/index.html create mode 100644 src/babel_explorer/web/templates/nodenorm.html create mode 100644 src/babel_explorer/web/templates/test_concord.html create mode 100644 src/babel_explorer/web/templates/xrefs.html create mode 100644 tests/test_web.py create mode 100644 uv.lock diff --git a/CLAUDE.md b/CLAUDE.md index ae2e78f..61e49aa 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -43,6 +43,12 @@ 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 @@ -91,7 +97,15 @@ uv run ruff format 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. **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 ### Data Flow @@ -122,6 +136,7 @@ Tests live in `tests/` and are split into fast **unit tests** (mocked, no networ | `tests/test_downloader.py` | 22 | 3 | 1 | 26 | | `tests/test_babel_xrefs.py` | 22 | 8 | 1 | 31 | | `tests/test_nodenorm.py` | 18 | 5 | 0 | 23 | +| `tests/test_web.py` | 24 | 0 | 0 | 24 | ### Test Infrastructure @@ -147,4 +162,6 @@ Tests live in `tests/` and are split into fast **unit tests** (mocked, no networ - Test CURIEs: `tests/data/valid_curies.txt` - Downloaded Babel files: `data//duckdb/*.parquet` - Generated DuckDB databases: `data//output/duckdbs/` +- Web frontend: `src/babel_explorer/web/` +- Web templates: `src/babel_explorer/web/templates/` - Entry point: `src/babel_explorer/cli.py` diff --git a/pyproject.toml b/pyproject.toml index 922fa1b..aa4c4af 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", "pytest>=8.3.5", "ruff>=0.11.0", ] diff --git a/src/babel_explorer/cli.py b/src/babel_explorer/cli.py index 8dd5fc4..527c52c 100644 --- a/src/babel_explorer/cli.py +++ b/src/babel_explorer/cli.py @@ -82,5 +82,21 @@ def test_concord(curies, nodenorm_url): print(f"{curie}\t{identifier.curie}\t\t{identifier.biolink_type}") +@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 uvicorn + from babel_explorer.web import create_app + + app = create_app(local_dir=local_dir, babel_url=babel_url, nodenorm_url=nodenorm_url) + uvicorn.run(app, host=host, port=port, reload=reload) + + if __name__ == "__main__": cli() diff --git a/src/babel_explorer/web/__init__.py b/src/babel_explorer/web/__init__.py new file mode 100644 index 0000000..1a0b5e1 --- /dev/null +++ b/src/babel_explorer/web/__init__.py @@ -0,0 +1,29 @@ +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 = "data/2025nov19", + babel_url: str = "https://stars.renci.org:443/var/babel_outputs/2025nov19/", + nodenorm_url: str = "https://nodenormalization-sri.renci.org/", +) -> FastAPI: + app = FastAPI(title="Babel Explorer") + + app.state.templates = Jinja2Templates(directory=str(TEMPLATES_DIR)) + app.state.nodenorm_url = nodenorm_url + 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..017b259 --- /dev/null +++ b/src/babel_explorer/web/routes.py @@ -0,0 +1,306 @@ +import csv +import io +import logging + +from fastapi import APIRouter, Form, Query, Request +from fastapi.responses import JSONResponse, StreamingResponse + +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) + + +# --------------------------------------------------------------------------- +# 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}) + + +@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}) + + +# --------------------------------------------------------------------------- +# 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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": "; ".join(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, expand=expand, label_curies=labels) + has_labels = labels and len(xrefs) > 0 and hasattr(xrefs[0], "subj_label") + 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 = [] + seen = set() + for rec in records: + for name, _ in rec.extra_fields: + if name not in seen: + extra_names.append(name) + seen.add(name) + 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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), expand=expand, label_curies=labels) + results = [] + for xref in xrefs: + row = {"filename": xref.filename, "subj": xref.subj, "pred": xref.pred, "obj": xref.obj} + if hasattr(xref, "subj_label"): + 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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), expand=expand, label_curies=labels) + if labels and xrefs and hasattr(xrefs[0], "subj_label"): + 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 = [] + seen = set() + for rec in records: + for name, _ in rec.extra_fields: + if name not in seen: + extra_names.append(name) + seen.add(name) + 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 = NodeNorm(nodenorm_url) if nodenorm_url else request.app.state.nodenorm + 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..17e8c89 --- /dev/null +++ b/src/babel_explorer/web/templates/base.html @@ -0,0 +1,51 @@ + + + + + + {% 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. +
+ +
+
+ + +
+ + + + +
+ +
+{% 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..d92d971 --- /dev/null +++ b/src/babel_explorer/web/templates/nodenorm.html @@ -0,0 +1,25 @@ +{% extends "base.html" %} +{% block title %}NodeNorm - Babel Explorer{% endblock %} +{% block content %} +

NodeNorm Lookup

+

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

+ +
+
+ + +
+
+ + +
+ + + + +
+ +
+{% 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..a4a1399 --- /dev/null +++ b/src/babel_explorer/web/templates/test_concord.html @@ -0,0 +1,25 @@ +{% extends "base.html" %} +{% block title %}Test Concordance - Babel Explorer{% endblock %} +{% block content %} +

Test Concordance

+

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

+ +
+
+ + +
+
+ + +
+ + + + +
+ +
+{% 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. +
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+{% endblock %} diff --git a/tests/test_web.py b/tests/test_web.py new file mode 100644 index 0000000..546160c --- /dev/null +++ b/tests/test_web.py @@ -0,0 +1,213 @@ +"""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 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b/src/babel_explorer/core/nodenorm.py index 018f106..be32a17 100644 --- a/src/babel_explorer/core/nodenorm.py +++ b/src/babel_explorer/core/nodenorm.py @@ -28,6 +28,15 @@ def from_dict(d: dict): return identifier class NodeNorm: + # A list of NodeNorm instances to choose from. + URLs = { + "NodeNorm Dev": "https://nodenormalization-sri.renci.org/", + "NodeNorm Exp": "https://nodenormalization-exp.apps.renci.org/", + "Translator NodeNorm Production": "https://nodenorm.transltr.io/", + "Translator NodeNorm Test": "https://nodenorm.test.transltr.io/", + "Translator NodeNorm CI": "https://nodenorm.ci.transltr.io/", + } + def __init__(self, nodenorm_url: str=""): self.nodenorm_url = nodenorm_url From bdf9d191d5b947c6a268bc8b0dbb5d25e4e5f3c8 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 16 Feb 2026 17:35:49 -0500 Subject: [PATCH 03/41] Replace NodeNorm URL text input with dropdown from NodeNorm.URLs The NodeNorm and Test Concordance pages now show a select dropdown populated from NodeNorm.URLs (defaulting to NodeNorm Dev), with a "Custom URL..." option that reveals a free-text input. Co-Authored-By: Claude Opus 4.6 --- src/babel_explorer/web/routes.py | 10 ++++-- .../web/templates/nodenorm.html | 31 +++++++++++++++++-- .../web/templates/test_concord.html | 31 +++++++++++++++++-- 3 files changed, 66 insertions(+), 6 deletions(-) diff --git a/src/babel_explorer/web/routes.py b/src/babel_explorer/web/routes.py index 017b259..cdc0017 100644 --- a/src/babel_explorer/web/routes.py +++ b/src/babel_explorer/web/routes.py @@ -52,7 +52,10 @@ def index(request: Request): @router.get("/nodenorm") def nodenorm_page(request: Request): - return _render(request, "nodenorm.html", {"default_url": request.app.state.nodenorm_url}) + return _render(request, "nodenorm.html", { + "default_url": request.app.state.nodenorm_url, + "nodenorm_urls": NodeNorm.URLs, + }) @router.get("/xrefs") @@ -67,7 +70,10 @@ def ids_page(request: Request): @router.get("/test-concord") def test_concord_page(request: Request): - return _render(request, "test_concord.html", {"default_url": request.app.state.nodenorm_url}) + return _render(request, "test_concord.html", { + "default_url": request.app.state.nodenorm_url, + "nodenorm_urls": NodeNorm.URLs, + }) # --------------------------------------------------------------------------- diff --git a/src/babel_explorer/web/templates/nodenorm.html b/src/babel_explorer/web/templates/nodenorm.html index d92d971..f563d3d 100644 --- a/src/babel_explorer/web/templates/nodenorm.html +++ b/src/babel_explorer/web/templates/nodenorm.html @@ -10,9 +10,19 @@

NodeNorm Lookup

- - + +
+ +
- - + +
+ + From cd3bb6d065117b45d44f8ceb90ccb65438cce3d9 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 16 Feb 2026 18:01:23 -0500 Subject: [PATCH 07/41] Document web frontend in CLAUDE.md and README.md Add web route table and NodeNorm dropdown details to CLAUDE.md. Add web frontend section to README.md covering startup, REST API examples, and CSV download endpoints. Co-Authored-By: Claude Opus 4.6 --- CLAUDE.md | 19 ++++++++++++++++--- README.md | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 3 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index 61e49aa..2d13b82 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -109,11 +109,24 @@ uv run ruff format ### Data Flow -1. User provides CURIEs via CLI +1. User provides CURIEs via CLI or web UI 2. BabelDownloader ensures required Parquet files are downloaded 3. BabelXRefs queries files using DuckDB 4. If `--labels` or `--expand` flags are set, NodeNorm is queried for additional metadata -5. Results are printed to stdout +5. Results are printed to stdout (CLI) or rendered as HTML tables / JSON / CSV (web) + +### 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 @@ -136,7 +149,7 @@ Tests live in `tests/` and are split into fast **unit tests** (mocked, no networ | `tests/test_downloader.py` | 22 | 3 | 1 | 26 | | `tests/test_babel_xrefs.py` | 22 | 8 | 1 | 31 | | `tests/test_nodenorm.py` | 18 | 5 | 0 | 23 | -| `tests/test_web.py` | 24 | 0 | 0 | 24 | +| `tests/test_web.py` | 25 | 0 | 0 | 25 | ### Test Infrastructure diff --git a/README.md b/README.md index b545c8c..f422b16 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,43 @@ uv run babel-explorer ids MONDO:0004979 uv run babel-explorer test-concord MONDO:0004979 HP:0000001 ``` +## Web Frontend + +babel-explorer includes a web interface built with FastAPI, htmx, and Bootstrap 5. It exposes all four tools — NodeNorm, XRefs, IDs, and Test Concordance — through a browser UI, a JSON REST API, and CSV downloads. + +```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. + ## 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. From 0bcdc483709bdc32fe45b805f361d4ce9405f8c0 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 02:05:34 -0400 Subject: [PATCH 08/41] Document frontend deployment architecture: split by data dependency DB-dependent tools (XRefs, IDs) stay on the FastAPI/htmx server (Kubernetes); API-only tools (NodeNorm, Test Concordance) move to static GitHub Pages with direct browser fetch calls. This avoids proxying CORS-enabled APIs through the server for no benefit and establishes a reusable pattern for translator_sdk web demos. Co-Authored-By: Claude Opus 4.6 --- README.md | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a37c327..d6ab084 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ uv run babel-explorer test-concord MONDO:0004979 HP:0000001 ## Web Frontend -babel-explorer includes a web interface built with FastAPI, htmx, and Bootstrap 5. It exposes all four tools — NodeNorm, XRefs, IDs, and Test Concordance — through a browser UI, a JSON REST API, and CSV downloads. +babel-explorer includes a web interface built with FastAPI, htmx, and Bootstrap 5. The server hosts the database-dependent tools (XRefs, IDs) through a browser UI, a JSON REST API, and CSV downloads. The API-only tools (NodeNorm, Test Concordance) are served as static pages via GitHub Pages — see [Architecture: Frontend Deployment](#architecture-frontend-deployment) for details. ```bash # Start the web server (default: http://127.0.0.1:8000) @@ -67,6 +67,38 @@ 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) + +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) + +**NodeNorm** and **Test Concordance** are served as static HTML + vanilla JS from the `docs/` directory on the `main` branch, deployed via GitHub Pages. These pages call the NodeNorm API directly from the browser using `fetch()` — no server required. + +A `config.js` file in `docs/` holds the Kubernetes server URL so that the static pages can cross-link to the server-hosted tools (and vice versa). Both sites share Bootstrap 5 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. From 801ceed5009cc49a21d9ad39c198b77d9f098a5a Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:17:11 -0400 Subject: [PATCH 09/41] Scaffold Astro + Vue web frontend and shared endpoint config - Initialize Astro project in web/ with Vue 3 integration - Create config/translator-endpoints.json as single source of truth for NodeNorm and NameRes deployment URLs across all environments - Update nodenorm.py to load URLs from shared config instead of hardcoding them - Add node_modules/ and web/dist/ to .gitignore Co-Authored-By: Claude Opus 4.6 --- .gitignore | 4 + config/translator-endpoints.json | 16 + src/babel_explorer/core/nodenorm.py | 29 +- web/astro.config.mjs | 11 + web/package-lock.json | 6036 +++++++++++++++++++++++++++ web/package.json | 19 + web/public/favicon.ico | Bin 0 -> 655 bytes web/public/favicon.svg | 9 + web/src/pages/index.astro | 17 + web/tsconfig.json | 13 + 10 files changed, 6146 insertions(+), 8 deletions(-) create mode 100644 config/translator-endpoints.json create mode 100644 web/astro.config.mjs create mode 100644 web/package-lock.json create mode 100644 web/package.json create mode 100644 web/public/favicon.ico create mode 100644 web/public/favicon.svg create mode 100644 web/src/pages/index.astro create mode 100644 web/tsconfig.json diff --git a/.gitignore b/.gitignore index 67d8b31..15311f2 100644 --- a/.gitignore +++ b/.gitignore @@ -191,6 +191,10 @@ 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/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/src/babel_explorer/core/nodenorm.py b/src/babel_explorer/core/nodenorm.py index 2cef8c5..3974f37 100644 --- a/src/babel_explorer/core/nodenorm.py +++ b/src/babel_explorer/core/nodenorm.py @@ -1,9 +1,28 @@ 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 class Identifier: curie: str @@ -30,14 +49,8 @@ def from_dict(d: dict): class NodeNorm: - # A list of NodeNorm instances to choose from. - URLs = { - "NodeNorm Dev": "https://nodenormalization-sri.renci.org/", - "NodeNorm Exp": "https://nodenormalization-exp.apps.renci.org/", - "Translator NodeNorm Production": "https://nodenorm.transltr.io/", - "Translator NodeNorm Test": "https://nodenorm.test.transltr.io/", - "Translator NodeNorm CI": "https://nodenorm.ci.transltr.io/", - } + # A list of NodeNorm instances to choose from, loaded from config/translator-endpoints.json. + URLs = _load_nodenorm_urls() def __init__(self, nodenorm_url: str = "", timeout: int = 30): self.nodenorm_url = nodenorm_url diff --git a/web/astro.config.mjs b/web/astro.config.mjs new file mode 100644 index 0000000..4cacd15 --- /dev/null +++ b/web/astro.config.mjs @@ -0,0 +1,11 @@ +// @ts-check +import { defineConfig } from 'astro/config'; +import vue from '@astrojs/vue'; + +// https://astro.build/config +export default defineConfig({ + integrations: [vue()], + // GitHub Pages deployment settings — update these for your repo + site: 'https://TranslatorSRI.github.io', + base: '/babel-explorer', +}); diff --git a/web/package-lock.json b/web/package-lock.json new file mode 100644 index 0000000..2635996 --- /dev/null +++ b/web/package-lock.json @@ -0,0 +1,6036 @@ +{ + "name": "web", + "version": "0.0.1", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "web", + "version": "0.0.1", + "dependencies": { + "@astrojs/vue": "^6.0.1", + "astro": "^6.0.8", + "vue": "^3.5.31" + }, + "engines": { + 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/dev/null +++ b/web/package.json @@ -0,0 +1,19 @@ +{ + "name": "web", + "type": "module", + "version": "0.0.1", + "engines": { + "node": ">=22.12.0" + }, + "scripts": { + "dev": "astro dev", + "build": "astro build", + "preview": "astro preview", + "astro": "astro" + }, + "dependencies": { + "@astrojs/vue": "^6.0.1", + "astro": "^6.0.8", + "vue": "^3.5.31" + } +} diff --git a/web/public/favicon.ico b/web/public/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..7f48a94d16071d6c8d06478c7458ab12e675019c GIT binary patch literal 655 zcmV;A0&x9_P)Rl-XF(A`bsas&GH{e7U1}Ri zJr5jR8B2*Jd6$=$AqgTM2o2FV$WZ9|#jJ3mmpEs{jB0ps@*Kxv}=RB|IJih8Z&fqwCG`%bN0000#bW%=J zQ=IH#a_&L{B{_6Lu_3m>0bMN%+@aOmN_3G~H^8EGi>+bXO=;-|Z`uFnf==AdP z{Oj-S=ltmI=<4`LcLE*&009F@L_t(|+I`d4ZUZ3@1<*Uo7H^LoCw6-8z4wsbd;b4l zA}zMFtOw2mLX6O5Mgl}(5P=uOM4%=tnuHiuAp%(G<c=npm$Fz%eL + + + diff --git a/web/src/pages/index.astro b/web/src/pages/index.astro new file mode 100644 index 0000000..561196b --- /dev/null +++ b/web/src/pages/index.astro @@ -0,0 +1,17 @@ +--- + +--- + + + + + + + + + Astro + + +

Astro

+ + 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 From 5cba309986cbf94c42f3e31a2f3e105b59e228d8 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:23:40 -0400 Subject: [PATCH 10/41] Add layout, navbar, landing page, types, and CURIE link utilities - BaseLayout.astro + Navbar.astro matching Python frontend's Bootstrap dark-navbar style - Landing page with tool card grid - TypeScript types for NodeNorm API responses - CURIE link-out support using biolink-model prefix map (v4.3.7) - CurieLink.vue shared component for linked CURIEs - web/README.md documenting dual-frontend architecture - Fix .gitignore lib/ rule to not exclude web/src/lib/ Co-Authored-By: Claude Opus 4.6 --- .gitignore | 5 +- web/README.md | 51 ++++++++++++++++++++ web/src/components/Navbar.astro | 30 ++++++++++++ web/src/components/shared/CurieLink.vue | 16 +++++++ web/src/layouts/BaseLayout.astro | 28 +++++++++++ web/src/lib/curie-links.ts | 64 +++++++++++++++++++++++++ web/src/lib/types.ts | 48 +++++++++++++++++++ web/src/pages/index.astro | 41 ++++++++++------ 8 files changed, 267 insertions(+), 16 deletions(-) create mode 100644 web/README.md create mode 100644 web/src/components/Navbar.astro create mode 100644 web/src/components/shared/CurieLink.vue create mode 100644 web/src/layouts/BaseLayout.astro create mode 100644 web/src/lib/curie-links.ts create mode 100644 web/src/lib/types.ts diff --git a/.gitignore b/.gitignore index 15311f2..53b4f8c 100644 --- a/.gitignore +++ b/.gitignore @@ -17,8 +17,9 @@ dist/ downloads/ eggs/ .eggs/ -lib/ -lib64/ +# Python distribution lib directories (not web/src/lib/) +/lib/ +/lib64/ parts/ sdist/ var/ diff --git a/web/README.md b/web/README.md new file mode 100644 index 0000000..4ac8995 --- /dev/null +++ b/web/README.md @@ -0,0 +1,51 @@ +# 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, Test Concordance | `web/` | +| **Python frontend** | FastAPI + htmx | Kubernetes | XRefs, IDs | `src/babel_explorer/web/` | + +The split follows data dependencies: tools that only call external APIs (NodeNorm, NameRes) 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. + +## Development + +```bash +cd web +npm install +npm run dev +``` + +This starts a local dev server at `http://localhost:4321`. + +## 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 is deployed to the `gh-pages` branch via GitHub Actions (triggered on new releases). GitHub Pages serves it at `https://TranslatorSRI.github.io/babel-explorer/`. + +## 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. + +CURIE link-outs use the [biolink-model prefix map](https://github.com/biolink/biolink-model), fetched at runtime and cached. The biolink model version is configurable in `src/lib/curie-links.ts`. + +## Adding a New Tool + +1. Create a new Astro page in `src/pages/` (e.g. `test-concord.astro`) +2. Create Vue components 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` diff --git a/web/src/components/Navbar.astro b/web/src/components/Navbar.astro new file mode 100644 index 0000000..2ca9080 --- /dev/null +++ b/web/src/components/Navbar.astro @@ -0,0 +1,30 @@ +--- +interface Props { + activePage?: string; +} +const { activePage = '' } = Astro.props; +const base = import.meta.env.BASE_URL; +--- + + 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/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/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/types.ts b/web/src/lib/types.ts new file mode 100644 index 0000000..f751ef3 --- /dev/null +++ b/web/src/lib/types.ts @@ -0,0 +1,48 @@ +/** 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[]; + description?: string[]; +} + +/** A normalized node returned by the NodeNorm API for one input CURIE. */ +export interface NormalizedNode { + id: { identifier: string; label?: string }; + equivalent_identifiers: NormalizedIdentifier[]; + /** Top-level biolink type hierarchy. */ + type: string[]; + information_content?: number; + /** Top-level descriptions (only present when description=true). */ + 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/pages/index.astro b/web/src/pages/index.astro index 561196b..2a4ccc4 100644 --- a/web/src/pages/index.astro +++ b/web/src/pages/index.astro @@ -1,17 +1,30 @@ --- - +import BaseLayout from '../layouts/BaseLayout.astro'; +const base = import.meta.env.BASE_URL; --- - - - - - - - - Astro - - -

Astro

- - + +

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 +
+
+
+
+ From 5df2958f9e4fe15bf35d67a3d8b5175bc7d08d89 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:27:55 -0400 Subject: [PATCH 11/41] Implement NodeNorm single-instance lookup (Feature 1) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - nodenorm-api.ts: fetch wrapper for NodeNorm get_normalized_nodes - NodeNormApp.vue: root Vue island orchestrating form + results - NodeNormForm.vue: textarea, instance dropdown, API option toggles - NodeNormResults.vue: accordion container with column visibility - CurieResultCard.vue: per-CURIE accordion card with adaptive detail (full table for ≤10 equiv IDs, prefix summary + expand for more) - EquivalentIdTable.vue: striped table with togglable columns - ColumnVisibility.vue: page-wide column show/hide controls - nodenorm.astro: Astro page hosting the Vue island Co-Authored-By: Claude Opus 4.6 --- .../components/nodenorm/ColumnVisibility.vue | 32 +++++ .../components/nodenorm/CurieResultCard.vue | 120 ++++++++++++++++++ .../components/nodenorm/EquivalentIdTable.vue | 44 +++++++ web/src/components/nodenorm/NodeNormApp.vue | 90 +++++++++++++ web/src/components/nodenorm/NodeNormForm.vue | 89 +++++++++++++ .../components/nodenorm/NodeNormResults.vue | 34 +++++ web/src/lib/nodenorm-api.ts | 49 +++++++ web/src/pages/nodenorm.astro | 15 +++ 8 files changed, 473 insertions(+) create mode 100644 web/src/components/nodenorm/ColumnVisibility.vue create mode 100644 web/src/components/nodenorm/CurieResultCard.vue create mode 100644 web/src/components/nodenorm/EquivalentIdTable.vue create mode 100644 web/src/components/nodenorm/NodeNormApp.vue create mode 100644 web/src/components/nodenorm/NodeNormForm.vue create mode 100644 web/src/components/nodenorm/NodeNormResults.vue create mode 100644 web/src/lib/nodenorm-api.ts create mode 100644 web/src/pages/nodenorm.astro diff --git a/web/src/components/nodenorm/ColumnVisibility.vue b/web/src/components/nodenorm/ColumnVisibility.vue new file mode 100644 index 0000000..3e15bc5 --- /dev/null +++ b/web/src/components/nodenorm/ColumnVisibility.vue @@ -0,0 +1,32 @@ + + + diff --git a/web/src/components/nodenorm/CurieResultCard.vue b/web/src/components/nodenorm/CurieResultCard.vue new file mode 100644 index 0000000..b5c2723 --- /dev/null +++ b/web/src/components/nodenorm/CurieResultCard.vue @@ -0,0 +1,120 @@ + + + diff --git a/web/src/components/nodenorm/EquivalentIdTable.vue b/web/src/components/nodenorm/EquivalentIdTable.vue new file mode 100644 index 0000000..4b1f729 --- /dev/null +++ b/web/src/components/nodenorm/EquivalentIdTable.vue @@ -0,0 +1,44 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormApp.vue b/web/src/components/nodenorm/NodeNormApp.vue new file mode 100644 index 0000000..651598f --- /dev/null +++ b/web/src/components/nodenorm/NodeNormApp.vue @@ -0,0 +1,90 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormForm.vue b/web/src/components/nodenorm/NodeNormForm.vue new file mode 100644 index 0000000..0d643df --- /dev/null +++ b/web/src/components/nodenorm/NodeNormForm.vue @@ -0,0 +1,89 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormResults.vue b/web/src/components/nodenorm/NodeNormResults.vue new file mode 100644 index 0000000..a348a10 --- /dev/null +++ b/web/src/components/nodenorm/NodeNormResults.vue @@ -0,0 +1,34 @@ + + + diff --git a/web/src/lib/nodenorm-api.ts b/web/src/lib/nodenorm-api.ts new file mode 100644 index 0000000..ac529a8 --- /dev/null +++ b/web/src/lib/nodenorm-api.ts @@ -0,0 +1,49 @@ +import type { ApiOptions, 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, +): 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()); + if (!resp.ok) { + throw new Error(`NodeNorm returned HTTP ${resp.status}: ${resp.statusText}`); + } + return resp.json(); +} + +/** + * 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/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. +

+ + + From df0b1751546cfb4202bb292c7bc4817b34a16ad5 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:32:19 -0400 Subject: [PATCH 12/41] Add summary card showing aggregate stats across all CURIEs SummaryCard.vue displays normalization success count, shared biolink types across all results, and per-type breakdown. Wired into NodeNormResults above the accordion. Co-Authored-By: Claude Opus 4.6 --- .../components/nodenorm/NodeNormResults.vue | 2 + web/src/components/nodenorm/SummaryCard.vue | 66 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 web/src/components/nodenorm/SummaryCard.vue diff --git a/web/src/components/nodenorm/NodeNormResults.vue b/web/src/components/nodenorm/NodeNormResults.vue index a348a10..856fc17 100644 --- a/web/src/components/nodenorm/NodeNormResults.vue +++ b/web/src/components/nodenorm/NodeNormResults.vue @@ -1,5 +1,6 @@ + + From 2925362276231af94c02b965d8fba1fb4ca07401 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:35:24 -0400 Subject: [PATCH 13/41] Add multi-instance comparison mode (Feature 2) - Mode toggle in NodeNormForm: "Single Instance" / "Compare Instances" - Compare mode shows checkboxes to select multiple NodeNorm deployments - NodeNormApp fetches from all selected instances in parallel using Promise.allSettled - ComparisonView renders side-by-side table: rows = CURIEs, columns = instances, with preferred ID, label, types, equiv count per cell - Rows where instances disagree on preferred ID are highlighted Co-Authored-By: Claude Opus 4.6 --- .../components/nodenorm/ComparisonView.vue | 89 +++++++++++++++++ web/src/components/nodenorm/NodeNormApp.vue | 68 +++++++++++-- web/src/components/nodenorm/NodeNormForm.vue | 97 +++++++++++++++---- 3 files changed, 230 insertions(+), 24 deletions(-) create mode 100644 web/src/components/nodenorm/ComparisonView.vue diff --git a/web/src/components/nodenorm/ComparisonView.vue b/web/src/components/nodenorm/ComparisonView.vue new file mode 100644 index 0000000..0341067 --- /dev/null +++ b/web/src/components/nodenorm/ComparisonView.vue @@ -0,0 +1,89 @@ + + + diff --git a/web/src/components/nodenorm/NodeNormApp.vue b/web/src/components/nodenorm/NodeNormApp.vue index 651598f..77f8292 100644 --- a/web/src/components/nodenorm/NodeNormApp.vue +++ b/web/src/components/nodenorm/NodeNormApp.vue @@ -5,6 +5,7 @@ import { fetchNormalizedNodes, parseCuries } from '../../lib/nodenorm-api'; import { loadPrefixMap } from '../../lib/curie-links'; import NodeNormForm from './NodeNormForm.vue'; import NodeNormResults from './NodeNormResults.vue'; +import ComparisonView from './ComparisonView.vue'; import endpoints from '../../../../config/translator-endpoints.json'; // Build instance list from shared config @@ -25,13 +26,20 @@ const instances: NodeNormInstance[] = Object.entries(endpoints.nodenorm).map( ); // State +const mode = ref<'single' | 'compare'>('single'); const loading = ref(false); const error = ref(null); -const results = ref(null); const queriedCuries = ref([]); const visibleColumns = reactive(new Set(['type'])); const prefixMap = ref>({}); +// Single-instance results +const singleResults = ref(null); + +// Multi-instance comparison results +const comparisonResults = ref>(new Map()); +const comparisonInstances = ref([]); + onMounted(async () => { prefixMap.value = await loadPrefixMap(); }); @@ -44,7 +52,7 @@ function toggleColumn(col: string) { } } -async function handleSubmit(payload: { curies: string; instanceUrl: string; options: ApiOptions }) { +async function handleSubmit(payload: { curies: string; instanceUrls: string[]; options: ApiOptions }) { const curies = parseCuries(payload.curies); if (curies.length === 0) { error.value = 'No valid CURIEs provided.'; @@ -53,11 +61,42 @@ async function handleSubmit(payload: { curies: string; instanceUrl: string; opti loading.value = true; error.value = null; - results.value = null; + singleResults.value = null; + comparisonResults.value = new Map(); queriedCuries.value = curies; try { - results.value = await fetchNormalizedNodes(payload.instanceUrl, curies, payload.options); + if (mode.value === 'single') { + singleResults.value = await fetchNormalizedNodes(payload.instanceUrls[0], curies, payload.options); + } else { + // Compare mode: fetch from all selected instances in parallel + const settled = await Promise.allSettled( + payload.instanceUrls.map((url) => fetchNormalizedNodes(url, curies, payload.options)), + ); + + const resultMap = new Map(); + const errors: string[] = []; + + for (let i = 0; i < payload.instanceUrls.length; i++) { + const result = settled[i]; + const url = payload.instanceUrls[i]; + if (result.status === 'fulfilled') { + resultMap.set(url, result.value); + } else { + const inst = instances.find((inst) => inst.url === url); + errors.push(`${inst?.name ?? url}: ${result.reason}`); + } + } + + comparisonResults.value = resultMap; + comparisonInstances.value = payload.instanceUrls + .map((url) => instances.find((inst) => inst.url === url)) + .filter((inst): inst is NodeNormInstance => inst != null); + + if (errors.length > 0) { + error.value = `Some instances failed: ${errors.join('; ')}`; + } + } } catch (e) { error.value = e instanceof Error ? e.message : String(e); } finally { @@ -70,21 +109,38 @@ async function handleSubmit(payload: { curies: string; instanceUrl: string; opti
{{ error }}
-
+ +
Results ({{ queriedCuries.length }} CURIE{{ queriedCuries.length !== 1 ? 's' : '' }})
+ + +
+
+ Comparison ({{ queriedCuries.length }} CURIE{{ queriedCuries.length !== 1 ? 's' : '' }} + across {{ comparisonInstances.length }} instance{{ comparisonInstances.length !== 1 ? 's' : '' }}) +
+ +
diff --git a/web/src/components/nodenorm/NodeNormForm.vue b/web/src/components/nodenorm/NodeNormForm.vue index 0d643df..e61f07d 100644 --- a/web/src/components/nodenorm/NodeNormForm.vue +++ b/web/src/components/nodenorm/NodeNormForm.vue @@ -6,10 +6,12 @@ import { DEFAULT_API_OPTIONS } from '../../lib/types'; const props = defineProps<{ instances: NodeNormInstance[]; loading: boolean; + mode: 'single' | 'compare'; }>(); const emit = defineEmits<{ - submit: [payload: { curies: string; instanceUrl: string; options: ApiOptions }]; + submit: [payload: { curies: string; instanceUrls: string[]; options: ApiOptions }]; + 'update:mode': [mode: 'single' | 'compare']; }>(); const curies = ref(''); @@ -18,10 +20,31 @@ const customUrl = ref(''); const showCustom = computed(() => selectedInstance.value === '__custom__'); const options = ref({ ...DEFAULT_API_OPTIONS }); +// For compare mode: track which instances are selected +const compareSelected = ref>(new Set([props.instances[0]?.url ?? ''])); + +function toggleCompareInstance(url: string) { + if (compareSelected.value.has(url)) { + compareSelected.value.delete(url); + } else { + compareSelected.value.add(url); + } +} + function onSubmit() { - const url = showCustom.value ? customUrl.value : selectedInstance.value; - if (!curies.value.trim() || !url.trim()) return; - emit('submit', { curies: curies.value, instanceUrl: url, options: { ...options.value } }); + if (!curies.value.trim()) return; + + let urls: string[]; + if (props.mode === 'compare') { + urls = [...compareSelected.value]; + if (urls.length === 0) return; + } else { + const url = showCustom.value ? customUrl.value : selectedInstance.value; + if (!url.trim()) return; + urls = [url]; + } + + emit('submit', { curies: curies.value, instanceUrls: urls, options: { ...options.value } }); } @@ -38,22 +61,60 @@ function onSubmit() { >
+ +
+
+ + +
+
+
- - - + + + + +
From 51d32b69f12932d88f4d68c99fc2f8212509c138 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 26 Mar 2026 03:42:49 -0400 Subject: [PATCH 14/41] Add FUTURE.md and fix base URL trailing slash in navigation MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - FUTURE.md documents deferred features: deep diff comparison, URL state persistence, CSV export, additional tools, testing, CI deploy - Fix navbar and landing page links missing slash between base path and page name (e.g. /babel-explorernodenorm → /babel-explorer/nodenorm) - Add trailing slash to base in astro.config.mjs Co-Authored-By: Claude Opus 4.6 --- web/FUTURE.md | 55 +++++++++++++++++++++++++++++++++ web/astro.config.mjs | 2 +- web/src/components/Navbar.astro | 3 +- web/src/pages/index.astro | 3 +- 4 files changed, 60 insertions(+), 3 deletions(-) create mode 100644 web/FUTURE.md diff --git a/web/FUTURE.md b/web/FUTURE.md new file mode 100644 index 0000000..4e20555 --- /dev/null +++ b/web/FUTURE.md @@ -0,0 +1,55 @@ +# Future Work + +Features and improvements deferred from the initial implementation. + +## NodeNorm Tool + +### Deep Diff in Comparison View +The current comparison view shows preferred ID, label, types, and equiv count per instance. 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** for unit tests (API client, CURIE parsing, prefix map logic) +- **Playwright** for E2E tests (form submission, result rendering, comparison mode) + +### 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/astro.config.mjs b/web/astro.config.mjs index 4cacd15..b5cf2c5 100644 --- a/web/astro.config.mjs +++ b/web/astro.config.mjs @@ -7,5 +7,5 @@ export default defineConfig({ integrations: [vue()], // GitHub Pages deployment settings — update these for your repo site: 'https://TranslatorSRI.github.io', - base: '/babel-explorer', + base: '/babel-explorer/', }); diff --git a/web/src/components/Navbar.astro b/web/src/components/Navbar.astro index 2ca9080..5828c5c 100644 --- a/web/src/components/Navbar.astro +++ b/web/src/components/Navbar.astro @@ -3,7 +3,8 @@ interface Props { activePage?: string; } const { activePage = '' } = Astro.props; -const base = import.meta.env.BASE_URL; +const rawBase = import.meta.env.BASE_URL; +const base = rawBase.endsWith('/') ? rawBase : rawBase + '/'; ---