Add NodeNorm web frontends: GitHub Pages and Python-based - #4

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gaurav wants to merge 112 commits into

basic-implementation-in-uvfrom

add-nodenorm-frontend

Commits on Dec 2, 2025

Initial commit
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d30c459
This initializes a uv package in this repository.
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fcc27c2
Added basic CLI.
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876353d
Add /data to the .gitignore.
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ec1d1f0

Commits on Dec 3, 2025

Initial implementation of a basic xref query-er.
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eff8f26

Commits on Dec 4, 2025

Added a method to look up a particular identifier.
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4d04e2a
Added CURIE expansion/recursive lookup.
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8531cb7
Added a basic ConcordTester.
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a1aeec6
Added labels via NodeNorm.
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bb1eb99

Commits on Dec 15, 2025

Renamed repository.
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58c5c85

Commits on Jan 8, 2026

Midnight commit: attempting to improve expansion.
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40c3338
Added some improvements.
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8c41112

Commits on Feb 14, 2026

Added a CLAUDE.md by Claude.ai.
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239c89f
Reorganized file slightly.
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8132fe1
Claude wrote some tests.
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bd00972
Improved downloader using Claude.
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9cc06bc
Added MD5 download functionality.
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da8bb0c

Commits on Feb 15, 2026

Removed empty model file.
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8f36b74
Attempted to rename this package to babel-explorer.
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0534fd8
Add comprehensive pytest suite for all core modules

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0b3a9f5

Commits on Feb 16, 2026

Add FastAPI + htmx web frontend for all tools

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4e6dd33
Added a list of NodeNorm URLs.
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b50daf0
Replace NodeNorm URL text input with dropdown from NodeNorm.URLs

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bdf9d19
Fix --reload by passing app factory as import string to uvicorn

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711a4ad
Fixed description display in web.
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92a21ea
Add API Docs and GitHub links to navbar

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11510a0
Document web frontend in CLAUDE.md and README.md

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cd3bb6d

Commits on Feb 17, 2026

Merge branch 'main' into basic-implementation-in-uv
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8535202

Commits on Mar 2, 2026

Added uv.lock (not sure why it wasn't added previously).
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ff0dacc
Update CLAUDE.md

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bacc72d
Update pyproject.toml
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96d9609
Update src/babel_explorer/core/babel_xrefs.py

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0c33e7e
Update src/babel_explorer/core/nodenorm.py

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1aff013
Replace MD5 checksumming with HTTP header caching and freshness window

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af76c15

Commits on Mar 3, 2026

Added some CURIEs to test.
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fb41da0
Partially changed --expand to --recurse.
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5c544a2
More fully changed --expand to --recurse.
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280212a
Add pytest-xdist for parallel test execution

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b522e6e
Replace Python recursion in get_curie_xrefs with DuckDB WITH RECURSIVE

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e137c31
Fix xdist race condition: skip test-data cleanup in parallel runs

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b115d02
Made output a bit prettier.
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5a0f758

Commits on Mar 16, 2026

Update src/babel_explorer/core/nodenorm.py

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be2fa36
Simplify babel_xrefs: extract helper, remove dead fetches, fix default arg

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2b2aa7f
Fix LabeledCrossReference: make it a frozen dataclass subclass

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3cdd19c
Fix BabelDownloader: use tempfile.gettempdir() when local_path is None

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c7a3f16
Fix test-concord: guard against None from get_clique_identifiers

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c6635bc
Potential fix for pull request finding

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d74110e
Potential fix for pull request finding

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4338bdc
Potential fix for pull request finding

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be3e427
Potential fix for pull request finding

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f8b718b
Potential fix for pull request finding

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48c8e96
Potential fix for pull request finding

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8fb37d6
Potential fix for pull request finding

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49f5c3b
Fix DuckDB connection leaks by using context managers

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c952c12
Fix and simplify test mocks for context manager protocol

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b0539bb
Add configurable HTTP timeout to NodeNorm and BabelDownloader

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6319212
Fix _etag_matches docstring to match actual behavior

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b634d11
Got rid of ignore_curies_in_expansion, which is no longer used.
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a7eb8c1
Add ruff CI and fix all lint errors

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7163a64
Rename lint workflow to CI and add unit test job

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f9e549e
Improved documentation.
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7d1d5ca
Add tests for parse_duration() in cli.py

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0d9e32c
Add CliRunner tests for xrefs, ids, and test-concord commands

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0ca35eb

Commits on Mar 26, 2026

Reformatted code with ruff.
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17782a2
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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27ec599
Document frontend deployment architecture: split by data dependency

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0bcdc48
Scaffold Astro + Vue web frontend and shared endpoint config

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801ceed
Add layout, navbar, landing page, types, and CURIE link utilities

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5cba309
Implement NodeNorm single-instance lookup (Feature 1)

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5df2958
Add summary card showing aggregate stats across all CURIEs

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df0b175
Add multi-instance comparison mode (Feature 2)

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2925362
Add FUTURE.md and fix base URL trailing slash in navigation

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51d32b6
Update CLAUDE.md, README.md, and web/README.md for dual-frontend architecture

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78890cf

Commits on Mar 27, 2026

Fix expand/recurse param bug and deduplicate route helpers

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e1d03f2

Commits on Mar 28, 2026

Reformatted code with `ruff`.
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60a09c9
Add Vitest tests for Astro/Vue frontend and fix description type bug

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a5e3f27
Fix description field types and expand test fixtures for conflation

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8b934ea
Rename npm package from "web" to "babel-explorer"

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8d86ca8
Update CLAUDE.md, web/README.md, web/tests/README.md with recent changes

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e6fea59
Add URL state persistence and Share button to NodeNorm page

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08ca86e
Update docs to reflect URL state persistence feature (77 tests)

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c5d9085
Unify NodeNorm UI: remove mode toggle, add expandable table rows

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2f7bf0a
Replace per-instance SummaryCards with unified ResultsSummary component

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e443ae5
Update docs to reflect unified NodeNorm UI (99 tests)

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c9f9eb9

Commits on Mar 30, 2026

Update src/babel_explorer/cli.py

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d34c5c3
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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d97572d
Cache get_identifier() locals in _to_labeled_xref; root-anchor lib/ in .gitignore

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ec0a71c
Fix bugs and gaps identified in PR #1 code review

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67be81e
Run integration tests on push to master and weekly on Tuesdays

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4199ae2
Add module, class, and method docstrings to new files in PR #1

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17f6b09

Commits on Apr 1, 2026

Fix LabeledCrossReference biolink_type fields to list[str]; simplify map to listcomp

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8216b0b
Address PR #1 review: frozen Identifier, atomic rename, fail-open HEAD, type fixes

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ac418ff
Sync CLAUDE.md with current code

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06cd300
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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4bfd9cb
Fix hashing crash, cache loss, stale hasResults, and TOCTOU races

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9b383a1
Separate query/results panes into cards; add JSON export; collapse advanced options

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4374a09
Fix Show Columns toggle: gate type badges in main row on visibleColumns

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a3b24ea
Make Types tile an interactive filter using most-specific type only

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09f2a67
Merge branch 'basic-implementation-in-uv' of github.com:TranslatorSRI/babel-explorer into basic-implementation-in-uv
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46f0863
Address PR #1 review: fix six correctness and quality issues

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bf1c48c

Commits on Apr 2, 2026

Renamed "equiv. IDs" to "equivalent IDs".
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b8123f7
Fixed missed equiv ID.
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10eacdd
Show taxa in collapsed card header when Taxa toggle is on

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0ca7d10
Fix query pane not reflecting URL params on shared link open

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6034d1a
Add GitHub Actions workflow to deploy web/ to GitHub Pages

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5e2e273
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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c622ca5
Activate on all pull requests.
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bc6aae5
Cleaned up GitHub Pages deploy triggers.
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d472d9c

Commits on Apr 3, 2026

Display direct biolink types (from individual_types) as linked badges

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6407404
Fix ComparisonView to use direct types for display and filtering

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d68b936

Commits on Apr 6, 2026

Add raw API link to expanded NodeNorm result panels

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bdadff5
Updated package-lock.json.
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df00ecc