Add NameRes lookup tool to Astro/Vue frontend - #6

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gaurav wants to merge 116 commits into

add-nodenorm-frontendfrom

add-nameres-frontend

Commits on Dec 2, 2025

Initial commit
gaurav
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98135e8
This initializes a uv package in this repository.
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0f5400b
Added basic CLI.
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d3ffc97
Add /data to the .gitignore.
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c2ff184

Commits on Dec 3, 2025

Initial implementation of a basic xref query-er.
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e238b8b

Commits on Dec 4, 2025

Added a method to look up a particular identifier.
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18479d6
Added CURIE expansion/recursive lookup.
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7317bfb
Added a basic ConcordTester.
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642dd21
Added labels via NodeNorm.
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75db5b2

Commits on Dec 15, 2025

Renamed repository.
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d4130b7

Commits on Jan 8, 2026

Midnight commit: attempting to improve expansion.
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eddd497
Added some improvements.
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3a55a23

Commits on Feb 14, 2026

Added a CLAUDE.md by Claude.ai.
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e45e2f0
Reorganized file slightly.
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46e829f
Claude wrote some tests.
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0fb11c5
Improved downloader using Claude.
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7876189
Added MD5 download functionality.
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f3d6e52

Commits on Feb 15, 2026

Removed empty model file.
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76907ba
Attempted to rename this package to babel-explorer.
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8e3ba7c
Add comprehensive pytest suite for all core modules

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cf3394d

Commits on Feb 16, 2026

Add FastAPI + htmx web frontend for all tools

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91b76a5
Added a list of NodeNorm URLs.
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a18a141
Replace NodeNorm URL text input with dropdown from NodeNorm.URLs

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dd78b26
Fix --reload by passing app factory as import string to uvicorn

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66c5058
Fixed description display in web.
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92dcee0
Add API Docs and GitHub links to navbar

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d9a48b0
Document web frontend in CLAUDE.md and README.md

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204b635

Commits on Feb 17, 2026

Merge branch 'main' into basic-implementation-in-uv
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26f217c

Commits on Mar 2, 2026

Added uv.lock (not sure why it wasn't added previously).
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7950034
Update CLAUDE.md

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47535d3
Update pyproject.toml
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a0719fa
Update src/babel_explorer/core/babel_xrefs.py

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ab67878
Update src/babel_explorer/core/nodenorm.py

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96523ca
Replace MD5 checksumming with HTTP header caching and freshness window

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bf11732

Commits on Mar 3, 2026

Added some CURIEs to test.
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d983de5
Partially changed --expand to --recurse.
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93086b1
More fully changed --expand to --recurse.
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d374760
Add pytest-xdist for parallel test execution

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26b6f9d
Replace Python recursion in get_curie_xrefs with DuckDB WITH RECURSIVE

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bb756cf
Fix xdist race condition: skip test-data cleanup in parallel runs

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e7ca380
Made output a bit prettier.
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4c3870b

Commits on Mar 16, 2026

Update src/babel_explorer/core/nodenorm.py

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1cc5c7b
Simplify babel_xrefs: extract helper, remove dead fetches, fix default arg

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d1ec8fe
Fix LabeledCrossReference: make it a frozen dataclass subclass

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ed1a27d
Fix BabelDownloader: use tempfile.gettempdir() when local_path is None

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afd722d
Fix test-concord: guard against None from get_clique_identifiers

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26cef00
Potential fix for pull request finding

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bdceca8
Potential fix for pull request finding

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2f439bc
Potential fix for pull request finding

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612e1ce
Potential fix for pull request finding

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52075ca
Potential fix for pull request finding

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59c2c3c
Potential fix for pull request finding

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f2677fd
Potential fix for pull request finding

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f1c2857
Fix DuckDB connection leaks by using context managers

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dd194e9
Fix and simplify test mocks for context manager protocol

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cafe303
Add configurable HTTP timeout to NodeNorm and BabelDownloader

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45250ab
Fix _etag_matches docstring to match actual behavior

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7d67f00
Got rid of ignore_curies_in_expansion, which is no longer used.
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597ab30
Add ruff CI and fix all lint errors

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ab0aa33
Rename lint workflow to CI and add unit test job

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ae8a424
Improved documentation.
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5a5f00e
Add tests for parse_duration() in cli.py

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b7a3f93
Add CliRunner tests for xrefs, ids, and test-concord commands

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54b6c5b

Commits on Mar 26, 2026

Reformatted code with ruff.
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1ce6428
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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440241e
Document frontend deployment architecture: split by data dependency

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eb63fe7
Scaffold Astro + Vue web frontend and shared endpoint config

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17ae8b2
Add layout, navbar, landing page, types, and CURIE link utilities

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5b33a00
Implement NodeNorm single-instance lookup (Feature 1)

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802b9aa
Add summary card showing aggregate stats across all CURIEs

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139ff6c
Add multi-instance comparison mode (Feature 2)

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a4fe711
Add FUTURE.md and fix base URL trailing slash in navigation

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282ac82
Update CLAUDE.md, README.md, and web/README.md for dual-frontend architecture

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58a3d7d

Commits on Mar 27, 2026

Fix expand/recurse param bug and deduplicate route helpers

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9d5759f

Commits on Mar 28, 2026

Reformatted code with `ruff`.
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986886c
Add Vitest tests for Astro/Vue frontend and fix description type bug

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d874a97
Fix description field types and expand test fixtures for conflation

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a56b05f
Rename npm package from "web" to "babel-explorer"

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72e2d06
Update CLAUDE.md, web/README.md, web/tests/README.md with recent changes

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ba3d084
Add URL state persistence and Share button to NodeNorm page

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a015ca6
Update docs to reflect URL state persistence feature (77 tests)

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1fef630
Unify NodeNorm UI: remove mode toggle, add expandable table rows

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a29ce81
Replace per-instance SummaryCards with unified ResultsSummary component

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6d278a9
Update docs to reflect unified NodeNorm UI (99 tests)

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a5045e9

Commits on Mar 30, 2026

Update src/babel_explorer/cli.py

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f54561a
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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18b6b10
Cache get_identifier() locals in _to_labeled_xref; root-anchor lib/ in .gitignore

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4481350
Fix bugs and gaps identified in PR #1 code review

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43a004d
Run integration tests on push to master and weekly on Tuesdays

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6d2eb1f
Add module, class, and method docstrings to new files in PR #1

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e3d3434

Commits on Apr 1, 2026

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

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807bfb2
Address PR #1 review: frozen Identifier, atomic rename, fail-open HEAD, type fixes

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06c3833
Sync CLAUDE.md with current code

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14fe2eb
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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73178a8
Fix hashing crash, cache loss, stale hasResults, and TOCTOU races

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0a7c535
Separate query/results panes into cards; add JSON export; collapse advanced options

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b46cc07
Fix Show Columns toggle: gate type badges in main row on visibleColumns

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20369bf
Make Types tile an interactive filter using most-specific type only

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d294f4c
Merge branch 'basic-implementation-in-uv' of github.com:TranslatorSRI/babel-explorer into basic-implementation-in-uv
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6f5dcfa
Address PR #1 review: fix six correctness and quality issues

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7d8faa8

Commits on Apr 2, 2026

Renamed "equiv. IDs" to "equivalent IDs".
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dcb0867
Fixed missed equiv ID.
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7f62ef5
Show taxa in collapsed card header when Taxa toggle is on

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f63d2d2
Fix query pane not reflecting URL params on shared link open

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8639713
Add GitHub Actions workflow to deploy web/ to GitHub Pages

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047790d
Merge branch 'basic-implementation-in-uv' into add-nodenorm-frontend
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23c2d65
Activate on all pull requests.
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cf25067
Cleaned up GitHub Pages deploy triggers.
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db1e78e

Commits on Apr 3, 2026

Display direct biolink types (from individual_types) as linked badges

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eed5b08
Fix ComparisonView to use direct types for display and filtering

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6aa812a
Add NameRes lookup tool to Astro/Vue frontend

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0a9f29b
Updated defaults once again.
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58a8a99

Commits on Apr 6, 2026