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fetchAliases returns { rows, partial, totalSize }, but Explorer treated
the return value as an array and called .forEach on it directly. That
threw a TypeError on the first namespace, which the surrounding bare
catch swallowed. Since setAliasMap() runs inside that try after the
loop, it never executed, so aliasMap stayed empty and every collection
rendered "-" in the Name column.
Read aliases.rows instead, matching how ExplorerAliases consumes the
same value.
gtars renamed the two RAM-residency fields on StoreStats (n_sequences_loaded -> n_sequences_in_memory, n_collections_loaded -> n_collections_in_memory) and now returns an ImportReport from add_sequence_collections_from_fastas instead of a bare list. The old names read as per-run ingest counters but were nothing of the kind: a build that ingested 74 collections reported `n_sequences_loaded: 0`, which looked like silent data loss. Update the bulk `store add` path to read report.collections, and emit the real per-run counters — n_sequences_written, n_sequences_deduped, n_collections_new — alongside the existing results/count. These are what a build report should quote; the `store stats` numbers describe current RAM residency and say nothing about what a run added. Fix the `store stats` docstring, which listed only three of the five keys and showed an example output missing one of them. Requires gtars with ImportReport (unreleased).
Collections have no name -- SequenceCollectionMetadata carries only digests and n_sequences -- so a "Name" column asserted a property that does not exist. Rename it to "Alias", which is what the data actually is and what the API, store layout, and aliases page already call it. Extract the alias lookup into services/aliases.js and reuse it in StoreOverview, which previously showed bare digests with no label at all. Where a collection carries aliases in several namespaces, prefer one by namespace instead of concatenating them: vgp, for example, has five, which rendered as an unreadable comma-joined cell. The priority order mirrors the probe list in vrs/vrsWorker.js. Remaining aliases stay available as a title tooltip. Namespaces are pure convention -- gtars treats one as the opaque stem of an aliases/collections/*.tsv filename -- so the ordering is a UI preference, not a spec.
add_sequence_collections_from_fastas returns an ImportReport rather than a list of (metadata, was_new) pairs, and PyImportReport defines neither __iter__ nor __getitem__, so iterating it and calling len() on it both raised TypeError. Read .collections for the per-file results, and surface the report's per-run ingest counters in the JSON output. Also update the stats docstring, which still advertised n_collections_loaded: that key is now n_collections_in_memory, and the docstring now says what those gauges actually measure -- RAM residency at the moment stats() is called, typically 0 for a disk-backed store -- so they stop being read as ingest counts.
…#106) Bumps [react-router-dom](https://github.com/remix-run/react-router/tree/HEAD/packages/react-router-dom) from 7.18.0 to 7.18.2. - [Release notes](https://github.com/remix-run/react-router/releases) - [Changelog](https://github.com/remix-run/react-router/blob/react-router-dom@7.18.2/packages/react-router-dom/CHANGELOG.md) - [Commits](https://github.com/remix-run/react-router/commits/react-router-dom@7.18.2/packages/react-router-dom) --- updated-dependencies: - dependency-name: react-router-dom dependency-version: 7.18.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [react-dom](https://github.com/react/react/tree/HEAD/packages/react-dom) from 19.2.7 to 19.2.8. - [Release notes](https://github.com/react/react/releases) - [Changelog](https://github.com/react/react/blob/main/CHANGELOG.md) - [Commits](https://github.com/react/react/commits/v19.2.8/packages/react-dom) --- updated-dependencies: - dependency-name: react-dom dependency-version: 19.2.8 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [globals](https://github.com/sindresorhus/globals) from 17.7.0 to 17.8.0. - [Release notes](https://github.com/sindresorhus/globals/releases) - [Commits](sindresorhus/globals@v17.7.0...v17.8.0) --- updated-dependencies: - dependency-name: globals dependency-version: 17.8.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [eslint](https://github.com/eslint/eslint) from 10.5.0 to 10.8.0. - [Release notes](https://github.com/eslint/eslint/releases) - [Commits](eslint/eslint@v10.5.0...v10.8.0) --- updated-dependencies: - dependency-name: eslint dependency-version: 10.8.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
# Conflicts: # refget/cli/store.py
Seqcol store app factory
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Release 0.12.0 from dev.
What's in this release
seqcolapi moved into the refget package. The API server code now lives at
refget/seqcolapi/and ships in the wheel, so you can run it straight from a pip install (uvicorn refget.seqcolapi.main:store_app). The old top-levelseqcolapi/directory remains as a compatibility shim, so existing deployments keep working.New app factory.
refget.seqcolapi.create_seqcol_app()builds a complete, mountable seqcol API app from a RefgetStore. Therefget store servecommand and the Docker deployments now use this same factory, so they all serve identical routes (including/service-info).Lighter install. The base
pip install refgetno longer pulls in database or web-server packages. Optional extras cover the rest:refget[seqcolapi]for the store-backed web service (fastapi + uvicorn only),refget[db]for the PostgreSQL layer, andrefget[seqcolapi-db]for both. Missing extras now produce a clear error telling you what to install.Store CLI improvements.
store addreports what each run actually imported (new collections, sequences written, sequences deduplicated), tracking the renamed gtars stats keys.Frontend fixes. Collection aliases shown in the store overview, fixed blank Name column in the collections explorer, plus dependency updates (react 19.2.8, react-router-dom 7.18.2, eslint 10.8.0).
Version bumped to 0.12.0.