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Seqcol store app factory - #101

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nsheff wants to merge 21 commits into
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seqcol-store-app-factory
Open

Seqcol store app factory#101
nsheff wants to merge 21 commits into
devfrom
seqcol-store-app-factory

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@nsheff

@nsheff nsheff commented Jul 25, 2026

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Moves seqcolapi server code into the refget package proper, as a module with gated.

also some other improvements to gating and stuff.

@nsheff
nsheff changed the base branch from master to dev July 25, 2026 22:19
nsheff added 12 commits July 25, 2026 18:25
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.
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