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"Error: Invalid argument: Column family not found: storage" when searching old (v0.9.5) index with latest (v0.9.12) plugin #580

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matthuska opened this issue Jan 9, 2025 · 2 comments · May be fixed by #581

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@matthuska
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I have an index that was created using sourmash_plugin_branchwater v0.9.5 which I could search without any errors. After updating the plugin to v0.9.12, I now get the error:

Error: Invalid argument: Column family not found: storage

The search command being used is:

$ sourmash scripts manysearch --ksize 21 --moltype DNA --scaled 1000 --cores 1 --threshold 0.9 --output <whatever> input.sig path/to/old/rocks.db/

@luizirber already found the change that is causing the error (roughly: a new rockdb column was added, which is supposed to automatically be added to older indexes but the index is being opened read-only).

@ctb
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ctb commented Jan 9, 2025

replicated locally!

@ctb
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ctb commented Jan 9, 2025

Per Luiz on slack:

hmm, the storage column was added to support adding signatures to the same rocksdb index, but it should be auto-created (empty) if you don't internalize the signatures
it's around here: https://github.com/sourmash-bio/sourmash/blob/b499152d9405256764cd288b690c162a88e14d03/src/core/src/index/revindex/disk_revindex.rs#L131-L133

let me check if the plugin is trying to open the DB as read-only
hmm, yes:

let db = RevIndex::open(index, true, None)?;

let db = RevIndex::open(index, true, None)?;

@ctb ctb linked a pull request Jan 9, 2025 that will close this issue
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