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Refgenie

The readonly store and concurrent access

RefgetStore exists in two types. RefgetStore is the one you use from a script or the CLI: it lazy-loads, so a read of something not yet resident quietly fetches it. ReadonlyRefgetStore is the one you use behind a server: its read methods borrow immutably, so a single instance can be shared across many threads at once.

The two types exist because those goals conflict. Lazy loading mutates the store, and a method that mutates cannot be called concurrently from several threads without a lock. Serving requests through a lock serializes them, which defeats the point of a fast local store. The readonly type resolves this by moving all the loading to a startup phase and leaving the request path with nothing left to mutate.

What into_readonly() gives you

Section titled “What into_readonly() gives you”

RefgetStore is a thin wrapper over a ReadonlyRefgetStore. Converting between them is a move, not a copy or a rebuild:

let mut store = RefgetStore::open_local("/path/to/store")?;
store.load_all_collections()?;
let readonly: ReadonlyRefgetStore = store.into_readonly();
let shared = std::sync::Arc::new(readonly);

The wrapper’s lazy-loading read methods are gone; what remains is the inner store, whose query methods take &self. Because it holds no interior state requiring exclusive access on the read path, Arc<ReadonlyRefgetStore> can be cloned into every request handler and read from concurrently. Partial reads from .seq files go through a small internal file-descriptor cache guarded by a mutex, but the lock is held only long enough to look up or insert a handle; the actual positioned read happens outside it, so concurrent readers are not serialized.

The Python binding follows the same shape:

from refget.store import RefgetStore


store = RefgetStore.open_local("/path/to/store")
store.load_all_collections()
readonly = store.into_readonly()

In Python, into_readonly() consumes the original: the source object is left holding an empty in-memory store and should not be used afterward. ReadonlyRefgetStore in Python has no constructor and no mutating methods at all; it is obtainable only through this call.

What “readonly” does and does not mean

Section titled “What “readonly” does and does not mean”

The name describes the read path, not the whole type. Two clarifications matter for deploying it correctly.

In Rust, ReadonlyRefgetStore still has &mut self methods. load_sequence, load_all_collections, clear, enable_persistence, add_sequence_collection, and remove_collection all exist on it. What the type guarantees is that its queries take &self. Once you place it in an Arc those mutating methods are unreachable, because Arc hands out shared references only. So the accurate framing is: reads are &self, and the value is safe to share across threads once you have finished mutating it and wrapped it.

It does not lazy-load. This is the constraint that catches people. A method that takes &self cannot promote a Stub record to Full, so anything not loaded before conversion stays unavailable. get_collection on a collection that was never loaded returns an error telling you to call load_collection() or load_all_collections() first; it does not go and fetch it.

That makes preloading the caller’s responsibility, and what to preload depends on which endpoints you serve:

ServingPreload before into_readonly()
Collection listing and level 1 attribute digestsNothing beyond opening the store; collection metadata comes from collections.rgci
Collection level 2, comparison, attribute lookupload_all_collections()
Sequences and substrings from a local storeload_all_collections(); sequence bytes are read from .seq files on demand even for Stub records
Sequences and substrings from a remote storeload_all_collections() and load_all_sequences()

The remote case deserves care. A remote store defers its sequence index (see How RefgetStore defers loading), so a readonly store converted from a freshly opened remote store has no sequences visible at all until the index is loaded. In Rust, load_sequence_index() loads just the index without downloading any sequence bytes. The Python binding does not currently expose that method, so the practical options in Python are load_all_sequences(), which downloads every sequence into the cache, or a single load_sequence(digest) call, which pulls the index plus that one sequence. Serving sequence bytes from a remote-backed readonly store in Python effectively means mirroring the data locally first.

The SeqColService trait

Section titled “The SeqColService trait”

On the Rust side, the read-only operations a GA4GH sequence collections API server needs from its backend are captured in a trait:

pub trait SeqColService {
    fn get_collection_level1(&self, digest: &str) -> Result<CollectionLevel1>;
    fn get_collection_level2(&self, digest: &str) -> Result<CollectionLevel2>;
    fn compare(&self, digest_a: &str, digest_b: &str) -> Result<SeqColComparison>;
    fn compare_with_level2(&self, digest_a: &str, external: &CollectionLevel2)
        -> Result<SeqColComparison>;
    fn find_collections_by_attribute(&self, attr_name: &str, attr_digest: &str)
        -> Result<Vec<String>>;
    fn get_attribute(&self, attr_name: &str, attr_digest: &str)
        -> Result<Option<serde_json::Value>>;
    fn list_collections(&self, page: usize, page_size: usize, filters: &[(&str, &str)])
        -> Result<PagedResult<SequenceCollectionMetadata>>;
    fn collection_count(&self) -> usize;
}

Every method takes &self and returns a concrete type, which makes the trait object-safe: a server can hold Arc<dyn SeqColService> and stay agnostic about what is behind it. A filesystem-backed store, a Postgres-backed service, a proxy to a remote API, or an in-memory mock in a test can all satisfy the same interface.

ReadonlyRefgetStore is the only implementation of SeqColService in the codebase. In particular the mutable RefgetStore does not implement it, and cannot: the trait requires &self methods, and RefgetStore’s equivalents take &mut self so they can lazy-load. This is a deliberate compile-time push toward the readonly type for anything server-shaped.

The trait is a Rust-level interface and is not exposed through the Python bindings. Python has an analogous but separate abstraction: the SeqColBackend protocol in the refget package, implemented by RefgetStoreBackend (store-backed) and RefgetDBAgent (Postgres-backed).

Section titled “Related reading”