@gmod/bam 7.9.0 → 7.9.1

package/esm/bamFile.js

@@ -6,7 +6,7 @@ import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { parseHeaderText } from "./sam.js";
-import { appendInRange, parseRefSeqs } from "./util.js";
+import { appendInRange, parseRefSeqs, throwIfAborted } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 // Ceiling on GROWING the header read. A million contigs is roughly 10MB of
@@ -259,6 +259,7 @@ export default class BamFile {
      * it for every other query still holding that read. See ADR 0006.
      */
     async getRecordsForRange(chr, min, max, opts) {
+        throwIfAborted(opts?.signal);
         const chrId = await this.getSeqId(chr, opts);
         if (chrId === undefined || !this.index) {
             return [];
@@ -268,23 +269,83 @@ export default class BamFile {
     }
     // Read a chunk, publish it to the cache, and keep the in-flight promise
     // discoverable while it runs.
-    _startChunkRead(cacheKey, chunk, opts) {
-        const promise = this._readChunkFeatures(chunk, opts).then(entry => {
+    //
+    // The read runs under this entry's own controller rather than any one
+    // caller's signal, because the read is shared: it must survive until every
+    // caller waiting on it has given up. joinChunkRead is what registers them.
+    _startChunkRead(cacheKey, chunk) {
+        const controller = new AbortController();
+        const promise = this._readChunkFeatures(chunk, {
+            signal: controller.signal,
+        }).then(entry => {
             this.chunkFeatureCache.set(cacheKey, entry);
             return entry;
         });
-        const inFlight = { promise, signal: opts.signal };
+        const inFlight = {
+            promise,
+            signals: new Set(),
+            pinned: false,
+            controller,
+            dispose: new AbortController(),
+            settled: false,
+        };
         this.inFlightChunks.set(cacheKey, inFlight);
-        // Only clear our own entry: a retry may already have replaced it. `.then(f,
-        // f)` rather than `.finally(f)` so the handler's own promise never carries
-        // an unhandled rejection.
+        // `.then(f, f)` rather than `.finally(f)` so the handler's own promise never
+        // carries an unhandled rejection.
         const clear = () => {
+            inFlight.settled = true;
+            // nothing reads these once the read has settled, and holding them would
+            // pin each caller's AbortController behind this entry
+            inFlight.dispose.abort();
+            inFlight.signals.clear();
+            // only clear our own entry: a later read for this chunk may have replaced it
             if (this.inFlightChunks.get(cacheKey) === inFlight) {
                 this.inFlightChunks.delete(cacheKey);
             }
         };
         promise.then(clear, clear);
-        return promise;
+        return inFlight;
+    }
+    // Register a caller's interest, so the read survives until that caller has
+    // given up too.
+    //
+    // A caller with no signal cannot give up, so it pins the read: there is no
+    // longer any set of aborts that should stop it. That is the honest reading of
+    // a caller that never asked to be cancellable, and it means one signal-free
+    // query makes that chunk's read uncancellable for everyone joined to it.
+    joinChunkRead(inFlight, signal) {
+        if (signal === undefined) {
+            inFlight.pinned = true;
+        }
+        else if (signal.aborted) {
+            // A caller that has already given up is not a waiter, and must not be
+            // counted as one: an `abort` listener never fires on a signal that
+            // aborted before it was added, so nothing would ever take this signal
+            // back out of the set. The count would never reach zero and the read
+            // would be uncancellable for everyone joined to it, silently.
+            //
+            // `_cachedChunkFeatures` rejects such a caller before it reaches here,
+            // with no `await` in between, so this is unreachable today. It is here
+            // because this is the bug that shipped, and an invariant that fails this
+            // quietly should not rest on a check twenty lines away. `@gmod/cram`
+            // guards the same spot for the same reason; see its ADR 0003.
+            if (!inFlight.pinned && inFlight.signals.size === 0) {
+                inFlight.controller.abort(signal.reason);
+            }
+        }
+        else if (!inFlight.signals.has(signal)) {
+            // guarded so one signal joining twice — a viewAsPairs query reaching the
+            // same chunk for a read and for its mate — does not add two listeners
+            inFlight.signals.add(signal);
+            signal.addEventListener('abort', () => {
+                inFlight.signals.delete(signal);
+                if (!inFlight.pinned && inFlight.signals.size === 0) {
+                    inFlight.controller.abort(signal.reason);
+                }
+            }, 
+            // `once` covers the abort firing; `dispose` covers it never firing
+            { once: true, signal: inFlight.dispose.signal });
+        }
     }
     // Parsed records for a chunk, reading and decompressing it only on a miss.
     // Every path that wants a chunk's features goes through here — mate lookups
@@ -297,6 +358,14 @@ export default class BamFile {
     // each caller its own objects, but roughly doubles a warm query on dense data
     // — measured, and rejected, in that ADR.
     async _cachedChunkFeatures(chunk, opts) {
+        // Before anything else, including the cache hit. A caller reaches here with
+        // a signal that has already fired on the ordinary pan — the abort lands
+        // while blocksForRange is still reading the index, and nothing between
+        // there and here looks at it, since bai.ts and csi.ts never read the
+        // signal. Such a caller must not start a read it has no interest in, and
+        // must not be registered as a waiter on someone else's: see joinChunkRead.
+        // @gmod/cram checks in exactly this position, in SliceRecordCache.getOrFill.
+        throwIfAborted(opts.signal);
         const cacheKey = chunkCacheKey(chunk);
         const cached = this.chunkFeatureCache.get(cacheKey);
         if (cached) {
@@ -307,23 +376,35 @@ export default class BamFile {
         // they collapse onto very few chunk keys, so without this a query pays for
         // the same inflate several times over — the dominant cost of a cold query
         // (ADR 0003).
-        const pending = this.inFlightChunks.get(cacheKey);
-        if (!pending) {
-            return (await this._startChunkRead(cacheKey, chunk, opts)).features;
+        let pending = this.inFlightChunks.get(cacheKey);
+        // A read every caller has abandoned is on its way out but may not have
+        // noticed yet. Start a fresh one rather than joining one already doomed.
+        if (pending?.controller.signal.aborted && !pending.settled) {
+            if (this.inFlightChunks.get(cacheKey) === pending) {
+                this.inFlightChunks.delete(cacheKey);
+            }
+            pending = undefined;
+        }
+        pending ??= this._startChunkRead(cacheKey, chunk);
+        // Only a read still running has anything to cancel. Joining a settled one
+        // would add this caller to a set nothing will ever take it out of, since
+        // the entry drops its abort listeners when it settles.
+        if (!pending.settled) {
+            this.joinChunkRead(pending, opts.signal);
         }
         try {
-            return (await pending.promise).features;
+            const entry = await pending.promise;
+            // the read finished, but this caller gave up while waiting for it
+            throwIfAborted(opts.signal);
+            return entry.features;
         }
         catch (e) {
-            // The read we joined was started by another caller. If that caller
-            // aborted and we did not, the failure is theirs and says nothing about
-            // our query, so start over — which picks up the cache, joins a sibling's
-            // retry, or reads under our own signal. Any other failure (and our own
-            // abort) propagates as it would have without sharing.
-            if (!pending.signal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this._cachedChunkFeatures(chunk, opts);
+            // Prefer this caller's own cancellation to whatever the shared read
+            // reported. If we asked to stop, that is the answer we want — and when
+            // the read itself was cancelled it is because we, and everyone else,
+            // asked it to.
+            throwIfAborted(opts.signal);
+            throw e;
         }
     }
     async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
@@ -493,6 +574,20 @@ export default class BamFile {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
             signal: opts.signal,
         });
+        // The last chance to bail before the expensive part, and the reason it is
+        // worth having: honouring the signal is optional in the filehandle.
+        // `RemoteFile` hands it to `fetch`, but `LocalFile.read(length, position)`
+        // does not even take an options argument, so every read under it runs to
+        // completion and arrives here with the cancellation unnoticed. Without this
+        // a fully abandoned chunk still gets inflated and decoded — measured at 6
+        // chunks for one 20kb query on out.bam — which is the dominant cost of a
+        // cold query (ADR 0003), spent on records nobody will ever look at.
+        //
+        // Safe precisely because this is the SHARED signal, not a caller's: it
+        // fires only once every waiter has given up, so there is never a live
+        // caller left to be denied the result. @gmod/cram checks in the same place
+        // and for the same reason, before the decode loop in `_fetchRecords`.
+        throwIfAborted(opts.signal);
         const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
         return {
             features: this.readBamFeatures(data, cpositions, dpositions, chunk),

package/esm/bamFile.js.map

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package/esm/indexFile.d.ts

@@ -23,6 +23,13 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
     private setupP?;
+    /**
+     * The signal `setupP` was started under, while it is still in flight. The
+     * index is parsed once and shared by every query against the file, so without
+     * this the first query to arrive would own a read all the others depend on —
+     * see {@link parse}.
+     */
+    private setupSignal?;
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;
         renameRefSeq?: (a: string) => string;
@@ -36,7 +43,31 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
     protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
     protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
-    parse(opts?: BaseOpts): Promise<TParsed>;
+    /**
+     * Parse the index, or join the parse already running.
+     *
+     * The index is downloaded and parsed once for the life of this object, so it
+     * is the one read here that is shared between queries — and therefore the one
+     * place a cancellation can leak from the query that asked for it to a query
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
+     * without this the first query to arrive owns a read every other query
+     * depends on: when it pans away, every concurrent query fails with its abort.
+     *
+     * A caller that joined someone else's parse and saw it fail because *they*
+     * aborted starts over rather than inheriting the failure — once, then
+     * propagates. Bounding it at one attempt is what jbrowse's
+     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
+     * down, and for the reason it gives: the pathological case becomes one
+     * duplicate parse rather than a recursion whose depth depends on how the
+     * aborts interleave.
+     *
+     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    parse(opts?: BaseOpts, retried?: boolean): Promise<TParsed>;
+    private startParse;
     lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
     estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;

package/esm/indexFile.js

@@ -1,5 +1,5 @@
 import QuickLRU from '@jbrowse/quick-lru';
-import { optimizeChunks } from "./util.js";
+import { optimizeChunks, throwIfAborted } from "./util.js";
 // SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
 // LRU-cache the result of getIndices(refId) so repeated lookups for the same
 // reference don't re-walk the index bytes.
@@ -23,6 +23,13 @@ export default class IndexFile {
     filehandle;
     renameRefSeq;
     setupP;
+    /**
+     * The signal `setupP` was started under, while it is still in flight. The
+     * index is parsed once and shared by every query against the file, so without
+     * this the first query to arrive would own a read all the others depend on —
+     * see {@link parse}.
+     */
+    setupSignal;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
@@ -54,14 +61,66 @@ export default class IndexFile {
         }
         return optimizeChunks(chunks, this.getLowestChunk(ba, min));
     }
-    parse(opts = {}) {
-        if (!this.setupP) {
-            this.setupP = this._parse(opts).catch((e) => {
-                this.setupP = undefined;
+    /**
+     * Parse the index, or join the parse already running.
+     *
+     * The index is downloaded and parsed once for the life of this object, so it
+     * is the one read here that is shared between queries — and therefore the one
+     * place a cancellation can leak from the query that asked for it to a query
+     * that did not. `_parse` hands `opts` straight to `filehandle.readFile`, so
+     * without this the first query to arrive owns a read every other query
+     * depends on: when it pans away, every concurrent query fails with its abort.
+     *
+     * A caller that joined someone else's parse and saw it fail because *they*
+     * aborted starts over rather than inheriting the failure — once, then
+     * propagates. Bounding it at one attempt is what jbrowse's
+     * `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
+     * down, and for the reason it gives: the pathological case becomes one
+     * duplicate parse rather than a recursion whose depth depends on how the
+     * aborts interleave.
+     *
+     * A retry rather than the reference count `_cachedChunkFeatures` uses, for
+     * the reason `@gmod/cram` gives for the same split in `CraiIndex`: the index
+     * is parsed once for the life of the object, so there is no repeated waste to
+     * recover, and this is a dozen lines against restructuring the memo.
+     */
+    async parse(opts = {}, retried = false) {
+        throwIfAborted(opts.signal);
+        const pending = this.setupP;
+        if (!pending) {
+            return this.startParse(opts);
+        }
+        // read before awaiting: the owner is forgotten as soon as the parse settles
+        const ownerSignal = this.setupSignal;
+        try {
+            return await pending;
+        }
+        catch (e) {
+            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
                 throw e;
-            });
+            }
+            return this.parse(opts, true);
         }
-        return this.setupP;
+    }
+    startParse(opts) {
+        const pending = this._parse(opts);
+        this.setupP = pending;
+        this.setupSignal = opts.signal;
+        // Drop a rejection rather than keeping it, so one transient failure does not
+        // poison the index for the lifetime of the file. Both branches are
+        // identity-checked so a retry started after this settles is not cleared by
+        // the attempt it already replaced.
+        pending.then(() => {
+            if (this.setupP === pending) {
+                this.setupSignal = undefined;
+            }
+        }, () => {
+            if (this.setupP === pending) {
+                this.setupP = undefined;
+                this.setupSignal = undefined;
+            }
+        });
+        return pending;
     }
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);

package/esm/indexFile.js.map

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package/esm/util.d.ts

@@ -35,6 +35,26 @@ export interface BaseOpts {
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
+/**
+ * `signal.throwIfAborted()`, without requiring either that method or `reason`.
+ *
+ * Two reasons not to call the built-in directly. It assumes a *real*
+ * `AbortSignal`, and callers pass duck-typed ones — `test/csi.test.ts` casts a
+ * bare `{ aborted }` through `as AbortSignal`, which is a fair model of what
+ * consumers do; calling a missing method there is a `TypeError` rather than the
+ * cancellation the caller asked for, which is a strictly worse failure.
+ *
+ * And it sets a browser floor. `AbortSignal.prototype.throwIfAborted` and
+ * `AbortSignal.reason` are Safari 15.4 / Chrome 100 / Firefox 97 (March 2022) —
+ * higher than anything else in this dependency tree needs, since
+ * `generic-filehandle2` only ever forwards a signal to `fetch`, and higher than
+ * every sibling gmod library, which use plain `.aborted`. Three lines here
+ * keeps that floor where it was.
+ *
+ * Faithful to the spec otherwise: an aborted signal throws its `reason`
+ * whatever that is, and only synthesizes an `AbortError` when there is none.
+ */
+export declare function throwIfAborted(signal?: AbortSignal): void;
 export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;

package/esm/util.js

@@ -10,6 +10,33 @@ import { VirtualOffset } from "./virtualOffset.js";
  * underneath you. (The Chunk objects themselves are never mutated; a merged
  * span produces a new instance.)
  */
+/**
+ * `signal.throwIfAborted()`, without requiring either that method or `reason`.
+ *
+ * Two reasons not to call the built-in directly. It assumes a *real*
+ * `AbortSignal`, and callers pass duck-typed ones — `test/csi.test.ts` casts a
+ * bare `{ aborted }` through `as AbortSignal`, which is a fair model of what
+ * consumers do; calling a missing method there is a `TypeError` rather than the
+ * cancellation the caller asked for, which is a strictly worse failure.
+ *
+ * And it sets a browser floor. `AbortSignal.prototype.throwIfAborted` and
+ * `AbortSignal.reason` are Safari 15.4 / Chrome 100 / Firefox 97 (March 2022) —
+ * higher than anything else in this dependency tree needs, since
+ * `generic-filehandle2` only ever forwards a signal to `fetch`, and higher than
+ * every sibling gmod library, which use plain `.aborted`. Three lines here
+ * keeps that floor where it was.
+ *
+ * Faithful to the spec otherwise: an aborted signal throws its `reason`
+ * whatever that is, and only synthesizes an `AbortError` when there is none.
+ */
+export function throwIfAborted(signal) {
+    if (signal?.aborted) {
+        const { reason } = signal;
+        throw reason === undefined
+            ? new DOMException('This operation was aborted', 'AbortError')
+            : reason;
+    }
+}
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
     if (n === 0) {

package/esm/util.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.9.0",
+  "version": "7.9.1",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
@@ -62,7 +62,6 @@
     "@vitest/coverage-v8": "^4.1.8",
     "eslint": "^10.4.1",
     "eslint-plugin-import-x": "^4.16.2",
-    "eslint-plugin-unicorn": "^65.0.0",
     "git-cliff": "^2.13.1",
     "prettier": "^3.8.3",
     "rimraf": "^6.1.3",