@gmod/tabix 3.6.0 → 3.6.1

package/dist/indexFile.d.ts

@@ -49,14 +49,11 @@ export interface IndexData {
 }
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
-    private parseP?;
     /**
-     * The signal `parseP` 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}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    private parseSignal?;
+    private parseCache;
     constructor({ filehandle }: {
         filehandle: GenericFilehandle;
     });
@@ -124,28 +121,27 @@ export default abstract class IndexFile {
      * 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 `readIndexBytes`, 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.
+     * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so a bare
+     * memoized promise makes the first query to arrive the owner of 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.
+     * The same cache `ChunkCache` uses, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone and a bystander gets the parse already in flight rather
+     * than having to re-read the index. A rejection is dropped rather than
+     * cached, so a transient failure does not poison the index for the life of
+     * the file.
      *
-     * A retry rather than the reference count `ChunkCache` uses, because the
-     * index is parsed once for the life of the object: there is no repeated waste
-     * to recover, and this is a dozen lines against restructuring the memo.
-     * `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
-     * split for the same reason.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `readIndexBytes` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      *
      * @internal
      */
-    parse(opts?: Options, retried?: boolean): Promise<IndexData>;
-    private startParse;
+    parse(opts?: Options): Promise<IndexData>;
     /** @internal */
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/dist/indexFile.js

@@ -1,17 +1,15 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const shared_read_cache_1 = require("@gmod/shared-read-cache");
 const util_ts_1 = require("./util.js");
 class IndexFile {
     filehandle;
-    parseP;
     /**
-     * The signal `parseP` 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}.
+     * The parsed index, as a shared read — see {@link parse}. One entry, never
+     * evicted, which is what a memo is.
      */
-    parseSignal;
+    parseCache = new shared_read_cache_1.SharedReadCache({});
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
@@ -75,71 +73,36 @@ class IndexFile {
         }
         return (0, util_ts_1.optimizeChunks)(chunks, this.lowestOffset(ba, min, indexData));
     }
-    // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same owner-signal
-    // tracking and one-attempt retry, and the same reasoning below.
+    // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape and the same
+    // reasoning below.
     /**
      * 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 `readIndexBytes`, 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.
+     * that did not. `_parse` hands `opts` straight to `readIndexBytes`, so a bare
+     * memoized promise makes the first query to arrive the owner of 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.
+     * The same cache `ChunkCache` uses, for the same reason and with the same
+     * rule: the parse runs under a signal of its own and is cancelled only once
+     * every caller waiting on it has given up, so one query's abort is reported
+     * to that query alone and a bystander gets the parse already in flight rather
+     * than having to re-read the index. A rejection is dropped rather than
+     * cached, so a transient failure does not poison the index for the life of
+     * the file.
      *
-     * A retry rather than the reference count `ChunkCache` uses, because the
-     * index is parsed once for the life of the object: there is no repeated waste
-     * to recover, and this is a dozen lines against restructuring the memo.
-     * `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
-     * split for the same reason.
+     * The fill is per call rather than on the cache so that the caller who starts
+     * the parse has its `onProgress` reach `readIndexBytes` — the index is a
+     * whole-file read, and a determinate "downloading index" bar is what that
+     * callback exists for.
      *
      * @internal
      */
-    async parse(opts = {}, retried = false) {
-        (0, util_ts_1.throwIfAborted)(opts.signal);
-        const pending = this.parseP;
-        if (!pending) {
-            return this.startParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.parseSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.parse(opts, true);
-        }
-    }
-    startParse(opts) {
-        const pending = this._parse(opts);
-        this.parseP = pending;
-        this.parseSignal = 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.parseP === pending) {
-                this.parseSignal = undefined;
-            }
-        }, () => {
-            if (this.parseP === pending) {
-                this.parseP = undefined;
-                this.parseSignal = undefined;
-            }
-        });
-        return pending;
+    parse(opts = {}) {
+        return this.parseCache.get('index', opts.signal, signal => this._parse({ ...opts, signal }));
     }
     /** @internal */
     async hasRefSeq(seqId, opts = {}) {

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