@gmod/tabix 3.5.7 → 3.6.1

package/README.md

@@ -102,18 +102,19 @@ opening the file directly.
 
 ### `new TabixIndexedFile(args)`
 
-| Arg              | Type                 | Description                                                                                 |
-| ---------------- | -------------------- | ------------------------------------------------------------------------------------------- |
-| `path`           | `string?`            | Local file path                                                                             |
-| `url`            | `string?`            | Remote URL                                                                                  |
-| `filehandle`     | `GenericFilehandle?` | Custom filehandle (from [generic-filehandle2](https://github.com/GMOD/generic-filehandle2)) |
-| `tbiPath`        | `string?`            | TBI index path (defaults to `path + '.tbi'`)                                                |
-| `tbiUrl`         | `string?`            | TBI index URL                                                                               |
-| `tbiFilehandle`  | `GenericFilehandle?` | TBI index filehandle                                                                        |
-| `csiPath`        | `string?`            | CSI index path                                                                              |
-| `csiUrl`         | `string?`            | CSI index URL                                                                               |
-| `csiFilehandle`  | `GenericFilehandle?` | CSI index filehandle                                                                        |
-| `chunkCacheSize` | `number?`            | Chunk LRU cache budget, in _decompressed_ bytes (default 100 MiB)                           |
+| Arg                       | Type                 | Description                                                                                                                                                                                                                                   |
+| ------------------------- | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `path`                    | `string?`            | Local file path                                                                                                                                                                                                                               |
+| `url`                     | `string?`            | Remote URL                                                                                                                                                                                                                                    |
+| `filehandle`              | `GenericFilehandle?` | Custom filehandle (from [generic-filehandle2](https://github.com/GMOD/generic-filehandle2))                                                                                                                                                   |
+| `tbiPath`                 | `string?`            | TBI index path (defaults to `path + '.tbi'`)                                                                                                                                                                                                  |
+| `tbiUrl`                  | `string?`            | TBI index URL                                                                                                                                                                                                                                 |
+| `tbiFilehandle`           | `GenericFilehandle?` | TBI index filehandle                                                                                                                                                                                                                          |
+| `csiPath`                 | `string?`            | CSI index path                                                                                                                                                                                                                                |
+| `csiUrl`                  | `string?`            | CSI index URL                                                                                                                                                                                                                                 |
+| `csiFilehandle`           | `GenericFilehandle?` | CSI index filehandle                                                                                                                                                                                                                          |
+| `chunkCacheSize`          | `number?`            | Chunk LRU cache budget, in _decompressed_ bytes (default 1 GiB). A retention bound, not a bound on peak memory. Size it to hold several queries: below one query's working set the hit rate drops to zero while the memory is retained anyway |
+| `chunkCacheIdleTimeoutMs` | `number?`            | Drop a cached chunk once nothing has read it for this long (default 3 minutes, `0` disables). The only thing that lowers the cache while nothing is happening, and what makes the budget above a peak rather than a resting level             |
 
 ### `getLines(refName, start, end, opts)`
 

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` gets from
-     * `@gmod/abortable-promise-cache`, 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;
     }
@@ -75,78 +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 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` gets from
-     * `@gmod/abortable-promise-cache`, 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. Identity-checked so a retry
-        // started after this settles is not cleared by the attempt it replaced.
-        //
-        // Written as one try/catch rather than `.then(onFulfilled, onRejected)`
-        // because `unicorn/prefer-then-catch` rewrites the two-argument form to
-        // `.then(...).catch(...)`, which is not the same thing — that catch would
-        // also swallow anything the fulfilment handler threw.
-        void (async () => {
-            let failed = false;
-            try {
-                await pending;
-            }
-            catch {
-                failed = true;
-            }
-            if (this.parseP === pending) {
-                if (failed) {
-                    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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