npm - @gmod/tabix - Versions diffs - 3.6.0 → 3.6.1 - Mend

@gmod/tabix 3.6.0 → 3.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (16) hide show

package/dist/indexFile.d.ts +19 -23
package/dist/indexFile.js +23 -60
package/dist/indexFile.js.map +1 -1
package/dist/tabix-bundle.js +1 -1
package/dist/tabixIndexedFile.d.ts +13 -11
package/dist/tabixIndexedFile.js +15 -47
package/dist/tabixIndexedFile.js.map +1 -1
package/esm/indexFile.d.ts +19 -23
package/esm/indexFile.js +24 -61
package/esm/indexFile.js.map +1 -1
package/esm/tabixIndexedFile.d.ts +13 -11
package/esm/tabixIndexedFile.js +16 -48
package/esm/tabixIndexedFile.js.map +1 -1
package/package.json +2 -2
package/src/indexFile.ts +25 -64
package/src/tabixIndexedFile.ts +20 -54

package/dist/tabixIndexedFile.d.ts CHANGED Viewed

@@ -24,14 +24,11 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     chunkCache: SharedReadCache<Chunk, ReadChunk>;
-    private headerP?;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    private headerSignal?;
+    private headerCache;
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, }: {
         path?: string;
         filehandle?: GenericFilehandle;
@@ -134,16 +131,21 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and 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 caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
     private getParsedHeader;
-    private startHeaderParse;
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the
      * string form: this hands back the buffer, and holding one for the lifetime

package/dist/tabixIndexedFile.js CHANGED Viewed

@@ -193,14 +193,11 @@ class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    headerP;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    headerSignal;
+    headerCache = new shared_read_cache_1.SharedReadCache({});
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
@@ -454,51 +451,22 @@ class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and 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 caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
-    async getParsedHeader(opts = {}, retried = false) {
-        (0, util_ts_1.throwIfAborted)(opts.signal);
-        const pending = this.headerP;
-        if (!pending) {
-            return this.startHeaderParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.headerSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.getParsedHeader(opts, true);
-        }
-    }
-    startHeaderParse(opts) {
-        const pending = this.parseHeader(opts);
-        this.headerP = pending;
-        this.headerSignal = opts.signal;
-        // Drop a rejection rather than keeping it, so one transient failure does not
-        // poison the header 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.headerP === pending) {
-                this.headerSignal = undefined;
-            }
-        }, () => {
-            if (this.headerP === pending) {
-                this.headerP = undefined;
-                this.headerSignal = undefined;
-            }
-        });
-        return pending;
+    getParsedHeader(opts = {}) {
+        return this.headerCache.get('header', opts.signal, signal => this.parseHeader({ ...opts, signal }));
     }
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the

package/dist/tabixIndexedFile.js.map CHANGED Viewed

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package/esm/indexFile.d.ts CHANGED Viewed

@@ -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/esm/indexFile.js CHANGED Viewed

@@ -1,15 +1,13 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import { optimizeChunks, throwIfAborted } from "./util.js";
+import { SharedReadCache } from '@gmod/shared-read-cache';
+import { optimizeChunks } from "./util.js";
 export default 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 SharedReadCache({});
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
@@ -73,71 +71,36 @@ export default class IndexFile {
         }
         return 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) {
-        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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package/esm/tabixIndexedFile.d.ts CHANGED Viewed

@@ -24,14 +24,11 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     chunkCache: SharedReadCache<Chunk, ReadChunk>;
-    private headerP?;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    private headerSignal?;
+    private headerCache;
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize, chunkCacheIdleTimeoutMs, }: {
         path?: string;
         filehandle?: GenericFilehandle;
@@ -134,16 +131,21 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and 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 caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
     private getParsedHeader;
-    private startHeaderParse;
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the
      * string form: this hands back the buffer, and holding one for the lifetime

package/esm/tabixIndexedFile.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { SharedReadCache } from '@gmod/shared-read-cache';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import CSI from "./csi.js";
 import TBI from "./tbi.js";
-import { optimizeChunks, throwIfAborted } from "./util.js";
+import { optimizeChunks } from "./util.js";
 const TAB = 9;
 const NEWLINE = 10;
 const CARRIAGE_RETURN = 13;
@@ -188,14 +188,11 @@ export default class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    headerP;
     /**
-     * The signal `headerP` was started under, while it is still in flight. The
-     * header is parsed once and shared by every caller, so without this the first
-     * one to arrive would own a read all the others depend on — see
-     * {@link getParsedHeader}.
+     * The parsed header, as a shared read — see {@link getParsedHeader}. One
+     * entry, never evicted, which is what a memo is.
      */
-    headerSignal;
+    headerCache = new SharedReadCache({});
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, chunkCacheIdleTimeoutMs = DEFAULT_CHUNK_CACHE_IDLE_TIMEOUT_MS, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
@@ -449,51 +446,22 @@ export default class TabixIndexedFile {
      * charge of a read every later caller joins: when it aborted, they failed
      * with its cancellation, their own signals untouched.
      *
-     * 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. Same bounded retry, and the same reasoning, as
-     * `IndexFile.parse`.
+     * The same cache the chunk reads use, and 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 caller's abort is reported to that caller alone and a
+     * bystander gets the parse already in flight. There is no retry here because
+     * there is nothing to retry — the parse a bystander joined is not cancelled by
+     * someone else's abort. A rejection is dropped rather than cached, so a
+     * transient failure does not poison the header for the life of the file.
+     *
+     * The fill is per call rather than on the cache, so the caller that starts the
+     * parse has its `onProgress` reach the index download inside `getMetadata`.
      *
      * SYNC: ~/src/gmod/bam-js/src/bamFile.ts getHeader — same shape for the same
      * reason, on the header rather than the index.
      */
-    async getParsedHeader(opts = {}, retried = false) {
-        throwIfAborted(opts.signal);
-        const pending = this.headerP;
-        if (!pending) {
-            return this.startHeaderParse(opts);
-        }
-        // read before awaiting: the owner is forgotten as soon as the parse settles
-        const ownerSignal = this.headerSignal;
-        try {
-            return await pending;
-        }
-        catch (e) {
-            if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
-                throw e;
-            }
-            return this.getParsedHeader(opts, true);
-        }
-    }
-    startHeaderParse(opts) {
-        const pending = this.parseHeader(opts);
-        this.headerP = pending;
-        this.headerSignal = opts.signal;
-        // Drop a rejection rather than keeping it, so one transient failure does not
-        // poison the header 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.headerP === pending) {
-                this.headerSignal = undefined;
-            }
-        }, () => {
-            if (this.headerP === pending) {
-                this.headerP = undefined;
-                this.headerSignal = undefined;
-            }
-        });
-        return pending;
+    getParsedHeader(opts = {}) {
+        return this.headerCache.get('header', opts.signal, signal => this.parseHeader({ ...opts, signal }));
     }
     /**
      * The bytes of the commented header. Deliberately not memoized, unlike the

package/esm/tabixIndexedFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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