@jbrowse/core 4.1.15 → 4.2.1

package/esm/util/io/RemoteFileWithRangeCache.d.ts

@@ -1,6 +1,10 @@
 import { RemoteFile } from 'generic-filehandle2';
 export declare function clearCache(): void;
 export declare class RemoteFileWithRangeCache extends RemoteFile {
+    private cachedStat?;
+    stat(): Promise<{
+        size: number;
+    }>;
     private fetchRange;
     private getCachedRange;
     fetch(url: string | RequestInfo, init?: RequestInit): Promise<Response>;

package/esm/util/io/RemoteFileWithRangeCache.js

@@ -36,7 +36,7 @@ function limitConcurrency(fn) {
                 runNext();
             }, (err) => {
                 activeCount--;
-                reject(err);
+                reject(err instanceof Error ? err : new Error(String(err)));
                 runNext();
             });
         }
@@ -53,46 +53,75 @@ function cacheKey(url, chunkIndex) {
     return `${url}:${chunkIndex}`;
 }
 export class RemoteFileWithRangeCache extends RemoteFile {
+    cachedStat;
+    async stat() {
+        if (!this.cachedStat) {
+            await this.getCachedRange(this.url, 0, 1);
+        }
+        return this.cachedStat ?? { size: 0 };
+    }
     async fetchRange(url, start, end, signal) {
         const res = await super.fetch(url, {
             signal: signal ?? undefined,
             headers: { range: `bytes=${start}-${end}` },
         });
+        if (res.status === 416) {
+            return new Uint8Array(0);
+        }
         if (!res.ok) {
-            const errorMessage = `HTTP ${res.status} fetching ${url} bytes ${start}-${end}`;
             const hint = ' (should be 206 for range requests)';
-            throw new Error(`${errorMessage}${res.status === 200 ? hint : ''}`);
+            const msg = `HTTP ${res.status} fetching ${url} bytes ${start}-${end}${res.status === 200 ? hint : ''}`;
+            throw Object.assign(new Error(msg), { status: res.status });
+        }
+        if (!this.cachedStat) {
+            const contentRange = res.headers.get('content-range');
+            const match = contentRange ? /\/(\d+)$/.exec(contentRange) : null;
+            if (match) {
+                this.cachedStat = { size: parseInt(match[1], 10) };
+            }
         }
         return new Uint8Array(await res.arrayBuffer());
     }
     async getCachedRange(url, start, length, signal) {
         const startChunk = Math.floor(start / CHUNK_SIZE);
         const endChunk = Math.floor((start + length - 1) / CHUNK_SIZE);
-        const chunkCount = endChunk - startChunk + 1;
-        const chunks = await Promise.all(Array.from({ length: chunkCount }, (_, i) => {
-            const idx = startChunk + i;
-            const key = cacheKey(url, idx);
-            const existing = getCached(key);
-            if (existing) {
-                return Promise.resolve(existing);
+        let effectiveEndChunk = endChunk;
+        for (let i = startChunk; i < endChunk; i++) {
+            const c = getCached(cacheKey(url, i));
+            if (c !== undefined && c.length < CHUNK_SIZE) {
+                effectiveEndChunk = i;
+                break;
             }
-            return limitConcurrency(async () => {
-                const alreadyCached = getCached(key);
-                if (alreadyCached) {
-                    return alreadyCached;
+        }
+        const chunkCount = effectiveEndChunk - startChunk + 1;
+        const runs = [];
+        for (let i = 0; i < chunkCount; i++) {
+            if (!getCached(cacheKey(url, startChunk + i))) {
+                const lastRun = runs[runs.length - 1];
+                if (lastRun?.end === i - 1) {
+                    lastRun.end = i;
                 }
-                const chunkStart = idx * CHUNK_SIZE;
-                const chunkEnd = chunkStart + CHUNK_SIZE - 1;
-                const data = await this.fetchRange(url, chunkStart, chunkEnd, signal);
-                putCached(key, data);
-                return data;
-            });
-        }));
+                else {
+                    runs.push({ start: i, end: i });
+                }
+            }
+        }
+        await Promise.all(runs.map(run => limitConcurrency(async () => {
+            const runStartChunk = startChunk + run.start;
+            const runEndChunk = startChunk + run.end;
+            const rangeStart = runStartChunk * CHUNK_SIZE;
+            const rangeEnd = (runEndChunk + 1) * CHUNK_SIZE - 1;
+            const data = await this.fetchRange(url, rangeStart, rangeEnd, signal);
+            for (let i = run.start; i <= run.end; i++) {
+                const offset = (i - run.start) * CHUNK_SIZE;
+                putCached(cacheKey(url, startChunk + i), data.subarray(offset, offset + CHUNK_SIZE));
+            }
+        })));
         const offsetInFirstChunk = start - startChunk * CHUNK_SIZE;
         const result = new Uint8Array(length);
         let written = 0;
-        for (const [i, chunk_] of chunks.entries()) {
-            const chunk = chunk_;
+        for (let i = 0; i < chunkCount; i++) {
+            const chunk = getCached(cacheKey(url, startChunk + i));
             const sourceStart = i === 0 ? offsetInFirstChunk : 0;
             const available = chunk.length - sourceStart;
             const needed = length - written;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "4.1.15",
+  "version": "4.2.1",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -484,9 +484,9 @@
     "@jbrowse/mobx-state-tree": "^5.6.0",
     "@jbrowse/quick-lru": "^7.3.5",
     "@leeoniya/ufuzzy": "^1.0.19",
-    "@mui/icons-material": "^7.3.9",
-    "@mui/material": "^7.3.9",
-    "@mui/system": "^7.3.9",
+    "@mui/icons-material": "^7.3.10",
+    "@mui/material": "^7.3.10",
+    "@mui/system": "^7.3.10",
     "@mui/types": "^7.4.12",
     "@mui/x-data-grid": "^8.28.2",
     "@types/file-saver-es": "^2.0.3",
@@ -495,7 +495,7 @@
     "copy-to-clipboard": "^3.3.3",
     "deepmerge": "^4.3.1",
     "detect-node": "^2.1.0",
-    "dompurify": "^3.3.3",
+    "dompurify": "^3.4.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-saver-es": "^2.0.5",