loom-browser 0.0.14 → 0.0.16

package/dist/loom-react.esm.js

@@ -9877,50 +9877,95 @@ function createGenomeSync(config) {
     return new GenomeImpl(id, config.chromSizes, { name, sequence, cytobands: config.cytobands, nameSet: config.nameSet });
 }
 // ─── Sequence resolution ────��─────────────────────────────────���──────────────
+/**
+ * Wrap a primary SequenceProvider with a fallback.
+ *
+ * On each request, tries `primary` first. If it throws (and the signal was
+ * not aborted), tries `fallback`. If both fail, the primary error is thrown
+ * so the caller sees the error from their configured source.
+ *
+ * The caching layer (createCachedSequence) wraps the combined provider,
+ * so successful fallback results are cached normally — subsequent requests
+ * for the same region won't re-attempt the primary.
+ */
+function createFallbackProvider(primary, fallback) {
+    return async (locus, signal) => {
+        try {
+            return await primary(locus, signal);
+        }
+        catch (primaryErr) {
+            if (signal === null || signal === void 0 ? void 0 : signal.aborted)
+                throw primaryErr;
+            console.warn('[loom] Primary sequence source failed, trying fallback:', primaryErr.message);
+            try {
+                return await fallback(locus, signal);
+            }
+            catch (_a) {
+                // Both failed — throw the primary error (more relevant to the user's config)
+                throw primaryErr;
+            }
+        }
+    };
+}
 /**
  * Resolve a sequence provider from config.
  *
- * Exactly one sequence source must be set. Throws if multiple are provided.
- * Sources: sequenceProvider, twoBitURL, fastaURL, ucscGenome.
- * When none is set, falls back to UCSC API via `id` if available.
+ * If a custom `sequenceProvider` is set, it is used directly. Otherwise,
+ * all available sources (twoBitURL, fastaURL, ucscGenome/id) are chained
+ * as a prioritized fallback list:
+ *
+ *   1. twoBitURL  — most efficient (binary range requests)
+ *   2. fastaURL   — reliable CDN fallback (igv.org hosts FASTA for common genomes)
+ *   3. UCSC API   — last resort (api.genome.ucsc.edu REST endpoint)
+ *
+ * This mirrors igv.js genomes3.json which provides both twoBitURL and fastaURL
+ * for common genomes. On networks where one server is unreachable (e.g.,
+ * hgdownload.soe.ucsc.edu blocked but igv.org reachable), the chain
+ * automatically falls through to the next available source.
  */
 function resolveSequenceProvider(config) {
     var _a;
-    const sources = [
-        config.sequenceProvider && 'sequenceProvider',
-        config.twoBitURL && 'twoBitURL',
-        config.fastaURL && 'fastaURL',
-        config.ucscGenome && 'ucscGenome',
-    ].filter(Boolean);
-    if (sources.length > 1) {
-        throw new Error(`GenomeConfig has multiple sequence sources: ${sources.join(', ')}. ` +
-            'Set exactly one of: sequenceProvider, twoBitURL, fastaURL, or ucscGenome.');
-    }
+    // Custom provider — use directly, no chaining
     if (config.sequenceProvider) {
         return config.sequenceProvider;
     }
+    // Build prioritized provider list from available config fields
+    const providers = [];
     if (config.twoBitURL) {
-        return createCachedSequence(createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl));
+        providers.push(createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl));
     }
     if (config.fastaURL) {
-        return createCachedSequence(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
+        providers.push(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
     }
-    // UCSC API — explicit ucscGenome, or implicit via id
     const ucscGenome = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
     if (ucscGenome) {
-        return createCachedSequence((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
+        providers.push((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
     }
-    return undefined;
+    if (providers.length === 0)
+        return undefined;
+    if (providers.length === 1)
+        return createCachedSequence(providers[0]);
+    // Chain all providers: try each in order, fall back on failure
+    const chained = providers.reduceRight((fallback, primary) => createFallbackProvider(primary, fallback));
+    return createCachedSequence(chained);
 }
 // ─── Pre-built singletons ��─────────��─────────────────────────────────────────
 /**
- * Pre-built hg38 genome with UCSC sequence API.
+ * Pre-built hg38 genome with triple-fallback sequence chain.
  *
  * This is the default genome used by HeadlessGenomeBrowser when no genome
- * is specified. Equivalent to igv.js's default behavior of loading hg38.
+ * is specified. Sequence sources are tried in order:
+ *   1. 2-bit from hgdownload.soe.ucsc.edu (most efficient, binary range requests)
+ *   2. Indexed FASTA from igv.org (reliable CDN, reachable on restricted networks)
+ *   3. UCSC REST API from api.genome.ucsc.edu (last resort)
+ *
+ * URLs match igv.js genomes3.json configuration for hg38.
  */
 const hg38Genome = createGenomeSync({
     id: 'hg38',
+    twoBitURL: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit',
+    fastaURL: 'https://igv.org/genomes/data/hg38/hg38.fa',
+    indexURL: 'https://igv.org/genomes/data/hg38/hg38.fa.fai',
     chromSizes: hg38ChromSizes,
 });
 
@@ -22102,10 +22147,12 @@ function isZoomAware(track) {
  * tracks point to the same URL/region.
  */
 function dataSourceCacheKey(config) {
-    var _a, _b, _c, _d, _e;
+    var _a, _b, _c, _d, _e, _f;
     switch (config.type) {
         case 'bigwig':
             return `bigwig:${config.url}:${(_a = config.windowFunction) !== null && _a !== void 0 ? _a : 'mean'}`;
+        case 'bigbed':
+            return `bigbed:${config.url}`;
         case 'gtx':
             return `gtx:${config.url}:${config.experimentId}`;
         case 'ucsc':
@@ -22113,13 +22160,9 @@ function dataSourceCacheKey(config) {
         case 'text':
             return `text:${config.url}:${(_d = config.format) !== null && _d !== void 0 ? _d : ''}:${(_e = config.indexURL) !== null && _e !== void 0 ? _e : ''}`;
         case 'memory':
-            // Each memory data source is unique — no deduplication.
             return `memory:${Math.random()}`;
-        default: {
-            // Unknown type — resolve via URL inference, then compute key from resolved config
-            const resolved = resolveDataSourceConfig(config);
-            return dataSourceCacheKey(resolved);
-        }
+        default:
+            return `unknown:${config.type}:${(_f = config.url) !== null && _f !== void 0 ? _f : Math.random()}`;
     }
 }