loom-browser 0.0.14 → 0.0.15

package/dist/loom-react.esm.js

@@ -9877,15 +9877,49 @@ 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.
+ *
+ * When twoBitURL is used and a genome ID is available, the UCSC REST API is
+ * automatically added as a fallback — if the 2-bit server is unreachable,
+ * the API is tried instead.
  */
 function resolveSequenceProvider(config) {
-    var _a;
+    var _a, _b;
     const sources = [
         config.sequenceProvider && 'sequenceProvider',
         config.twoBitURL && 'twoBitURL',
@@ -9900,13 +9934,20 @@ function resolveSequenceProvider(config) {
         return config.sequenceProvider;
     }
     if (config.twoBitURL) {
-        return createCachedSequence(createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl));
+        const primary = createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl);
+        // Add UCSC REST API fallback when a genome ID is known
+        const genomeId = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
+        if (genomeId) {
+            const fallback = (locus, signal) => fetchSequence(locus, { genome: genomeId }, signal);
+            return createCachedSequence(createFallbackProvider(primary, fallback));
+        }
+        return createCachedSequence(primary);
     }
     if (config.fastaURL) {
         return createCachedSequence(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;
+    const ucscGenome = (_b = config.ucscGenome) !== null && _b !== void 0 ? _b : config.id;
     if (ucscGenome) {
         return createCachedSequence((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
     }
@@ -9914,13 +9955,15 @@ function resolveSequenceProvider(config) {
 }
 // ─── Pre-built singletons ��─────────��─────────────────────────────────────────
 /**
- * Pre-built hg38 genome with UCSC sequence API.
+ * Pre-built hg38 genome with 2-bit sequence (UCSC API fallback).
  *
  * 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. Matches igv.js's default behavior: 2-bit file as primary
+ * sequence source, with UCSC REST API as automatic fallback for resilience.
  */
 const hg38Genome = createGenomeSync({
     id: 'hg38',
+    twoBitURL: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit',
     chromSizes: hg38ChromSizes,
 });
 
@@ -22102,10 +22145,12 @@ 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}:${config.experimentId}`;
         case 'ucsc':
@@ -22113,13 +22158,9 @@ function dataSourceCacheKey(config) {
         case 'text':
             return `text:${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()}`;
     }
 }