@vitessce/config 3.9.2 → 3.9.4

package/dist/index.js

@@ -2374,6 +2374,9 @@ function get_ctr(data_type) {
     let [, kind, chars] = match;
     return (kind === "U" ? UnicodeStringArray : ByteStringArray).bind(null, Number(chars));
   }
+  if (data_type === "string") {
+    return globalThis.Array;
+  }
   let ctr = {
     int8: Int8Array,
     int16: Int16Array,
@@ -2495,7 +2498,7 @@ function is_dtype(dtype, query) {
   let is_boolean = dtype === "bool";
   if (query === "boolean")
     return is_boolean;
-  let is_string = dtype.startsWith("v2:U") || dtype.startsWith("v2:S");
+  let is_string = dtype.startsWith("v2:U") || dtype.startsWith("v2:S") || dtype === "string";
   if (query === "string")
     return is_string;
   let is_bigint = dtype === "int64" || dtype === "uint64";
@@ -2945,7 +2948,7 @@ async function load_codecs(chunk_meta) {
   return { array_to_array, array_to_bytes, bytes_to_bytes };
 }
 function is_typed_array_like_meta(meta) {
-  return meta.data_type !== "v2:object";
+  return meta.data_type !== "v2:object" && meta.data_type !== "string";
 }
 class NodeNotFoundError extends Error {
   constructor(context, options = {}) {
@@ -3029,7 +3032,7 @@ function create_sharded_chunk_getter(location, shard_shape, encode_shard_key, sh
     codecs: sharding_config.index_codecs
   });
   let cache = {};
-  return async (chunk_coord) => {
+  return async (chunk_coord, options) => {
     let shard_coord = chunk_coord.map((d, i) => Math.floor(d / index_shape[i]));
     let shard_path = location.resolve(encode_shard_key(shard_coord)).path;
     let index;
@@ -3040,7 +3043,7 @@ function create_sharded_chunk_getter(location, shard_shape, encode_shard_key, sh
       let index_size = 16 * index_shape.reduce((a, b) => a * b, 1);
       let bytes = await get_range(shard_path, {
         suffixLength: index_size + checksum_size
-      });
+      }, options);
       index = cache[shard_path] = bytes ? await index_codec.decode(bytes) : null;
     }
     if (index === null) {
@@ -3056,7 +3059,7 @@ function create_sharded_chunk_getter(location, shard_shape, encode_shard_key, sh
     return get_range(shard_path, {
       offset: Number(offset),
       length: Number(length)
-    });
+    }, options);
   };
 }
 var _a;
@@ -4077,6 +4080,13 @@ async function unzip(source) {
     entries: Object.fromEntries(entries.map((v) => [v.name, v]))
   };
 }
+function isZipEntryInternal(entry) {
+  if (!("compressionMethod" in entry) || !("_rawEntry" in entry)) {
+    return false;
+  }
+  const rawEntry = entry._rawEntry;
+  return typeof entry.compressionMethod === "number" && typeof rawEntry === "object" && rawEntry !== null && "relativeOffsetOfLocalHeader" in rawEntry && typeof rawEntry.relativeOffsetOfLocalHeader === "number";
+}
 class BlobReader2 {
   constructor(blob) {
     this.blob = blob;
@@ -4120,6 +4130,7 @@ class HTTPRangeReader {
 }
 class ZipFileStore {
   constructor(reader, opts = {}) {
+    this.reader = reader;
     this.info = unzip(reader).then((info) => {
       if (opts.transformEntries) {
         info.entries = opts.transformEntries(info.entries);
@@ -4127,12 +4138,46 @@ class ZipFileStore {
       return info;
     });
   }
+  /**
+   * Compute the byte offset where entry data begins in the zip file.
+   * This requires reading the local file header to get filename and extra field lengths.
+   */
+  async getEntryDataOffset(entry) {
+    const localHeaderOffset = entry._rawEntry.relativeOffsetOfLocalHeader;
+    const header = await this.reader.read(localHeaderOffset, 30);
+    const fileNameLength = header[26] + header[27] * 256;
+    const extraFieldLength = header[28] + header[29] * 256;
+    return localHeaderOffset + 30 + fileNameLength + extraFieldLength;
+  }
   async get(key) {
     let entry = (await this.info).entries[strip_prefix(key)];
     if (!entry)
       return;
     return new Uint8Array(await entry.arrayBuffer());
   }
+  async getRange(key, range) {
+    const entry = (await this.info).entries[strip_prefix(key)];
+    if (!entry)
+      return void 0;
+    if (!isZipEntryInternal(entry)) {
+      throw new Error("ZipFileStore.getRange requires internal unzipit properties that are not available. This may indicate an incompatible version of unzipit.");
+    }
+    if (entry.compressionMethod !== 0) {
+      const bytes = await this.get(key);
+      if (!bytes)
+        return void 0;
+      if ("suffixLength" in range) {
+        return bytes.slice(-range.suffixLength);
+      }
+      return bytes.slice(range.offset, range.offset + range.length);
+    }
+    const dataOffset = await this.getEntryDataOffset(entry);
+    if ("suffixLength" in range) {
+      const start = dataOffset + entry.size - range.suffixLength;
+      return this.reader.read(start, range.suffixLength);
+    }
+    return this.reader.read(dataOffset + range.offset, range.length);
+  }
   async has(key) {
     return strip_prefix(key) in (await this.info).entries;
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "3.9.2",
+  "version": "3.9.4",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -16,12 +16,12 @@
     "dist-tsc"
   ],
   "dependencies": {
-    "zarrita": "0.5.4",
-    "@zarrita/storage": "0.1.3",
-    "@vitessce/constants-internal": "3.9.2",
-    "@vitessce/utils": "3.9.2",
-    "@vitessce/globals": "3.9.2",
-    "@vitessce/zarr-utils": "3.9.2"
+    "zarrita": "0.6.1",
+    "@zarrita/storage": "0.1.4",
+    "@vitessce/constants-internal": "3.9.4",
+    "@vitessce/zarr-utils": "3.9.4",
+    "@vitessce/utils": "3.9.4",
+    "@vitessce/globals": "3.9.4"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.mjs",