@vitessce/all 3.3.10 → 3.3.12

package/dist/{deflate-7c420d06.js → deflate-a6707a9d.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{hglib-abd4a9d9.js → hglib-9dacf5bc.js}

@@ -1,6 +1,6 @@
 import React__default from "react";
 import ReactDOM__default from "react-dom";
-import { c as commonjsGlobal, o as objectAssign, g as getDefaultExportFromCjs, e as earcut, b as getAugmentedNamespace } from "./index-b2bb1d08.js";
+import { c as commonjsGlobal, o as objectAssign, g as getDefaultExportFromCjs, e as earcut, b as getAugmentedNamespace } from "./index-ac567918.js";
 function _mergeNamespaces(n, m) {
   for (var i = 0; i < m.length; i++) {
     const e = m[i];

package/dist/{index-b2bb1d08.js → index-ac567918.js}

@@ -122362,13 +122362,13 @@ var gOPD = Object.getOwnPropertyDescriptor;
 var defineProperty$1 = Object.defineProperty;
 var TypeErr = TypeError;
 var getProto$1 = Object.getPrototypeOf;
-var regex$3 = /a/;
+var regex$2 = /a/;
 var shim$2 = function shimFlags() {
   if (!supportsDescriptors || !getProto$1) {
     throw new TypeErr("RegExp.prototype.flags requires a true ES5 environment that supports property descriptors");
   }
   var polyfill2 = getPolyfill$1();
-  var proto = getProto$1(regex$3);
+  var proto = getProto$1(regex$2);
   var descriptor2 = gOPD(proto, "flags");
   if (!descriptor2 || descriptor2.get !== polyfill2) {
     defineProperty$1(proto, "flags", {
@@ -156406,16 +156406,16 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-221c7288.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-67b71961.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-306e279c.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-fbdbcd71.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-7e1ceac4.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-7c420d06.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-d95ea21b.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-54fe9485.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-e90de519.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-94fc740e.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-a6707a9d.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-440a0758.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-1fa73516.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-6f012708.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -205595,7 +205595,8 @@ var ZarrMultivecDataFetcher = function ZarrMultivecDataFetcher2(HGC, ...args) {
       this.dataConfig = dataConfig;
       this.trackUid = slugid.nice();
       if (dataConfig.url) {
-        this.store = new FetchStore$1(dataConfig.url);
+        const { url, options = {} } = dataConfig;
+        this.store = new FetchStore$1(url, options);
         this.storeRoot = Promise.resolve(root(this.store));
       }
       if (dataConfig.row !== void 0) {
@@ -205767,7 +205768,7 @@ const HIGLASS_BUNDLE_VERSION = "1.11.13";
 const HIGLASS_CSS_URL = `https://unpkg.com/${HIGLASS_PKG_NAME}@${HIGLASS_BUNDLE_VERSION}/dist/hglib.css`;
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./hglib-abd4a9d9.js").then((n3) => n3.h);
+  const { HiGlassComponent } = await import("./hglib-9dacf5bc.js").then((n3) => n3.h);
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -205938,7 +205939,7 @@ function GenomicProfilesSubscriber(props2) {
   const [width2, height2, containerRef] = useGridItemSize();
   const loaders = useLoaders();
   const [{ dataset, obsSetColor: cellSetColor, obsSetSelection: cellSetSelection }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.GENOMIC_PROFILES], coordinationScopes);
-  const [genomicProfilesAttrs, genomicProfilesStatus, genomicProfilesUrls] = useGenomicProfilesData(loaders, dataset, true, {}, {}, {});
+  const [genomicProfilesAttrs, genomicProfilesStatus, genomicProfilesUrls, genomicProfilesRequestInit] = useGenomicProfilesData(loaders, dataset, true, {}, {}, {});
   const isReady = useReady([genomicProfilesStatus]);
   const urls2 = useUrls([genomicProfilesUrls]);
   const hgViewConfig = useMemo(() => {
@@ -206006,12 +206007,14 @@ function GenomicProfilesSubscriber(props2) {
       const setInSelection = isPath ? cellSetSelection == null ? void 0 : cellSetSelection.find((s2) => isEqual$4(s2, trackUid)) : false;
       const setColor = isPath ? (_a3 = cellSetColor == null ? void 0 : cellSetColor.find((s2) => isEqual$4(s2.path, trackUid))) == null ? void 0 : _a3.color : null;
       const trackUidString = isPath ? trackUid.join("__") : trackUid;
+      const options = genomicProfilesRequestInit ? { overrides: genomicProfilesRequestInit } : void 0;
       const track = {
         type: "horizontal-bar",
         uid: `bar-track-${trackUidString}`,
         data: {
           type: "zarr-multivec",
           url,
+          options,
           row: i2
         },
         options: {
@@ -265021,10 +265024,10 @@ class AnnDataSource extends ZarrDataSource {
     throw new Error("Keys for encoding-type or encoding-version not found in AnnDataSource._loadString");
   }
 }
-const regex$2 = /^mod\/([^/]*)\/(.*)$/;
+const regex$1 = /^mod\/([^/]*)\/(.*)$/;
 function getModPrefix(arrPath) {
   if (arrPath) {
-    const matches2 = arrPath.match(regex$2);
+    const matches2 = arrPath.match(regex$1);
     if (matches2 && matches2.length === 3) {
       return `mod/${matches2[1]}/`;
     }
@@ -265086,12 +265089,17 @@ class MuDataSource extends AnnDataSource {
     return this.varAlias[varPath];
   }
 }
-const regex$1 = /^table\/([^/]*)\/(.*)$/;
+const pluralRegex = /^tables\/([^/]*)\/(.*)$/;
+const singularRegex = /^table\/([^/]*)\/(.*)$/;
 function getTablePrefix(arrPath) {
   if (arrPath) {
-    const matches2 = arrPath.match(regex$1);
-    if (matches2 && matches2.length === 3) {
-      return `table/${matches2[1]}/`;
+    const pluralMatches = arrPath.match(pluralRegex);
+    if (pluralMatches && pluralMatches.length === 3) {
+      return `tables/${pluralMatches[1]}/`;
+    }
+    const singularMatches = arrPath.match(singularRegex);
+    if (singularMatches && singularMatches.length === 3) {
+      return `table/${singularMatches[1]}/`;
     }
   }
   return "table/table/";
@@ -265290,7 +265298,33 @@ class MatrixZarrAsObsFeatureMatrixLoader extends AbstractTwoStepLoader {
     return Promise.all([this.loadAttrs(), this.loadArr()]).then(([attrs, arr]) => Promise.resolve(new LoaderResult({ obsIndex: attrs.data.rows, featureIndex: attrs.data.cols, obsFeatureMatrix: arr }, null)));
   }
 }
-const toObject = (data2) => ({ data: data2 });
+class IncorrectDataTypeError extends Error {
+  constructor(message) {
+    super(message);
+    this.name = "IncorrectDataTypeError";
+  }
+}
+function convertBigInt64ArrayToInt32Array(arr) {
+  if (!(arr instanceof BigInt64Array)) {
+    throw new IncorrectDataTypeError("Expected a BigInt64Array");
+  }
+  const out = new Int32Array(arr.length);
+  const view = new Int32Array(arr.buffer);
+  for (let i2 = 0; i2 < arr.length; i2++) {
+    out[i2] = view[i2 * 2];
+  }
+  return out;
+}
+const maybeDowncastInt64 = (data2) => {
+  try {
+    return convertBigInt64ArrayToInt32Array(data2);
+  } catch (error2) {
+    if (error2 instanceof IncorrectDataTypeError) {
+      return data2;
+    }
+    throw error2;
+  }
+};
 const concatenateColumnVectors = (arr) => {
   const numCols = arr.length;
   const numRows = arr[0].length;
@@ -265305,6 +265339,7 @@ const concatenateColumnVectors = (arr) => {
   }
   return new TypedArray2(view.buffer);
 };
+const toObject = (data2) => ({ data: data2 });
 class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
   getOptions() {
     return this.options;
@@ -265404,9 +265439,10 @@ class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
       const { data: rowIndices } = await get$6(indexArr, [
         slice$4(startRowIndex, endRowIndex)
       ]);
-      const { data: cellXGeneData } = await get$6(cellXGeneArr, [
+      let { data: cellXGeneData } = await get$6(cellXGeneArr, [
         slice$4(startRowIndex, endRowIndex)
       ]);
+      cellXGeneData = maybeDowncastInt64(cellXGeneData);
       for (let rowIndex = 0; rowIndex < rowIndices.length; rowIndex += 1) {
         geneData[rowIndices[rowIndex]] = cellXGeneData[rowIndex];
       }
@@ -265443,10 +265479,11 @@ class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
     this._sparseMatrix = this._openSparseArrays().then(async (sparseArrays) => {
       const { path: matrix2 } = this.getOptions();
       const { shape: shape2 } = await this.dataSource.getJson(`${matrix2}/.zattrs`);
-      const [rows, cols, cellXGene] = await Promise.all(sparseArrays.map(async (arr) => {
+      let [rows, cols, cellXGene] = await Promise.all(sparseArrays.map(async (arr) => {
         const { data: data2 } = await createZarrArrayAdapter(arr).getRaw(null);
         return data2;
       }));
+      cellXGene = maybeDowncastInt64(cellXGene);
       const cellXGeneMatrix = new Float32Array(shape2[0] * shape2[1]).fill(0);
       let row = 0;
       rows.forEach((_, index2) => {
@@ -265474,10 +265511,11 @@ class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
     this._sparseMatrix = this._openSparseArrays().then(async (sparseArrays) => {
       const { path: matrix2 } = this.getOptions();
       const { shape: shape2 } = await this.dataSource.getJson(`${matrix2}/.zattrs`);
-      const [cols, rows, cellXGene] = await Promise.all(sparseArrays.map(async (arr) => {
+      let [cols, rows, cellXGene] = await Promise.all(sparseArrays.map(async (arr) => {
         const { data: data2 } = await createZarrArrayAdapter(arr).getRaw(null);
         return data2;
       }));
+      cellXGene = maybeDowncastInt64(cellXGene);
       const cellXGeneMatrix = new Float32Array(shape2[0] * shape2[1]).fill(0);
       let col = 0;
       cols.forEach((_, index2) => {
@@ -265517,7 +265555,7 @@ class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
         if (!this.arr) {
           this.arr = open(storeRoot.resolve(matrix2), { kind: "array" });
         }
-        this.cellXGene = this.arr.then((z2) => createZarrArrayAdapter(z2).getRaw(null)).then(({ data: data2 }) => toObject(data2));
+        this.cellXGene = this.arr.then((z2) => createZarrArrayAdapter(z2).getRaw(null)).then(({ data: data2 }) => toObject(maybeDowncastInt64(data2)));
       }
     } else if (encodingType === "csr_matrix") {
       this.cellXGene = this._loadCSRSparseCellXGene().then(async (cellXGene) => {
@@ -265564,7 +265602,7 @@ class ObsFeatureMatrixAnndataLoader extends AbstractTwoStepLoader {
         this.arr = open(storeRoot.resolve(matrix2), { kind: "array" });
       }
       const indices = await this._getGeneIndices(selection);
-      genes = await Promise.all(indices.map((index2) => this.arr.then((z2) => get$6(z2, [null, index2])).then(({ data: data2 }) => data2)));
+      genes = await Promise.all(indices.map((index2) => this.arr.then((z2) => get$6(z2, [null, index2])).then(({ data: data2 }) => maybeDowncastInt64(data2))));
     }
     return { data: genes, url: null };
   }
@@ -266609,8 +266647,8 @@ class GenomicProfilesZarrLoader extends AbstractTwoStepLoader {
     return this.attrs;
   }
   load() {
-    const { url } = this;
-    return this.loadAttrs().then((attrs) => Promise.resolve(new LoaderResult(attrs, url)));
+    const { url, requestInit: requestInit2 } = this;
+    return this.loadAttrs().then((attrs) => Promise.resolve(new LoaderResult(attrs, url, null, requestInit2)));
   }
 }
 class OmeTiffSource {

package/dist/index.js

@@ -1,4 +1,4 @@
-import { f, P, h, d, V, z } from "./index-b2bb1d08.js";
+import { f, P, h, d, V, z } from "./index-ac567918.js";
 import { useCoordination } from "@vitessce/vit-s";
 import "react";
 import "react-dom";

package/dist/{jpeg-7e1ceac4.js → jpeg-94fc740e.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-54fe9485.js → lerc-1fa73516.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-b2bb1d08.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder, L as LercParameters, a as LercAddCompression } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-67b71961.js → lzw-fbdbcd71.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-d95ea21b.js → packbits-440a0758.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-221c7288.js → raw-306e279c.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-e90de519.js → webimage-6f012708.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-b2bb1d08.js";
+import { B as BaseDecoder } from "./index-ac567918.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.3.10",
+  "version": "3.3.12",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,27 +18,27 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.3.10",
-    "@vitessce/csv": "3.3.10",
-    "@vitessce/description": "3.3.10",
-    "@vitessce/feature-list": "3.3.10",
-    "@vitessce/genomic-profiles": "3.3.10",
-    "@vitessce/heatmap": "3.3.10",
-    "@vitessce/json": "3.3.10",
-    "@vitessce/layer-controller": "3.3.10",
-    "@vitessce/layer-controller-beta": "3.3.10",
-    "@vitessce/obs-sets-manager": "3.3.10",
-    "@vitessce/ome-tiff": "3.3.10",
-    "@vitessce/plugins": "3.3.10",
-    "@vitessce/scatterplot-gating": "3.3.10",
-    "@vitessce/schemas": "3.3.10",
-    "@vitessce/scatterplot-embedding": "3.3.10",
-    "@vitessce/spatial": "3.3.10",
-    "@vitessce/statistical-plots": "3.3.10",
-    "@vitessce/status": "3.3.10",
-    "@vitessce/spatial-beta": "3.3.10",
-    "@vitessce/zarr": "3.3.10",
-    "@vitessce/vit-s": "3.3.10"
+    "@vitessce/constants-internal": "3.3.12",
+    "@vitessce/csv": "3.3.12",
+    "@vitessce/feature-list": "3.3.12",
+    "@vitessce/genomic-profiles": "3.3.12",
+    "@vitessce/description": "3.3.12",
+    "@vitessce/heatmap": "3.3.12",
+    "@vitessce/layer-controller": "3.3.12",
+    "@vitessce/layer-controller-beta": "3.3.12",
+    "@vitessce/json": "3.3.12",
+    "@vitessce/obs-sets-manager": "3.3.12",
+    "@vitessce/plugins": "3.3.12",
+    "@vitessce/scatterplot-embedding": "3.3.12",
+    "@vitessce/ome-tiff": "3.3.12",
+    "@vitessce/schemas": "3.3.12",
+    "@vitessce/scatterplot-gating": "3.3.12",
+    "@vitessce/spatial": "3.3.12",
+    "@vitessce/spatial-beta": "3.3.12",
+    "@vitessce/statistical-plots": "3.3.12",
+    "@vitessce/status": "3.3.12",
+    "@vitessce/zarr": "3.3.12",
+    "@vitessce/vit-s": "3.3.12"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",