@genome-spy/core 0.72.0 → 0.74.0

package/dist/src/data/sources/urlSource.js

@@ -1,5 +1,5 @@
 import { read } from "vega-loader";
-import { getFormat, responseType } from "./dataUtils.js";
+import { getFormat, hasGzipExtension, responseType } from "./dataUtils.js";
 import DataSource from "./dataSource.js";
 import {
     activateExprRefProps,
@@ -7,14 +7,13 @@ import {
 } from "../../paramRuntime/paramUtils.js";
 import { concatUrl } from "../../utils/url.js";
 
+const gzipMimeTypes = new Set(["application/gzip", "application/x-gzip"]);
+const textDecoder = new TextDecoder();
+
 /**
- * @param {Partial<import("../../spec/data.js").Data>} data
- * @returns {data is import("../../spec/data.js").UrlData}
+ * Loads eager data from URLs and transparently decompresses gzip-compatible
+ * payloads before handing them to the registered format reader.
  */
-export function isUrlData(data) {
-    return "url" in data;
-}
-
 export default class UrlSource extends DataSource {
     /**
      * @param {import("../../spec/data.js").UrlData} params
@@ -48,6 +47,7 @@ export default class UrlSource extends DataSource {
      */
     async #loadUrlsFromFile(props) {
         const listUrl = concatUrl(this.baseUrl, props.urlsFromFile);
+        const format = { type: props.type ?? "tsv" };
 
         const result = await fetch(listUrl);
 
@@ -56,10 +56,14 @@ export default class UrlSource extends DataSource {
                 `Cannot load "${listUrl}": ${result.status} ${result.statusText}`
             );
         }
-        const text = await result.text();
+        const content = await readResponseBody(
+            result,
+            listUrl,
+            responseType(format.type)
+        );
 
         const files = /** @type {string[] | {url: string}[]} */ (
-            read(text, { type: props.type ?? "tsv" })
+            read(content, format)
         )
             .map((u) => (typeof u === "string" ? u : u.url))
             .map((u) => concatUrl(listUrl, u));
@@ -94,14 +98,11 @@ export default class UrlSource extends DataSource {
                 if (!result.ok) {
                     throw new Error(`${result.status} ${result.statusText}`);
                 }
-                // @ts-ignore
-                return typeof result[type] == "function"
-                    ? // @ts-ignore
-                      result[type]()
-                    : result.text();
+                return await readResponseBody(result, url, type);
             } catch (e) {
                 throw new Error(
-                    `Could not load data: ${url}. Reason: ${e.message}`
+                    `Could not load data: ${url}. Reason: ${e.message}`,
+                    { cause: e }
                 );
             }
         };
@@ -124,7 +125,9 @@ export default class UrlSource extends DataSource {
                 }
             } catch (e) {
                 console.warn(e);
-                throw new Error(`Cannot parse: ${url}: ${e.message}`);
+                throw new Error(`Cannot parse: ${url}: ${e.message}`, {
+                    cause: e,
+                });
             }
         };
 
@@ -140,3 +143,122 @@ export default class UrlSource extends DataSource {
         this.complete();
     }
 }
+
+/**
+ * @param {Partial<import("../../spec/data.js").Data>} data
+ * @returns {data is import("../../spec/data.js").UrlData}
+ */
+export function isUrlData(data) {
+    return "url" in data;
+}
+
+/**
+ * @param {Uint8Array} bytes
+ */
+function hasGzipMagic(bytes) {
+    return (
+        bytes.length >= 10 &&
+        bytes[0] == 0x1f &&
+        bytes[1] == 0x8b &&
+        bytes[2] == 0x08 &&
+        (bytes[3] & 0xe0) == 0
+    );
+}
+
+/**
+ * @param {string | null} contentType
+ */
+function isGzipMimeType(contentType) {
+    if (!contentType) {
+        return false;
+    }
+
+    return gzipMimeTypes.has(contentType.split(";")[0].trim().toLowerCase());
+}
+
+/**
+ * @param {string | null} contentEncoding
+ */
+function hasGzipContentEncoding(contentEncoding) {
+    if (!contentEncoding) {
+        return false;
+    }
+
+    return contentEncoding
+        .toLowerCase()
+        .split(",")
+        .some((encoding) => encoding.trim() == "gzip");
+}
+
+/**
+ * @param {Uint8Array} bytes
+ * @returns {ArrayBuffer}
+ */
+function toArrayBuffer(bytes) {
+    return new Uint8Array(bytes).buffer;
+}
+
+/**
+ * @param {Uint8Array} bytes
+ */
+async function decompressGzip(bytes) {
+    if (typeof DecompressionStream != "function") {
+        throw new Error(
+            "Gzip-compressed URL data requires DecompressionStream support."
+        );
+    }
+
+    const body = new Response(toArrayBuffer(bytes)).body;
+    if (!body) {
+        throw new Error(
+            "Cannot create a readable stream for gzip decompression."
+        );
+    }
+
+    const stream = body.pipeThrough(new DecompressionStream("gzip"));
+    return new Uint8Array(await new Response(stream).arrayBuffer());
+}
+
+/**
+ * @param {Response} response
+ * @param {string} url
+ * @param {string} type
+ */
+async function readResponseBody(response, url, type) {
+    const gzipHint =
+        hasGzipExtension(url) ||
+        isGzipMimeType(response.headers.get("content-type")) ||
+        hasGzipContentEncoding(response.headers.get("content-encoding"));
+
+    if (!gzipHint) {
+        return readResponseUsingType(response, type);
+    }
+
+    const bytes = new Uint8Array(await response.arrayBuffer());
+    const bodyBytes = hasGzipMagic(bytes) ? await decompressGzip(bytes) : bytes;
+    return deserializeBytes(bodyBytes, type);
+}
+
+/**
+ * @param {Response} response
+ * @param {string} type
+ */
+function readResponseUsingType(response, type) {
+    // @ts-ignore
+    return typeof response[type] == "function"
+        ? // @ts-ignore
+          response[type]()
+        : response.text();
+}
+
+/**
+ * @param {Uint8Array} bytes
+ * @param {string} type
+ */
+function deserializeBytes(bytes, type) {
+    if (type == "arrayBuffer") {
+        return toArrayBuffer(bytes);
+    } else {
+        return textDecoder.decode(bytes);
+    }
+}

package/dist/src/data/transforms/aggregate.d.ts

@@ -16,6 +16,7 @@ export default class AggregateTransform extends Transform {
      * @type {string[]}
      */
     as: string[];
+    #private;
 }
 import Transform from "./transform.js";
 //# sourceMappingURL=aggregate.d.ts.map

package/dist/src/data/transforms/aggregate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,KAFU,CAAC,CAAC,GAAG,EAAE,gCAAO,KAAK,MAAM,CAAC,EAAE,CAEzB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;CAiFnB;sBA5GqB,gBAAgB"}
+{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,KAFU,CAAC,CAAC,GAAG,EAAE,gCAAO,KAAK,MAAM,CAAC,EAAE,CAEzB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;;CAuGnB;sBAlIqB,gBAAgB"}

package/dist/src/data/transforms/aggregate.js

@@ -64,16 +64,10 @@ export default class AggregateTransform extends Transform {
     }
 
     /**
-     *
-     * @param {import("../flowNode.js").Datum} datum
+     * Propagate the current buffer as one aggregated batch.
      */
-    handle(datum) {
-        this.buffer.push(datum);
-    }
-
-    complete() {
+    #flushBuffer() {
         const params = this.params;
-
         const groupby = params?.groupby;
 
         if (groupby?.length > 0) {
@@ -107,6 +101,34 @@ export default class AggregateTransform extends Transform {
 
             this._propagate(datum);
         }
+    }
+
+    /**
+     *
+     * @param {import("../flowNode.js").Datum} datum
+     */
+    handle(datum) {
+        this.buffer.push(datum);
+    }
+
+    /**
+     * Flush the current batch before downstream nodes switch to a new facet.
+     *
+     * @param {import("../../types/flowBatch.js").FlowBatch} flowBatch
+     */
+    beginBatch(flowBatch) {
+        if (this.buffer.length > 0) {
+            this.#flushBuffer();
+            this.buffer = [];
+        }
+
+        super.beginBatch(flowBatch);
+    }
+
+    complete() {
+        if (this.buffer.length > 0) {
+            this.#flushBuffer();
+        }
 
         super.complete();
     }

package/dist/src/data/transforms/aggregateOps.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAEA;;GAEG;AACH,6BAFU,MAAM,CAAC,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAWxH"}
+{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAWA;;GAEG;AACH,6BAFU,MAAM,CAAC,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAaxH"}

package/dist/src/data/transforms/aggregateOps.js

@@ -1,4 +1,13 @@
-import { count, max, mean, median, min, sum, variance } from "d3-array";
+import {
+    count,
+    max,
+    mean,
+    median,
+    min,
+    quantile,
+    sum,
+    variance,
+} from "d3-array";
 
 /**
  * @type {Record<import("../../spec/transform.js").AggregateOp, (arr: any[], accessor?: (datum: any) => number) => number>}
@@ -10,7 +19,9 @@ const AGGREGATE_OPS = {
     min,
     max,
     mean,
+    q1: (arr, accessor) => quantile(arr, 0.25, accessor),
     median,
+    q3: (arr, accessor) => quantile(arr, 0.75, accessor),
     variance,
 };
 

package/dist/src/data/transforms/coverage.js

@@ -147,7 +147,7 @@ export default class CoverageTransform extends Transform {
         };
 
         const flushQueue = () => {
-            let edge = 0;
+            let edge;
             while ((edge = ends.peekValue()) !== undefined) {
                 pushSegment(prevEdge, edge, coverage);
                 prevEdge = edge;
@@ -166,7 +166,7 @@ export default class CoverageTransform extends Transform {
         this.handle = (datum) => {
             const start = startAccessor(datum);
 
-            let edge = 0;
+            let edge;
             while ((edge = ends.peekValue()) !== undefined && edge < start) {
                 pushSegment(prevEdge, edge, coverage);
                 prevEdge = edge;

package/dist/src/data/transforms/filter.js

@@ -17,7 +17,7 @@ export default class FilterTransform extends Transform {
     }
 
     initialize() {
-        let expression = "";
+        let expression;
 
         if (isExprFilterParams(this.params)) {
             expression = this.params.expr;

package/dist/src/data/transforms/filterScoredLabels.d.ts

@@ -5,6 +5,12 @@ export default class FilterScoredLabelsTransform extends Transform {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params: import("../../spec/transform.js").FilterScoredLabelsParams, view: import("../../view/view.js").default);
+    /**
+     * The transform emits only labels that fit in the current visible interval,
+     * so downstream x/y values derived from its output must not feed back into
+     * shared-domain resolution.
+     */
+    get domainSensitiveScaleChannels(): ("x" | "y")[];
     params: import("../../spec/transform.js").FilterScoredLabelsParams;
     /** @type {any[]} */
     _data: any[];

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAkD9C;IA7CG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA8B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBAhKqB,gBAAgB;2BAFX,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAcI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAkD9C;IA9DD;;;;OAIG;IACH,kDAEC;IAUG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA8B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBAzKqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -10,6 +10,15 @@ export default class FilterScoredLabelsTransform extends Transform {
         return BEHAVIOR_COLLECTS;
     }
 
+    /**
+     * The transform emits only labels that fit in the current visible interval,
+     * so downstream x/y values derived from its output must not feed back into
+     * shared-domain resolution.
+     */
+    get domainSensitiveScaleChannels() {
+        return [this.channel];
+    }
+
     /**
      *
      * @param {import("../../spec/transform.js").FilterScoredLabelsParams} params

package/dist/src/data/transforms/measureText.d.ts

@@ -14,6 +14,7 @@ export default class MeasureTextTransform extends Transform {
      * @param {any} datum
      */
     handle: (datum: any) => void;
+    font: import("../../fonts/bmFontManager.js").FontEntry;
 }
 import Transform from "./transform.js";
 //# sourceMappingURL=measureText.d.ts.map

package/dist/src/data/transforms/measureText.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"measureText.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/measureText.js"],"names":[],"mappings":"AAOA;;GAEG;AACH;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,iBAAiB,wBACnD,OAAO,gBAAgB,EAAE,oBAAoB,EA8CvD;IAzCG,4DAAoB;IA4BpB;;;OAGG;IACH,gBAFW,GAAG,UAUb;CAER;sBA7DqB,gBAAgB"}
+{"version":3,"file":"measureText.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/measureText.js"],"names":[],"mappings":"AAKA;;GAEG;AACH;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,iBAAiB,wBACnD,OAAO,gBAAgB,EAAE,oBAAoB,EA4CvD;IAvCG,4DAAoB;IA0BpB;;;OAGG;IACH,gBAFW,GAAG,UAUb;IAOD,uDAMkC;CAEzC;sBAxEqB,gBAAgB"}

package/dist/src/data/transforms/measureText.js

@@ -1,6 +1,4 @@
 import { BEHAVIOR_MODIFIES } from "../flowNode.js";
-import fontMetadata from "../../fonts/Lato-Regular.json" with { type: "json" };
-import getMetrics from "../../fonts/bmFontMetrics.js";
 import { field } from "../../utils/field.js";
 import Transform from "./transform.js";
 import { isExprRef } from "../../paramRuntime/paramUtils.js";
@@ -23,10 +21,8 @@ export default class MeasureTextTransform extends Transform {
 
         this.params = params;
 
-        const metrics = getMetrics(fontMetadata);
         const accessor = field(params.field);
         const as = params.as;
-        // TODO: Support custom fonts.
 
         let size = 0;
 
@@ -56,11 +52,24 @@ export default class MeasureTextTransform extends Transform {
         this.handle = (datum) => {
             const text = accessor(datum);
             if (text !== undefined) {
-                datum[as] = metrics.measureWidth(text, size);
+                datum[as] = this.font.metrics.measureWidth(text, size);
             } else {
                 datum[as] = 0;
             }
             this._propagate(datum);
         };
     }
+
+    initialize() {
+        const fontManager = this.paramRuntimeProvider.context.fontManager;
+        // Resolve the font during flow initialization so viewDataInit's global
+        // font wait also covers measureText before any rows are propagated.
+        this.font = this.params.font
+            ? fontManager.getFont(
+                  this.params.font,
+                  this.params.fontStyle,
+                  this.params.fontWeight
+              )
+            : fontManager.getDefaultFont();
+    }
 }

package/dist/src/data/transforms/pileup.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pileup.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/pileup.js"],"names":[],"mappings":"AASA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,YAAY,EAMxD;IADG,uDAAoB;CAyG3B;sBAzHqB,gBAAgB"}
+{"version":3,"file":"pileup.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/pileup.js"],"names":[],"mappings":"AAQA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,YAAY,EAMxD;IADG,uDAAoB;CAyG3B;sBAzHqB,gBAAgB"}

package/dist/src/data/transforms/pileup.js

@@ -1,4 +1,3 @@
-/* eslint-disable no-unmodified-loop-condition */
 import FlatQueue from "flatqueue";
 import { isNumber } from "vega-util";
 import { field } from "../../utils/field.js";
@@ -68,7 +67,7 @@ export default class PileupTransform extends Transform {
                 const preferredLane = preferredOrder.indexOf(
                     preferenceAccessor(datum)
                 );
-                let lane = -1;
+                let lane;
                 if (preferredLane >= 0 && freeLaneMap[preferredLane] < start) {
                     lane = preferredLane;
                 } else {

package/dist/src/data/transforms/regexFold.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"regexFold.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/regexFold.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,eAAe,EA6I3D;IAxIG,0DAAoB;IAyHhB,gBALO,GAAG,UAKe;CAgBpC;sBA3JqB,gBAAgB"}
+{"version":3,"file":"regexFold.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/regexFold.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,eAAe,EA4I3D;IAvIG,0DAAoB;IAwHhB,gBALO,GAAG,UAKe;CAgBpC;sBA1JqB,gBAAgB"}

package/dist/src/data/transforms/regexFold.js

@@ -107,7 +107,6 @@ export default class RegexFoldTransform extends Transform {
                 ...as.map((a, i) => JSON.stringify(a) + `: datum[attrs[${i}]]`),
             ];
 
-            // eslint-disable-next-line no-new-func
             create = /** @type {any} */ (
                 new Function(
                     "datum",

package/dist/src/embedFactory.d.ts

@@ -0,0 +1,13 @@
+/**
+ * @param {new (container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions) => import("./genomeSpy.js").default} GenomeSpy
+ * @returns {(el: HTMLElement | string, spec: import("./spec/root.js").RootSpec | string, options?: import("./types/embedApi.js").EmbedOptions) => Promise<import("./types/embedApi.js").EmbedResult>}
+ */
+export function createEmbed(GenomeSpy: new (container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions) => import("./genomeSpy.js").default): (el: HTMLElement | string, spec: import("./spec/root.js").RootSpec | string, options?: import("./types/embedApi.js").EmbedOptions) => Promise<import("./types/embedApi.js").EmbedResult>;
+/**
+ * Loads the spec from the given url and sets the baseUrl if it is not
+ * defined in the spec.
+ *
+ * @param {string} url
+ */
+export function loadSpec(url: string): Promise<any>;
+//# sourceMappingURL=embedFactory.d.ts.map

package/dist/src/embedFactory.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"embedFactory.d.ts","sourceRoot":"","sources":["../../src/embedFactory.js"],"names":[],"mappings":"AAKA;;;GAGG;AACH,uCAHW,KAAK,SAAS,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,gBAAgB,EAAE,OAAO,GAC7J,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,GAAG,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,CAAC,OAAO,qBAAqB,EAAE,WAAW,CAAC,CAmFpM;AAaD;;;;;GAKG;AACH,8BAFW,MAAM,gBAmBhB"}

package/dist/src/embedFactory.js

@@ -0,0 +1,127 @@
+import { isObject, isString } from "vega-util";
+
+import { fetchJson } from "./utils/fetchUtils.js";
+import inferSpecBaseUrl from "./utils/inferSpecBaseUrl.js";
+
+/**
+ * @param {new (container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions) => import("./genomeSpy.js").default} GenomeSpy
+ * @returns {(el: HTMLElement | string, spec: import("./spec/root.js").RootSpec | string, options?: import("./types/embedApi.js").EmbedOptions) => Promise<import("./types/embedApi.js").EmbedResult>}
+ */
+export function createEmbed(GenomeSpy) {
+    /**
+     * Embeds GenomeSpy into the DOM
+     *
+     * @param {HTMLElement | string} el
+     * @param {import("./spec/root.js").RootSpec | string} spec
+     * @param {import("./types/embedApi.js").EmbedOptions} [options]
+     * @returns {Promise<import("./types/embedApi.js").EmbedResult>}
+     */
+    return async function embed(el, spec, options = {}) {
+        /** @type {HTMLElement} */
+        let element;
+
+        if (isString(el)) {
+            element = document.querySelector(el);
+            if (!element) {
+                throw new Error(`No such element: ${el}`);
+            }
+        } else if (el instanceof HTMLElement) {
+            element = el;
+        } else {
+            throw new Error(`Invalid element: ${el}`);
+        }
+
+        /** @type {InstanceType<typeof GenomeSpy> | undefined} */
+        let genomeSpy;
+
+        try {
+            const specObject = isObject(spec) ? spec : await loadSpec(spec);
+
+            specObject.baseUrl ??= "";
+            specObject.width ??= "container";
+            specObject.padding ??= 10;
+
+            if (element == document.body) {
+                // Need to add a wrapper to make sizing behavior more stable
+                const wrapper = document.createElement("div");
+                wrapper.style.position = "fixed";
+                wrapper.style.inset = "0";
+                wrapper.style.overflow = "hidden";
+                element.appendChild(wrapper);
+                element = wrapper;
+            }
+
+            genomeSpy = new GenomeSpy(element, specObject, options);
+            applyOptions(genomeSpy, options);
+            await genomeSpy.launch();
+        } catch (e) {
+            element.innerText = e.toString();
+            console.error(e);
+        }
+
+        return {
+            finalize() {
+                genomeSpy.destroy();
+                while (element.firstChild) {
+                    element.firstChild.remove();
+                }
+            },
+
+            addEventListener(type, listener) {
+                genomeSpy.addEventListener(type, listener);
+            },
+
+            removeEventListener(type, listener) {
+                genomeSpy.removeEventListener(type, listener);
+            },
+
+            getScaleResolutionByName(name) {
+                return genomeSpy.getNamedScaleResolutions().get(name);
+            },
+
+            awaitVisibleLazyData:
+                genomeSpy.awaitVisibleLazyData.bind(genomeSpy),
+            getRenderedBounds: genomeSpy.getRenderedBounds.bind(genomeSpy),
+            updateNamedData: genomeSpy.updateNamedData.bind(genomeSpy),
+            getLogicalCanvasSize:
+                genomeSpy.getLogicalCanvasSize.bind(genomeSpy),
+            exportCanvas: genomeSpy.exportCanvas.bind(genomeSpy),
+        };
+    };
+}
+
+/**
+ *
+ * @param {import("./genomeSpy.js").default} genomeSpy
+ * @param {import("./types/embedApi.js").EmbedOptions} options options
+ */
+function applyOptions(genomeSpy, options) {
+    if (options.namedDataProvider) {
+        genomeSpy.registerNamedDataProvider(options.namedDataProvider);
+    }
+}
+
+/**
+ * Loads the spec from the given url and sets the baseUrl if it is not
+ * defined in the spec.
+ *
+ * @param {string} url
+ */
+export async function loadSpec(url) {
+    let spec;
+
+    try {
+        spec = /** @type {any} */ (await fetchJson(url));
+    } catch (e) {
+        throw new Error(
+            `Could not load or parse configuration: ${url}, reason: ${e.message}`,
+            { cause: e }
+        );
+    }
+
+    if (!spec.baseUrl) {
+        spec.baseUrl = inferSpecBaseUrl(url);
+    }
+
+    return spec;
+}

package/dist/src/encoder/accessor.d.ts

@@ -1,4 +1,7 @@
 /**
+ * Creates a raw accessor for a single channel definition branch and attaches
+ * metadata used by scale resolution and equality checks.
+ *
  * @param {import("../spec/channel.js").Channel} channel
  * @param {import("../spec/channel.js").ChannelDef | import("../spec/channel.js").Conditional<import("../spec/channel.js").ChannelDef>} channelDef
  * @param {{ createExpression: (expr: string) => import("../paramRuntime/types.js").ExprRefFunction }} paramRuntime
@@ -7,18 +10,6 @@
 export function createAccessor(channel: import("../spec/channel.js").Channel, channelDef: import("../spec/channel.js").ChannelDef | import("../spec/channel.js").Conditional<import("../spec/channel.js").ChannelDef>, paramRuntime: {
     createExpression: (expr: string) => import("../paramRuntime/types.js").ExprRefFunction;
 }): import("../types/encoder.js").Accessor;
-/**
- * Returns an array of acessors and their predicates. A returned array with
- * a single element indicates that no conditions are present.
- * The default accessor is always the last element in the array.
- *
- * @param {import("../spec/channel.js").Channel} channel
- * @param {import("../spec/channel.js").ChannelDef} channelDef
- * @param {{ createExpression: (expr: string) => import("../paramRuntime/types.js").ExprRefFunction }} paramRuntime
- */
-export function createConditionalAccessors(channel: import("../spec/channel.js").Channel, channelDef: import("../spec/channel.js").ChannelDef, paramRuntime: {
-    createExpression: (expr: string) => import("../paramRuntime/types.js").ExprRefFunction;
-}): import("../types/encoder.js").Accessor<import("../spec/channel.js").Scalar>[];
 /**
  * @param {import("../types/encoder.js").Accessor} accessor
  * @returns {accessor is import("../types/encoder.js").ScaleAccessor}

package/dist/src/encoder/accessor.d.ts.map

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