@genome-spy/core 0.45.0 → 0.46.1

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

@@ -16,6 +16,10 @@ export default class CoverageTransform extends FlowNode {
         return BEHAVIOR_CLONES;
     }
 
+    /**
+     * @typedef {import("../flowNode.js").Datum} Datum
+     */
+
     /**
      * @param {import("../../spec/transform.js").CoverageParams} params
      */
@@ -34,30 +38,30 @@ export default class CoverageTransform extends FlowNode {
         this.weightAccessor = params.weight ? field(params.weight) : (d) => 1;
 
         this.as = {
-            coverage: params.as || "coverage",
-            start: params.asStart || params.start,
-            end: params.asEnd || params.end,
-            chrom: params.asChrom || params.chrom,
+            coverage: params.as ?? "coverage",
+            start: params.asStart ?? params.start,
+            end: params.asEnd ?? params.end,
+            chrom: params.asChrom ?? params.chrom,
         };
 
-        // eslint-disable-next-line no-new-func
-        this.createSegment = /** @type {function} */ (
-            new Function(
-                "start",
-                "end",
-                "coverage",
-                "chrom",
-                "return {" +
-                    Object.entries(this.as)
-                        .filter(([param, prop]) => prop)
-                        .map(
-                            ([param, prop]) =>
-                                `${JSON.stringify(prop)}: ${param}`
-                        )
-                        .join(", ") +
-                    "};"
-            )
-        );
+        this.createSegment =
+            /** @type {(start: Number, end: Number, coverage: Number, chrom?: string) => Datum} */ (
+                new Function(
+                    "start",
+                    "end",
+                    "coverage",
+                    "chrom",
+                    "return {" +
+                        Object.entries(this.as)
+                            .filter(([param, prop]) => prop)
+                            .map(
+                                ([param, prop]) =>
+                                    `${JSON.stringify(prop)}: ${param}`
+                            )
+                            .join(", ") +
+                        "};"
+                )
+            );
 
         /**
          * End pos as priority, weight as value
@@ -82,7 +86,7 @@ export default class CoverageTransform extends FlowNode {
         const chromAccessor = this.chromAccessor;
         const weightAccessor = this.weightAccessor;
 
-        /** @type {import("../flowNode.js").Datum} used for merging adjacent segment */
+        /** @type {Datum} used for merging adjacent segment */
         let bufferedSegment;
 
         /** @type {string} */
@@ -96,12 +100,20 @@ export default class CoverageTransform extends FlowNode {
         let coverage = 0;
 
         /** @type {number} */
-        let prevEdge;
+        let prevEdge = NaN;
 
         /** End pos as priority, weight as value */
         const ends = this.ends;
         ends.clear();
 
+        /**
+         * @param {Datum} segment
+         */
+        const propagate = (segment) => {
+            this._propagate(segment);
+            bufferedSegment = null;
+        };
+
         /**
          * @param {number} start
          * @param {number} end
@@ -119,7 +131,7 @@ export default class CoverageTransform extends FlowNode {
                     bufferedSegment[asEnd] = end;
                     extended = true;
                 } else if (bufferedSegment[asCoverage] != 0) {
-                    this._propagate(bufferedSegment);
+                    propagate(bufferedSegment);
                 }
             }
 
@@ -140,15 +152,16 @@ export default class CoverageTransform extends FlowNode {
                 prevEdge = edge;
                 coverage -= ends.pop();
             }
-            prevEdge = undefined;
+            prevEdge = NaN;
 
             if (bufferedSegment) {
-                this._propagate(bufferedSegment);
-                bufferedSegment = undefined;
+                propagate(bufferedSegment);
             }
         };
 
-        /** @param {Record<string, any>} datum */
+        /**
+         * @param {Datum} datum
+         */
         this.handle = (datum) => {
             const start = startAccessor(datum);
 
@@ -168,7 +181,7 @@ export default class CoverageTransform extends FlowNode {
                 }
             }
 
-            if (prevEdge !== undefined) {
+            if (!isNaN(prevEdge)) {
                 pushSegment(prevEdge, start, coverage);
             }
             prevEdge = start;
@@ -189,7 +202,7 @@ export default class CoverageTransform extends FlowNode {
          */
         this.beginBatch = (flowBatch) => {
             flushQueue();
-            prevChrom = undefined;
+            prevChrom = null;
             super.beginBatch(flowBatch);
         };
     }

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

@@ -2,11 +2,12 @@ export default class FilterTransform extends FlowNode {
     /**
      *
      * @param {import("../../spec/transform.js").FilterParams} params
+     * @param {import("../flowNode.js").ParamMediatorProvider} paramMediatorProvider
      */
-    constructor(params: import("../../spec/transform.js").FilterParams);
+    constructor(params: import("../../spec/transform.js").FilterParams, paramMediatorProvider: import("../flowNode.js").ParamMediatorProvider);
     params: import("../../spec/transform.js").FilterParams;
-    /** @type {(datum: any) => boolean} */
-    predicate: (datum: any) => boolean;
+    /** @type {import("../../view/paramMediator.js").ExprRefFunction} */
+    predicate: import("../../view/paramMediator.js").ExprRefFunction;
 }
 import FlowNode from "../flowNode.js";
 //# sourceMappingURL=filter.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AAGA;IACI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,YAAY,EAQxD;IAJG,uDAAoB;IAEpB,sCAAsC;IACtC,mBADmB,GAAG,KAAK,OAAO,CACR;CAmBjC;qBA/BoB,gBAAgB"}
+{"version":3,"file":"filter.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filter.js"],"names":[],"mappings":"AAEA;IACI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,YAAY,yBAC9C,OAAO,gBAAgB,EAAE,qBAAqB,EASxD;IAJG,uDAAoB;IAEpB,oEAAoE;IACpE,WADW,OAAO,6BAA6B,EAAE,eAAe,CACtC;CAiBjC;qBA/BoB,gBAAgB"}

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

@@ -1,24 +1,23 @@
-import createFunction from "../../utils/expression.js";
 import FlowNode from "../flowNode.js";
 
 export default class FilterTransform extends FlowNode {
     /**
      *
      * @param {import("../../spec/transform.js").FilterParams} params
+     * @param {import("../flowNode.js").ParamMediatorProvider} paramMediatorProvider
      */
-    constructor(params) {
-        super();
+    constructor(params, paramMediatorProvider) {
+        super(paramMediatorProvider);
+
         this.params = params;
 
-        /** @type {(datum: any) => boolean} */
+        /** @type {import("../../view/paramMediator.js").ExprRefFunction} */
         this.predicate = undefined;
     }
 
     initialize() {
-        this.predicate = createFunction(
-            this.params.expr,
-            this.getGlobalObject()
-        );
+        this.predicate = this.paramMediator.createExpression(this.params.expr);
+        this.predicate.addListener(() => this.repropagate());
     }
 
     /**

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

@@ -1,7 +1,9 @@
 import { expect, test } from "vitest";
-import { processData } from "../flowTestUtils.js";
+import { makeParamMediatorProvider, processData } from "../flowTestUtils.js";
 import FilterTransform from "./filter.js";
 
+test.todo("Implement stub for ParamMediator");
+
 test("FilterTransform filter rows", () => {
     const data = [1, 2, 3, 4, 5, 6].map((x) => ({ x }));
 
@@ -11,7 +13,7 @@ test("FilterTransform filter rows", () => {
         expr: "datum.x > 3 && datum.x != 5",
     };
 
-    const t = new FilterTransform(filterParams);
+    const t = new FilterTransform(filterParams, makeParamMediatorProvider());
     t.initialize();
 
     expect(processData(t, data)).toEqual([4, 6].map((x) => ({ x })));

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

@@ -2,12 +2,13 @@ export default class FormulaTransform extends FlowNode {
     /**
      *
      * @param {import("../../spec/transform.js").FormulaParams} params
+     * @param {import("../flowNode.js").ParamMediatorProvider} paramMediatorProvider
      */
-    constructor(params: import("../../spec/transform.js").FormulaParams);
+    constructor(params: import("../../spec/transform.js").FormulaParams, paramMediatorProvider: import("../flowNode.js").ParamMediatorProvider);
     params: import("../../spec/transform.js").FormulaParams;
     as: string;
-    /** @type {(datum: any) => any} */
-    fn: (datum: any) => any;
+    /** @type {import("../../view/paramMediator.js").ExprRefFunction} */
+    fn: import("../../view/paramMediator.js").ExprRefFunction;
 }
 import FlowNode from "../flowNode.js";
 //# sourceMappingURL=formula.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"formula.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/formula.js"],"names":[],"mappings":"AAGA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,aAAa,EAUzD;IANG,wDAAoB;IAEpB,WAAmB;IAEnB,kCAAkC;IAClC,YADmB,GAAG,KAAK,GAAG,CACX;CAe1B;qBAjC2C,gBAAgB"}
+{"version":3,"file":"formula.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/formula.js"],"names":[],"mappings":"AAEA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,aAAa,yBAC/C,OAAO,gBAAgB,EAAE,qBAAqB,EAWxD;IANG,wDAAoB;IAEpB,WAAmB;IAEnB,oEAAoE;IACpE,IADW,OAAO,6BAA6B,EAAE,eAAe,CAC7C;CAgB1B;qBApC2C,gBAAgB"}

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

@@ -1,4 +1,3 @@
-import createFunction from "../../utils/expression.js";
 import FlowNode, { BEHAVIOR_MODIFIES } from "../flowNode.js";
 
 export default class FormulaTransform extends FlowNode {
@@ -9,19 +8,22 @@ export default class FormulaTransform extends FlowNode {
     /**
      *
      * @param {import("../../spec/transform.js").FormulaParams} params
+     * @param {import("../flowNode.js").ParamMediatorProvider} paramMediatorProvider
      */
-    constructor(params) {
-        super();
+    constructor(params, paramMediatorProvider) {
+        super(paramMediatorProvider);
+
         this.params = params;
 
         this.as = params.as;
 
-        /** @type {(datum: any) => any} */
+        /** @type {import("../../view/paramMediator.js").ExprRefFunction} */
         this.fn = undefined;
     }
 
     initialize() {
-        this.fn = createFunction(this.params.expr, this.getGlobalObject());
+        this.fn = this.paramMediator.createExpression(this.params.expr);
+        this.fn.addListener(() => this.repropagate());
     }
 
     /**

package/dist/src/data/transforms/formula.test.js

@@ -1,15 +1,21 @@
-import { expect, test } from "vitest";
-import { processData } from "../flowTestUtils.js";
+import { expect, test, test } from "vitest";
+import { makeParamMediatorProvider, processData } from "../flowTestUtils.js";
 import FormulaTransform from "./formula.js";
 
+test.todo("Implement stub for ParamMediator");
+
 test("FormulaTransform", () => {
     const data = [{ a: 2 }, { a: 3 }];
 
-    const t = new FormulaTransform({
-        type: "formula",
-        expr: "datum.a * 2",
-        as: "b",
-    });
+    const t = new FormulaTransform(
+        {
+            type: "formula",
+            expr: "datum.a * 2",
+            as: "b",
+        },
+        makeParamMediatorProvider()
+    );
+
     t.initialize();
 
     expect(processData(t, data)).toEqual([

package/dist/src/genomeSpy.d.ts

@@ -73,9 +73,12 @@ export default class GenomeSpy {
     /**
      * Views that are currently loading data using lazy sources.
      *
-     * @type {Map<View, boolean>}
+     * @type {Map<View, { status: import("./types/viewContext.js").DataLoadingStatus, detail?: string }>}
      */
-    _loadingViews: Map<import("./view/view.js").default, boolean>;
+    _loadingViews: Map<import("./view/view.js").default, {
+        status: import("./types/viewContext.js").DataLoadingStatus;
+        detail?: string;
+    }>;
     /**
      * @type {HTMLElement}
      */

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

@@ -1 +1 @@
-{"version":3,"file":"genomeSpy.d.ts","sourceRoot":"","sources":["../../src/genomeSpy.js"],"names":[],"mappings":"AA8CA;IACI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA2FpD;IAxFG,uBAA0B;IAC1B,oDAAsB;IAItB,6BAA6B;IAC7B,uBADW,CAAC,MAAM,IAAI,CAAC,EAAE,CACM;IAE/B,sCAAsC;IACtC,wCAAgB;IAEhB,iCAA4C;IAC5C,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,QAAU,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,qEAF0B,OAAO,CAE8B;IAE/D,2CAA2C;IAC3C,mBADW,4BAA4B,CACL;IAClC,2CAA2C;IAC3C,iBADW,4BAA4B,CACP;IAEhC,oDAAoD;IACpD,6BAAgC;IAEhC;;;OAGG;IACH,eAFU;QAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC;QAAC,KAAK,EAAE,OAAO,oBAAoB,EAAE,KAAK,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAEpF;IAE9B,uBAA+C;IAE/C;;;OAGG;IACH,oBAFU,IAAI,MAAM,EAAE,QAAU,aAAa,KAAE,IAAI,CAAC,EAAE,CAAC,CAEpB;IAEnC;;;;;;OAMG;IACH,yCAFkC,GAAG,KAAK,IAAI,GAEd;IAEhC;;;OAGG;IACH,kDAFkC,GAAG,KAAK,IAAI,GAEL;IAEzC,oFAAoF;IACpF,iBADW,OAAO,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,2CAAyB;IAEzB;;;;OAIG;IACH,8DAA8B;IAE9B;;OAEG;IACH,wBAFU,WAAW,CAEkB;IA2C3C;;;OAGG;IACH,2CAFkB,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAaf;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAQb;IAED;;;OAGG;IACH,iCAyCC;IA0DG,uBAOC;IAGD,mCAGE;IAOF,sCAEE;IAGF,iBAAyC;IAW7C;;OAEG;IACH,gBAuBC;IAED,sCA8MC;IAED;;;OAGG;IACH,UAFa,QAAQ,OAAO,CAAC,CA6B5B;IAED,4BA6IC;IAjIe,iCAAoC;IAmIpD;;;OAGG;IACH,kBAHW,MAAM,KACN,MAAM,QAiEhB;IAED;;;;;;;OAOG;IACH,oDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;IAED,sBAyCC;IAED,kBAIC;IAED,iCAOC;IAED,iCASC;IAED,qFAWC;;CACJ;;;;iCA15BY,eAAe,GAAG,YAAY,GAAG,QAAQ,GAAG,gBAAgB;4BAjC7C,uBAAuB;4BA2BP,uBAAuB;qBAZ9C,qBAAqB;wBAIlB,yBAAyB;yCARR,yDAAyD;oBAYvD,oBAAoB;wBAdvC,qBAAqB;oBAXzB,uBAAuB;qBAStB,oBAAoB"}
+{"version":3,"file":"genomeSpy.d.ts","sourceRoot":"","sources":["../../src/genomeSpy.js"],"names":[],"mappings":"AA8CA;IACI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA2FpD;IAxFG,uBAA0B;IAC1B,oDAAsB;IAItB,6BAA6B;IAC7B,uBADW,CAAC,MAAM,IAAI,CAAC,EAAE,CACM;IAE/B,sCAAsC;IACtC,wCAAgB;IAEhB,iCAA4C;IAC5C,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,QAAU,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,qEAF0B,OAAO,CAE8B;IAE/D,2CAA2C;IAC3C,mBADW,4BAA4B,CACL;IAClC,2CAA2C;IAC3C,iBADW,4BAA4B,CACP;IAEhC,oDAAoD;IACpD,6BAAgC;IAEhC;;;OAGG;IACH,eAFU;QAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC;QAAC,KAAK,EAAE,OAAO,oBAAoB,EAAE,KAAK,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAEpF;IAE9B,uBAA+C;IAE/C;;;OAGG;IACH,oBAFU,IAAI,MAAM,EAAE,QAAU,aAAa,KAAE,IAAI,CAAC,EAAE,CAAC,CAEpB;IAEnC;;;;;;OAMG;IACH,yCAFkC,GAAG,KAAK,IAAI,GAEd;IAEhC;;;OAGG;IACH,kDAFkC,GAAG,KAAK,IAAI,GAEL;IAEzC,oFAAoF;IACpF,iBADW,OAAO,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,2CAAyB;IAEzB;;;;OAIG;IACH;gBAF8B,OAAO,wBAAwB,EAAE,iBAAiB;iBAAW,MAAM;OAEnE;IAE9B;;OAEG;IACH,wBAFU,WAAW,CAEkB;IA2C3C;;;OAGG;IACH,2CAFkB,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAaf;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAQb;IAED;;;OAGG;IACH,iCAqDC;IA0DG,uBAOC;IAGD,mCAGE;IAOF,sCAEE;IAGF,iBAAyC;IAW7C;;OAEG;IACH,gBAuBC;IAED,sCA8MC;IAED;;;OAGG;IACH,UAFa,QAAQ,OAAO,CAAC,CA6B5B;IAED,4BA6IC;IAjIe,iCAAoC;IAmIpD;;;OAGG;IACH,kBAHW,MAAM,KACN,MAAM,QAiEhB;IAED;;;;;;;OAOG;IACH,oDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;IAED,sBA6CC;IAED,kBAIC;IAED,iCAOC;IAED,iCASC;IAED,qFAWC;;CACJ;;;;iCA16BY,eAAe,GAAG,YAAY,GAAG,QAAQ,GAAG,gBAAgB;4BAjC7C,uBAAuB;4BA2BP,uBAAuB;qBAZ9C,qBAAqB;wBAIlB,yBAAyB;yCARR,yDAAyD;oBAYvD,oBAAoB;wBAdvC,qBAAqB;oBAXzB,uBAAuB;qBAStB,oBAAoB"}

package/dist/src/genomeSpy.js

@@ -1,5 +1,5 @@
 import { formats as vegaFormats } from "vega-loader";
-import { html, render } from "lit";
+import { html, nothing, render } from "lit";
 import { styleMap } from "lit/directives/style-map.js";
 import SPINNER from "./img/90-ring-with-bg.svg";
 
@@ -139,7 +139,7 @@ export default class GenomeSpy {
         /**
          * Views that are currently loading data using lazy sources.
          *
-         * @type {Map<View, boolean>}
+         * @type {Map<View, { status: import("./types/viewContext.js").DataLoadingStatus, detail?: string }>}
          */
         this._loadingViews = new Map();
 
@@ -250,7 +250,9 @@ export default class GenomeSpy {
         const indicators = [];
 
         const isSomethingVisible = () =>
-            [...this._loadingViews.values()].some((v) => v);
+            [...this._loadingViews.values()].some(
+                (v) => v.status == "loading" || v.status == "error"
+            );
 
         for (const [view, status] of this._loadingViews) {
             const c = view.coords;
@@ -263,9 +265,18 @@ export default class GenomeSpy {
                 };
                 indicators.push(
                     html`<div style=${styleMap(style)}>
-                        <div class=${status ? "loading" : ""}>
-                            <img src="${SPINNER}" alt="" />
-                            <span>Loading...</span>
+                        <div class=${status.status}>
+                            ${status.status == "error"
+                                ? html`<span
+                                      >Loading
+                                      failed${status.detail
+                                          ? html`: ${status.detail}`
+                                          : nothing}</span
+                                  >`
+                                : html`
+                                      <img src="${SPINNER}" alt="" />
+                                      <span>Loading...</span>
+                                  `}
                         </div>
                     </div>`
                 );
@@ -274,6 +285,7 @@ export default class GenomeSpy {
 
         // Do some hacks to stop css animations of the loading indicators.
         // Otherwise they fire animation frames even when their opacity is zero.
+        // TODO: Instead of this, replace the animated spinners with static images.
         if (isSomethingVisible()) {
             this.loadingIndicatorsElement.style.display = "block";
         } else {
@@ -437,8 +449,8 @@ export default class GenomeSpy {
             getNamedDataFromProvider: this.getNamedDataFromProvider.bind(this),
             getCurrentHover: () => this._currentHover,
 
-            setDataLoadingStatus: (view, status) => {
-                this._loadingViews.set(view, status);
+            setDataLoadingStatus: (view, status, detail) => {
+                this._loadingViews.set(view, { status, detail });
                 this._updateLoadingIndicators();
             },
 
@@ -920,6 +932,10 @@ export default class GenomeSpy {
             Rectangle.create(0, 0, canvasSize.width, canvasSize.height)
         );
 
+        // The view coordinates may have not been known during the initial data loading.
+        // Thus, update them so that possible error messages are shown in the correct place.
+        this._updateLoadingIndicators();
+
         this.broadcast("layoutComputed");
     }
 

package/dist/src/marks/mark.d.ts.map

@@ -1 +1 @@
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package/dist/src/marks/mark.js

@@ -1224,6 +1224,17 @@ class RangeMap extends InternMap {
      * @param {Map<K, import("../gl/dataToVertices.js").RangeEntry>} anotherMap
      */
     migrateEntries(anotherMap) {
+        for (const [key, value] of this.entries()) {
+            // Buffered draw calls maintain direct references to the range entries.
+            // Thus, they cannot just be deleted, but instead, their counts and offsets
+            // must be zeroed.
+            if (!anotherMap.has(key)) {
+                value.offset = 0;
+                value.count = 0;
+                value.xIndex = undefined;
+            }
+        }
+
         for (const [key, value] of anotherMap.entries()) {
             Object.assign(this.get(key), value);
         }

package/dist/src/spec/view.d.ts

@@ -124,6 +124,11 @@ export interface ViewSpecBase extends ResolveSpec {
      */
     description?: string | string[];
 
+    /**
+     * Optional base URL for constructing request URLs. When set, all views
+     * deeper in the hierarchy inherit this base URL, using it for importing
+     * loading data and importing specifications.
+     */
     baseUrl?: string;
 
     /**
@@ -151,6 +156,12 @@ export interface ViewSpecBase extends ResolveSpec {
      * **Default:** `false` for children of `layer`, `true` for others.
      */
     configurableVisibility?: boolean;
+
+    /**
+     * Templates that can be reused within the view specification by importing
+     * them with the template key.
+     */
+    templates?: Record<string, ViewSpec>;
 }
 
 export interface UnitSpec extends ViewSpecBase, AggregateSamplesSpec {
@@ -165,7 +176,7 @@ export interface AggregateSamplesSpec {
 
 export interface LayerSpec extends ViewSpecBase, AggregateSamplesSpec {
     view?: ViewBackground;
-    layer: (LayerSpec | UnitSpec)[];
+    layer: (LayerSpec | UnitSpec | ImportSpec)[];
 }
 
 export interface FacetSpec extends ViewSpecBase {
@@ -218,39 +229,71 @@ export type ViewSpec =
     | ConcatSpec
     | SampleSpec;
 
-export interface ImportParams {
-    url?: string;
+export interface UrlImport {
+    /**
+     * Imports a specification from the specified URL.
+     */
+    url: string;
+}
+
+export interface TemplateImport {
+    /**
+     * Imports a specification from the current view hierarchy, searching
+     * first in the current view, then ascending through ancestors.
+     */
+    template: string;
+}
 
+export interface ImportSpec {
     /**
-     * Name for the imported view. Overrides the name defined in the imported spec.
+     * The name given to the imported view. This property overrides the name
+     * specified in the imported specification.
      */
     name?: string;
 
     /**
-     * Dynamic variables that parameterize a visualization. Parameters defined here
-     * override the parameters defined in the imported spec.
+     * Dynamic variables that parameterize a visualization. Parameters defined
+     * here override the parameters defined in the imported specification.
      */
     params?: VariableParameter[] | Record<string, any>;
-}
 
-export interface ImportSpec {
-    import: ImportParams;
+    /**
+     * The method to import a specification.
+     */
+    import: UrlImport | TemplateImport;
 }
 
 export interface ConcatBase extends ViewSpecBase {
+    /**
+     * The gap between the views, in pixels.
+     */
     spacing?: number;
 }
 
 export interface VConcatSpec extends ConcatBase {
+    /**
+     * Specifies views that will be concatenated vertically.
+     */
     vconcat: (ViewSpec | ImportSpec)[];
 }
 
 export interface HConcatSpec extends ConcatBase {
+    /**
+     * Specifies views that will be concatenated horizontally.
+     */
     hconcat: (ViewSpec | ImportSpec)[];
 }
 
 export interface ConcatSpec extends ConcatBase {
+    /**
+     * Specifies views that will be concatenated into a grid that wraps when
+     * the specified number of columns are used.
+     */
     concat: (ViewSpec | ImportSpec)[];
+
+    /**
+     * The number of columns in the grid.
+     */
     columns: number;
 }
 

package/dist/src/styles/genome-spy.css.d.ts

@@ -1,3 +1,3 @@
 export default css;
-declare const css: "\n.genome-spy {\n  font-family: system-ui, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";\n  position: relative;\n  display: flex;\n  flex-direction: column;\n}\n.genome-spy .canvas-wrapper {\n  position: relative;\n  flex-grow: 1;\n  overflow: hidden;\n}\n.genome-spy canvas {\n  transform: scale(1, 1);\n  opacity: 1;\n  transition: transform 0.6s, opacity 0.6s;\n}\n.genome-spy .loading-message {\n  position: absolute;\n  inset: 0;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-message .message {\n  color: #666;\n  opacity: 0;\n  transition: opacity 0.7s;\n}\n.genome-spy .loading > canvas {\n  transform: scale(0.95, 0.95);\n  opacity: 0;\n}\n.genome-spy .loading > .loading-message .message {\n  opacity: 1;\n}\n.genome-spy .loading > .loading-message .message .ellipsis {\n  animation: blinker 1s linear infinite;\n}\n@keyframes blinker {\n  50% {\n    opacity: 0;\n  }\n}\n.genome-spy .loading-indicators {\n  position: absolute;\n  inset: 0;\n  user-select: none;\n  pointer-events: none;\n}\n.genome-spy .loading-indicators div {\n  position: absolute;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-indicators div > div {\n  font-size: 11px;\n  transition: opacity 0.2s;\n  background: white;\n  padding: 2px 5px;\n  display: flex;\n  border-radius: 3px;\n  gap: 0.5em;\n  opacity: 0;\n}\n.genome-spy .loading-indicators div > div.loading {\n  opacity: 0.5;\n}\n.genome-spy .loading-indicators div > div > * {\n  display: block;\n}\n.genome-spy .loading-indicators div > div img {\n  width: 1.5em;\n  height: 1.5em;\n}\n.genome-spy .tooltip {\n  position: absolute;\n  max-width: 450px;\n  overflow: hidden;\n  background: #f6f6f6;\n  padding: 10px;\n  font-size: 13px;\n  box-shadow: 0px 3px 15px 0px rgba(0, 0, 0, 0.21);\n  pointer-events: none;\n  z-index: 100;\n}\n.genome-spy .tooltip > :last-child {\n  margin-bottom: 0;\n}\n.genome-spy .tooltip > .title {\n  padding-bottom: 5px;\n  margin-bottom: 5px;\n  border-bottom: 1px dashed #b6b6b6;\n}\n.genome-spy .tooltip .summary {\n  font-size: 12px;\n}\n.genome-spy .tooltip table {\n  border-collapse: collapse;\n}\n.genome-spy .tooltip table:first-child {\n  margin-top: 0;\n}\n.genome-spy .tooltip table th,\n.genome-spy .tooltip table td {\n  padding: 2px 0.4em;\n  vertical-align: top;\n}\n.genome-spy .tooltip table th:first-child,\n.genome-spy .tooltip table td:first-child {\n  padding-left: 0;\n}\n.genome-spy .tooltip table th {\n  text-align: left;\n  font-weight: bold;\n}\n.genome-spy .tooltip .color-legend {\n  display: inline-block;\n  width: 0.8em;\n  height: 0.8em;\n  margin-left: 0.4em;\n  box-shadow: 0px 0px 3px 1px white;\n}\n.genome-spy .tooltip .attributes .hovered {\n  background-color: #e0e0e0;\n}\n.genome-spy .tooltip .na {\n  color: #aaa;\n  font-style: italic;\n  font-size: 80%;\n}\n.genome-spy .gene-track-tooltip .summary {\n  font-size: 90%;\n}\n.genome-spy .message-box {\n  display: flex;\n  align-items: center;\n  justify-content: center;\n  position: absolute;\n  top: 0;\n  height: 100%;\n  width: 100%;\n}\n.genome-spy .message-box > div {\n  border: 1px solid red;\n  padding: 10px;\n  background: #fff0f0;\n}\n\n.gs-input-binding {\n  display: grid;\n  grid-template-columns: max-content max-content;\n  column-gap: 1em;\n  row-gap: 0.3em;\n  justify-items: start;\n}\n.gs-input-binding > select,\n.gs-input-binding > input:not([type=checkbox]) {\n  width: 100%;\n}\n.gs-input-binding input[type=range] + span {\n  display: inline-block;\n  margin-left: 0.3em;\n  min-width: 2.2em;\n  font-variant-numeric: tabular-nums;\n}\n.gs-input-binding input[type=range],\n.gs-input-binding input[type=radio] {\n  vertical-align: text-bottom;\n}\n.gs-input-binding .radio-group {\n  display: flex;\n  align-items: center;\n}\n.gs-input-binding .description {\n  max-width: 26em;\n  grid-column: 1/-1;\n  color: #777;\n  font-size: 90%;\n  margin-top: -0.5em;\n}\n\n.gs-input-bindings {\n  flex-basis: content;\n  font-size: 14px;\n  padding: 10px;\n}\n";
+declare const css: "\n.genome-spy {\n  font-family: system-ui, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";\n  position: relative;\n  display: flex;\n  flex-direction: column;\n}\n.genome-spy .canvas-wrapper {\n  position: relative;\n  flex-grow: 1;\n  overflow: hidden;\n}\n.genome-spy canvas {\n  transform: scale(1, 1);\n  opacity: 1;\n  transition: transform 0.6s, opacity 0.6s;\n}\n.genome-spy .loading-message {\n  position: absolute;\n  inset: 0;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-message .message {\n  color: #666;\n  opacity: 0;\n  transition: opacity 0.7s;\n}\n.genome-spy .loading > canvas {\n  transform: scale(0.95, 0.95);\n  opacity: 0;\n}\n.genome-spy .loading > .loading-message .message {\n  opacity: 1;\n}\n.genome-spy .loading > .loading-message .message .ellipsis {\n  animation: blinker 1s linear infinite;\n}\n@keyframes blinker {\n  50% {\n    opacity: 0;\n  }\n}\n.genome-spy .loading-indicators {\n  position: absolute;\n  inset: 0;\n  user-select: none;\n  pointer-events: none;\n}\n.genome-spy .loading-indicators div {\n  position: absolute;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-indicators div > div {\n  font-size: 11px;\n  transition: opacity 0.2s;\n  background: white;\n  padding: 2px 5px;\n  display: flex;\n  border-radius: 3px;\n  gap: 0.5em;\n  opacity: 0;\n}\n.genome-spy .loading-indicators div > div.loading {\n  opacity: 0.5;\n}\n.genome-spy .loading-indicators div > div.error {\n  opacity: 0.8;\n  color: firebrick;\n}\n.genome-spy .loading-indicators div > div > * {\n  display: block;\n}\n.genome-spy .loading-indicators div > div img {\n  width: 1.5em;\n  height: 1.5em;\n}\n.genome-spy .tooltip {\n  position: absolute;\n  max-width: 450px;\n  overflow: hidden;\n  background: #f6f6f6;\n  padding: 10px;\n  font-size: 13px;\n  box-shadow: 0px 3px 15px 0px rgba(0, 0, 0, 0.21);\n  pointer-events: none;\n  z-index: 100;\n}\n.genome-spy .tooltip > :last-child {\n  margin-bottom: 0;\n}\n.genome-spy .tooltip > .title {\n  padding-bottom: 5px;\n  margin-bottom: 5px;\n  border-bottom: 1px dashed #b6b6b6;\n}\n.genome-spy .tooltip .summary {\n  font-size: 12px;\n}\n.genome-spy .tooltip table {\n  border-collapse: collapse;\n}\n.genome-spy .tooltip table:first-child {\n  margin-top: 0;\n}\n.genome-spy .tooltip table th,\n.genome-spy .tooltip table td {\n  padding: 2px 0.4em;\n  vertical-align: top;\n}\n.genome-spy .tooltip table th:first-child,\n.genome-spy .tooltip table td:first-child {\n  padding-left: 0;\n}\n.genome-spy .tooltip table th {\n  text-align: left;\n  font-weight: bold;\n}\n.genome-spy .tooltip .color-legend {\n  display: inline-block;\n  width: 0.8em;\n  height: 0.8em;\n  margin-left: 0.4em;\n  box-shadow: 0px 0px 3px 1px white;\n}\n.genome-spy .tooltip .attributes .hovered {\n  background-color: #e0e0e0;\n}\n.genome-spy .tooltip .na {\n  color: #aaa;\n  font-style: italic;\n  font-size: 80%;\n}\n.genome-spy .gene-track-tooltip .summary {\n  font-size: 90%;\n}\n.genome-spy .message-box {\n  display: flex;\n  align-items: center;\n  justify-content: center;\n  position: absolute;\n  top: 0;\n  height: 100%;\n  width: 100%;\n}\n.genome-spy .message-box > div {\n  border: 1px solid red;\n  padding: 10px;\n  background: #fff0f0;\n}\n\n.gs-input-binding {\n  display: grid;\n  grid-template-columns: max-content max-content;\n  column-gap: 1em;\n  row-gap: 0.3em;\n  justify-items: start;\n}\n.gs-input-binding > select,\n.gs-input-binding > input:not([type=checkbox]) {\n  width: 100%;\n}\n.gs-input-binding input[type=range] + span {\n  display: inline-block;\n  margin-left: 0.3em;\n  min-width: 2.2em;\n  font-variant-numeric: tabular-nums;\n}\n.gs-input-binding input[type=range],\n.gs-input-binding input[type=radio] {\n  vertical-align: text-bottom;\n}\n.gs-input-binding .radio-group {\n  display: flex;\n  align-items: center;\n}\n.gs-input-binding .description {\n  max-width: 26em;\n  grid-column: 1/-1;\n  color: #777;\n  font-size: 90%;\n  margin-top: -0.5em;\n}\n\n.gs-input-bindings {\n  flex-basis: content;\n  font-size: 14px;\n  padding: 10px;\n}\n";
 //# sourceMappingURL=genome-spy.css.d.ts.map

package/dist/src/styles/genome-spy.css.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"genome-spy.css.d.ts","sourceRoot":"","sources":["../../../src/styles/genome-spy.css.js"],"names":[],"mappings":";AAAA,6iIA4LE"}
+{"version":3,"file":"genome-spy.css.d.ts","sourceRoot":"","sources":["../../../src/styles/genome-spy.css.js"],"names":[],"mappings":";AAAA,yoIAgME"}

package/dist/src/styles/genome-spy.css.js

@@ -67,6 +67,10 @@ const css = `
 .genome-spy .loading-indicators div > div.loading {
   opacity: 0.5;
 }
+.genome-spy .loading-indicators div > div.error {
+  opacity: 0.8;
+  color: firebrick;
+}
 .genome-spy .loading-indicators div > div > * {
   display: block;
 }

package/dist/src/styles/genome-spy.scss

@@ -88,6 +88,11 @@ $font-family: system-ui, "Segoe UI", Roboto, Helvetica, Arial, sans-serif,
                     opacity: 0.5;
                 }
 
+                &.error {
+                    opacity: 0.8;
+                    color: firebrick;
+                }
+
                 > * {
                     display: block;
                 }

package/dist/src/types/viewContext.d.ts

@@ -18,6 +18,8 @@ export interface Hover {
     datum: Datum;
 }
 
+export type DataLoadingStatus = "loading" | "complete" | "error";
+
 /**
  * ViewContext provides essential data and interfaces to View classes.
  */
@@ -74,9 +76,14 @@ export default interface ViewContext {
      * The status is shown in the UI somewhere within or near the view.
      *
      * @param view The view where the data source is located.
-     * @param status true if loading, false if not loading.
+     * @param status
+     * @param detail Details about the error, if any.
      */
-    setDataLoadingStatus: (view: View, status: boolean) => void;
+    setDataLoadingStatus: (
+        view: View,
+        status: DataLoadingStatus,
+        detail?: string
+    ) => void;
 
     /**
      * Returns true if the view is configured to be visible.

package/dist/src/utils/expression.js

@@ -49,7 +49,7 @@ function buildFunctions(codegen) {
 
 const cg = codegenExpression({
     forbidden: [],
-    allowed: ["datum"],
+    allowed: ["datum", "undefined"],
     globalvar: "globalObject",
     fieldvar: "datum",
     functions: buildFunctions,