@genome-spy/core 0.45.0 → 0.46.1

package/dist/src/data/flowNode.js

@@ -18,7 +18,9 @@ export const BEHAVIOR_MODIFIES = 1 << 1;
  */
 export const BEHAVIOR_COLLECTS = 1 << 2;
 
-const ROOT_CONTEXT_OBJECT = {};
+/**
+ * @typedef {{paramMediator: import("../view/paramMediator.js").default}} ParamMediatorProvider
+ */
 
 /**
  * This is heavily inspired by Vega's and Vega-Lite's data flow system.
@@ -27,11 +29,24 @@ const ROOT_CONTEXT_OBJECT = {};
  * @typedef {Datum[]} Data
  */
 export default class FlowNode {
+    /**
+     * An object that provides a paramMediator. (Most likely a View)
+     *
+     * @type {ParamMediatorProvider}
+     * @protected
+     */
+    paramMediatorProvider = null;
+
     get behavior() {
         return 0;
     }
 
-    constructor() {
+    /**
+     * @param {ParamMediatorProvider} [paramMediatorProvider]
+     */
+    constructor(paramMediatorProvider) {
+        this.paramMediatorProvider = paramMediatorProvider;
+
         /** @type {FlowNode[]} */
         this.children = [];
 
@@ -66,7 +81,7 @@ export default class FlowNode {
      * Dynamically updates the propagator method to allow the JavaScript engine
      * to employ optimizations such as inlining.
      */
-    _updatePropagator() {
+    #updatePropagator() {
         this._propagate = Function(
             "children",
             range(this.children.length)
@@ -96,7 +111,7 @@ export default class FlowNode {
         }
         this.children.push(child);
         child.setParent(this);
-        this._updatePropagator();
+        this.#updatePropagator();
         return this;
     }
 
@@ -131,7 +146,7 @@ export default class FlowNode {
 
         newParent.parent = this.parent;
         this.parent.children[this.parent.children.indexOf(this)] = newParent;
-        this.parent._updatePropagator();
+        this.parent.#updatePropagator();
         this.parent = undefined;
         newParent.addChild(this);
     }
@@ -145,7 +160,7 @@ export default class FlowNode {
         if (index > -1) {
             this.children.splice(index, 1);
             child.parent = undefined;
-            this._updatePropagator();
+            this.#updatePropagator();
         } else {
             throw new Error("Trying to remove an unknown child node!");
         }
@@ -164,7 +179,7 @@ export default class FlowNode {
             const child = this.children[0];
             child.setParent(this.parent);
             this.parent.children[this.parent.children.indexOf(this)] = child;
-            this.parent._updatePropagator();
+            this.parent.#updatePropagator();
             this.setParent(undefined);
             this.children.length = 0;
         } else {
@@ -219,19 +234,6 @@ export default class FlowNode {
         } \n${childTree}`;
     }
 
-    /**
-     * The global object for expressions (in formula and filter transforms).
-     * Nodes in the hierarchy may extend the object using Object.create to
-     * introduce variables that are visible downstream the flow.
-     *
-     * @returns {Record<string, any>}
-     */
-    getGlobalObject() {
-        return this.parent
-            ? this.parent.getGlobalObject()
-            : ROOT_CONTEXT_OBJECT;
-    }
-
     /**
      *
      * @param {Datum} datum
@@ -260,9 +262,40 @@ export default class FlowNode {
         }
     }
 
+    /**
+     * @returns {import("../view/paramMediator.js").default}
+     * @protected
+     */
+    get paramMediator() {
+        if (this.paramMediatorProvider) {
+            return this.paramMediatorProvider.paramMediator;
+        }
+
+        if (!this.parent) {
+            throw new Error("Cannot find paramMediator!");
+        }
+        return this.parent.paramMediator;
+    }
+
+    /**
+     * Repropagates the stored data. If this node has no stored data,
+     * find the nearest ancestor that has and repropagate from there.
+     * @protected
+     */
+    repropagate() {
+        if (this.parent) {
+            this.parent.repropagate();
+        } else {
+            throw new Error(
+                "Cannot repropagate data, no FlowNode with stored data found!"
+            );
+        }
+    }
+
     /**
      *
      * @param {any} datum
+     * @protected
      */
     _propagate(datum) {
         // Implementation is set dynamically in add/removeChild

package/dist/src/data/flowTestUtils.d.ts

@@ -1,3 +1,8 @@
+/**
+ *
+ * @returns {import("./flowNode.js").ParamMediatorProvider}
+ */
+export function makeParamMediatorProvider(): import("./flowNode.js").ParamMediatorProvider;
 /**
  *
  * @param {import("./flowNode.js").default} flowNode

package/dist/src/data/flowTestUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"flowTestUtils.d.ts","sourceRoot":"","sources":["../../../src/data/flowTestUtils.js"],"names":[],"mappings":"AAGA;;;;GAIG;AACH,sCAHW,OAAO,eAAe,EAAE,OAAO,QAC/B,GAAG,EAAE,mCAcf;AAED;;GAEG;AACH;IACI;;;OAGG;IACH,kBAFW,GAAG,EAAE,EAKf;IADG,YAAgB;IAGpB,iBAMC;CACJ;AAED;;GAEG;AACH;IACI;;;OAGG;IACH,eAFW,MAAM,EAWhB;CACJ;qBA7DoB,eAAe"}
+{"version":3,"file":"flowTestUtils.d.ts","sourceRoot":"","sources":["../../../src/data/flowTestUtils.js"],"names":[],"mappings":"AAIA;;;GAGG;AACH,6CAFa,OAAO,eAAe,EAAE,qBAAqB,CAMzD;AAED;;;;GAIG;AACH,sCAHW,OAAO,eAAe,EAAE,OAAO,QAC/B,GAAG,EAAE,mCAcf;AAED;;GAEG;AACH;IACI;;;OAGG;IACH,kBAFW,GAAG,EAAE,EAKf;IADG,YAAgB;IAGpB,iBAMC;CACJ;AAED;;GAEG;AACH;IACI;;;OAGG;IACH,eAFW,MAAM,EAWhB;CACJ;qBAvEoB,eAAe"}

package/dist/src/data/flowTestUtils.js

@@ -1,6 +1,17 @@
+import ParamMediator from "../view/paramMediator.js";
 import Collector from "./collector.js";
 import FlowNode from "./flowNode.js";
 
+/**
+ *
+ * @returns {import("./flowNode.js").ParamMediatorProvider}
+ */
+export function makeParamMediatorProvider() {
+    return {
+        paramMediator: new ParamMediator(),
+    };
+}
+
 /**
  *
  * @param {import("./flowNode.js").default} flowNode

package/dist/src/data/sources/dataSource.d.ts

@@ -1,4 +1,13 @@
 export default class DataSource extends FlowNode {
+    /**
+     * @param {import("../../view/view.js").default} view
+     */
+    constructor(view: import("../../view/view.js").default);
+    /**
+     * @type {import("../../view/view.js").default}
+     * @protected
+     */
+    protected view: import("../../view/view.js").default;
     /**
      * Returns a string that identifies a data source. Data sources with the
      * same identifier can be merged.
@@ -6,6 +15,14 @@ export default class DataSource extends FlowNode {
      * @return {string}
      */
     get identifier(): string;
+    /**
+     * Sets the loading status of the data source. The status is shown in the UI.
+     *
+     * @param {import("../../types/viewContext.js").DataLoadingStatus} status
+     * @param {string} [detail] The error message
+     * @protected
+     */
+    protected setLoadingStatus(status: import("../../types/viewContext.js").DataLoadingStatus, detail?: string): void;
     load(): Promise<void>;
 }
 import FlowNode from "../flowNode.js";

package/dist/src/data/sources/dataSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataSource.js"],"names":[],"mappings":"AAEA;IACI;;;;;OAKG;IACH,yBAEC;IAUD,sBAEC;CACJ;qBAxBoB,gBAAgB"}
+{"version":3,"file":"dataSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataSource.js"],"names":[],"mappings":"AAEA;IAOI;;OAEG;IACH,kBAFW,OAAO,oBAAoB,EAAE,OAAO,EAM9C;IAbD;;;OAGG;IACH,gBAHU,OAAO,oBAAoB,EAAE,OAAO,CAGzC;IAWL;;;;;OAKG;IACH,yBAEC;IAED;;;;;;OAMG;IACH,mCAJW,OAAO,4BAA4B,EAAE,iBAAiB,WACtD,MAAM,QAKhB;IAcD,sBAEC;CAKJ;qBA1DoB,gBAAgB"}

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

@@ -1,6 +1,21 @@
 import FlowNode from "../flowNode.js";
 
 export default class DataSource extends FlowNode {
+    /**
+     * @type {import("../../view/view.js").default}
+     * @protected
+     */
+    view;
+
+    /**
+     * @param {import("../../view/view.js").default} view
+     */
+    constructor(view) {
+        super();
+
+        this.view = view;
+    }
+
     /**
      * Returns a string that identifies a data source. Data sources with the
      * same identifier can be merged.
@@ -11,6 +26,21 @@ export default class DataSource extends FlowNode {
         return undefined;
     }
 
+    /**
+     * Sets the loading status of the data source. The status is shown in the UI.
+     *
+     * @param {import("../../types/viewContext.js").DataLoadingStatus} status
+     * @param {string} [detail] The error message
+     * @protected
+     */
+    setLoadingStatus(status, detail) {
+        this.view.context.setDataLoadingStatus(this.view, status, detail);
+    }
+
+    get paramMediator() {
+        return this.view.paramMediator;
+    }
+
     /**
      *
      * @param {import("../flowNode.js").Datum} datum
@@ -22,4 +52,8 @@ export default class DataSource extends FlowNode {
     async load() {
         // override
     }
+
+    repropagate() {
+        this.load();
+    }
 }

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

@@ -16,7 +16,7 @@ export default class InlineSource extends DataSource {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params, view) {
-        super();
+        super(view);
 
         this.params = params;
 

package/dist/src/data/sources/lazy/bigBedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,mBADmB,MAAM,UAAU;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CA8EpC;qCAtHoC,+BAA+B"}
+{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,mBADmB,MAAM,UAAU;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CAoFpC;qCA5HoC,+BAA+B"}

package/dist/src/data/sources/lazy/bigBedSource.js

@@ -72,6 +72,7 @@ export default class BigBedSource extends SingleAxisWindowedSource {
                     ),
                 });
 
+                this.setLoadingStatus("loading");
                 this.bbi
                     .getHeader()
                     .then(async (header) => {
@@ -88,11 +89,16 @@ export default class BigBedSource extends SingleAxisWindowedSource {
                                 );
                         }
 
+                        this.setLoadingStatus("complete");
                         resolve();
                     })
                     .catch((e) => {
                         // Load empty data
                         this.load();
+                        this.setLoadingStatus(
+                            "error",
+                            `${withoutExprRef(this.params.url)}: ${e.message}`
+                        );
                         reject(e);
                     });
             });

package/dist/src/data/sources/lazy/bigWigSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bigWigSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigWigSource.js"],"names":[],"mappings":"AAOA;;GAEG;AACH;IAOI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IATG,mDAA6B;IA8CjC;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAqBlB;IAED;;;OAGG;IAEH,uBAJW,MAAM,EAAE,kBACR,MAAM,iBA2BhB;;CACJ;qCA9IoC,+BAA+B"}
+{"version":3,"file":"bigWigSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigWigSource.js"],"names":[],"mappings":"AAOA;;GAEG;AACH;IAOI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IATG,mDAA6B;IA2DjC;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAqBlB;IAED;;;OAGG;IAEH,uBAJW,MAAM,EAAE,kBACR,MAAM,iBA2BhB;;CACJ;qCA3JoC,+BAA+B"}

package/dist/src/data/sources/lazy/bigWigSource.js

@@ -55,7 +55,7 @@ export default class BigWigSource extends SingleAxisWindowedSource {
     }
 
     #initialize() {
-        this.initializedPromise = new Promise((resolve) => {
+        this.initializedPromise = new Promise((resolve, reject) => {
             Promise.all([
                 import("@gmod/bbi"),
                 import("generic-filehandle"),
@@ -69,20 +69,33 @@ export default class BigWigSource extends SingleAxisWindowedSource {
                     ),
                 });
 
-                this.#bbi.getHeader().then((header) => {
-                    this.#reductionLevels =
-                        /** @type {{reductionLevel: number}[]} */ (
-                            header.zoomLevels
-                        )
-                            .map((z) => z.reductionLevel)
-                            .reverse();
-
-                    // Add the non-reduced level. Not sure if this is the best way to do it.
-                    // Afaik, the non-reduced bin size is not available in the header.
-                    this.#reductionLevels.push(1);
-
-                    resolve();
-                });
+                this.setLoadingStatus("loading");
+                this.#bbi
+                    .getHeader()
+                    .then((header) => {
+                        this.#reductionLevels =
+                            /** @type {{reductionLevel: number}[]} */ (
+                                header.zoomLevels
+                            )
+                                .map((z) => z.reductionLevel)
+                                .reverse();
+
+                        // Add the non-reduced level. Not sure if this is the best way to do it.
+                        // Afaik, the non-reduced bin size is not available in the header.
+                        this.#reductionLevels.push(1);
+
+                        this.setLoadingStatus("complete");
+                        resolve();
+                    })
+                    .catch((e) => {
+                        // Load empty data
+                        this.load();
+                        this.setLoadingStatus(
+                            "error",
+                            `${withoutExprRef(this.params.url)}: ${e.message}`
+                        );
+                        reject(e);
+                    });
             });
         });
 

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts

@@ -12,7 +12,6 @@ export default class SingleAxisLazySource extends DataSource {
      * @protected
      */
     protected initializedPromise: Promise<void>;
-    view: import("../../../view/view.js").default;
     /** @type {import("../../../spec/channel.js").PrimaryPositionalChannel}  */
     channel: import("../../../spec/channel.js").PrimaryPositionalChannel;
     scaleResolution: import("../../../view/scaleResolution.js").default;
@@ -35,13 +34,6 @@ export default class SingleAxisLazySource extends DataSource {
      * @abstract
      */
     onDomainChanged(domain: number[], complexDomain: import("../../../spec/genome.js").ChromosomalLocus[]): void;
-    /**
-     * Sets the loading status of the data source. The status is shown in the UI.
-     *
-     * @param {boolean} status true if loading, false otherwise
-     * @protected
-     */
-    protected setLoadingStatus(status: boolean): void;
     /**
      * TODO: Get rid of this method.
      * Rendering should be requested by the collector.

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EAiDrE;IAzDD;;;OAGG;IACH,4CAAuC;IASnC,8CAAgB;IAYhB,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,oEAA4D;IA+BhE;;;OAGG;IACH,wBAWC;IAED;;;;OAIG;IACH,oEAEC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,mCAHW,OAAO,QAKjB;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;OAKG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBAtJsB,kBAAkB"}
+{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IAvDD;;;OAGG;IACH,4CAAuC;IAmBnC,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,oEAA4D;IA+BhE;;;OAGG;IACH,wBAWC;IAED;;;;OAIG;IACH,oEAEC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;OAKG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBA1IsB,kBAAkB"}

package/dist/src/data/sources/lazy/singleAxisLazySource.js

@@ -17,9 +17,7 @@ export default class SingleAxisLazySource extends DataSource {
      * @param {import("../../../spec/channel.js").PrimaryPositionalChannel} channel
      */
     constructor(view, channel) {
-        super();
-
-        this.view = view;
+        super(view);
 
         if (!channel) {
             throw new Error(
@@ -102,16 +100,6 @@ export default class SingleAxisLazySource extends DataSource {
         // Override me
     }
 
-    /**
-     * Sets the loading status of the data source. The status is shown in the UI.
-     *
-     * @param {boolean} status true if loading, false otherwise
-     * @protected
-     */
-    setLoadingStatus(status) {
-        this.view.context.setDataLoadingStatus(this.view, status);
-    }
-
     /**
      * TODO: Get rid of this method.
      * Rendering should be requested by the collector.

package/dist/src/data/sources/lazy/singleAxisWindowedSource.js

@@ -111,7 +111,7 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
         // Abort previous requests
         this.#abortController.abort();
 
-        this.setLoadingStatus(true);
+        this.setLoadingStatus("loading");
 
         this.#abortController = new AbortController();
         const signal = this.#abortController.signal;
@@ -129,13 +129,13 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
             );
 
             if (!signal.aborted) {
-                this.setLoadingStatus(false);
+                this.setLoadingStatus("complete");
                 return resultByChrom;
             }
         } catch (e) {
             if (!signal.aborted) {
                 // TODO: Nice reporting of errors
-                this.setLoadingStatus(false);
+                this.setLoadingStatus("error", e.message);
                 throw e;
             }
         }

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

@@ -22,7 +22,7 @@ export default class NamedSource extends DataSource {
      * @param {function(string):any[]} provider Function that retrieves a dataset using a name
      */
     constructor(params, view, provider) {
-        super();
+        super(view);
 
         this.provider = provider;
         this.params = params;

package/dist/src/data/sources/sequenceSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sequenceSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/sequenceSource.js"],"names":[],"mappings":"AAMA;;;GAGG;AACH,0CAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,0DAKpD;AAED;IACI;;;;OAIG;IACH,oBAHW,OAAO,oBAAoB,EAAE,iBAAiB,QAC9C,OAAO,oBAAoB,EAAE,OAAO,EAgB9C;IAZG,sDAIC;IAUL,0BAcC;CAKJ;uBAnDsB,iBAAiB"}
+{"version":3,"file":"sequenceSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/sequenceSource.js"],"names":[],"mappings":"AAMA;;;GAGG;AACH,0CAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,0DAKpD;AAED;IACI;;;;OAIG;IACH,oBAHW,OAAO,oBAAoB,EAAE,iBAAiB,QAC9C,OAAO,oBAAoB,EAAE,OAAO,EAiB9C;IAZG,sDAIC;IAUL,0BAcC;CAKJ;uBApDsB,iBAAiB"}

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

@@ -19,7 +19,8 @@ export default class SequenceSource extends DataSource {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params, view) {
-        super();
+        super(view);
+
         this.sequence = activateExprRefProps(
             view.paramMediator,
             params.sequence,

package/dist/src/data/sources/urlSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AAQA;;;GAGG;AACH,gCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,gDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CA0DxC;uBApFsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AAQA;;;GAGG;AACH,gCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,gDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CA8DxC;uBAxFsB,iBAAiB"}

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

@@ -20,7 +20,7 @@ export default class UrlSource extends DataSource {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params, view) {
-        super();
+        super(view);
 
         this.params = activateExprRefProps(view.paramMediator, params, () =>
             this.load()
@@ -55,9 +55,7 @@ export default class UrlSource extends DataSource {
                     .load(url)
                     .catch((/** @type {Error} */ e) => {
                         // TODO: Include baseurl in the error message. Should be normalized, however.
-                        throw new Error(
-                            `Cannot fetch: ${this.baseUrl}${url}: ${e.message}`
-                        );
+                        throw new Error(`${url}: ${e.message}`);
                     })
             );
 
@@ -78,9 +76,15 @@ export default class UrlSource extends DataSource {
             }
         };
 
+        this.setLoadingStatus("loading");
         this.reset();
 
-        await Promise.all(urls.map((url) => load(url).then(readAndParse)));
+        try {
+            await Promise.all(urls.map((url) => load(url).then(readAndParse)));
+            this.setLoadingStatus("complete");
+        } catch (e) {
+            this.setLoadingStatus("error", e.message);
+        }
 
         this.complete();
     }

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

@@ -2,6 +2,7 @@
  * Clones the data objects that pass through.
  */
 export default class CloneTransform extends FlowNode {
+    constructor();
     /** @param {any} datum */
     handle: (datum: any) => void;
     /**

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

@@ -1 +1 @@
-{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;IAYY,yBAAyB;IACzB,gBALQ,GAAG,UAK2C;IAO1D;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAQtD;CAER;qBAtCsD,gBAAgB"}
+{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;IAKI,cA2BC;IApBO,yBAAyB;IACzB,gBALQ,GAAG,UAK2C;IAO1D;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAQtD;CAER;qBAtCsD,gBAAgB"}

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

@@ -8,6 +8,9 @@
  * segments and calculates weighted averages.
  */
 export default class CoverageTransform extends FlowNode {
+    /**
+     * @typedef {import("../flowNode.js").Datum} Datum
+     */
     /**
      * @param {import("../../spec/transform.js").CoverageParams} params
      */
@@ -25,7 +28,7 @@ export default class CoverageTransform extends FlowNode {
         end: string;
         chrom: string;
     };
-    createSegment: Function;
+    createSegment: (start: number, end: number, coverage: number, chrom?: string) => import("../flowNode.js").Datum;
     /**
      * End pos as priority, weight as value
      *

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

@@ -1 +1 @@
-{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":";AAKA;;;;;;;GAOG;AACH;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,sBADoB,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,uBADoB,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAGD,wBAgBC;IAED;;;;OAIG;IACH,MAFU,UAAU,MAAM,CAAC,CAEA;CAiIlC;qBAhMyC,gBAAgB;sBAHpC,WAAW"}
+{"version":3,"file":"coverage.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/coverage.js"],"names":[],"mappings":";AAKA;;;;;;;GAOG;AACH;IAKI;;OAEG;IAEH;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,cAAc,EAgD1D;IA5CG,yDAAoB;IAEpB,mDAAwC;IACxC,iDAAoC;IAEpC,mCAAmC;IACnC,sBADoB,GAAG,KAAE,MAAM,CAGT;IACtB,mCAAmC;IACnC,uBADoB,GAAG,KAAE,MAAM,CACsC;IAErE;;;;;MAKC;IAED,sEACsE,MAAM,oCAgBvE;IAEL;;;;OAIG;IACH,MAFU,UAAU,MAAM,CAAC,CAEA;CA0IlC;qBA7MyC,gBAAgB;sBAHpC,WAAW"}