@genome-spy/core 0.66.1 → 0.68.0

package/dist/src/genomeSpy/loadingIndicatorManager.js

@@ -5,45 +5,67 @@ import SPINNER from "../img/90-ring-with-bg.svg";
 export default class LoadingIndicatorManager {
     /** @type {HTMLElement} */
     #loadingIndicatorsElement;
+
     /**
-     * @type {Map<import("../view/view.js").default, { status: import("../types/viewContext.js").DataLoadingStatus, detail?: string }>}
+     * @type {import("./loadingStatusRegistry.js").default}
      */
-    #loadingViews;
+    #loadingStatusRegistry;
+
+    /** @type {(() => void) | null} */
+    #unsubscribe = null;
 
     /**
      * @param {HTMLElement} loadingIndicatorsElement
+     * @param {import("./loadingStatusRegistry.js").default} loadingStatusRegistry
      */
-    constructor(loadingIndicatorsElement) {
+    constructor(loadingIndicatorsElement, loadingStatusRegistry) {
         this.#loadingIndicatorsElement = loadingIndicatorsElement;
 
-        /**
-         * @type {Map<import("../view/view.js").default, { status: import("../types/viewContext.js").DataLoadingStatus, detail?: string }>}
-         */
-        this.#loadingViews = new Map();
-    }
+        this.#loadingStatusRegistry = loadingStatusRegistry;
 
-    /**
-     * @param {import("../view/view.js").default} view
-     * @param {import("../types/viewContext.js").DataLoadingStatus} status
-     * @param {string} [detail]
-     */
-    setDataLoadingStatus(view, status, detail) {
-        this.#loadingViews.set(view, { status, detail });
+        this.#unsubscribe = this.#loadingStatusRegistry.subscribe(() =>
+            this.updateLayout()
+        );
         this.updateLayout();
     }
 
+    destroy() {
+        if (this.#unsubscribe) {
+            this.#unsubscribe();
+            this.#unsubscribe = null;
+        }
+    }
+
     updateLayout() {
         /** @type {import("lit").TemplateResult[]} */
         const indicators = [];
 
-        const isSomethingVisible = () =>
-            [...this.#loadingViews.values()].some(
-                (v) => v.status == "loading" || v.status == "error"
-            );
+        const isSomethingVisible = () => {
+            for (const [, status] of this.#loadingStatusRegistry.entries()) {
+                if (status.status == "loading" || status.status == "error") {
+                    return true;
+                }
+            }
+            return false;
+        };
+
+        /** @type {{ status: import("../types/viewContext.js").DataLoadingStatus, detail?: string } | undefined} */
+        let fallbackStatus;
+        let hasVisibleWithCoords = false;
+
+        for (const [view, status] of this.#loadingStatusRegistry.entries()) {
+            const isVisible =
+                status.status == "loading" || status.status == "error";
 
-        for (const [view, status] of this.#loadingViews) {
             const c = view.coords;
+            if (!c && isVisible && !fallbackStatus) {
+                fallbackStatus = status;
+            }
             if (c) {
+                if (isVisible) {
+                    hasVisibleWithCoords = true;
+                }
+
                 const style = {
                     left: `${c.x}px`,
                     top: `${c.y}px`,
@@ -70,6 +92,32 @@ export default class LoadingIndicatorManager {
             }
         }
 
+        if (fallbackStatus && !hasVisibleWithCoords) {
+            const style = {
+                left: "0px",
+                top: "0px",
+                width: "100%",
+                height: "100%",
+            };
+            indicators.push(
+                html`<div style=${styleMap(style)}>
+                    <div class=${fallbackStatus.status}>
+                        ${fallbackStatus.status == "error"
+                            ? html`<span
+                                  >Loading
+                                  failed${fallbackStatus.detail
+                                      ? html`: ${fallbackStatus.detail}`
+                                      : nothing}</span
+                              >`
+                            : html`
+                                  <img src="${SPINNER}" alt="" />
+                                  <span>Loading...</span>
+                              `}
+                    </div>
+                </div>`
+            );
+        }
+
         // 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.

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

@@ -0,0 +1,52 @@
+/**
+ * @typedef {import("../view/view.js").default} View
+ * @typedef {import("../types/viewContext.js").DataLoadingStatus} DataLoadingStatus
+ * @typedef {{ status: DataLoadingStatus, detail?: string }} LoadingStatus
+ * @typedef {{ view: View, status: DataLoadingStatus, detail?: string }} LoadingStatusChange
+ */
+/**
+ * Central registry for per-view loading status that decouples data sources
+ * from UI rendering. Consumers can subscribe to changes and query the current
+ * status map when needed (e.g., for overlay rendering).
+ */
+export default class LoadingStatusRegistry {
+    /**
+     * @param {View} view
+     * @param {DataLoadingStatus} status
+     * @param {string} [detail]
+     */
+    set(view: View, status: DataLoadingStatus, detail?: string): void;
+    /**
+     * @param {View} view
+     */
+    delete(view: View): void;
+    /**
+     * @param {View} view
+     * @returns {LoadingStatus | undefined}
+     */
+    get(view: View): LoadingStatus | undefined;
+    /**
+     * @returns {IterableIterator<[View, LoadingStatus]>}
+     */
+    entries(): IterableIterator<[View, LoadingStatus]>;
+    /**
+     * Subscribe to status changes.
+     *
+     * @param {(change: LoadingStatusChange) => void} listener
+     * @returns {() => void} Unsubscribe callback
+     */
+    subscribe(listener: (change: LoadingStatusChange) => void): () => void;
+    #private;
+}
+export type View = import("../view/view.js").default;
+export type DataLoadingStatus = import("../types/viewContext.js").DataLoadingStatus;
+export type LoadingStatus = {
+    status: DataLoadingStatus;
+    detail?: string;
+};
+export type LoadingStatusChange = {
+    view: View;
+    status: DataLoadingStatus;
+    detail?: string;
+};
+//# sourceMappingURL=loadingStatusRegistry.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/src/genomeSpy/loadingStatusRegistry.js

@@ -0,0 +1,86 @@
+/**
+ * @typedef {import("../view/view.js").default} View
+ * @typedef {import("../types/viewContext.js").DataLoadingStatus} DataLoadingStatus
+ * @typedef {{ status: DataLoadingStatus, detail?: string }} LoadingStatus
+ * @typedef {{ view: View, status: DataLoadingStatus, detail?: string }} LoadingStatusChange
+ */
+
+/**
+ * Central registry for per-view loading status that decouples data sources
+ * from UI rendering. Consumers can subscribe to changes and query the current
+ * status map when needed (e.g., for overlay rendering).
+ */
+export default class LoadingStatusRegistry {
+    /** @type {Map<View, LoadingStatus>} */
+    #statuses = new Map();
+
+    /** @type {Set<(change: LoadingStatusChange) => void>} */
+    #listeners = new Set();
+
+    /**
+     * @param {View} view
+     * @param {DataLoadingStatus} status
+     * @param {string} [detail]
+     */
+    set(view, status, detail) {
+        if (!view) {
+            throw new Error("LoadingStatusRegistry.set requires a view.");
+        }
+
+        this.#statuses.set(view, { status, detail });
+
+        const change = { view, status, detail };
+        for (const listener of this.#listeners) {
+            listener(change);
+        }
+    }
+
+    /**
+     * @param {View} view
+     */
+    delete(view) {
+        const previous = this.#statuses.get(view);
+        if (!previous) {
+            return;
+        }
+
+        this.#statuses.delete(view);
+
+        const change = {
+            view,
+            status: previous.status,
+            detail: previous.detail,
+        };
+        for (const listener of this.#listeners) {
+            listener(change);
+        }
+    }
+
+    /**
+     * @param {View} view
+     * @returns {LoadingStatus | undefined}
+     */
+    get(view) {
+        return this.#statuses.get(view);
+    }
+
+    /**
+     * @returns {IterableIterator<[View, LoadingStatus]>}
+     */
+    entries() {
+        return this.#statuses.entries();
+    }
+
+    /**
+     * Subscribe to status changes.
+     *
+     * @param {(change: LoadingStatusChange) => void} listener
+     * @returns {() => void} Unsubscribe callback
+     */
+    subscribe(listener) {
+        this.#listeners.add(listener);
+        return () => {
+            this.#listeners.delete(listener);
+        };
+    }
+}

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

@@ -1 +1 @@
-{"version":3,"file":"viewContextFactory.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewContextFactory.js"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;;;;;;;;GASG;AACH,2CALW,OAAO,CAAC,WAAW,CAAC,GAAG;IAC7B,6BAA6B,CAAC,EAAE,CAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,QAAQ,GAAG,OAAO,iBAAiB,EAAE,UAAU,EAAE,YAAY,CAAC,EAAE,OAAO,0BAA0B,EAAE,OAAO,EAAE,UAAU,CAAC,EAAE,OAAO,iBAAiB,EAAE,OAAO,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,CAAC,IAAI,EAAE,OAAO,iBAAiB,EAAE,QAAQ,KAAK,IAAI,KAAK,OAAO,CAAC,OAAO,iBAAiB,EAAE,OAAO,CAAC,CAAA;CACvX,GACS,WAAW,CAkEvB;0BA7EY,OAAO,yBAAyB,EAAE,OAAO"}
+{"version":3,"file":"viewContextFactory.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewContextFactory.js"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;;;;;;;;GASG;AACH,2CALW,OAAO,CAAC,WAAW,CAAC,GAAG;IAC7B,6BAA6B,CAAC,EAAE,CAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,QAAQ,GAAG,OAAO,iBAAiB,EAAE,UAAU,EAAE,YAAY,CAAC,EAAE,OAAO,0BAA0B,EAAE,OAAO,EAAE,UAAU,CAAC,EAAE,OAAO,iBAAiB,EAAE,OAAO,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,CAAC,IAAI,EAAE,OAAO,iBAAiB,EAAE,QAAQ,KAAK,IAAI,KAAK,OAAO,CAAC,OAAO,iBAAiB,EAAE,OAAO,CAAC,CAAA;CACvX,GACS,WAAW,CAiEvB;0BA5EY,OAAO,yBAAyB,EAAE,OAAO"}

package/dist/src/genomeSpy/viewContextFactory.js

@@ -58,7 +58,6 @@ export function createViewContext(options) {
         "updateTooltip",
         "getNamedDataFromProvider",
         "getCurrentHover",
-        "setDataLoadingStatus",
         "addKeyboardListener",
         "addBroadcastListener",
         "removeBroadcastListener",

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

@@ -9,4 +9,14 @@
  * @returns {Promise<import("../data/dataFlow.js").default>}
  */
 export function initializeViewData(viewRoot: import("../view/view.js").default, dataFlow: import("../data/dataFlow.js").default, fontManager: import("../fonts/bmFontManager.js").default, onDataFlowBuilt: (dataFlow: import("../data/dataFlow.js").default) => void): Promise<import("../data/dataFlow.js").default>;
+/**
+ * Initializes data flow and graphics for visible views that were previously
+ * skipped. Intended for view-visibility toggles.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export function initializeVisibleViewData(viewRoot: import("../view/view.js").default, dataFlow: import("../data/dataFlow.js").default, fontManager: import("../fonts/bmFontManager.js").default): Promise<import("../data/dataFlow.js").default>;
 //# sourceMappingURL=viewDataInit.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"viewDataInit.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewDataInit.js"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,6CANW,OAAO,iBAAiB,EAAE,OAAO,YACjC,OAAO,qBAAqB,EAAE,OAAO,eACrC,OAAO,2BAA2B,EAAE,OAAO,mBAC3C,CAAC,QAAQ,EAAE,OAAO,qBAAqB,EAAE,OAAO,KAAK,IAAI,GACvD,OAAO,CAAC,OAAO,qBAAqB,EAAE,OAAO,CAAC,CA0B1D"}
+{"version":3,"file":"viewDataInit.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewDataInit.js"],"names":[],"mappings":"AAOA;;;;;;;;;GASG;AACH,6CANW,OAAO,iBAAiB,EAAE,OAAO,YACjC,OAAO,qBAAqB,EAAE,OAAO,eACrC,OAAO,2BAA2B,EAAE,OAAO,mBAC3C,CAAC,QAAQ,EAAE,OAAO,qBAAqB,EAAE,OAAO,KAAK,IAAI,GACvD,OAAO,CAAC,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAkC1D;AAED;;;;;;;;GAQG;AACH,oDALW,OAAO,iBAAiB,EAAE,OAAO,YACjC,OAAO,qBAAqB,EAAE,OAAO,eACrC,OAAO,2BAA2B,EAAE,OAAO,GACzC,OAAO,CAAC,OAAO,qBAAqB,EAAE,OAAO,CAAC,CA2E1D"}

package/dist/src/genomeSpy/viewDataInit.js

@@ -3,6 +3,7 @@ import {
     loadViewSubtreeData,
 } from "../data/flowInit.js";
 import { finalizeSubtreeGraphics } from "../view/viewUtils.js";
+import { VISIT_SKIP } from "../view/view.js";
 
 /**
  * Initializes the view data pipeline: builds the flow graph, awaits fonts,
@@ -20,9 +21,13 @@ export async function initializeViewData(
     fontManager,
     onDataFlowBuilt
 ) {
+    const visibilityPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => view.isConfiguredVisible();
     const { dataFlow: builtDataFlow, graphicsPromises } = initializeViewSubtree(
         viewRoot,
-        dataFlow
+        dataFlow,
+        visibilityPredicate
     );
     onDataFlowBuilt(builtDataFlow);
 
@@ -33,9 +38,168 @@ export async function initializeViewData(
     await fontManager.waitUntilReady();
 
     // Find all data sources and initiate loading.
-    await loadViewSubtreeData(viewRoot, new Set(builtDataFlow.dataSources));
+    await loadViewSubtreeData(
+        viewRoot,
+        new Set(builtDataFlow.dataSources),
+        visibilityPredicate
+    );
+
+    await finalizeSubtreeGraphics(graphicsPromises);
+
+    return builtDataFlow;
+}
+
+/**
+ * Initializes data flow and graphics for visible views that were previously
+ * skipped. Intended for view-visibility toggles.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export async function initializeVisibleViewData(
+    viewRoot,
+    dataFlow,
+    fontManager
+) {
+    // Initialize dataflow/graphics for views that have become visible since the
+    // initial load, while avoiding unnecessary data source reloads. If a view
+    // attaches downstream of an already completed collector, repropagate that
+    // collector instead of reloading the source.
+    const visibilityPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => view.isConfiguredVisible();
+    const visibleViews = collectVisibleViews(viewRoot, visibilityPredicate);
+    const viewsToInitialize = visibleViews.filter(
+        (view) => view.getDataInitializationState() === "none"
+    );
+
+    if (viewsToInitialize.length === 0) {
+        return dataFlow;
+    }
+
+    const viewsToInitializeSet = new Set(viewsToInitialize);
+    const viewInitializationPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => viewsToInitializeSet.has(view);
+
+    /** @type {Set<import("../data/collector.js").default>} */
+    const collectorsToRepropagate = new Set();
+    /** @type {import("../view/view.js").default[]} */
+    const viewsNeedingLoad = [];
+    for (const view of viewsToInitialize) {
+        if (view.spec.data) {
+            viewsNeedingLoad.push(view);
+            continue;
+        }
+        const collector = findCompletedAncestorCollector(view);
+        if (collector) {
+            collectorsToRepropagate.add(collector);
+        } else {
+            viewsNeedingLoad.push(view);
+        }
+    }
+
+    const { dataFlow: builtDataFlow, graphicsPromises } = initializeViewSubtree(
+        viewRoot,
+        dataFlow,
+        visibilityPredicate,
+        viewInitializationPredicate
+    );
+
+    await fontManager.waitUntilReady();
+
+    for (const collector of collectorsToRepropagate) {
+        collector.repropagate();
+    }
+
+    if (viewsNeedingLoad.length) {
+        const dataSourceRoots = collectDataSourceRoots(viewsNeedingLoad);
+        await Promise.all(
+            Array.from(dataSourceRoots.entries()).map(
+                ([subtreeRoot, dataSources]) =>
+                    loadViewSubtreeData(subtreeRoot, dataSources, undefined, {
+                        // If a source is already loading, schedule a reload so new branches
+                        // added during lazy init receive a complete data propagation.
+                        queueReload: true,
+                    })
+            )
+        );
+    }
 
     await finalizeSubtreeGraphics(graphicsPromises);
 
     return builtDataFlow;
 }
+
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {(view: import("../view/view.js").default) => boolean} viewFilter
+ * @returns {import("../view/view.js").default[]}
+ */
+function collectVisibleViews(viewRoot, viewFilter) {
+    /** @type {import("../view/view.js").default[]} */
+    const views = [];
+    viewRoot.visit((view) => {
+        if (!viewFilter(view)) {
+            return VISIT_SKIP;
+        }
+        views.push(view);
+    });
+    return views;
+}
+
+/**
+ * @param {import("../view/view.js").default[]} views
+ * @returns {Map<import("../view/view.js").default, Set<import("../data/sources/dataSource.js").default>>}
+ */
+function collectDataSourceRoots(views) {
+    /** @type {Map<import("../view/view.js").default, Set<import("../data/sources/dataSource.js").default>>} */
+    const roots = new Map();
+
+    for (const view of views) {
+        let current = view;
+        while (current && !current.flowHandle?.dataSource) {
+            current = current.dataParent;
+        }
+
+        if (!current?.flowHandle?.dataSource) {
+            if (view.spec.data) {
+                throw new Error(
+                    "No data source found for view " + view.getPathString()
+                );
+            }
+            // Some views are data-less (constants or references); they don't
+            // participate in data loading but still need graphics init.
+            continue;
+        }
+
+        let dataSources = roots.get(current);
+        if (!dataSources) {
+            dataSources = new Set();
+            roots.set(current, dataSources);
+        }
+        dataSources.add(current.flowHandle.dataSource);
+    }
+
+    return roots;
+}
+
+/**
+ * Finds the nearest completed collector in the dataParent chain.
+ *
+ * @param {import("../view/view.js").default} view
+ * @returns {import("../data/collector.js").default | undefined}
+ */
+function findCompletedAncestorCollector(view) {
+    let current = view.dataParent;
+    while (current) {
+        const collector = current.flowHandle?.collector;
+        if (collector) {
+            return collector.completed ? collector : undefined;
+        }
+        current = current.dataParent;
+    }
+    return undefined;
+}

package/dist/src/genomeSpy/viewDataInit.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=viewDataInit.test.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"viewDataInit.test.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewDataInit.test.js"],"names":[],"mappings":""}

package/dist/src/genomeSpy.d.ts

@@ -66,8 +66,6 @@ export default class GenomeSpy {
      * @param {any} [payload]
      */
     broadcast(type: BroadcastEventType, payload?: any): void;
-    loadingMessageElement: HTMLElement;
-    loadingIndicatorsElement: HTMLElement;
     tooltip: import("./utils/ui/tooltip.js").default;
     /**
      * Unregisters all listeners, removes all created dom elements, removes all css classes from the container
@@ -78,6 +76,7 @@ export default class GenomeSpy {
      * @returns {Promise<boolean>} true if the launch was successful
      */
     launch(): Promise<boolean>;
+    initializeVisibleViewData(): Promise<void>;
     registerMouseEvents(): void;
     /**
      * This method should be called in a mouseMove handler. If not called, the

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

@@ -1 +1 @@
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