@genome-spy/core 0.64.0 → 0.65.0

package/dist/src/view/view.js

@@ -86,6 +86,11 @@ export default class View {
      */
     opacityFunction = defaultOpacityFunction;
 
+    /**
+     * @type {(() => void)[]}
+     */
+    #disposers = [];
+
     /**
      * Coords of the view for each facet, recorded during the last layout rendering pass.
      * Most views have only one facet, so the map is usually of size 1.
@@ -136,6 +141,11 @@ export default class View {
             ...options,
         };
 
+        /**
+         * @type {import("../data/flowHandle.js").FlowHandle | undefined}
+         */
+        this.flowHandle = undefined;
+
         /**
          * Whether GridView or equivalent should draw axis and grid lines for this view.
          * TODO: Use view options for this.
@@ -497,7 +507,7 @@ export default class View {
     }
 
     /**
-     * Get all descendants of this view in depth-first order.
+     * Get this view and all descendants in depth-first order.
      */
     getDescendants() {
         /** @type {View[]} */
@@ -508,6 +518,52 @@ export default class View {
         return descendants;
     }
 
+    /**
+     * Release resources owned by this view.
+     */
+    dispose() {
+        for (const disposer of this.#disposers) {
+            disposer();
+        }
+        this.#disposers.length = 0;
+
+        const handle = this.flowHandle;
+
+        if (handle?.collector) {
+            this.context.dataFlow.pruneCollectorBranch(handle.collector);
+            this.context.dataFlow.removeCollector(handle.collector);
+        }
+
+        if (
+            handle?.dataSource &&
+            handle.dataSource.view === this &&
+            !handle.dataSource.identifier
+        ) {
+            this.context.dataFlow.removeDataSource(handle.dataSource);
+        }
+
+        this.flowHandle = undefined;
+    }
+
+    /**
+     * @param {() => void} disposer
+     */
+    registerDisposer(disposer) {
+        this.#disposers.push(disposer);
+    }
+
+    /**
+     * Dispose this view and all descendants in post-order.
+     */
+    disposeSubtree() {
+        /** @type {Visitor} */
+        const visitor = () => undefined;
+        visitor.postOrder = (view) => {
+            view.dispose();
+        };
+        this.visit(visitor);
+    }
+
     /**
      * Called after all scales in the view hierarchy have been resolved.
      */

package/dist/src/view/viewDispose.test.d.ts

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

package/dist/src/view/viewDispose.test.d.ts.map

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

package/dist/src/view/viewDispose.test.js

@@ -0,0 +1,110 @@
+import { describe, expect, test } from "vitest";
+
+import ConcatView from "./concatView.js";
+import DataSource from "../data/sources/dataSource.js";
+import UnitView from "./unitView.js";
+import View from "./view.js";
+import { create, createTestViewContext } from "./testUtils.js";
+
+class DisposableView extends View {
+    /** @type {boolean} */
+    disposed = false;
+
+    /**
+     * @param {string} name
+     * @param {import("../types/viewContext.js").default} context
+     * @param {import("./containerView.js").default} layoutParent
+     * @param {import("./view.js").default} dataParent
+     */
+    constructor(name, context, layoutParent, dataParent) {
+        /** @type {import("../spec/view.js").LayerSpec} */
+        const spec = { name, layer: [] };
+        super(spec, context, layoutParent, dataParent, name);
+    }
+
+    dispose() {
+        super.dispose();
+        this.disposed = true;
+    }
+}
+
+describe("View disposal", () => {
+    test("removes scale and axis resolutions for disposed unit views", async () => {
+        /** @type {import("../spec/view.js").UnitSpec} */
+        const spec = {
+            data: {
+                values: [
+                    {
+                        x: 1,
+                        y: 2,
+                    },
+                ],
+            },
+            mark: "point",
+            encoding: {
+                x: { field: "x", type: "quantitative" },
+                y: { field: "y", type: "quantitative" },
+            },
+        };
+
+        const view = await create(spec, UnitView);
+
+        expect(view.getScaleResolution("x")).toBeDefined();
+        expect(view.getAxisResolution("x")).toBeDefined();
+
+        view.disposeSubtree();
+
+        expect(view.getScaleResolution("x")).toBeUndefined();
+        expect(view.getAxisResolution("x")).toBeUndefined();
+    });
+
+    test("disposes replaced grid children", () => {
+        const context = createTestViewContext();
+        const parent = new ConcatView(
+            { hconcat: [] },
+            context,
+            null,
+            null,
+            "c"
+        );
+
+        const childA = new DisposableView("a", context, parent, parent);
+        const childB = new DisposableView("b", context, parent, parent);
+        parent.setChildren([childA, childB]);
+
+        const childC = new DisposableView("c", context, parent, parent);
+        parent.setChildren([childC]);
+
+        expect(childA.disposed).toBe(true);
+        expect(childB.disposed).toBe(true);
+        expect(childC.disposed).toBe(false);
+
+        const childD = new DisposableView("d", context, parent, parent);
+        parent.replaceChild(childC, childD);
+
+        expect(childC.disposed).toBe(true);
+        expect(childD.disposed).toBe(false);
+    });
+
+    test("removes dataflow hosts on dispose", () => {
+        const context = createTestViewContext();
+        const parent = new ConcatView(
+            { hconcat: [] },
+            context,
+            null,
+            null,
+            "c"
+        );
+        const child = new DisposableView("a", context, parent, parent);
+
+        const dataSource = new DataSource(child);
+        context.dataFlow.addDataSource(dataSource);
+        child.flowHandle = { dataSource };
+
+        expect(child.flowHandle.dataSource).toBe(dataSource);
+
+        child.disposeSubtree();
+
+        expect(child.flowHandle).toBeUndefined();
+    });
+});

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

@@ -35,11 +35,11 @@ export function checkForDuplicateScaleNames(root: View): void;
  */
 export function setImplicitScaleNames(root: View): void;
 /**
- * @param {View} root
- * @param {import("../data/dataFlow.js").default<View>} [existingFlow] Add data flow
- *      graphs to an existing DataFlow object.
+ * @param {Promise<import("../marks/mark.js").default>[]} graphicsPromises
+ * @param {() => boolean} [shouldFinalize]
+ * @returns {Promise<void>}
  */
-export function initializeData(root: View, existingFlow?: import("../data/dataFlow.js").default<View>): Promise<import("../data/dataFlow.js").default<View>>;
+export function finalizeSubtreeGraphics(graphicsPromises: Promise<import("../marks/mark.js").default>[], shouldFinalize?: () => boolean): Promise<void>;
 /**
  *
  * @param {View} view

package/dist/src/view/viewUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AAWA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,GAC9E,IAAI,IAAI,aAAa,CAIjC;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,GACjF,IAAI,IAAI,YAAY,CAOhC;AAED;;;GAGG;AACH,+BAFW,IAAI,6EAMd;AAED;;;;GAIG;AACH,wCAFW,IAAI,UASd;AAED;;GAEG;AACH,kDAFW,IAAI,QAiBd;AAED;;;;;;;GAOG;AACH,4CAFW,IAAI,QAUd;AAED;;;;GAIG;AACH,qCAJW,IAAI,iBACJ,OAAO,qBAAqB,EAAE,OAAO,CAAC,IAAI,CAAC,wDAcrD;AAED;;;GAGG;AACH,wCAFW,IAAI;UAGO,QAAQ;aAAW,OAAO,oBAAoB,EAAE,OAAO;WAAS,OAAO,oBAAoB,EAAE,KAAK;UAAQ,OAAO,oBAAoB,EAAE,IAAI;IAqBhK;AAED;;;;;GAKG;AACH,2CALW,OAAO,iBAAiB,EAAE,UAAU,WACpC,MAAM,eACN,OAAO,yBAAyB,EAAE,OAAO,GACvC,OAAO,CAAC,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CAsCvD;AAED;;GAEG;AACH,yCAFW,CAAS,IAAI,EAAJ,IAAI,EAAE,IAAM,EAAN,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;;;;GAMG;AACH,4CAJW,IAAI,QACJ,MAAM,GACJ,IAAI,EAAE,CAalB;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAED;;GAEG;AACH,8CAFW,OAAO,WAAW,EAAE,OAAO;;;EAoBrC;iBA3Q4C,WAAW;qBAFnC,eAAe"}
+{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AASA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,GAC9E,IAAI,IAAI,aAAa,CAIjC;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,GACjF,IAAI,IAAI,YAAY,CAOhC;AAED;;;GAGG;AACH,+BAFW,IAAI,6EAMd;AAED;;;;GAIG;AACH,wCAFW,IAAI,UASd;AAED;;GAEG;AACH,kDAFW,IAAI,QAiBd;AAED;;;;;;;GAOG;AACH,4CAFW,IAAI,QAUd;AAED;;;;GAIG;AACH,0DAJW,OAAO,CAAC,OAAO,kBAAkB,EAAE,OAAO,CAAC,EAAE,mBAC7C,MAAM,OAAO,GACX,OAAO,CAAC,IAAI,CAAC,CAmBzB;AAED;;;GAGG;AACH,wCAFW,IAAI;UAGO,QAAQ;aAAW,OAAO,oBAAoB,EAAE,OAAO;WAAS,OAAO,oBAAoB,EAAE,KAAK;UAAQ,OAAO,oBAAoB,EAAE,IAAI;IAqBhK;AAED;;;;;GAKG;AACH,2CALW,OAAO,iBAAiB,EAAE,UAAU,WACpC,MAAM,eACN,OAAO,yBAAyB,EAAE,OAAO,GACvC,OAAO,CAAC,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CAsCvD;AAED;;GAEG;AACH,yCAFW,CAAS,IAAI,EAAJ,IAAI,EAAE,IAAM,EAAN,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;;;;GAMG;AACH,4CAJW,IAAI,QACJ,MAAM,GACJ,IAAI,EAAE,CAalB;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAED;;GAEG;AACH,8CAFW,OAAO,WAAW,EAAE,OAAO;;;EAoBrC;iBA/Q4C,WAAW;qBAFnC,eAAe"}

package/dist/src/view/viewUtils.js

@@ -3,8 +3,6 @@ import { isObject, isString } from "vega-util";
 import UnitView from "./unitView.js";
 // eslint-disable-next-line no-unused-vars
 import View, { VISIT_SKIP, VISIT_STOP } from "./view.js";
-import { buildDataFlow } from "./flowBuilder.js";
-import { optimizeDataFlow } from "../data/flowOptimizer.js";
 import { isFieldDef, primaryPositionalChannels } from "../encoder/encoder.js";
 import { rollup } from "d3-array";
 import { concatUrl, getDirectory } from "../utils/url.js";
@@ -93,21 +91,27 @@ export function setImplicitScaleNames(root) {
 }
 
 /**
- * @param {View} root
- * @param {import("../data/dataFlow.js").default<View>} [existingFlow] Add data flow
- *      graphs to an existing DataFlow object.
+ * @param {Promise<import("../marks/mark.js").default>[]} graphicsPromises
+ * @param {() => boolean} [shouldFinalize]
+ * @returns {Promise<void>}
  */
-export async function initializeData(root, existingFlow) {
-    const flow = buildDataFlow(root, existingFlow);
-    optimizeDataFlow(flow);
-    flow.initialize();
-
-    /** @type {Promise<void>[]} */
-    const promises = flow.dataSources.map((dataSource) => dataSource.load());
-
-    await Promise.all(promises);
+export function finalizeSubtreeGraphics(
+    graphicsPromises,
+    shouldFinalize = () => true
+) {
+    return Promise.allSettled(graphicsPromises).then((results) => {
+        if (!shouldFinalize()) {
+            return;
+        }
 
-    return flow;
+        for (const result of results) {
+            if ("value" in result) {
+                result.value.finalizeGraphicsInitialization();
+            } else if ("reason" in result) {
+                console.error(result.reason);
+            }
+        }
+    });
 }
 
 /**

package/dist/src/view/viewUtils.test.d.ts

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

package/dist/src/view/viewUtils.test.d.ts.map

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

package/dist/src/view/viewUtils.test.js

@@ -0,0 +1,87 @@
+import { describe, expect, test, vi } from "vitest";
+
+import { createTestViewContext } from "./testUtils.js";
+import { finalizeSubtreeGraphics } from "./viewUtils.js";
+import { initializeViewSubtree } from "../data/flowInit.js";
+
+describe("initializeViewSubtree", () => {
+    test("initializes data flow for a subtree only", async () => {
+        const context = createTestViewContext();
+
+        /** @type {import("../spec/view.js").HConcatSpec} */
+        const spec = {
+            hconcat: [
+                {
+                    data: {
+                        values: [{ x: 1 }],
+                    },
+                    mark: "point",
+                    encoding: {
+                        x: { field: "x", type: "quantitative" },
+                    },
+                },
+                {
+                    data: {
+                        values: [{ x: 2 }],
+                    },
+                    mark: "point",
+                    encoding: {
+                        x: { field: "x", type: "quantitative" },
+                    },
+                },
+            ],
+        };
+
+        const root = await context.createOrImportView(spec, null, null, "root");
+        const concatRoot = /** @type {import("./concatView.js").default} */ (
+            root
+        );
+        const child = concatRoot.children[0];
+        const otherChild = concatRoot.children[1];
+
+        const { dataSources, graphicsPromises, unitViews } =
+            initializeViewSubtree(child, context.dataFlow);
+
+        expect(dataSources.size).toBe(1);
+        expect(unitViews.length).toBe(1);
+        expect(graphicsPromises.length).toBe(0);
+
+        expect(child.flowHandle?.dataSource).toBeDefined();
+        expect(otherChild.flowHandle?.dataSource).toBeUndefined();
+    });
+});
+
+describe("finalizeSubtreeGraphics", () => {
+    test("finalizes marks when allowed", async () => {
+        const markA = /** @type {import("../marks/mark.js").default} */ (
+            /** @type {unknown} */ ({
+                finalizeGraphicsInitialization: vi.fn(),
+            })
+        );
+        const markB = /** @type {import("../marks/mark.js").default} */ (
+            /** @type {unknown} */ ({
+                finalizeGraphicsInitialization: vi.fn(),
+            })
+        );
+
+        await finalizeSubtreeGraphics([
+            Promise.resolve(markA),
+            Promise.resolve(markB),
+        ]);
+
+        expect(markA.finalizeGraphicsInitialization).toHaveBeenCalledTimes(1);
+        expect(markB.finalizeGraphicsInitialization).toHaveBeenCalledTimes(1);
+    });
+
+    test("skips finalization when predicate is false", async () => {
+        const mark = /** @type {import("../marks/mark.js").default} */ (
+            /** @type {unknown} */ ({
+                finalizeGraphicsInitialization: vi.fn(),
+            })
+        );
+
+        await finalizeSubtreeGraphics([Promise.resolve(mark)], () => false);
+
+        expect(mark.finalizeGraphicsInitialization).not.toHaveBeenCalled();
+    });
+});

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.64.0",
+  "version": "0.65.0",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -36,14 +36,12 @@
     "postpack": "node scripts/postpack.mjs"
   },
   "dependencies": {
-    "@gmod/bam": "^4.0.1",
-    "@gmod/bbi": "^5.0.2",
-    "@gmod/bed": "^2.1.3",
-    "@gmod/bgzf-filehandle": "^1.5.5",
-    "@gmod/gff": "^1.3.0",
-    "@gmod/indexedfasta": "^2.1.1",
-    "@gmod/tabix": "^1.6.1",
-    "@gmod/vcf": "^6.0.0",
+    "@gmod/bam": "^7.0.5",
+    "@gmod/bbi": "^7.1.0",
+    "@gmod/bed": "^2.1.7",
+    "@gmod/indexedfasta": "^4.0.7",
+    "@gmod/tabix": "^3.1.2",
+    "@gmod/vcf": "^6.1.0",
     "@types/d3-array": "^3.2.2",
     "@types/d3-dsv": "^3.0.7",
     "@types/d3-ease": "^3.0.2",
@@ -56,6 +54,8 @@
     "d3-format": "^3.1.0",
     "events": "^3.3.0",
     "flatqueue": "^2.0.3",
+    "generic-filehandle2": "^2.0.14",
+    "gff-nostream": "^2.0.0",
     "internmap": "^2.0.3",
     "lit": "^3.3.0",
     "twgl.js": "^4.19.1",
@@ -67,5 +67,5 @@
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "a1edb39d7a50b3a2b05c9ee0d860170065fd5ad6"
+  "gitHead": "15ad2aca88eff4e1ba45a6956c3f2a04a01e6d26"
 }

package/dist/bundle/__vite-browser-external-C--ziKoh.js

@@ -1,8 +0,0 @@
-const e = {}, t = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
-  __proto__: null,
-  default: e
-}, Symbol.toStringTag, { value: "Module" }));
-export {
-  e as L,
-  t as _
-};

package/dist/bundle/_commonjsHelpers-DjF3Plf2.js

@@ -1,26 +0,0 @@
-function n(e) {
-  return e && e.__esModule && Object.prototype.hasOwnProperty.call(e, "default") ? e.default : e;
-}
-function c(e) {
-  if (e.__esModule) return e;
-  var o = e.default;
-  if (typeof o == "function") {
-    var t = function r() {
-      return this instanceof r ? Reflect.construct(o, arguments, this.constructor) : o.apply(this, arguments);
-    };
-    t.prototype = o.prototype;
-  } else t = {};
-  return Object.defineProperty(t, "__esModule", { value: !0 }), Object.keys(e).forEach(function(r) {
-    var u = Object.getOwnPropertyDescriptor(e, r);
-    Object.defineProperty(t, r, u.get ? u : {
-      enumerable: !0,
-      get: function() {
-        return e[r];
-      }
-    });
-  }), t;
-}
-export {
-  c as a,
-  n as g
-};