@genome-spy/core 0.29.0 → 0.30.2

package/package.json

@@ -7,17 +7,20 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.29.0",
+  "version": "0.30.2",
   "main": "dist/index.js",
-  "module": "src/index.js",
+  "module": "dist/index.es.js",
   "exports": {
-    ".": "./src/index.js",
+    ".": {
+      "import": "./dist/index.es.js",
+      "require": "./dist/index.js"
+    },
     "./*": "./src/*",
-    "./schema.json": "./dist/schema.json"
+    "./schema.json": "./dist/schema.json",
+    "./style.css": "./dist/style.css"
   },
   "files": [
-    "dist/",
-    "src/"
+    "dist/"
   ],
   "repository": {
     "type": "git",
@@ -53,5 +56,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "465004bcc575262ef7cee3932502a3bfee1da4e1"
+  "gitHead": "26530163d4f60172bfe45c45cd488c54a69942ca"
 }

package/src/data/collector.js

@@ -1,183 +0,0 @@
-import { InternMap } from "internmap";
-import { group } from "d3-array";
-import { compare } from "vega-util";
-import iterateNestedMaps from "../utils/iterateNestedMaps";
-import FlowNode, { isFacetBatch } from "./flowNode";
-import { field } from "../utils/field";
-import { asArray } from "../utils/arrayUtils";
-
-/**
- * Collects (materializes) the data that flows through this node.
- * The collected data can be optionally grouped and sorted.
- *
- * Grouping is primarily intended for handling faceted data.
- *
- * @typedef {import("../spec/transform").CollectParams} CollectParams
- * @typedef {import("./flowNode").Data} Data
- */
-export default class Collector extends FlowNode {
-    /**
-     * @param {CollectParams} [params]
-     */
-    constructor(params) {
-        super();
-
-        this.params = params ?? { type: "collect" };
-
-        /** @type {(function(Collector):void)[]} */
-        this.observers = [];
-
-        /** @type {Map<any | any[], Data>} TODO: proper type for key */
-        this.facetBatches = undefined;
-
-        this._init();
-    }
-
-    _init() {
-        /** @type {Data} */
-        this._data = [];
-
-        // TODO: Consider nested maps
-        this.facetBatches = new InternMap([], JSON.stringify);
-        this.facetBatches.set(undefined, this._data);
-    }
-
-    reset() {
-        super.reset();
-        this._init();
-    }
-
-    /**
-     *
-     * @param {import("./flowNode").Datum} datum
-     */
-    handle(datum) {
-        this._data.push(datum);
-    }
-
-    /**
-     * @param {import("./flowBatch").FlowBatch} flowBatch
-     */
-    beginBatch(flowBatch) {
-        if (isFacetBatch(flowBatch)) {
-            this._data = [];
-            this.facetBatches.set(asArray(flowBatch.facetId), this._data);
-        }
-    }
-
-    complete() {
-        const sort = this.params?.sort;
-        // Vega's "compare" function is incredibly slow (uses megamorphic field accessor)
-        // TODO: Implement a replacement for static data types
-        const comparator = sort ? compare(sort.field, sort.order) : undefined;
-
-        /** @param {any[]} data */
-        const sortData = (data) => {
-            if (comparator) {
-                data.sort(comparator);
-            }
-        };
-
-        if (this.params.groupby?.length) {
-            if (this.facetBatches.size > 1) {
-                throw new Error("TODO: Support faceted data!");
-            }
-
-            const accessors = this.params.groupby.map((fieldName) =>
-                field(fieldName)
-            );
-            // @ts-ignore
-            const groups = group(this._data, ...accessors);
-
-            this.facetBatches.clear();
-            for (const [key, data] of iterateNestedMaps(groups)) {
-                this.facetBatches.set(key, data);
-            }
-        }
-
-        for (const data of this.facetBatches.values()) {
-            // TODO: Only sort if not already sorted
-            sortData(data);
-        }
-
-        if (this.children.length) {
-            for (const [key, data] of this.facetBatches.entries()) {
-                if (key) {
-                    /** @type {import("./flowBatch").FacetBatch} */
-                    const facetBatch = { type: "facet", facetId: key };
-                    for (const child of this.children) {
-                        child.beginBatch(facetBatch);
-                    }
-                }
-                for (const datum of data) {
-                    this._propagate(datum);
-                }
-            }
-        }
-
-        super.complete();
-
-        for (const observer of this.observers) {
-            observer(this);
-        }
-    }
-
-    /**
-     * @returns {Iterable<import("./flowNode").Datum>}
-     */
-    getData() {
-        this._checkStatus();
-
-        switch (this.facetBatches.size) {
-            case 0:
-                return [];
-            case 1:
-                return [...this.facetBatches.values()][0];
-            default: {
-                const groups = this.facetBatches;
-                return {
-                    [Symbol.iterator]: function* generator() {
-                        for (const data of groups.values()) {
-                            for (let i = 0; i < data.length; i++) {
-                                yield data[i];
-                            }
-                        }
-                    },
-                };
-            }
-        }
-    }
-
-    /**
-     *
-     * @param {(datum: import("./flowNode").Datum) => void} visitor
-     */
-    visitData(visitor) {
-        this._checkStatus();
-
-        for (const data of this.facetBatches.values()) {
-            for (let i = 0; i < data.length; i++) {
-                visitor(data[i]);
-            }
-        }
-    }
-
-    /**
-     * Returns the total number of data items collected.
-     */
-    getItemCount() {
-        let count = 0;
-        for (const data of this.facetBatches.values()) {
-            count += data.length;
-        }
-        return count;
-    }
-
-    _checkStatus() {
-        if (!this.completed) {
-            throw new Error(
-                "Data propagation is not completed! No data are available."
-            );
-        }
-    }
-}

package/src/data/collector.test.js

@@ -1,84 +0,0 @@
-import { expect, test } from "vitest";
-
-import Collector from "./collector";
-
-const data = [1, 5, 2, 4, 3].map((x) => ({ x }));
-
-test("Collector collects data", () => {
-    const collector = new Collector();
-
-    for (const d of data) {
-        collector.handle(d);
-    }
-    collector.complete();
-
-    expect(collector.getData()).toEqual(data);
-});
-
-test("Collector collects and sorts data", () => {
-    const collector = new Collector({
-        type: "collect",
-        sort: { field: ["x"] },
-    });
-
-    for (const d of data) {
-        collector.handle(d);
-    }
-    collector.complete();
-
-    expect([...collector.getData()]).toEqual(
-        [1, 2, 3, 4, 5].map((x) => ({ x }))
-    );
-});
-
-test("Collector collects, groups, and sorts data", () => {
-    const collector = new Collector({
-        type: "collect",
-        sort: { field: ["x"] },
-        groupby: ["a", "b"],
-    });
-
-    const data = [
-        { a: 1, b: 1, x: 1 },
-        { a: 1, b: 2, x: 2 },
-        { a: 1, b: 2, x: 3 },
-        { a: 2, b: 1, x: 4 },
-        { a: 2, b: 1, x: 5 },
-        { a: 2, b: 2, x: 6 },
-    ];
-
-    for (const d of data) {
-        collector.handle(d);
-    }
-    collector.complete();
-
-    const cd = [...collector.getData()];
-
-    expect(cd.map((d) => ({ x: d.x }))).toEqual(
-        [1, 2, 3, 4, 5, 6].map((x) => ({ x }))
-    );
-
-    /** @param {any[]} group*/
-    const getGroupX = (group) =>
-        collector.facetBatches.get(group).map((d) => d.x);
-
-    expect(getGroupX([1, 1])).toEqual([1]);
-    expect(getGroupX([1, 2])).toEqual([2, 3]);
-    expect(getGroupX([2, 1])).toEqual([4, 5]);
-    expect(getGroupX([2, 2])).toEqual([6]);
-
-    expect(new Set(collector.facetBatches.keys())).toEqual(
-        new Set([
-            [1, 1],
-            [1, 2],
-            [2, 1],
-            [2, 2],
-        ])
-    );
-});
-
-test("Collector throws on incomplete flow", () => {
-    const collector = new Collector();
-
-    expect(() => collector.getData()).toThrow();
-});

package/src/data/dataFlow.js

@@ -1,148 +0,0 @@
-/**
- *
- * @typedef {import("./sources/dataSource").default} DataSource
- * @typedef {import("./collector").default} Collector
- */
-
-import NamedSource from "./sources/namedSource";
-
-/**
- * @template H A key (string, object, whatever) that is used to retrieve
- *      data sources and collectors.
- */
-export default class DataFlow {
-    constructor() {
-        /** @type {Map<H, DataSource>} */
-        this._dataSourcesByHost = new Map();
-
-        /** @type {Map<H, Collector>} */
-        this._collectorsByHost = new Map();
-
-        /** @type {Map<H, (function(Collector):void)[]>} */
-        this._observers = new Map();
-    }
-
-    get dataSources() {
-        return [...new Set(this._dataSourcesByHost.values()).values()];
-    }
-
-    get collectors() {
-        return [...this._collectorsByHost.values()];
-    }
-
-    /**
-     * Adds a callback function that will be called when a collector has completed.
-     *
-     * @param {function(Collector):void} callback
-     * @param {H} key
-     */
-    addObserver(callback, key) {
-        let arr = this._observers.get(key);
-        if (!arr) {
-            arr = [];
-            this._observers.set(key, arr);
-        }
-
-        arr.push(callback);
-    }
-
-    /**
-     *
-     * @param {Collector} collector
-     * @param {H} key
-     */
-    _relayObserverCallback(collector, key) {
-        const arr = this._observers.get(key);
-        if (arr) {
-            for (const callback of arr) {
-                // eslint-disable-next-line callback-return
-                callback(collector);
-            }
-        }
-    }
-
-    /**
-     *
-     * @param {DataSource} dataSource
-     * @param {H} key
-     */
-    addDataSource(dataSource, key) {
-        this._dataSourcesByHost.set(key, dataSource);
-    }
-
-    /**
-     *
-     * @param {H} key
-     */
-    findDataSourceByKey(key) {
-        return this._dataSourcesByHost.get(key);
-    }
-
-    /**
-     *
-     * @param {string} name
-     */
-    findNamedDataSource(name) {
-        /** @type {NamedSource} */
-        let namedSource;
-        /** @type {H[]} */
-        let hosts = [];
-
-        // Note: If a named sources with the same name are present at multiple locations in the
-        // view hierarchy, the should actually be exactly the same instance. It's arranged that
-        // way in the data flow optimization phase.
-
-        for (const [host, dataSource] of this._dataSourcesByHost.entries()) {
-            if (dataSource instanceof NamedSource) {
-                if (name == dataSource.identifier) {
-                    if (namedSource && namedSource !== dataSource) {
-                        // TODO: Write a test case for this and remove the runtime check.
-                        throw new Error(
-                            `Found multiple instances of named data: ${name}. Data flow optimization is broken (it's a bug).`
-                        );
-                    }
-                    namedSource = dataSource;
-                    hosts.push(host);
-                }
-            }
-        }
-
-        if (namedSource) {
-            return {
-                dataSource: namedSource,
-                hosts,
-            };
-        }
-    }
-
-    /**
-     *
-     * @param {Collector} collector
-     * @param {H} key
-     */
-    addCollector(collector, key) {
-        this._collectorsByHost.set(key, collector);
-        collector.observers.push((collector) =>
-            this._relayObserverCallback(collector, key)
-        );
-    }
-
-    /**
-     *
-     * @param {H} key
-     */
-    findCollectorByKey(key) {
-        return this._collectorsByHost.get(key);
-    }
-
-    /**
-     * Allows the flow nodes to perform final initialization after the flow
-     * structure has been built and optimized.
-     * Must be called before any data are to be propagated.
-     */
-    initialize() {
-        for (const ds of this.dataSources) {
-            ds.visit((node) => node.initialize());
-        }
-    }
-}

package/src/data/dataFlow.test.js

@@ -1,5 +0,0 @@
-import { describe, test } from "vitest";
-
-describe("DataFlow", () => {
-    test.todo("TODO");
-});

package/src/data/facetNode.js

@@ -1,17 +0,0 @@
-import FlowNode from "./flowNode";
-
-/**
- * @typedef {object} FacetParams
- * @prop {string[]} groupby
- */
-export default class FacetNode extends FlowNode {
-    /**
-     * @param {FacetParams} params
-     */
-    constructor(params) {
-        super();
-
-        /** @type {Map<any | any[], FlowNode>} */
-        this.subflows = new Map();
-    }
-}

package/src/data/flow.test.js

@@ -1,72 +0,0 @@
-import { describe, expect, test } from "vitest";
-import FilterTransform from "./transforms/filter";
-import FormulaTransform from "./transforms/formula";
-import Collector from "./collector";
-import { SynchronousSequenceSource } from "./flowTestUtils";
-
-describe("Test flow graphs", () => {
-    test("Trivial graph: sequence to collector", () => {
-        const source = new SynchronousSequenceSource(5);
-        const collector = new Collector();
-        source.addChild(collector);
-
-        source.dispatch();
-
-        expect(collector.getData()).toEqual(
-            [0, 1, 2, 3, 4].map((d) => ({
-                data: d,
-            }))
-        );
-    });
-
-    test("Trivial branching: sequence to two collectors", () => {
-        const source = new SynchronousSequenceSource(5);
-        const collector1 = new Collector();
-        source.addChild(collector1);
-        const collector2 = new Collector();
-        source.addChild(collector2);
-
-        source.dispatch();
-
-        expect(collector1.getData()).not.toBe(collector2._data);
-
-        expect(collector1.getData()).toEqual(
-            [0, 1, 2, 3, 4].map((d) => ({
-                data: d,
-            }))
-        );
-
-        expect(collector2.getData()).toEqual(
-            [0, 1, 2, 3, 4].map((d) => ({
-                data: d,
-            }))
-        );
-    });
-
-    test("Longer chain of nodes", () => {
-        const source = new SynchronousSequenceSource(10);
-        const filter = new FilterTransform({
-            type: "filter",
-            expr: "datum.data < 5",
-        });
-        const formula = new FormulaTransform({
-            type: "formula",
-            expr: "datum.data * 2",
-            as: "data",
-        });
-        const collector = new Collector();
-
-        source.addChild(filter);
-        filter.addChild(formula);
-        formula.addChild(collector);
-
-        source.visit((node) => node.initialize());
-        source.dispatch();
-
-        expect(collector.getData()).toEqual(
-            [0, 2, 4, 6, 8].map((d) => ({
-                data: d,
-            }))
-        );
-    });
-});

package/src/data/flowBatch.d.ts

@@ -1,40 +0,0 @@
-import { Field } from "../spec/transform";
-
-export interface FlowBatchBase {
-    type: string;
-}
-
-/**
- * Indicates that the contents of a new file will be propagated. The fields of
- * the file may or may not differ from the previous file. The data items within
- * a single batch must have homogenous fields.
- *
- * FlowNodes can react to FileBatches and, for example, clear their internal
- * states that expect specific fields in a specific layout.
- */
-export interface FileBatch {
-    type: "file";
-
-    /**
-     * An absolute or relative url where the file was loaded from.
-     */
-    url?: string;
-}
-
-/**
- * Indicates that a new group/facet will be propagated. All data items that
- * belong to a specific facet must be propagated within a single batch.
- */
-export interface FacetBatch {
-    type: "facet";
-
-    facetId: any | any[];
-
-    /**
-     * The field or fields that were used for partitioning the data.
-     * May be missing if partitioning is not based on the fields.
-     */
-    facetField?: Field | Field[];
-}
-
-export type FlowBatch = FileBatch | FacetBatch;