@genome-spy/core 0.17.0 → 0.19.0

package/dist/{genome-spy-schema.json → schema.json}

@@ -2851,6 +2851,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "aggregateSamples": {
               "items": {
                 "anyOf": [
@@ -3010,6 +3013,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "aggregateSamples": {
               "items": {
                 "anyOf": [
@@ -3172,6 +3178,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "baseUrl": {
               "type": "string"
             },
@@ -3322,6 +3331,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "baseUrl": {
               "type": "string"
             },
@@ -3471,6 +3483,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "baseUrl": {
               "type": "string"
             },
@@ -3620,6 +3635,9 @@
         {
           "additionalProperties": false,
           "properties": {
+            "$schema": {
+              "type": "string"
+            },
             "baseUrl": {
               "type": "string"
             },

package/package.json

@@ -7,12 +7,13 @@
   },
   "contributors": [],
   "license": "BSD-2-Clause",
-  "version": "0.17.0",
+  "version": "0.19.0",
   "main": "dist/index.js",
   "module": "src/index.js",
   "exports": {
     ".": "./src/index.js",
-    "./*": "./src/*"
+    "./*": "./src/*",
+    "./schema.json": "./dist/schema.json"
   },
   "files": [
     "dist/",
@@ -20,16 +21,16 @@
   ],
   "repository": {
     "type": "git",
-    "url": "github:tuner/genome-spy",
+    "url": "github:genome-spy/genome-spy",
     "directory": "packages/core"
   },
   "scripts": {
     "dev": "node dev-server.js",
-    "build": "vite build",
-    "prepublishOnly": "npm run build && npm run build:schema",
+    "build": "vite build && npm run build:schema",
+    "prepublishOnly": "npm run build",
     "test:tsc": "tsc -p tsconfig.json",
     "checkSpec": "tsc --allowJs --checkJs --strict --noEmit --moduleResolution node --target es6 src/spec/root.d.ts",
-    "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/genome-spy-schema.json"
+    "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/schema.json"
   },
   "dependencies": {
     "@types/d3-array": "^3.0.2",
@@ -51,5 +52,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "32db7f46f77206140bd624344e9465d32a94bd07"
+  "gitHead": "282eb640bf4c29be3755ef5de3992b8d76ad5f4c"
 }

package/src/data/collector.js

@@ -27,7 +27,7 @@ export default class Collector extends FlowNode {
         /** @type {(function(Collector):void)[]} */
         this.observers = [];
 
-        /** @type {Map<any | any[], Data>} */
+        /** @type {Map<any | any[], Data>} TODO: proper type for key */
         this.facetBatches = undefined;
 
         this._init();
@@ -59,8 +59,6 @@ export default class Collector extends FlowNode {
      * @param {import("./flowBatch").FlowBatch} flowBatch
      */
     beginBatch(flowBatch) {
-        // TODO: Propagate batches to children(?)
-
         if (isFacetBatch(flowBatch)) {
             this._data = [];
             this.facetBatches.set(asArray(flowBatch.facetId), this._data);
@@ -103,7 +101,14 @@ export default class Collector extends FlowNode {
         }
 
         if (this.children.length) {
-            for (const data of this.facetBatches.values()) {
+            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);
                 }

package/src/data/flowOptimizer.js

@@ -1,3 +1,4 @@
+import Collector from "./collector";
 import { BEHAVIOR_CLONES } from "./flowNode";
 import CloneTransform from "./transforms/clone";
 
@@ -31,6 +32,11 @@ export function validateLinks(node, parent = undefined) {
  * @param {FlowNode} node
  */
 export function removeRedundantCloneTransforms(node, cloneRequired = false) {
+    if (node instanceof Collector) {
+        // If an object is modified downstream of Collector, it must be cloned
+        cloneRequired = true;
+    }
+
     if (node instanceof CloneTransform) {
         if (cloneRequired) {
             cloneRequired = false;

package/src/genome/genome.js

@@ -257,15 +257,27 @@ export default class Genome {
     parseInterval(str) {
         // TODO: consider changing [0-9XY] to support other species besides humans
         const matches = str.match(
-            /^(chr[0-9A-Z]+):([0-9,]+)-(?:(chr[0-9A-Z]+):)?([0-9,]+)$/
+            /^(chr[0-9A-Z]+)(?::([0-9,]+)(?:-(?:(chr[0-9A-Z]+):)?([0-9,]+))?)?$/
         );
 
         if (matches) {
             const startChr = matches[1];
+
+            if (matches.slice(2).every((x) => x === undefined)) {
+                const chrom = this.getChromosome(startChr);
+                if (chrom) {
+                    return [chrom.continuousStart, chrom.continuousEnd];
+                }
+                return;
+            }
+
             const endChr = matches[3] || startChr;
 
             const startIndex = parseInt(matches[2].replace(/,/g, ""));
-            const endIndex = parseInt(matches[4].replace(/,/g, ""));
+            const endIndex =
+                matches[4] !== undefined
+                    ? parseInt(matches[4].replace(/,/g, ""))
+                    : startIndex;
 
             return [
                 this.toContinuous(startChr, startIndex - 1),

package/src/genome/genome.test.js

@@ -150,3 +150,38 @@ describe("C. elegans genome, chromosome names prefixed with 'chr'", () => {
         expect(g.toContinuous("III", 10)).toEqual(30351865);
     });
 });
+
+describe("Parse interval strings", () => {
+    const chromosomes = [
+        { name: "chr1", size: 1000 },
+        { name: "chr2", size: 2000 },
+        { name: "chr3", size: 3000 },
+        { name: "chrX", size: 4000 },
+    ];
+
+    const g = new Genome({ name: "random", contigs: chromosomes });
+
+    test("Parses a single chromosome, returns an interval spanning the chromosome", () => {
+        expect(g.parseInterval("chr2")).toEqual([1000, 3000]);
+    });
+
+    test("Returns undefined on unknown chromosome", () => {
+        expect(g.parseInterval("chrZ")).toBeUndefined();
+    });
+
+    test("Parses a single coordinate without a thousand separator", () => {
+        expect(g.parseInterval("chr2:1500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses a single coordinate with a thousand separator", () => {
+        expect(g.parseInterval("chr2:1,500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses an interval within a single chromosome", () => {
+        expect(g.parseInterval("chr2:1,500-1,700")).toEqual([2499, 2700]);
+    });
+
+    test("Parses an interval spanning multiple chromosomes", () => {
+        expect(g.parseInterval("chr2:1,500-chr3:1,500")).toEqual([2499, 4500]);
+    });
+});

package/src/spec/root.d.ts

@@ -2,6 +2,8 @@ import { GenomeConfig } from "./genome";
 import { ViewSpec } from "./view";
 
 interface RootConfig {
+    $schema?: string;
+
     genome?: GenomeConfig;
 
     baseUrl?: string;

package/src/utils/addBaseUrl.js

@@ -0,0 +1,19 @@
+/**
+ * @param {string} url
+ * @param {string} baseUrl
+ */
+export default function addBaseUrl(url, baseUrl) {
+    // Regex copied from vega-loader
+    if (!baseUrl || /^(data:|([A-Za-z]+:)?\/\/)/.test(url)) {
+        return url;
+    }
+
+    if (!url.startsWith("/")) {
+        if (!baseUrl.endsWith("/")) {
+            baseUrl += "/";
+        }
+        return baseUrl + url;
+    }
+
+    return url;
+}

package/src/utils/addBaseUrl.test.js

@@ -0,0 +1,21 @@
+import addBaseUrl from "./addBaseUrl";
+
+test("addBaseUrl adds baseUrl when needed", () => {
+    expect(addBaseUrl("foo.html", "https://site.com/")).toEqual(
+        "https://site.com/foo.html"
+    );
+    expect(addBaseUrl("foo.html", "https://site.com")).toEqual(
+        "https://site.com/foo.html"
+    );
+    expect(addBaseUrl("bar/foo.html", "https://site.com/")).toEqual(
+        "https://site.com/bar/foo.html"
+    );
+    expect(addBaseUrl("../foo.html", "https://site.com/bar/")).toEqual(
+        "https://site.com/bar/../foo.html"
+    );
+});
+
+test("addBaseUrl doesn't add baseUrl when not needed", () => {
+    expect(addBaseUrl("/foo.html", "https://site.com/")).toEqual("/foo.html");
+    expect(addBaseUrl("foo.html", undefined)).toEqual("foo.html");
+});

package/src/view/unitView.js

@@ -17,6 +17,7 @@ import {
 import createDomain from "../utils/domainArray";
 import AxisResolution from "./axisResolution";
 import { isAggregateSamplesSpec } from "./viewFactory";
+import { peek } from "../utils/arrayUtils";
 
 /**
  *
@@ -337,10 +338,13 @@ export default class UnitView extends ContainerView {
         if (isAggregateSamplesSpec(this.spec)) {
             // TODO: Support multiple
             for (const sumSpec of this.spec.aggregateSamples) {
-                sumSpec.transform = [
-                    ...(sumSpec.transform ?? []),
-                    { type: "mergeFacets" },
-                ];
+                const transform = sumSpec.transform ?? [];
+                if (transform.length && peek(transform).type != "collect") {
+                    // MergeFacets must be a direct child of Collector
+                    transform.push({ type: "collect" });
+                }
+                transform.push({ type: "mergeFacets" });
+                sumSpec.transform = transform;
 
                 sumSpec.encoding = {
                     ...(sumSpec.encoding ?? {}),