@genome-spy/app 1.2.0 → 1.3.0

package/dist/{svgRasterizer-DoRQEqFA.js → svgRasterizer-6OcftuoI.js}

@@ -1,7 +1,7 @@
 import { t as e } from "./rasterization-CFogVB3B.js";
 import { t } from "./rectangle-DZTR6NFQ.js";
-import { t as n } from "./layoutResult-D50MSHXR.js";
-import { t as r } from "./renderCanvas2D-DVjhp834.js";
+import { n } from "./color-jETn8xK_.js";
+import { t as r } from "./renderCanvas2D-Y7pkRzbC.js";
 import { n as i, t as a } from "./rasterImage-B4rPLaW9.js";
 //#region ../core/src/rendering/canvas2d/svgRasterizer.js
 function o() {

package/dist/{svgRasterizer-raDDhBF-.js → svgRasterizer-DkNRaCPs.js}

@@ -1,7 +1,7 @@
-import { t as e } from "./rasterization-DFj3Cvx4.js";
-import { t } from "./rectangle-Dl4Dy0hS.js";
-import { t as n } from "./layoutResult-D50MSHXR.js";
-import { t as r } from "./renderCanvas2D-Bfm1NHFu.js";
+import { t as e } from "./rasterization-QktH8Sn2.js";
+import { t } from "./rectangle-BAdoDPXu.js";
+import { n } from "./color-uTRRsy8i.js";
+import { t as r } from "./renderCanvas2D-CsRO78Pq.js";
 import { n as i, t as a } from "./rasterImage-B4rPLaW9.js";
 //#region ../core/src/rendering/canvas2d/svgRasterizer.js
 function o() {

package/dist/tableMetadataSourceAdapter-CUNwLsdi.js

@@ -0,0 +1,291 @@
+import { c as e, r as t, s as n } from "./flowOutput-D5qpxWe0.js";
+import { c as r, i, l as a, o, r as s, s as c } from "./metadataUtils-DxEPe0vj.js";
+//#region ../core/src/data/sources/inlineSource.js
+function l(e) {
+	return "values" in e;
+}
+var u = class extends t {
+	constructor(e, t) {
+		if (super(t), this.params = e, typeof e.values == "string" && !e?.format?.type) throw Error("Data format type (csv, dsv, ...) must be specified if a string is provided!");
+	}
+	get label() {
+		return "inlineSource";
+	}
+	isTrivial() {
+		let e = this.params.values, t = Array.isArray(e) ? e[0] : e;
+		return !!(t && Object.keys(t).length == 0 && t.constructor === Object);
+	}
+	updateDynamicData(e) {
+		this.#e(e);
+	}
+	loadSynchronously() {
+		this.#e(this.params.values);
+	}
+	#e(e) {
+		let t = [], n = (e) => e;
+		if (Array.isArray(e)) e.length > 0 && (t = e, n = y(e[0]));
+		else if (typeof e == "object") t = [e];
+		else if (typeof e == "string") t = a(e, m(p(this.params)));
+		else throw Error("\"values\" in data configuration is not an array, object, or a string!");
+		this.reset(), this.beginBatch({ type: "file" });
+		for (let e of t) this._propagate(n(e));
+		this.complete();
+	}
+	async load() {
+		this.loadSynchronously();
+	}
+}, d = /* @__PURE__ */ new Set([
+	"csv",
+	"tsv",
+	"dsv"
+]), f = /* @__PURE__ */ new Set([
+	"gz",
+	"bgz",
+	"bgzf"
+]);
+function p(e, t = []) {
+	if (!l(e) && !w(e)) return;
+	let n = { ...e.format };
+	if (n.type ??= w(e) && g(t), n.parse === void 0 && T(n.type) && (n.parse = "auto"), !n.type) throw Error("Format for the data source was not defined and it could not be inferred: " + JSON.stringify(e));
+	return n;
+}
+function m(e) {
+	let t = { ...e };
+	return (S(t) || C(t)) && t.columns && !("header" in t) && (t.header = t.columns), t;
+}
+function h(e) {
+	return r(e)?.responseType ?? "text";
+}
+function g(e) {
+	if (Array.isArray(e) && (e = e[0]), e) {
+		let t = v(e).split("/").pop()?.toLowerCase();
+		if (!t) return;
+		let n = t.split(".");
+		for (; n.length > 1 && f.has(n.at(-1));) n.pop();
+		let i = n.at(-1);
+		if (i && r(i)) return i;
+	}
+}
+function _(e) {
+	let t = v(e).split("/").pop()?.toLowerCase();
+	if (!t) return !1;
+	let n = t.split(".").at(-1);
+	return !!n && f.has(n);
+}
+function v(e) {
+	return e.replace(/[?#].*$/, "");
+}
+var y = (e) => typeof e == "object" ? x : b, b = (e) => ({ data: e }), x = (e) => e;
+function S(e) {
+	return e.type == "csv" || e.type == "tsv";
+}
+function C(e) {
+	return e.type == "dsv";
+}
+function w(e) {
+	return "url" in e;
+}
+function T(e) {
+	return d.has(e);
+}
+//#endregion
+//#region src/sampleView/metadata/metadataValidation.js
+function E(e, t) {
+	let n = /* @__PURE__ */ new Map();
+	function r(e, t = 1, r = null) {
+		let i = n.get(e);
+		i || (i = {
+			message: e,
+			count: 0,
+			cases: []
+		}, n.set(e, i)), i.count += t, r && i.cases.push(r);
+	}
+	let i = new Set(e), a = /* @__PURE__ */ new Set();
+	for (let e of t) {
+		if (!("sample" in e)) {
+			r(D);
+			continue;
+		}
+		if (e.sample == null || e.sample === "") {
+			r(O);
+			continue;
+		}
+		let t = String(e.sample);
+		a.has(t) && r(k, 1, t), a.add(t);
+	}
+	return a.size === 0 && r(A), n.size > 0 ? { error: Array.from(n.values()) } : { statistics: {
+		unknownSamples: a.difference(i),
+		notCoveredSamples: i.difference(a),
+		samplesInBoth: a.intersection(i)
+	} };
+}
+var D = "Missing sample field in metadata record", O = "Empty sample field in metadata record", k = "Duplicate sample IDs found in metadata", A = "No valid samples found in metadata";
+//#endregion
+//#region src/sampleView/metadata/metadataSourceAttributes.js
+function j(e, t) {
+	return t ? s(e, t, "/") : o([e], "/");
+}
+function M(e, t) {
+	let n = e.attributes;
+	if (!n) return {};
+	let r = e.attributeGroupSeparator, i = /* @__PURE__ */ new Set();
+	for (let e of t) {
+		let t = j(e, r), n = c(t, "/");
+		for (let e = 1; e <= n.length; e++) i.add(o(n.slice(0, e), "/"));
+	}
+	i.add("");
+	let a = {}, s = /* @__PURE__ */ new Map();
+	for (let [e, t] of Object.entries(n)) {
+		let n = j(e, r);
+		if (!i.has(n)) continue;
+		let o = s.get(n);
+		if (o) throw Error("Metadata source attributes has conflicting keys \"" + o + "\" and \"" + e + "\" that both resolve to \"" + n + "\".");
+		s.set(n, e), a[n] = { ...t };
+	}
+	return a;
+}
+//#endregion
+//#region ../core/src/utils/topK.js
+function N(e, t, r = (e) => +e, i = 0, a = e.length) {
+	let o = a - i;
+	if (t <= 0 || o <= 0) return [];
+	let s = new n(), c = 0;
+	for (; c < t && c < o; c++) s.push(c, r(e[i + c]));
+	for (; c < o; c++) {
+		let t = r(e[i + c]);
+		t > s.peekValue() && (s.push(c, t), s.pop());
+	}
+	let l = s.peekValue(), u = [], d = 0, f = 0;
+	for (c = 0; c < o; c++) r(e[i + c]) > l && d++;
+	let p = t - d;
+	for (c = 0; c < o; c++) {
+		let t = r(e[i + c]);
+		(t > l || t === l && f++ < p) && u.push(c);
+	}
+	return u.sort((t, n) => {
+		let a = r(e[i + t]), o = r(e[i + n]);
+		return a > o ? -1 : a < o ? 1 : t - n;
+	}), u.map((t) => e[i + t]);
+}
+//#endregion
+//#region src/sampleView/metadata/exampleValues.js
+function P(e, t) {
+	return N(e.map((e) => String(e ?? "").trim()).filter(Boolean), t, F);
+}
+function F(e) {
+	let t = 2166136261;
+	for (let n = 0; n < e.length; n += 1) t ^= e.charCodeAt(n), t = Math.imul(t, 16777619);
+	return t >>> 0;
+}
+//#endregion
+//#region src/sampleView/metadata/adapters/tableMetadataSourceAdapter.js
+var I = class {
+	#e;
+	#t;
+	#n;
+	#r;
+	#i;
+	constructor(e, t = {}) {
+		this.#e = e, this.#t = t.sampleIdField ?? (e.backend.backend === "data" ? e.backend.sampleIdField ?? "sample" : "sample"), this.#n = t.baseUrl, this.#i = /* @__PURE__ */ new Set([
+			this.#t,
+			...t.excludedColumns ?? [],
+			...e.excludeColumns ?? []
+		]);
+	}
+	async listColumns(e) {
+		let t = await this.#a(e), n = this.#t, r = /* @__PURE__ */ new Set();
+		for (let e of t) for (let t of Object.keys(e)) t !== n && (this.#c(t) || r.add(t));
+		return Array.from(r).map((e) => ({ id: e }));
+	}
+	async listSampleIds(e) {
+		return (await this.#a(e)).map((e) => String(e[this.#t] ?? ""));
+	}
+	async listSamples(e = {}, t) {
+		let n = await this.#a(t), r = this.#t;
+		return n.map((t) => {
+			let n = String(t[r] ?? ""), i = e.displayNameField ? t[e.displayNameField] : void 0;
+			return {
+				id: n,
+				displayName: i == null ? n : String(i)
+			};
+		});
+	}
+	async listIdentifierExamples(e, t) {
+		return [{
+			name: "column",
+			primary: !0,
+			examples: P((await this.listColumns(t)).map((e) => e.id), e)
+		}];
+	}
+	async resolveColumns(e, t) {
+		let n = await this.listColumns(t), r = new Set(n.map((e) => e.id)), i = [], a = /* @__PURE__ */ new Set();
+		for (let t of e) r.has(t) ? i.includes(t) || i.push(t) : a.add(t);
+		return {
+			columnIds: i,
+			missing: Array.from(a)
+		};
+	}
+	async fetchColumns(e, t) {
+		let n = await this.#a(t), r = this.#t, a = new Set(e.sampleIds);
+		for (let t of e.columnIds) if (this.#c(t)) throw Error("Column \"" + t + "\" is excluded by metadata source configuration.");
+		let o = [];
+		for (let t of n) {
+			let n = String(t[r] ?? "");
+			if (!a.has(n)) continue;
+			let i = { sample: n };
+			for (let n of e.columnIds) i[n] = t[n];
+			o.push(i);
+		}
+		if (o.length === 0) throw Error("Metadata source rows do not match any sample ids in the current view.");
+		let s = E(e.sampleIds, o);
+		if ("error" in s) {
+			let e = s.error[0];
+			throw Error("Invalid metadata source payload: " + String(e.message));
+		}
+		if (s.statistics.samplesInBoth.size === 0) throw Error("Metadata source rows do not match any sample ids in the current view.");
+		let c = M(this.#e, e.columnIds), l = e.groupPath ?? this.#e.groupPath, u = i(o, c, this.#e.attributeGroupSeparator, l);
+		return e.replace !== void 0 && (u.replace = e.replace), u;
+	}
+	async #a(e) {
+		return this.#r ||= this.loadRows(e).catch((e) => {
+			throw this.#r = void 0, e;
+		}), this.#r;
+	}
+	async loadRows(e) {
+		let t = this.#e.backend;
+		if (t.backend !== "data") throw Error("Table metadata loading requires a data backend.");
+		let n = t.data;
+		if ("url" in n) return this.#o(n, e);
+		if ("values" in n) return this.#s(n);
+		throw Error("Metadata source data backend supports only UrlData and InlineData.");
+	}
+	async #o(t, n) {
+		if (typeof t.url != "string") throw Error("Metadata source UrlData currently supports only string URLs.");
+		let r = e(this.#n, t.url), i = p(t, r), o = h(i.type), s;
+		try {
+			s = await fetch(r, { signal: n });
+		} catch (e) {
+			throw Error("Could not load metadata source: " + e.message, { cause: e });
+		}
+		if (!s.ok) throw Error("Could not load metadata source: " + s.status + " " + s.statusText);
+		let c;
+		return c = typeof s[o] == "function" ? await s[o]() : await s.text(), a(c, m(i));
+	}
+	async #s(e) {
+		let t = e.values, n = [];
+		if (Array.isArray(t)) {
+			if (t.length > 0) {
+				let e = y(t[0]);
+				n = t.map((t) => e(t));
+			}
+		} else if (typeof t == "object") n = [t];
+		else if (typeof t == "string") n = a(t, m(p(e)));
+		else throw Error("Inline metadata source values must be an array, object, or a string.");
+		return n;
+	}
+	#c(e) {
+		return this.#i.has(e);
+	}
+};
+//#endregion
+export { E as a, y as c, u as d, l as f, M as i, h as l, P as n, p as o, N as r, _ as s, I as t, m as u };