More refactoring and linting improvement. Fix Cytoscape test.

.eslintrc.json

@@ -37,6 +37,9 @@
 		"@typescript-eslint/no-explicit-any": ["off"],
 		"@typescript-eslint/no-this-alias": ["warn", { "allowedNames": ["thisView"] }],
 		"@typescript-eslint/no-shadow": ["warn"],
+		"@typescript-eslint/no-unused-vars": ["warn", { "argsIgnorePattern": "^_" }],
+		"@typescript-eslint/consistent-type-imports": ["error"],
+		"@typescript-eslint/consistent-type-exports": ["error"],
 		"no-shadow": ["off"],
 		"no-console": ["off"],
 		"no-duplicate-imports": ["error"],
@@ -45,6 +48,7 @@
 		"eol-last": ["error"],
 		"import/no-default-export": ["warn"],
 		"import/no-cycle": ["warn"],
+		"import/no-unresolved": ["error"],
 		"max-len": ["warn", 245],
 		"padded-blocks": ["error", "never"],
 		"space-in-parens": ["error"],
@@ -55,7 +59,6 @@
 		"no-control-regex": ["off"],
 		"curly": ["warn"],
 		"camelcase": ["warn"],
-		"@typescript-eslint/no-unused-vars": ["warn", { "argsIgnorePattern": "^_" }],
 		"prefer-const": ["warn"],
 		"comma-style": ["error", "last"],
 		"class-methods-use-this": ["off"],

js/browser/chaptersearch.ts

@@ -2,7 +2,7 @@
 import * as sparql from "../sparql";
 import * as util from "./util";
 import * as language from "../lang/language";
-import { Graph } from "./graph";
+import type { Graph } from "./graph";
 import MicroModal from "micromodal";
 
 const chapters: Map<string, Array<string>> = new Map();

js/browser/contextmenu.ts

@@ -1,7 +1,7 @@
 /** Creates the circular context menu that can be opened on top of a node/edge.
 Needs to be initialized before it can be used via the default export function.*/
 import { flatHelp } from "../help";
-import { MenuItem } from "./menuItem";
+import type { MenuItem } from "./menuItem";
 import cytoscape from "cytoscape";
 //{ Collection, EdgeSingular, NodeSingular, SingularElementReturnValue } from "cytoscape";
 import contextMenus from "cytoscape-context-menus";

js/browser/contextmenuEdges.ts

@@ -4,9 +4,9 @@ import * as util from "./util";
 import { EDGE } from "../edge";
 import * as language from "../lang/language";
 import { Graph } from "./graph";
-import { ContextMenu, MenuItem } from "./contextmenu";
+import { type MenuItem, ContextMenu } from "./contextmenu";
 import log from "loglevel";
-import { EdgeSingular } from "cytoscape";
+import type { EdgeSingular } from "cytoscape";
 
 /** Creates a human readable string of the triple that an edge represents.
  *  @param edge - the edge, whose label is determined

js/browser/contextmenuNodes.ts

@@ -4,7 +4,7 @@ import * as rdf from "../rdf";
 import { NODE } from "../node";
 import * as util from "./util";
 import { Graph, Direction } from "./graph";
-import { ContextMenu, MenuItem } from "./contextmenu";
+import { type MenuItem, ContextMenu } from "./contextmenu";
 import * as sparql from "../sparql";
 import * as language from "../lang/language";
 

js/browser/graph.ts

@@ -11,7 +11,8 @@ import * as language from "../lang/language";
 import { progress } from "./progress";
 import { View } from "./view";
 import MicroModal from "micromodal";
-import cytoscape, { Collection, NodeCollection, EdgeCollection, NodeSingular } from "cytoscape";
+import type { Core, Collection, NodeCollection, EdgeCollection, NodeSingular } from "cytoscape";
+import cytoscape from "cytoscape"; //eslint-disable-line no-duplicate-imports
 import type { Menu } from "./menu";
 import log from "loglevel";
 
@@ -27,11 +28,11 @@ export enum Direction {
 
 /** Cytoscape.js Graph Class with path operations and styling. */
 export class Graph {
-	cy: cytoscape.Core;
-	selectedNode: cytoscape.NodeSingular | null = null;
+	cy: Core;
+	selectedNode: NodeSingular | null = null;
 	starMode: boolean = false;
-	matchComponents: Array<cytoscape.Collection> = [];
-	pathSource: cytoscape.NodeSingular | null = null;
+	matchComponents: Array<Collection> = [];
+	pathSource: NodeSingular | null = null;
 	container: HTMLElement;
 	instancesLoaded: boolean = false;
 	menu: Menu = null;
@@ -84,7 +85,7 @@ export class Graph {
 	}
 	/**
     @param eles - the elements to assign the star mode css class to */
-	static starStyle(eles: cytoscape.Collection): void {
+	static starStyle(eles: Collection): void {
 		eles.removeClass("hidden");
 		//eles.addClass('starmode');
 		eles.select();
@@ -587,7 +588,7 @@ export class Graph {
 	}
 	/**Show close matches of the given nodes.
 	 * @param nodes - the nodes whose close matches are shown */
-	showCloseMatch(nodes: cytoscape.NodeCollection): void {
+	showCloseMatch(nodes: NodeCollection): void {
 		const edges = nodes.connectedEdges(".unfiltered").filter('[pl="closeMatch"]'); // ,[pl="narrowMatch"],[pl="narrowMatch"]
 		const matches = edges.connectedNodes(".unfiltered");
 		log.debug(

js/browser/load.ts

@@ -1,6 +1,6 @@
 /** Module for loading files both locally from the server and via upload from the client.*/
 import { View } from "./view";
-import { ViewJson, Session } from "./interface";
+import type { ViewJson, Session } from "./interface";
 import { config } from "../config";
 import { fromJSON } from "./state";
 import { VERSION } from "./util";

js/browser/save.ts

@@ -1,10 +1,10 @@
 /** Lets the user save files generated from the loaded graph. */
-import { ViewJson, Session } from "./interface";
+import type { ViewJson, Session } from "./interface";
 import { config } from "../config";
 import { toJSON } from "./state";
-import { View, State } from "./view";
+import { View, type State } from "./view";
 import { VERSION } from "./util";
-import { Graph } from "./graph";
+import type { Graph } from "./graph";
 import log from "loglevel";
 import c from "cytoscape";
 import svg from "cytoscape-svg";

js/browser/state.ts

@@ -1,3 +1,4 @@
+/** Application State, e.g. which filters and options are activated, which is imported from and exported to JSON. */
 import { Filter } from "./filter";
 import { menu } from "./menu";
 import { VERSION } from "./util";

js/browser/view.ts

@@ -6,7 +6,7 @@ import { edgeCommands } from "./contextmenuEdges";
 import { goldenLayout } from "./viewLayout";
 import { toJSON } from "./state";
 import log from "loglevel";
-import { ComponentConfig, ContentItem } from "golden-layout";
+import type { ComponentConfig, ContentItem } from "golden-layout";
 
 let viewCount: number = 0; // only used for the name, don't decrement on destroy to prevent name conflicts
 
@@ -31,16 +31,17 @@ function traverse(x: ContentItem, depth: number): Array<ContentItem> {
 	return removeTabsArray;
 }
 
-export interface State {
+interface ViewState {
 	title: string;
 	graph: Graph;
 	name: string;
 	cy: cytoscape.Core;
 }
 
+/** Tab that shows a graph. */
 export class View {
 	initialized: Promise<void>;
-	state: State;
+	state: ViewState;
 	readonly cyContainer: HTMLDivElement = document.createElement("div");
 	element: HTMLElement;
 	cxtMenu: ContextMenu;
@@ -53,7 +54,7 @@ export class View {
 
 	/** Returns the state of the active (focussed) view.
 	@returns The state of the active (focussed) view. */
-	static activeState(): State {
+	static activeState(): ViewState {
 		return (viewLayout as any).selectedItem?.getActiveContentItem()?.config?.componentState;
 	}
 

js/config.dist.ts

@@ -2,7 +2,7 @@
 Copy to js/config.ts after checkout and adapt to your preferences.
 */
 
-import { LogLevelDesc } from "loglevel";
+import type { LogLevelDesc } from "loglevel";
 
 export const config = {
 	defaultSubOntologies: ["meta", "bb", "ob", "ciox", "he", "it4it"],

js/layout.ts

@@ -7,13 +7,14 @@ import { timer } from "./timer";
 import { NODE } from "./node";
 import { config } from "./config";
 import log from "loglevel";
-import cytoscape, { ElementDefinition, LayoutOptions, NodeCollection } from "cytoscape";
+import type { ElementDefinition, LayoutOptions, NodeCollection, Layouts, Position } from "cytoscape";
+import cytoscape from "cytoscape"; //eslint-disable-line no-duplicate-imports
 import cytoscapeeuler from "cytoscape-euler";
 cytoscape.use(cytoscapeeuler);
 
 const ANIMATE_THRESHOLD = 500;
 
-let activeLayout: cytoscape.Layouts;
+let activeLayout: Layouts;
 
 /**
 @param layoutName - Cytoscape.js layout name
@@ -52,7 +53,7 @@ export function positions(nodes: NodeCollection): Array<Array<number>> {
 
 /** @param nodes - the nodes whose center is returned
 @returns the center point of the nodes */
-function center(nodes: cytoscape.NodeCollection): cytoscape.Position {
+function center(nodes: NodeCollection): Position {
 	const c = { x: 0.0, y: 0.0 };
 	for (let i = 0; i < nodes.length; i++) {
 		const pos = nodes[i].position();
@@ -76,20 +77,14 @@ function center(nodes: cytoscape.NodeCollection): cytoscape.Position {
 run(cy,{"name":"grid"},new Set(["meta","ciox"]))
 ```
 */
-export async function run(
-	cy: cytoscape.Core,
-	layoutConfig: LayoutOptions,
-	subs?: Array<string>,
-	separateSubs: boolean = false,
-	save: boolean = false
-): Promise<boolean> {
+export async function run(cy: Core, layoutConfig: LayoutOptions, subs?: Array<string>, separateSubs: boolean = false, save: boolean = false): Promise<boolean> {
 	if (cy.nodes().size() === 0) {
 		log.warn("layout.js#run: Graph empty. Nothing to layout.");
 		return false;
 	}
 	const layoutTimer = timer("layout");
 	if (separateSubs) {
-		const sources: Set<cytoscape.ElementDefinition> = new Set();
+		const sources: Set<ElementDefinition> = new Set();
 		const virtualEdges: Array<ElementDefinition> = [];
 
 		const nodes = cy.nodes();
@@ -168,7 +163,7 @@ in pos are set to position `{x:0,y:0}`, positions without matching node id are i
 @returns whether the layout could be successfully applied
 @example `presetLayout(cy,[["http://www.snik.eu...",{"x":0,"y":0}],...]);`
 */
-export async function presetLayout(cy: cytoscape.Core, pos: Array<cytoscape.Position>): Promise<boolean> {
+export async function presetLayout(cy: Core, pos: Array<Position>): Promise<boolean> {
 	const map = new Map(pos as any);
 	let hits = 0;
 	let misses = 0;
@@ -318,7 +313,7 @@ export function eulerVariable(len)
 */
 
 /** Layout for compound graphs */
-export const cose: cytoscape.LayoutOptions = {
+export const cose: LayoutOptions = {
 	name: "cose",
 	animate: true,
 	refresh: 50,

js/loadGraphFromSparql.ts

@@ -3,7 +3,7 @@ import * as sparql from "./sparql";
 import { timer } from "./timer";
 import { config } from "./config";
 import log from "loglevel";
-import cytoscape, { ElementDefinition } from "cytoscape";
+import type { ElementDefinition, Core } from "cytoscape";
 
 interface ClassBinding {
 	src: { value: string };
@@ -83,7 +83,7 @@ function parseLabels(s: string): object {
  * @param   from - a SPARQL FROM clause defining where to load the classes from
  * @returns nodes - representing the classes
  */
-async function createClassNodes(from: string): Promise<Array<cytoscape.ElementDefinition>> {
+async function createClassNodes(from: string): Promise<Array<ElementDefinition>> {
 	const bindings = await selectClasses(from);
 
 	const nodes: Array<ElementDefinition> = [];
@@ -146,7 +146,7 @@ async function selectInstances(from: string): Promise<Array<object>> {
  @returns cytoscape nodes for the instances */
 async function createInstanceNodes(from: string): Promise<Array<object>> {
 	const json = await selectInstances(from);
-	const nodes: Array<cytoscape.ElementDefinition> = [];
+	const nodes: Array<ElementDefinition> = [];
 	for (let i = 0; i < json.length; i++) {
 		nodes.push({
 			group: "nodes",
@@ -210,7 +210,7 @@ async function selectTriples(from: string, fromNamed: string, instances: boolean
  * @param  virtual   - whether to select virtual triples from domain and range statements
  * @returns SPARQL query result object
  */
-async function createEdges(from: string, fromNamed: string, instances: boolean, virtual: boolean): Promise<Array<cytoscape.ElementDefinition>> {
+async function createEdges(from: string, fromNamed: string, instances: boolean, virtual: boolean): Promise<Array<ElementDefinition>> {
 	const json = await selectTriples(from, fromNamed, instances, virtual);
 	const edges: Array<ElementDefinition> = [];
 	for (let i = 0; i < json.length; i++) {
@@ -238,7 +238,7 @@ async function createEdges(from: string, fromNamed: string, instances: boolean,
  * @param instances - whether to load instances in addition to the classes
  * @returns an array of nodes
  */
-async function createNodes(from: string, instances: boolean): Promise<Array<cytoscape.ElementDefinition>> {
+async function createNodes(from: string, instances: boolean): Promise<Array<ElementDefinition>> {
 	if (!instances) {
 		return createClassNodes(from);
 	}
@@ -256,7 +256,7 @@ async function createNodes(from: string, instances: boolean): Promise<Array<cyto
   @example
   loadGraphFromSparql(cy,new Set(["meta","bb"]))
   */
-export async function loadGraphFromSparql(cy: cytoscape.Core, graphs: Array<string>, instances: boolean = false, virtual: boolean = false): Promise<void> {
+export async function loadGraphFromSparql(cy: Core, graphs: Array<string>, instances: boolean = false, virtual: boolean = false): Promise<void> {
 	log.debug(`Loading graph from endpoint ${config.sparql.endpoint} with graphs ${graphs}.`);
 	const from = graphs.map((g) => `FROM <${g}>`).reduce((a, b) => a + "\n" + b, "");
 	const fromNamed = from.replace(/FROM/g, "FROM NAMED");

package.json

@@ -37,6 +37,7 @@
 		"c8": "^8.0.1",
 		"eslint": "^8.51.0",
 		"eslint-plugin-import": "^2.28.1",
+		"eslint-plugin-mocha": "^10.2.0",
 		"eslint-plugin-tsdoc": "^0.2.17",
 		"husky": "^8.0.3",
 		"lint-staged": "^15.0.1",
@@ -64,7 +65,7 @@
 		"preview": "vite preview",
 		"test": "vitest run",
 		"vitest": "vitest",
-		"lint": "eslint js --ext .ts",
+		"lint": "eslint js test --ext .ts",
 		"typecheck": "tsc --noEmit",
 		"doc": "typedoc --plugin typedoc-plugin-merge-modules",
 		"prepare": "husky install"

test/cytoscape.test.ts

@@ -2,9 +2,7 @@ import * as layout from "../js/layout";
 import { loadGraphFromSparql } from "../js/loadGraphFromSparql";
 import { SNIK } from "../js/sparql";
 import cytoscape from "cytoscape";
-import euler from "cytoscape-euler";
 import "isomorphic-fetch";
-cytoscape.use(euler);
 import chai from "chai";
 const assert = chai.assert;
 
@@ -20,22 +18,21 @@ describe("cytoscape", () => {
 	test("load graph from SPARQL", async () => {
 		await loadGraphFromSparql(cy, graphs);
 		assert.closeTo(cy.nodes().size(), 1134, 100);
+		console.log("sparql");
 	});
 	test("calculate layout", async () => {
-		// Causes "TypeError: Cannot read property 'pos' of undefined"
-		// see https://github.com/cytoscape/cytoscape.js-euler/issues/14
-		//layout.run(cy,layout.euler,subs);
+		assert(await layout.run(cy, layout.euler, subs));
 		// cose is more realistic for SNIK Graph but takes over a minute
-		//assert(layout.run(cy,layout.cose,subs));
+		//assert(await layout.run(cy,layout.cose,subs));
 		// use the faster grid layout
-		await layout.run(cy, layout.grid, subs);
+		//await layout.run(cy, layout.grid);
 
 		const nodes = cy.nodes();
 		for (let i = 0; i < nodes.size(); i++) {
 			for (let j = i + 1; j < nodes.size(); j += 10) {
 				assert(
 					JSON.stringify(nodes[i].position()) !== JSON.stringify(nodes[j].position()),
-					"2 nodes at the same position " + JSON.stringify(nodes[i].position())
+					`2 nodes ${i} and ${j} at the same position ` + JSON.stringify(nodes[i].position())
 				);
 			}
 		}

test/fuse.test.ts

@@ -1,10 +1,5 @@
-import { executionAsyncId } from "async_hooks";
-import { should } from "chai";
 import "isomorphic-fetch";
-import { search, createIndex } from "../js/fuse";
-//import chai from "chai";
-//chai.should();
-//const assert = chai.assert;
+import { search, createIndex } from "../js/fuseSearch";
 console.groupCollapsed;
 
 const SEARCH = {
@@ -22,7 +17,7 @@ describe("fuse#search", () => {
 		for (const key in SEARCH) {
 			const uris = (await search(key)).map((x) => x.item.uri);
 			const expectedUris = SEARCH[key];
-			if (expectedUris.length == 1) {
+			if (expectedUris.length === 1) {
 				expect(uris).toEqual(expectedUris);
 			} else {
 				expect(uris).toEqual(expect.arrayContaining(expectedUris));

tsconfig.json

@@ -30,6 +30,6 @@
 		"out": "doc",
 		"readme": "none"
 	},
-	"include": ["js/**/*", "globals.d.ts"],
+	"include": ["js/**/*", "test/**/*", "globals.d.ts"],
 	"exclude": ["node_modules"]
 }