cytoscape 3.34.3: cytoscape

Clean-room public code sample — generation instructions

Write a brand-new, minimal, self-contained code sample in this clean-room directory.
Do not copy, paraphrase, or reference any existing project source. Work only from this spec.

A csx.json manifest scaffold already exists. Do not recreate it from memory. Preserve its case.goal, packages and symbols; fill its empty case.contract with exact assertions and correct its environment, commands and verifierAdapter for the files you generate.

Goal: verify pkg:npm/cytoscape@3.34.3
Kind: HOW

Use EXACTLY these public packages and versions:
  - pkg:npm/cytoscape@3.34.3

Rules:
  - One focused purpose; the smallest project that proves the goal.
  - Include a contract test (test/contract.*) that runs OFFLINE and exits 0 exactly when the goal behavior works.
  - Pin every dependency with a lockfile so resolution is reproducible.
  - No secrets, credentials, or tokens. No real URLs (only example.com or localhost). No absolute paths.
  - No personal names, emails, company names, or project identifiers of any kind.
  - No binaries and no generated output (node_modules, dist, target, venv, .git, .env).
  - Keep it under 200 files and 256KB packed.

{"case":{"caseId":"case:sha256:985f2dd81575e1c330b156e0dcb2b246a426552d2bf3f8bab5132868e663a3b5","contract":["initializes headless Cytoscape core instance with nodes and edges and reports correct element counts","queries graph elements by id and reads node data attributes","traverses graph neighborhoods using connected edges and outgoers","adds elements dynamically to an existing graph instance","calculates shortest paths and distances between nodes using Dijkstra algorithm"],"goal":"verify pkg:npm/cytoscape@3.34.3","kind":"HOW","packages":["pkg:npm/cytoscape@3.34.3"],"schemaVersion":1,"symbols":["cytoscape"]},"contractCommand":["node","test/contract.mjs"],"environment":{"arch":"x64","distro":"ubuntu","ecosystem":"npm","libc":"glibc","libcVersion":"2.39","os":"linux","osVersionBucket":"24","packageManager":"npm","schemaVersion":1},"license":"MIT-0","packages":["pkg:npm/cytoscape@3.34.3"],"schemaVersion":1,"subject":"pkg:npm/cytoscape@3.34.3","symbols":["cytoscape"],"verifierAdapter":"node-typescript@1"}

{
  "name": "sample-cytoscape",
  "version": "1.0.0",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
    "": {
      "name": "sample-cytoscape",
      "version": "1.0.0",
      "license": "MIT-0",
      "dependencies": {
        "cytoscape": "3.34.3"
      }
    },
    "node_modules/cytoscape": {
      "version": "3.34.3",
      "resolved": "https://registry.npmjs.org/cytoscape/-/cytoscape-3.34.3.tgz",
      "integrity": "sha512-yfYGhRcGAntq6YBD583j4n0Eg3jIxvWmZtz/5uz9UYkeIStSlMxuUja+ec5j3iBD8nv1rwaOAYMW09tBdkSeaQ==",
      "license": "MIT",
      "engines": {
        "node": ">=0.10"
      }
    }
  }
}

{
  "name": "sample-cytoscape",
  "version": "1.0.0",
  "description": "Clean-room verification sample for pkg:npm/cytoscape@3.34.3",
  "type": "module",
  "main": "src/index.js",
  "license": "MIT-0",
  "dependencies": {
    "cytoscape": "3.34.3"
  }
}

{
  "schemaVersion": 1,
  "goal": "verify pkg:npm/cytoscape@3.34.3",
  "kind": "HOW",
  "packages": [
    "pkg:npm/cytoscape@3.34.3"
  ],
  "symbols": [
    "cytoscape"
  ]
}

import cytoscape from 'cytoscape';

/**
 * Creates a headless Cytoscape instance with given elements and options.
 * @param {Array<object>} elements - Initial graph elements (nodes and edges).
 * @param {object} [options={}] - Additional Cytoscape configuration options.
 * @returns {object} Cytoscape core instance.
 */
export function createGraph(elements = [], options = {}) {
  return cytoscape({
    headless: true,
    elements,
    ...options
  });
}

/**
 * Adds nodes and edges to an existing Cytoscape instance.
 * @param {object} cy - Cytoscape instance.
 * @param {Array<object>} elements - Elements to add.
 * @returns {object} Added elements collection.
 */
export function addElements(cy, elements) {
  return cy.add(elements);
}

/**
 * Computes the shortest path from a source selector to a target selector using Dijkstra.
 * @param {object} cy - Cytoscape instance.
 * @param {string} rootSelector - Selector for root node.
 * @param {string} targetSelector - Selector for target node.
 * @returns {{ path: object, distance: number }} Shortest path collection and distance.
 */
export function findShortestPath(cy, rootSelector, targetSelector) {
  const dijkstra = cy.elements().dijkstra(rootSelector);
  const targetNode = cy.$(targetSelector);
  return {
    path: dijkstra.pathTo(targetNode),
    distance: dijkstra.distanceTo(targetNode)
  };
}

export { cytoscape };

import assert from 'node:assert';
import cytoscape from 'cytoscape';
import { createGraph, addElements, findShortestPath } from '../src/index.js';

// 1. initializes headless Cytoscape core instance with nodes and edges and reports correct element counts
const cy = createGraph([
  { data: { id: 'a', label: 'Node A' } },
  { data: { id: 'b', label: 'Node B' } },
  { data: { id: 'ab', source: 'a', target: 'b' } }
]);
assert.strictEqual(typeof cytoscape, 'function', 'cytoscape export must be a factory function');
assert.strictEqual(typeof cytoscape.version, 'string', 'cytoscape must expose version string');
assert.strictEqual(cy.nodes().length, 2, 'cy.nodes().length must equal 2');
assert.strictEqual(cy.edges().length, 1, 'cy.edges().length must equal 1');

// 2. queries graph elements by id and reads node data attributes
const nodeA = cy.getElementById('a');
assert.strictEqual(nodeA.id(), 'a', 'nodeA id must be "a"');
assert.strictEqual(nodeA.data('label'), 'Node A', 'nodeA data label must be "Node A"');

// 3. traverses graph neighborhoods using connected edges and outgoers
const outgoers = nodeA.outgoers();
assert.strictEqual(outgoers.has(cy.getElementById('ab')), true, 'outgoers must include edge ab');
assert.strictEqual(outgoers.has(cy.getElementById('b')), true, 'outgoers must include target node b');

// 4. adds elements dynamically to an existing graph instance
addElements(cy, [
  { group: 'nodes', data: { id: 'c', label: 'Node C' } },
  { group: 'edges', data: { id: 'bc', source: 'b', target: 'c' } }
]);
assert.strictEqual(cy.nodes().length, 3, 'cy.nodes().length must equal 3 after add');
assert.strictEqual(cy.edges().length, 2, 'cy.edges().length must equal 2 after add');

// 5. calculates shortest paths and distances between nodes using Dijkstra algorithm
const { path: pathToC, distance } = findShortestPath(cy, '#a', '#c');
assert.strictEqual(pathToC.length, 5, 'path length from a to c must be 5 elements');
assert.strictEqual(distance, 2, 'distance from a to c must be 2');

console.log('Contract assertions passed.');