@opencor/opencor 0.20250813.0

package/package.json

@@ -0,0 +1,90 @@
+{
+  "author": {
+    "name": "Alan Garny",
+    "email": "a.garny@auckland.ac.nz"
+  },
+  "bugs": {
+    "url": "https://github.com/opencor/webapp/issues"
+  },
+  "description": "A Web-based modelling environment for organising, editing, simulating, and analysing CellML files.",
+  "files": [
+    "dist",
+    "src",
+    "README.md",
+    "LICENSE"
+  ],
+  "homepage": "https://opencor.ws/",
+  "keywords": [
+    "vue",
+    "component",
+    "opencor",
+    "cellml",
+    "sed-ml",
+    "omex",
+    "combine"
+  ],
+  "license": "Apache-2.0",
+  "main": "dist/opencor.umd.js",
+  "module": "dist/opencor.es.js",
+  "name": "@opencor/opencor",
+  "productName": "OpenCOR",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/opencor/webapp.git"
+  },
+  "type": "module",
+  "types": "dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/opencor.es.js",
+      "require": "./dist/opencor.umd.js"
+    },
+    "./style.css": "./dist/opencor.css"
+  },
+  "version": "0.20250813.0",
+  "peerDependencies": {
+    "vue": "^3.0.0"
+  },
+  "dependencies": {
+    "@primeuix/themes": "^1.2.3",
+    "@primevue/auto-import-resolver": "^4.3.7",
+    "@tailwindcss/postcss": "^4.1.11",
+    "@tailwindcss/vite": "^4.1.11",
+    "@vueuse/core": "^13.6.0",
+    "js-cookie": "^3.0.5",
+    "jsonschema": "^1.5.0",
+    "mathjs": "^14.6.0",
+    "plotly.js-gl2d-dist-min": "^3.1.0",
+    "primeicons": "^7.0.0",
+    "primevue": "^4.3.7",
+    "quill": "^2.0.3",
+    "tailwindcss": "^4.1.11",
+    "tailwindcss-primeui": "^0.6.1",
+    "ua-parser-js": "^2.0.4"
+  },
+  "devDependencies": {
+    "@types/js-cookie": "^3.0.6",
+    "@types/node": "^24.2.1",
+    "@types/plotly.js": "^3.0.3",
+    "@vitejs/plugin-vue": "^6.0.1",
+    "@vue/eslint-config-prettier": "^10.2.0",
+    "@vue/eslint-config-typescript": "^14.6.0",
+    "@vue/tsconfig": "^0.7.0",
+    "autoprefixer": "^10.4.21",
+    "eslint": "^9.33.0",
+    "prettier": "^3.6.2",
+    "unplugin-vue-components": "^29.0.0",
+    "vite": "^7.1.2"
+  },
+  "scripts": {
+    "build": "vite build",
+    "build:lib": "vite build --config vite.lib.config.ts && cp index.d.ts dist/index.d.ts",
+    "clean": "node scripts/clean.js",
+    "dev": "vite dev",
+    "format": "prettier --log-level silent --write . && clang-format -i src/libopencor/src/*",
+    "format:check": "prettier --check . && clang-format --dry-run -Werror src/libopencor/src/*",
+    "lint": "eslint --fix .",
+    "serve": "pnpm build && vite preview"
+  }
+}

package/src/App.vue

@@ -0,0 +1,27 @@
+<template>
+  <div id="app">
+    <OpenCOR />
+    <!-- <OpenCOR omex="https://raw.githubusercontent.com/opencor/webapp/refs/heads/main/tests/models/lorenz.omex"/> -->
+    <!-- <OpenCOR omex="https://raw.githubusercontent.com/opencor/webapp/refs/heads/main/tests/models/ui/lorenz.omex"/> -->
+    <!-- <OpenCOR omex="https://models.physiomeproject.org/workspace/b7c/rawfile/e0ae8d2d56aaaa091e23e1ee7e84cacbda1dfb6b/lorenz.omex"/> -->
+  </div>
+</template>
+
+<script setup lang="ts">
+import OpenCOR from './components/OpenCOR.vue'
+
+function updateViewportHeight() {
+  document.documentElement.style.setProperty('--vh', `${String(window.innerHeight * 0.01)}px`)
+}
+
+window.addEventListener('resize', updateViewportHeight)
+
+updateViewportHeight()
+</script>
+
+<style scoped>
+#app {
+  width: 100%;
+  height: calc(100 * var(--vh, 1vh));
+}
+</style>

package/src/assets/app.css

@@ -0,0 +1,14 @@
+@import './base.css';
+
+body {
+  background-color: var(--p-content-background);
+  color: var(--p-content-color);
+}
+
+a {
+  color: var(--p-button-link-color);
+}
+
+:focus {
+  outline: none !important;
+}

package/src/assets/base.css

@@ -0,0 +1,28 @@
+@import 'tailwindcss';
+@import 'tailwindcss-primeui';
+
+:root {
+  --border-color: var(--p-content-border-color);
+}
+
+body {
+  margin: 0;
+  font-family:
+    Inter,
+    -apple-system,
+    BlinkMacSystemFont,
+    'Segoe UI',
+    Roboto,
+    Oxygen,
+    Ubuntu,
+    Cantarell,
+    'Fira Sans',
+    'Droid Sans',
+    'Helvetica Neue',
+    sans-serif;
+  text-rendering: optimizeLegibility;
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
+  user-select: none;
+  overflow: hidden;
+}

package/src/assets/logo.svg

@@ -0,0 +1,17 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" id="OpenCOR logo" xml:space="preserve" height="704.92" width="828.12" version="1.1">
+    <defs>
+        <style>
+        @font-face {
+            font-family: "Brush Script MT";
+            src: 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+        }
+        </style>
+    </defs>
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+</svg>

package/src/common/common.ts

@@ -0,0 +1,86 @@
+import { UAParser } from 'ua-parser-js'
+
+import { electronApi } from './electronApi.js'
+
+// Some interfaces.
+
+export interface ISettingsGeneral {
+  checkForUpdatesAtStartup: boolean
+}
+
+export interface ISettings {
+  general: ISettingsGeneral
+}
+
+// Some methods to determine the operating system, whether the application is running on a mobile device, etc.
+
+const uaParser = new UAParser()
+
+export function isWindows(): boolean {
+  return uaParser.getOS().name === 'Windows'
+}
+
+export function isLinux(): boolean {
+  return uaParser.getOS().name === 'Linux'
+}
+
+export function isMacOs(): boolean {
+  return uaParser.getOS().name === 'macOS'
+}
+
+export function isMobile(): boolean {
+  return uaParser.getDevice().type === 'mobile'
+}
+
+// A method to determine whether the Ctrl or Cmd key is pressed, depending on the operating system.
+
+export function isCtrlOrCmd(event: KeyboardEvent): boolean {
+  return isMacOs() ? event.metaKey : event.ctrlKey
+}
+
+// A method to enable/disable the main menu.
+
+export function enableDisableMainMenu(enable: boolean): void {
+  electronApi?.enableDisableMainMenu(enable)
+}
+
+// A method to format a given number of milliseconds into a string.
+
+export function formatTime(time: number): string {
+  const ms = Math.floor(time % 1000)
+  const s = Math.floor((time / 1000) % 60)
+  const m = Math.floor((time / (1000 * 60)) % 60)
+  const h = Math.floor((time / (1000 * 60 * 60)) % 24)
+  const d = Math.floor((time / (1000 * 60 * 60 * 24)) % 24)
+  let res = ''
+
+  if (d !== 0 || ((h !== 0 || m !== 0 || s !== 0 || ms !== 0) && res !== '')) {
+    res += `${res === '' ? '' : ' '}${String(d)}d`
+  }
+
+  if (h !== 0 || ((m !== 0 || s !== 0 || ms !== 0) && res !== '')) {
+    res += `${res === '' ? '' : ' '}${String(h)}h`
+  }
+
+  if (m !== 0 || ((s !== 0 || ms !== 0) && res !== '')) {
+    res += `${res === '' ? '' : ' '}${String(m)}m`
+  }
+
+  if (s !== 0 || (ms !== 0 && res !== '')) {
+    res += `${res === '' ? '' : ' '}${String(s)}s`
+  }
+
+  if (ms !== 0 || res === '') {
+    res += `${res === '' ? '' : ' '}${String(ms)}ms`
+  }
+
+  return res
+}
+
+// A method to format an issue, i.e. make sure that it starts with a capital letter and ends with a period.
+
+export function formatIssue(issue: string): string {
+  issue = issue.charAt(0).toUpperCase() + issue.slice(1)
+
+  return issue.endsWith('.') ? issue : `${issue}.`
+}

package/src/common/constants.ts

@@ -0,0 +1,12 @@
+export const URI_SCHEME = 'opencor'
+export const FULL_URI_SCHEME = `${URI_SCHEME}://`
+
+export const SHORT_DELAY = 69
+export const MEDIUM_DELAY = 169
+export const LONG_DELAY = 369
+
+export const TOAST_LIFE = 3000
+
+const currentYear = new Date().getFullYear()
+
+export const COPYRIGHT = currentYear === 2025 ? '2025' : `2025-${String(currentYear)}`

package/src/common/electron.ts

@@ -0,0 +1,23 @@
+import { is } from '@electron-toolkit/utils'
+
+import electron from 'electron'
+
+export function isPackaged(): boolean {
+  return electron.app.isPackaged
+}
+
+export function isDevMode(): boolean {
+  return is.dev && !!process.env.ELECTRON_RENDERER_URL
+}
+
+export function isWindows(): boolean {
+  return process.platform === 'win32'
+}
+
+export function isLinux(): boolean {
+  return process.platform === 'linux'
+}
+
+export function isMacOs(): boolean {
+  return process.platform === 'darwin'
+}

package/src/common/electronApi.ts

@@ -0,0 +1,63 @@
+import { type ISettings } from './common.js'
+
+export interface ISplashScreenInfo {
+  copyright: string
+  version: string
+}
+
+interface IElectronApi {
+  // Note: this must be in sync with src/preload/index.ts.
+
+  // Some general methods.
+
+  operatingSystem: () => string
+
+  // Splash screen window.
+
+  onInitSplashScreenWindow: (callback: (info: ISplashScreenInfo) => void) => void
+
+  // Renderer process asking the main process to do something for it.
+
+  checkForUpdates: (atStartup: boolean) => void
+  downloadAndInstallUpdate: () => void
+  enableDisableMainMenu: (enable: boolean) => void
+  enableDisableFileCloseAndCloseAllMenuItems: (enable: boolean) => void
+  fileClosed: (filePath: string) => void
+  fileIssue: (filePath: string) => void
+  fileOpened: (filePath: string) => void
+  filePath: (file: File) => string
+  fileSelected(filePath: string): void
+  filesOpened(filePaths: string[]): void
+  installUpdateAndRestart: () => void
+  loadSettings: () => Promise<ISettings>
+  resetAll: () => void
+  saveSettings: (settings: ISettings) => void
+
+  // Renderer process listening to the main process.
+
+  onAbout: (callback: () => void) => void
+  onAction: (callback: (action: string) => void) => void
+  onCheckForUpdates: (callback: () => void) => void
+  onEnableDisableUi: (callback: (enable: boolean) => void) => void
+  onOpen: (callback: (filePath: string) => void) => void
+  onOpenRemote: (callback: () => void) => void
+  onOpenSampleLorenz: (callback: () => void) => void
+  onOpenSampleInteractiveLorenz: (callback: () => void) => void
+  onClose: (callback: () => void) => void
+  onCloseAll: (callback: () => void) => void
+  onResetAll: (callback: () => void) => void
+  onSelect: (callback: (filePath: string) => void) => void
+  onSettings: (callback: () => void) => void
+  onUpdateAvailable: (callback: (version: string) => void) => void
+  onUpdateCheckError: (callback: (issue: string) => void) => void
+  onUpdateDownloaded: (callback: () => void) => void
+  onUpdateDownloadError: (callback: (issue: string) => void) => void
+  onUpdateDownloadProgress: (callback: (percent: number) => void) => void
+  onUpdateNotAvailable: (callback: () => void) => void
+}
+
+interface IWindow {
+  electronApi: IElectronApi
+}
+
+export const electronApi: IElectronApi | undefined = (window as unknown as IWindow).electronApi

package/src/common/locCommon.ts

@@ -0,0 +1,170 @@
+import { electronApi } from './electronApi.js'
+import * as locApi from '../libopencor/locApi.js'
+
+// Some file-related methods.
+
+export function proxyUrl(url: string): string {
+  return `https://corsproxy.io/?url=${encodeURIComponent(url)}`
+}
+
+export function isRemoteFilePath(filePath: string): boolean {
+  return filePath.startsWith('http://') || filePath.startsWith('https://')
+}
+
+export function filePath(fileOrFilePath: string | File): string {
+  return fileOrFilePath instanceof File
+    ? electronApi !== undefined
+      ? electronApi.filePath(fileOrFilePath)
+      : fileOrFilePath.name
+    : fileOrFilePath
+}
+
+export function file(fileOrFilePath: string | File): Promise<locApi.File> {
+  if (typeof fileOrFilePath === 'string') {
+    if (isRemoteFilePath(fileOrFilePath)) {
+      return new Promise((resolve, reject) => {
+        fetch(proxyUrl(fileOrFilePath))
+          .then((response) => {
+            if (response.ok) {
+              return response.arrayBuffer()
+            }
+
+            throw new Error(`The server responded with a status of ${String(response.status)}.`)
+          })
+          .then((arrayBuffer) => {
+            const fileContents = new Uint8Array(arrayBuffer)
+
+            resolve(new locApi.File(filePath(fileOrFilePath), fileContents))
+          })
+          .catch((error: unknown) => {
+            reject(error instanceof Error ? error : new Error(String(error)))
+          })
+      })
+    }
+
+    return new Promise((resolve, reject) => {
+      if (electronApi !== undefined) {
+        resolve(new locApi.File(filePath(fileOrFilePath)))
+      } else {
+        reject(new Error('Local files cannot be opened.'))
+      }
+    })
+  }
+
+  return new Promise((resolve, reject) => {
+    fileOrFilePath
+      .arrayBuffer()
+      .then((arrayBuffer) => {
+        const fileContents = new Uint8Array(arrayBuffer)
+
+        resolve(new locApi.File(filePath(fileOrFilePath), fileContents))
+      })
+      .catch((error: unknown) => {
+        reject(error instanceof Error ? error : new Error(String(error)))
+      })
+  })
+}
+
+// A method to retrieve the simulation data information for a given name from an instance task.
+
+export enum ESimulationDataInfoType {
+  UNKNOWN,
+  VOI,
+  STATE,
+  RATE,
+  CONSTANT,
+  COMPUTED_CONSTANT,
+  ALGEBRAIC
+}
+
+export interface ISimulationDataInfo {
+  type: ESimulationDataInfoType
+  index: number
+}
+
+export function simulationDataInfo(instanceTask: locApi.SedInstanceTask, name: string): ISimulationDataInfo {
+  if (name === '') {
+    return {
+      type: ESimulationDataInfoType.UNKNOWN,
+      index: -1
+    }
+  }
+
+  if (name === instanceTask.voiName()) {
+    return {
+      type: ESimulationDataInfoType.VOI,
+      index: -1
+    }
+  }
+
+  for (let i = 0; i < instanceTask.stateCount(); i++) {
+    if (name === instanceTask.stateName(i)) {
+      return {
+        type: ESimulationDataInfoType.STATE,
+        index: i
+      }
+    }
+  }
+
+  for (let i = 0; i < instanceTask.rateCount(); i++) {
+    if (name === instanceTask.rateName(i)) {
+      return {
+        type: ESimulationDataInfoType.RATE,
+        index: i
+      }
+    }
+  }
+
+  for (let i = 0; i < instanceTask.constantCount(); i++) {
+    if (name === instanceTask.constantName(i)) {
+      return {
+        type: ESimulationDataInfoType.CONSTANT,
+        index: i
+      }
+    }
+  }
+
+  for (let i = 0; i < instanceTask.computedConstantCount(); i++) {
+    if (name === instanceTask.computedConstantName(i)) {
+      return {
+        type: ESimulationDataInfoType.COMPUTED_CONSTANT,
+        index: i
+      }
+    }
+  }
+
+  for (let i = 0; i < instanceTask.algebraicCount(); i++) {
+    if (name === instanceTask.algebraicName(i)) {
+      return {
+        type: ESimulationDataInfoType.ALGEBRAIC,
+        index: i
+      }
+    }
+  }
+
+  return {
+    type: ESimulationDataInfoType.UNKNOWN,
+    index: -1
+  }
+}
+
+// A method to retrieve the simulation data for a given name from an instance task.
+
+export function simulationData(instanceTask: locApi.SedInstanceTask, info: ISimulationDataInfo): number[] {
+  switch (info.type) {
+    case ESimulationDataInfoType.VOI:
+      return instanceTask.voi()
+    case ESimulationDataInfoType.STATE:
+      return instanceTask.state(info.index)
+    case ESimulationDataInfoType.RATE:
+      return instanceTask.rate(info.index)
+    case ESimulationDataInfoType.CONSTANT:
+      return instanceTask.constant(info.index)
+    case ESimulationDataInfoType.COMPUTED_CONSTANT:
+      return instanceTask.computedConstant(info.index)
+    case ESimulationDataInfoType.ALGEBRAIC:
+      return instanceTask.algebraic(info.index)
+    default:
+      return []
+  }
+}

package/src/common/settings.ts

@@ -0,0 +1,95 @@
+import jsCookie from 'js-cookie'
+
+import { type ISettings, type ISettingsGeneral } from './common.js'
+import { electronApi } from './electronApi.js'
+
+class Settings {
+  private static _instance: Settings | null = null
+  private _settings!: ISettings
+  private _isInitialised = false
+  private _initialisationListeners: (() => void)[] = []
+
+  private constructor() {
+    // Start with some default settings and then load them.
+    // Note: to have default settings is critical when running the desktop version of OpenCOR since they are loaded
+    //       asynchronously, so we need to ensure that our settings are always defined. This is not the case for the
+    //       web version of OpenCOR, where we can load our settings directly from the cookies.
+
+    this.reset()
+    this.load()
+  }
+
+  static instance(): Settings {
+    this._instance ??= new Settings()
+
+    return this._instance
+  }
+
+  private emitInitialised(): void {
+    this._isInitialised = true
+
+    this._initialisationListeners.forEach((callback) => {
+      callback()
+    })
+
+    this._initialisationListeners = []
+  }
+
+  onInitialised(callback: () => void): void {
+    if (this._isInitialised) {
+      callback()
+    } else {
+      this._initialisationListeners.push(callback)
+    }
+  }
+
+  load(): void {
+    if (electronApi !== undefined) {
+      void electronApi.loadSettings().then((settings: ISettings) => {
+        this._settings = settings
+
+        this.emitInitialised()
+      })
+    } else {
+      const cookieData = jsCookie.get('settings')
+
+      if (cookieData !== undefined) {
+        try {
+          this._settings = JSON.parse(cookieData)
+        } catch (error: unknown) {
+          console.error('Failed to parse settings from cookie, so resetting to defaults:', error)
+
+          this.reset()
+        }
+      }
+
+      this.emitInitialised()
+    }
+  }
+
+  save(): void {
+    if (electronApi !== undefined) {
+      electronApi.saveSettings(this._settings)
+    } else {
+      jsCookie.set('settings', JSON.stringify(this._settings), { expires: 365 })
+    }
+  }
+
+  reset(): void {
+    this._settings = {
+      general: {
+        checkForUpdatesAtStartup: true
+      }
+    }
+  }
+
+  toString(): string {
+    return JSON.stringify(this._settings, null, 2)
+  }
+
+  get general(): ISettingsGeneral {
+    return this._settings.general
+  }
+}
+
+export const settings = Settings.instance()