From 7ad47d75cf581f34dbdd352bfc35d627dd7ecde3 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Date: Fri, 19 Jan 2024 15:57:12 +0100
Subject: [PATCH]  - fix typescript issues

---
 .gitignore                                    |  2 +-
 examples/vue-copasi-ts/.gitignore             |  1 +
 .../vue-copasi-ts/src/copasi-plugin-type.ts   |  8 ++
 examples/vue-copasi-ts/src/copasi-plugin.js   |  8 +-
 examples/vue-copasi-ts/src/views/HomeView.vue | 16 +++-
 examples/vue-copasi-ts/tsconfig.node.json     |  2 +-
 js/copasi.d.ts                                | 94 +++++++++++++++++++
 7 files changed, 122 insertions(+), 9 deletions(-)
 create mode 100644 examples/vue-copasi-ts/src/copasi-plugin-type.ts
 create mode 100644 js/copasi.d.ts

diff --git a/.gitignore b/.gitignore
index 2a19cd2..0831134 100644
--- a/.gitignore
+++ b/.gitignore
@@ -62,4 +62,4 @@
 /dist-web/
 /em-build/
 
-.DS_Store
\ No newline at end of file
+.DS_Store
diff --git a/examples/vue-copasi-ts/.gitignore b/examples/vue-copasi-ts/.gitignore
index a19d957..3587447 100644
--- a/examples/vue-copasi-ts/.gitignore
+++ b/examples/vue-copasi-ts/.gitignore
@@ -32,5 +32,6 @@ coverage
 
 src/copasijs.js
 src/copasi.js
+src/copasi.d.ts
 src/copasijs.wasm
 src/copasijs.data
diff --git a/examples/vue-copasi-ts/src/copasi-plugin-type.ts b/examples/vue-copasi-ts/src/copasi-plugin-type.ts
new file mode 100644
index 0000000..f55986f
--- /dev/null
+++ b/examples/vue-copasi-ts/src/copasi-plugin-type.ts
@@ -0,0 +1,8 @@
+import type COPASI from "./copasi";
+
+export interface CopasiPlugin {
+    state: string;
+    module: any;
+    instance: COPASI|undefined;
+    version: string;
+}
\ No newline at end of file
diff --git a/examples/vue-copasi-ts/src/copasi-plugin.js b/examples/vue-copasi-ts/src/copasi-plugin.js
index c70b6cc..1bba722 100644
--- a/examples/vue-copasi-ts/src/copasi-plugin.js
+++ b/examples/vue-copasi-ts/src/copasi-plugin.js
@@ -1,7 +1,6 @@
 import { COPASI } from './copasi.js'
 import { createCpsModule } from './copasijs.js'
 import { reactive } from 'vue'
-
 /**
  * Install function for installing plugin into Vue 3 application.
  *
@@ -12,15 +11,18 @@ function install(app) {
   const copasi = reactive({
     state: 'loading',
     module: undefined,
-    instance: {version: 'loading'},
+    instance: undefined,
+    version: 'loading'
   })
 
   app.provide('$copasi', copasi)
 
   createCpsModule().then((module) => {
+    const c = new COPASI(module)
     copasi.state = 'ready'
     copasi.module = module
-    copasi.instance = new COPASI(module)
+    copasi.instance = c
+    copasi.version = c.version
     // console.log('initialized COPASI', copasi.instance.version)
   })
 }
diff --git a/examples/vue-copasi-ts/src/views/HomeView.vue b/examples/vue-copasi-ts/src/views/HomeView.vue
index 983c981..3e59982 100644
--- a/examples/vue-copasi-ts/src/views/HomeView.vue
+++ b/examples/vue-copasi-ts/src/views/HomeView.vue
@@ -1,15 +1,23 @@
 <script setup lang="ts">
 import { ref, onMounted, inject } from 'vue'
+import {type COPASI } from '../copasi'
+import {type CopasiPlugin } from '../copasi-plugin-type'
 
 // inject the COPASI object from the main app
-const copasi : any = inject('$copasi')
+const copasi : CopasiPlugin|undefined = inject('$copasi')
 
 const data: any = ref(null);
 const simData: any = ref(null);
-const model : string = ref('');
-const info = ref(null);
+const model : any = ref('');
+const info : any = ref(null);
 
 onMounted(async () => {
+
+  if (!copasi?.instance || copasi?.state == 'loading'){
+    // load the copasi object
+    return;
+  }
+
   if (!model.value){
       // download `brusselator.cps` model copied to 
       // /public folder
@@ -52,7 +60,7 @@ onMounted(async () => {
     <VuePlotly :data="data" :layout="layout" :display-mode-bar="false"></VuePlotly>
     <div>
       <p>Model: {{ info?.model.name }}</p>
-      <p >COPASI Version: {{copasi.instance.version}}</p>
+      <p >COPASI Version: {{copasi?.version}}</p>
     </div>
   </main>
 </template>
diff --git a/examples/vue-copasi-ts/tsconfig.node.json b/examples/vue-copasi-ts/tsconfig.node.json
index 4326dfa..c33d6bb 100644
--- a/examples/vue-copasi-ts/tsconfig.node.json
+++ b/examples/vue-copasi-ts/tsconfig.node.json
@@ -1,7 +1,7 @@
 {
   "extends": "@tsconfig/node18/tsconfig.json",
   "include": [
-    "vite.config.*",
+    "vite.config.ts",
     "vitest.config.*",
     "cypress.config.*",
     "nightwatch.conf.*",
diff --git a/js/copasi.d.ts b/js/copasi.d.ts
new file mode 100644
index 0000000..f067cfd
--- /dev/null
+++ b/js/copasi.d.ts
@@ -0,0 +1,94 @@
+import type exp from "constants";
+
+export interface SimResult {
+    num_variables: number;
+    recorded_steps: number;
+    titles: string[];
+    columns: string[];
+}
+
+export interface SpeciesInfo {
+    compartment: string;
+    concentration: number;
+    id: string;
+    name: string;
+    initial_concentration: number;
+    initial_particle_number: number;
+    particle_number: number;
+    type: string;
+}
+
+export interface CompartmentInfo {
+    id: string;
+    name: string;
+    size: number;
+    type: string;
+}
+export interface LocalParamterInfo {
+    name: string;
+    value: number;
+}
+
+export interface ReactionInfo {
+    id: string;
+    name: string;
+    reversible: boolean;
+    scheme: string;
+    local_paramters: LocalParamterInfo[];
+}
+
+export interface ModelName
+{
+    name: string;
+    notes: string;
+}
+
+export interface GlobalParamterInfo {   
+    name: string;
+    value: number;
+    initial_value: number;
+    id: string;
+    type: string;
+}
+
+export interface ModelInfo {
+    species: SpeciesInfo[];
+    compartments: CompartmentInfo[];
+    reactions: ReactionInfo[];
+    global_parameters: GlobalParamterInfo[];
+    model : ModelName;
+    time: number;
+    status: string;
+    messages: string;
+}
+
+export default class COPASI {
+    constructor(module: any);
+    reset(): void;
+    readonly version: string;
+    _vectorToArray(v: any): any[];
+    loadExample(path: string) : ModelInfo;
+    loadModel(modelCode: string): ModelInfo;
+    simulate() : object;
+    simulate2D() : number[][];
+    simulateEx(startTime : number, endTime : number, numPoints : number) : SimResult;
+    simulateEx2D(startTime : number, endTime : number, numPoints : number) : number[][];
+    simulateYaml(yamlProcessingOptions : string|object) : SimResult;
+    simulateYaml2D(yamlProcessingOptions : string|object) : SimResult;
+    readonly floatingSpeciesConcentrations : number[];
+    readonly ratesOfChange : number[];
+    readonly floatingSpeciesNames : string[];
+    readonly boundarySpeciesConcentrations : number[];
+    readonly boundarySpeciesNames : string[];
+    readonly reactionNames : string[];
+    readonly reactionRates : number[];
+    readonly compartmentNames : string[];
+    readonly compartmentSizes : number[];
+    readonly globalParameterNames : string[];
+    readonly globalParameterValues : number[];
+    readonly localParameterNames : string[];
+    readonly localParameterValues : number[];
+}
+
+export {COPASI};
+export default COPASI;
\ No newline at end of file