Merge branch 'feature/custom-database-foundations' into develop

.github/workflows/lint.yml

@@ -5,10 +5,12 @@ on: [push]
 jobs:
   lint:
     runs-on: ubuntu-latest
-    
+
     steps:
     - uses: actions/checkout@v1
-    - uses: actions/setup-node@v1
+    - uses: actions/setup-node@v2
+      with:
+        node-version: 16
     - name: Cache node modules
       uses: actions/cache@v1
       with:

link_with_web_components_watch.js

@@ -10,7 +10,8 @@ const chokidar = require('chokidar');
 const fs = require('fs');
 const path = require('path');
 
-const directory = './../unipept-web-components/dist'
+const distDirectory = './../unipept-web-components/dist'
+const typesDirectory = './../unipept-web-components/types';
 
 const errHandler = function(err) {
     if (err) {
@@ -21,7 +22,7 @@ const errHandler = function(err) {
 console.log("Watching file system for changes...");
 
 // Watch for changes to the web components directory.
-chokidar.watch(directory).on('all', (event, currentPath) => {
+chokidar.watch(distDirectory).on('all', (event, currentPath) => {
     if (!currentPath.includes('/node_modules') && !currentPath.includes('/.git')) {
         const filteredPath = currentPath.replace('../unipept-web-components', './node_modules/unipept-web-components');
         const directory = path.dirname(filteredPath);
@@ -40,3 +41,21 @@ chokidar.watch(directory).on('all', (event, currentPath) => {
         console.log(event, currentPath);
     }
 });
+
+chokidar.watch(typesDirectory).on('all', (event, currentPath) => {
+    const filteredPath = currentPath.replace('../unipept-web-components', './node_modules/unipept-web-components');
+    const directory = path.dirname(filteredPath);
+    switch(event) {
+        case 'add':
+            fs.mkdirSync(directory, { recursive: true }, errHandler);
+            fs.copyFile(currentPath, filteredPath, errHandler);
+            break;
+        case 'change':
+            fs.copyFile(currentPath, filteredPath, errHandler);
+            break;
+        case 'unlink':
+            fs.unlink(filteredPath, errHandler);
+            break;
+    }
+    console.log(event, currentPath);
+});

package.json

@@ -1,6 +1,6 @@
 {
   "name": "unipept-desktop",
-  "version": "1.2.1",
+  "version": "1.2.2",
   "private": true,
   "author": "Unipept Team (Ghent University)",
   "description": "A desktop equivalent of unipept.ugent.be. This app aims at high-throughput analysis of metaproteomics samples.",
@@ -25,6 +25,7 @@
     "@babel/preset-env": "^7.6.0",
     "@types/async": "^3.2.3",
     "@types/better-sqlite3": "^5.4.0",
+    "@types/dockerode": "^3.2.3",
     "@types/electron-devtools-installer": "^2.2.0",
     "@types/follow-redirects": "^1.13.0",
     "@types/marked": "^2.0.2",
@@ -39,6 +40,7 @@
     "better-sqlite3": "^7.1.2",
     "chokidar": "^3.3.1",
     "core-js": "^2.6.9",
+    "dockerode": "^3.3.0",
     "electron-devtools-installer": "^3.1.1",
     "electron-log": "^4.2.2",
     "electron-updater": "4.3.4",
@@ -49,16 +51,16 @@
     "marked": "^2.0.3",
     "node-abi": "^2.19.3",
     "regenerator-runtime": "^0.13.3",
-    "shared-memory-datastructures": "0.1.8",
-    "unipept-web-components": "^1.4.3",
+    "shared-memory-datastructures": "0.1.9",
+    "unipept-web-components": "^1.5.0",
     "uuid": "^7.0.3",
     "vue": "^2.6.12",
     "vue-class-component": "^7.1.0",
     "vue-fullscreen": "^2.1.5",
     "vue-property-decorator": "^8.2.2",
     "vue-router": "^3.1.3",
     "vue-styleguidist": "^4.2.3",
-    "vuetify": "^2.1.1",
+    "vuetify": "^2.5.8",
     "vuex": "^3.1.1",
     "whatwg-fetch": "^3.0.0",
     "yauzl": "^2.10.0"
@@ -93,7 +95,7 @@
     "vue-cli-plugin-styleguidist": "^4.2.3",
     "vue-cli-plugin-vuetify": "^0.6.3",
     "vue-template-compiler": "^2.6.12",
-    "vuetify-loader": "^1.2.2",
+    "vuetify-loader": "^1.7.3",
     "worker-loader": "^3.0.2"
   },
   "eslintConfig": {

src/App.vue

@@ -11,7 +11,6 @@
             <!-- Navigation drawer for managing the currently selected peptides / experiments / etc. Is positioned on
                  the left side -->
             <Toolbar
-                v-on:activate-dataset="onActivateDataset"
                 v-on:update:toolbar-width="onToolbarWidthUpdated">
             </Toolbar>
 
@@ -79,9 +78,11 @@ import {
     Assay,
     ProteomicsAssay,
     NetworkConfiguration,
-    AssayData,
-    QueueManager
+    QueueManager,
+    AssayAnalysisStatus
 } from "unipept-web-components";
+import DockerCommunicator from "@/logic/communication/docker/DockerCommunicator";
+import BootstrapApplication from "@/logic/application/BootstrapApplication";
 
 const electron = require("electron");
 const ipcRenderer = electron.ipcRenderer;
@@ -101,8 +102,8 @@ const { app } = require("electron").remote;
         assaysInProgress: {
             get(): Assay[] {
                 return this.$store.getters.assays
-                    .filter((a: AssayData) => a.analysisMetaData.progress < 1)
-                    .map((a: AssayData) => a.assay);
+                    .filter((a: AssayAnalysisStatus) => !a.analysisReady)
+                    .map((a: AssayAnalysisStatus) => a.assay);
             }
         },
         isMini: {
@@ -124,6 +125,7 @@ export default class App extends Vue implements ErrorListener {
     private updatedColor: string = "info";
 
     private toolbarWidth: number = 210;
+
     // Has this component been initialized before?
     private static previouslyInitialized: boolean = false;
 
@@ -182,7 +184,7 @@ export default class App extends Vue implements ErrorListener {
             electron.remote.BrowserWindow.getAllWindows()[0].setProgressBar(-1);
         } else {
             const average: number = assays.reduce(
-                (prev: number, currentAssay: Assay) => prev + this.$store.getters.assayData(currentAssay).analysisMetaData.progress, 0
+                (prev: number, currentAssay: Assay) => prev + this.$store.getters["assayData"](currentAssay).originalProgress.value, 0
             ) / assays.length;
             electron.remote.BrowserWindow.getAllWindows()[0].setProgressBar(average);
         }
@@ -196,14 +198,8 @@ export default class App extends Vue implements ErrorListener {
         this.loading = true;
         let configurationManager = new ConfigurationManager();
         try {
-            let config: Configuration = await configurationManager.readConfiguration();
-            NetworkConfiguration.BASE_URL = config.apiSource;
-            // Make sure that the old Unipept URL is no longer being used...
-            if (NetworkConfiguration.BASE_URL === "https://unipept.ugent.be") {
-                NetworkConfiguration.BASE_URL = "https://api.unipept.ugent.be";
-            }
-            NetworkConfiguration.PARALLEL_API_REQUESTS = config.maxParallelRequests;
-            QueueManager.initializeQueue(config.maxLongRunningTasks);
+            const appBootstrap = new BootstrapApplication(this.$store);
+            appBootstrap.loadApplicationComponents();
         } catch (err) {
             // TODO: show a proper error message to the user in case this happens
             console.error(err)
@@ -218,10 +214,6 @@ export default class App extends Vue implements ErrorListener {
     private onToolbarWidthUpdated(newValue: number) {
         this.toolbarWidth = newValue;
     }
-
-    private onActivateDataset(value: ProteomicsAssay) {
-        this.$store.dispatch("setActiveDataset", value);
-    }
 }
 </script>