Upgrade dependencies to latest version

electron.vite.config.ts

@@ -7,7 +7,8 @@ export default defineConfig({
         plugins: [externalizeDepsPlugin()],
         resolve: {
             alias: {
-                "@common": resolve("src/common")
+                "@common": resolve("src/common"),
+                "@main": resolve("src/main")
             }
         },
     },
@@ -16,7 +17,8 @@ export default defineConfig({
         resolve: {
             alias: {
                 "@common": resolve("src/common"),
-                "@preload": resolve("src/preload")
+                "@preload": resolve("src/preload"),
+                "@main": resolve("src/main")
             }
         },
     },

package.json

@@ -28,14 +28,20 @@
     "@electron-toolkit/preload": "^2.0.0",
     "@electron-toolkit/utils": "^1.0.2",
     "@electron/remote": "^2.0.10",
-    "better-sqlite3": "^8.5.0",
+    "@types/async": "^3.2.21",
+    "@types/better-sqlite3": "^7.6.5",
+    "@types/uuid": "^9.0.4",
+    "async": "^3.2.4",
+    "better-sqlite3": "^9.1.1",
     "compare-versions": "^6.1.0",
-    "electron-updater": "^5.3.0",
+    "electron-updater": "^6.1.4",
     "follow-redirects": "^1.15.2",
     "marked": "^7.0.1",
     "pinia": "^2.1.6",
+    "unipept-web-components": "^2.1.3",
+    "uuid": "^9.0.1",
     "vue-router": "4",
-    "vuetify": "^3.3.9"
+    "vuetify": "^3.4.0"
   },
   "devDependencies": {
     "@electron-toolkit/tsconfig": "^1.0.1",
@@ -46,9 +52,9 @@
     "@types/node": "^18.16.16",
     "@vitejs/plugin-vue": "^4.2.3",
     "@vue/eslint-config-typescript": "^11.0.3",
-    "electron": "^24.4.1",
-    "electron-builder": "^23.6.0",
-    "electron-vite": "^1.0.23",
+    "electron": "^27.0.4",
+    "electron-builder": "^24.6.4",
+    "electron-vite": "^1.0.28",
     "eslint": "^8.42.0",
     "eslint-plugin-vue": "^9.14.1",
     "less": "^4.1.3",

src/common/assay/AssayManager.ts

@@ -0,0 +1,35 @@
+import { Assay } from "unipept-web-components";
+
+export default interface AssayManager {
+    /**
+     * Read all peptides and metadata for this assay from the datasource given in the constructor of this class. If the
+     * given assay does not exist yet, an error will be thrown.
+     *
+     * @param assayName Name of the assay that should be read. If no file with the associated name exists in the
+     * provided directory, an error will be thrown.
+     * @throws { Error } If no assay with the given name exists or could be find using the information provided.
+     */
+    loadAssay(
+        assayName: string
+    ): Promise<Assay>;
+
+    /**
+     * Write all peptides and metadata for this assay to the datasource given in the constructor of this class. If the
+     * given assay already exists, it will be overwritten.
+     *
+     * @param assay Assay object for which all information should be persistently stored.
+     */
+    writeAssay(
+        assay: Assay
+    ): Promise<void>;
+
+    /**
+     * Remove all peptides and metadata for this assay from the datasource given in the constructor of this class. If no
+     * assay with the given name exists, nothing will happen.
+     *
+     * @param assayName Name of the assay object that should be removed.
+     */
+    removeAssay(
+        assayName: string
+    ): Promise<void>;
+}

src/common/project/Project.ts

@@ -0,0 +1,9 @@
+import Study from "@common/study/Study";
+
+export default class Project {
+    constructor(
+        public readonly name: string,
+        public readonly location: string,
+        public readonly studies: Study[],
+    ) {}
+}

src/common/project/RecentProject.ts

@@ -0,0 +1,11 @@
+export default class RecentProject {
+    public readonly name: string;
+    public readonly path: string;
+    public lastOpened: Date;
+
+    constructor(name: string, path: string, lastOpened: Date) {
+        this.name = name;
+        this.path = path;
+        this.lastOpened = lastOpened;
+    }
+}

src/common/search-configuration/SearchConfiguration.ts

@@ -0,0 +1,14 @@
+export default class SearchConfiguration {
+    constructor(
+        public equateIl: boolean = true,
+        public filterDuplicates: boolean = true,
+        public enableMissingCleavageHandling: boolean = false,
+        public id?: string
+    ) {}
+
+    public toString() {
+        return [this.equateIl, this.filterDuplicates, this.enableMissingCleavageHandling].map(
+            t => t.toString()
+        ).join(",");
+    }
+}