No more FS access in workers

unipept · Oct 5, 2020 · 1ccc6c5 · 1ccc6c5
1 parent 94185e9
commit 1ccc6c5
Show file tree

Hide file tree

Showing 46 changed files with 548 additions and 782 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -17,8 +17,6 @@ jobs:
       - uses: actions/setup-node@v1
       - name: Install dependencies
         run: npm install
-      - name: Patch dependencies
-        run: npx patch-package
       - name: Build application for ${{ matrix.os }}
         run: npm run electron:publish
         env:

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "unipept-desktop",
-  "version": "0.3.1",
+  "version": "0.4.0",
   "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.",
@@ -43,11 +43,9 @@
     "follow-redirects": "^1.11.0",
     "jquery": "^3.4.1",
     "node-abi": "^2.18.0",
-    "patch-package": "^6.2.2",
     "regenerator-runtime": "^0.13.3",
     "shared-memory-datastructures": "0.1.8",
-    "threads": "^1.4.1",
-    "unipept-web-components": "file:unipept-web-components-1.2.2.tgz",
+    "unipept-web-components": "1.2.3",
     "uuid": "^7.0.3",
     "vue": "^2.6.12",
     "vue-class-component": "^7.1.0",
@@ -85,7 +83,6 @@
     "sass-loader": "^7.1.0",
     "speed-measure-webpack-plugin": "^1.3.3",
     "style-loader": "^1.0.0",
-    "threads-plugin": "^1.3.1",
     "typescript": "^3.9.5",
     "vue-cli-plugin-electron-builder": "^2.0.0-rc.4",
     "vue-cli-plugin-styleguidist": "^4.2.3",

diff --git a/patches/better-sqlite3+7.0.1.patch b/patches/better-sqlite3+7.0.1.patch
diff --git a/patches/bindings+1.5.0.patch b/patches/bindings+1.5.0.patch
diff --git a/src/App.vue b/src/App.vue
@@ -71,7 +71,6 @@ import ConfigurationManager from "./logic/configuration/ConfigurationManager";
 import Configuration from "./logic/configuration/Configuration";
 import ErrorListener from "@/logic/filesystem/ErrorListener";
 const electron = require("electron");
-import Worker from "worker-loader?inline=fallback!./logic/system/DesktopWorker.worker";
 import {
     Assay,
     ProteomicsAssay,
@@ -205,7 +204,7 @@ export default class App extends Vue implements ErrorListener {
             let config: Configuration = await configurationManager.readConfiguration();
             NetworkConfiguration.BASE_URL = config.apiSource;
             NetworkConfiguration.PARALLEL_API_REQUESTS = config.maxParallelRequests;
-            QueueManager.initializeQueue(config.maxLongRunningTasks, () => new Worker());
+            QueueManager.initializeQueue(config.maxLongRunningTasks);
             await this.$store.dispatch("setUseNativeTitlebar", config.useNativeTitlebar);
         } catch (err) {
             // TODO: show a proper error message to the user in case this happens

diff --git a/src/background.ts b/src/background.ts
@@ -27,7 +27,7 @@ async function createWindow() {
     let options = {
         width: 1200,
         height: 1000,
-        webPreferences: { nodeIntegration: true, nodeIntegrationInWorker: true, enableRemoteModule: true },
+        webPreferences: { nodeIntegration: true, enableRemoteModule: true },
         show: false
     };
 

diff --git a/src/components/navigation-drawers/AssayItem.vue b/src/components/navigation-drawers/AssayItem.vue
@@ -356,7 +356,7 @@ export default class AssayItem extends Vue {
         newAssay.setSearchConfiguration(searchConfiguration);
         const metadataWriter = new AssayFileSystemMetaDataWriter(
             `${this.$store.getters.projectLocation}${this.study.getName()}`,
-            this.$store.getters.database,
+            this.$store.getters.dbManager,
             this.study
         );
         await newAssay.accept(metadataWriter);
@@ -371,8 +371,7 @@ export default class AssayItem extends Vue {
         this.removeConfirmationActive = false;
         const assayDestroyer = new AssayFileSystemDestroyer(
             `${this.$store.getters.projectLocation}${this.study.getName()}`,
-            this.$store.getters.database,
-            this.$store.getters.databaseFile
+            this.$store.getters.dbManager
         );
         await this.assay.accept(assayDestroyer);
     }

diff --git a/src/components/navigation-drawers/StudyItem.vue b/src/components/navigation-drawers/StudyItem.vue
@@ -246,7 +246,7 @@ export default class StudyItem extends Vue {
         // Completely destroy this study and wait for the file system watcher to pick the change up.
         const studyDestroyer = new StudyFileSystemRemover(
             `${this.$store.getters.projectLocation}${this.study.getName()}`,
-            this.$store.getters.database
+            this.$store.getters.dbManager
         );
         await this.study.accept(studyDestroyer);
     }
@@ -270,7 +270,7 @@ export default class StudyItem extends Vue {
                 // Write metadata to disk
                 const metaDataWriter = new AssayFileSystemMetaDataWriter(
                     `${this.$store.getters.projectLocation}${this.study.getName()}`,
-                    this.$store.getters.database,
+                    this.$store.getters.dbManager,
                     this.study
                 );
 
@@ -301,7 +301,7 @@ export default class StudyItem extends Vue {
             // Write metadata to disk
             const metaDataWriter = new AssayFileSystemMetaDataWriter(
                 `${this.$store.getters.projectLocation}${this.study.getName()}`,
-                this.$store.getters.database,
+                this.$store.getters.dbManager,
                 this.study
             );
 
@@ -310,7 +310,7 @@ export default class StudyItem extends Vue {
             // Write the assay to disk. It will automatically be picked up by the file system watchers
             const assaySerializer = new AssayFileSystemDataWriter(
                 `${this.$store.getters.projectLocation}${this.study.getName()}`,
-                this.$store.getters.database
+                this.$store.getters.dbManager
             );
 
             await assay.accept(assaySerializer);

diff --git a/src/logic/communication/DesktopAssayProcessor.ts b/src/logic/communication/DesktopAssayProcessor.ts
@@ -17,14 +17,14 @@ import ProcessedAssayManager from "@/logic/filesystem/assay/processed/ProcessedA
 import { Database } from "better-sqlite3";
 import { ShareableMap } from "shared-memory-datastructures";
 import MetadataCommunicator from "@/logic/communication/metadata/MetadataCommunicator";
+import DatabaseManager from "@/logic/filesystem/database/DatabaseManager";
 
 export default class DesktopAssayProcessor implements AssayProcessor {
     private pept2DataCommunicator: Pept2DataCommunicator;
     private cancelled: boolean = false;
 
     constructor(
-        private readonly db: Database,
-        private readonly dbFile: string,
+        private readonly dbManager: DatabaseManager,
         private readonly assay: ProteomicsAssay,
         private readonly progressListener?: ProgressListener
     ) {}
@@ -62,7 +62,7 @@ export default class DesktopAssayProcessor implements AssayProcessor {
         peptideCountTable: CountTable<Peptide>,
         forceUpdate: boolean
     ): Promise<[ShareableMap<Peptide, PeptideData>, PeptideTrust]> {
-        const processedAssayManager = new ProcessedAssayManager(this.db, this.dbFile);
+        const processedAssayManager = new ProcessedAssayManager(this.dbManager);
         const processingResult = await processedAssayManager.readProcessingResults(this.assay);
 
         if (processingResult !== null && !forceUpdate) {