Merge pull request #164 from unipept/fix/demo-project-unreadable

Fix for unreadable demo projects
unipept · Mar 30, 2022 · 97ef36a · 97ef36a
2 parents 40b2b73 + c248a14
commit 97ef36a
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Showing 5 changed files with 40 additions and 19 deletions.
diff --git a/src/App.vue b/src/App.vue
@@ -22,9 +22,6 @@
                     'left': isMini ? '55px' : (toolbarWidth + 55) + 'px'
                 }"
                 class="main-container">
-                <v-alert type="warning" class="ma-2" v-if="isDemoProjectActive">
-                    You are currently browsing the demo project. Changes made to this project will not be saved.
-                </v-alert>
                 <router-view style="min-height: 100%;"></router-view>
                 <v-dialog v-model="errorDialog" persistent max-width="600">
                     <v-card>
@@ -130,12 +127,6 @@ export default class App extends Vue implements ErrorListener {
     private showHomePageDialog: boolean = true;
     private errorDialog: boolean = false;
 
-    get isDemoProjectActive(): boolean {
-        const projectLocation: string = this.$store.getters.projectLocation;
-        const tempPath: string = app.getPath("temp");
-        return projectLocation && projectLocation.includes(tempPath);
-    }
-
     async mounted() {
         // Connect with the electron-renderer thread and listen to navigation events that take place. All navigation
         // should pass through the Vue app.

diff --git a/src/components/pages/analysis/AnalysisPage.vue b/src/components/pages/analysis/AnalysisPage.vue
@@ -8,11 +8,16 @@
                 'float': 'right'
             }">
 
+            <v-alert type="warning" class="ma-2" v-if="isDemoProjectActive">
+                You are currently browsing the demo project. Changes made to this project will not be saved.
+            </v-alert>
+
             <!-- Show analysis results for the currently selected assay if it's ready with processing -->
             <v-container
                 v-if="!errorStatus && activeAssay && activeAssay.analysisReady"
                 fluid
                 class="pt-0">
+
                 <router-view></router-view>
             </v-container>
 
@@ -142,6 +147,8 @@ import CreateAssayDialog from "@/components/assay/CreateAssayDialog.vue";
 import ProgressReportSummary from "@/components/analysis/ProgressReportSummary.vue";
 import { Watch } from "vue-property-decorator";
 
+const { app } = require("electron").remote;
+
 @Component({
     components: {
         ProgressReportSummary,
@@ -194,6 +201,12 @@ export default class AnalysisPage extends Vue {
         return this.activeAssay?.originalProgress;
     }
 
+    get isDemoProjectActive(): boolean {
+        const projectLocation: string = this.$store.getters.projectLocation;
+        const tempPath: string = app.getPath("temp");
+        return projectLocation && projectLocation.includes(tempPath);
+    }
+
     private reanalyse() {
         if (this.activeAssay) {
             this.$store.dispatch("analyseAssay", this.activeAssay.assay);

diff --git a/src/logic/filesystem/assay/AssayFileSystemDataReader.ts b/src/logic/filesystem/assay/AssayFileSystemDataReader.ts
@@ -1,5 +1,13 @@
 import FileSystemAssayVisitor from "@/logic/filesystem/assay/FileSystemAssayVisitor";
-import { ProteomicsAssay, IOException, QueueManager, Assay, Study, SearchConfiguration } from "unipept-web-components";
+import {
+    ProteomicsAssay,
+    IOException,
+    QueueManager,
+    Assay,
+    Study,
+    SearchConfiguration,
+    NetworkConfiguration
+} from "unipept-web-components";
 import { promises as fs } from "fs";
 import Worker from "worker-loader?inline=fallback!./AssayFileSystemDataReader.worker";
 import { Database } from "better-sqlite3";
@@ -10,6 +18,7 @@ import DatabaseManager from "@/logic/filesystem/database/DatabaseManager";
 import AnalysisSourceSerializer from "@/logic/filesystem/analysis/AnalysisSourceSerializer";
 import SearchConfigManager from "@/logic/filesystem/configuration/SearchConfigManager";
 import StorageMetadataManager from "@/logic/filesystem/metadata/StorageMetadataManager";
+import CachedOnlineAnalysisSource from "@/logic/communication/analysis/CachedOnlineAnalysisSource";
 
 export default class AssayFileSystemDataReader extends FileSystemAssayVisitor {
     private static inProgress: Promise<string[]>;
@@ -67,7 +76,6 @@ export default class AssayFileSystemDataReader extends FileSystemAssayVisitor {
 
             const searchConfigMng = new SearchConfigManager(this.dbManager);
 
-            mpAssay.setName(assayRow.name);
             mpAssay.setSearchConfiguration(await searchConfigMng.readSearchConfig(assayRow.configuration_id));
             mpAssay.setAnalysisSource(
                 await AnalysisSourceSerializer.deserializeAnalysisSource(
@@ -82,8 +90,15 @@ export default class AssayFileSystemDataReader extends FileSystemAssayVisitor {
                 mpAssay.setDate(metadata.analysisDate);
             }
         } else {
-            // Throw an exception, the assay was not found in the database
-            throw new IOException("Requested assay was not found in the database!");
+            mpAssay.setSearchConfiguration(new SearchConfiguration());
+            mpAssay.setAnalysisSource(
+                new CachedOnlineAnalysisSource(
+                    NetworkConfiguration.BASE_URL,
+                    mpAssay,
+                    this.dbManager,
+                    this.projectLocation
+                )
+            );
         }
     }
 }
diff --git a/src/logic/filesystem/assay/AssayFileSystemDataWriter.ts b/src/logic/filesystem/assay/AssayFileSystemDataWriter.ts
@@ -23,8 +23,6 @@ export default class AssayFileSystemDataWriter extends FileSystemAssayVisitor {
     }
 
     public async visitProteomicsAssay(mpAssay: ProteomicsAssay): Promise<void> {
-        console.log("Visit from writer...");
-
         // Write search configuration to database
         const config = mpAssay.getSearchConfiguration();
 

diff --git a/src/logic/filesystem/study/StudyFileSystemDataReader.ts b/src/logic/filesystem/study/StudyFileSystemDataReader.ts
@@ -2,10 +2,11 @@ import FileSystemStudyVisitor from "./FileSystemStudyVisitor";
 import * as fs from "fs";
 import path from "path";
 import AssayFileSystemDataReader from "@/logic/filesystem/assay/AssayFileSystemDataReader";
-import { Study, Assay, ProteomicsAssay, AssayVisitor, IOException } from "unipept-web-components";
+import { Study, Assay, ProteomicsAssay, AssayVisitor, IOException, NetworkConfiguration } from "unipept-web-components";
 import { Database } from "better-sqlite3";
 import DatabaseManager from "@/logic/filesystem/database/DatabaseManager";
 import AssayFileSystemDataWriter from "@/logic/filesystem/assay/AssayFileSystemDataWriter";
+import CachedOnlineAnalysisSource from "@/logic/communication/analysis/CachedOnlineAnalysisSource";
 
 
 /**
@@ -34,7 +35,7 @@ export default class StudyFileSystemDataReader extends FileSystemStudyVisitor {
             for (const file of files.filter(name => name.endsWith(".pep"))) {
                 const assayName: string = path.basename(file).replace(".pep", "");
 
-                let assay: Assay;
+                let assay: ProteomicsAssay;
 
                 const row = await this.dbManager.performQuery<any>((db: Database) => {
                     return db.prepare(
@@ -54,12 +55,15 @@ export default class StudyFileSystemDataReader extends FileSystemStudyVisitor {
                     assay = new ProteomicsAssay();
                     assay.setName(assayName);
 
-                    const assayVisitor: AssayVisitor = new AssayFileSystemDataWriter(
+                    const assayReader = new AssayFileSystemDataReader(this.studyPath, this.dbManager, this.projectLocation);
+                    await assay.accept(assayReader);
+
+                    const assayWriter: AssayVisitor = new AssayFileSystemDataWriter(
                         this.studyPath,
                         this.dbManager,
                         study
                     );
-                    await assay.accept(assayVisitor);
+                    await assay.accept(assayWriter);
                 }
 
                 study.addAssay(assay);