Merge pull request #115 from unipept/fix/search-settings-transaction

Fix incorrect search settings sync when unexpected close of application
unipept · Jan 11, 2021 · 4f79c88 · 4f79c88
2 parents c97fada + d2dd334
commit 4f79c88
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Showing 10 changed files with 40 additions and 52 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -47,7 +47,7 @@
     "node-abi": "^2.19.3",
     "regenerator-runtime": "^0.13.3",
     "shared-memory-datastructures": "0.1.8",
-    "unipept-web-components": "1.3.0",
+    "unipept-web-components": "^1.3.1",
     "uuid": "^7.0.3",
     "vue": "^2.6.12",
     "vue-class-component": "^7.1.0",

diff --git a/src/components/analysis/AnalysisSummary.vue b/src/components/analysis/AnalysisSummary.vue
@@ -186,8 +186,7 @@ export default class AnalysisSummary extends Vue {
 
     private update() {
         const config = new SearchConfiguration(this.equateIl, this.filterDuplicates, this.missedCleavage);
-        this.assay.setSearchConfiguration(config);
-        this.$store.dispatch("processAssay", [this.assay, true]);
+        this.$store.dispatch("processAssay", [this.assay, true, config]);
     }
 
     private getHumanReadableAssayDate(): string {

diff --git a/src/components/navigation-drawers/AssayItem.vue b/src/components/navigation-drawers/AssayItem.vue
@@ -322,7 +322,7 @@ export default class AssayItem extends Vue {
     }
 
     private reanalyse() {
-        this.$store.dispatch("processAssay", [this.assay, true]);
+        this.$store.dispatch("processAssay", [this.assay, true, this.assay.getSearchConfiguration()]);
     }
 
     private selectAssay() {

diff --git a/src/components/pages/analysis/AnalysisPage.vue b/src/components/pages/analysis/AnalysisPage.vue
@@ -142,7 +142,11 @@ export default class AnalysisPage extends Vue {
 
     private reanalyse() {
         if (this.activeAssay) {
-            this.$store.dispatch("processAssay", [this.activeAssay, true]);
+            this.$store.dispatch("processAssay", [
+                this.activeAssay,
+                true,
+                this.activeAssay.getSearchConfiguration()
+            ]);
         }
     }
 

diff --git a/src/logic/communication/DesktopAssayProcessor.ts b/src/logic/communication/DesktopAssayProcessor.ts
@@ -9,6 +9,7 @@ import {
     AssayProcessor,
     PeptideData,
     NetworkConfiguration,
+    SearchConfiguration
 } from "unipept-web-components";
 
 import CachedCommunicationSource from "@/logic/communication/source/CachedCommunicationSource";
@@ -29,9 +30,14 @@ export default class DesktopAssayProcessor implements AssayProcessor {
 
     public async processAssay(
         countTable: CountTable<Peptide>,
-        forceUpdate: boolean = false
+        forceUpdate: boolean = false,
+        searchSettings: SearchConfiguration
     ): Promise<CommunicationSource> {
-        const [pept2DataResponses, peptideTrust] = await this.getPept2Data(countTable, forceUpdate);
+        const [pept2DataResponses, peptideTrust] = await this.getPept2Data(
+            countTable,
+            forceUpdate,
+            searchSettings
+        );
         this.setProgress(1);
 
         if (this.isCancelled()) {
@@ -58,7 +64,8 @@ export default class DesktopAssayProcessor implements AssayProcessor {
 
     private async getPept2Data(
         peptideCountTable: CountTable<Peptide>,
-        forceUpdate: boolean
+        forceUpdate: boolean,
+        searchSettings: SearchConfiguration
     ): Promise<[ShareableMap<Peptide, PeptideData>, PeptideTrust]> {
         const processedAssayManager = new ProcessedAssayManager(this.dbManager);
         const processingResult = await processedAssayManager.readProcessingResults(this.assay);
@@ -81,26 +88,27 @@ export default class DesktopAssayProcessor implements AssayProcessor {
 
             await this.pept2DataCommunicator.process(
                 peptideCountTable,
-                this.assay.getSearchConfiguration(),
+                searchSettings,
                 pept2DataProgressNotifier
             );
 
             if (!this.cancelled) {
                 // @ts-ignore
                 const pept2ResponseMap: ShareableMap<string, PeptideData> = this.pept2DataCommunicator.getPeptideResponseMap(
-                    this.assay.getSearchConfiguration()
+                    searchSettings
                 );
                 const trust = await this.pept2DataCommunicator.getPeptideTrust(
                     peptideCountTable,
-                    this.assay.getSearchConfiguration()
+                    searchSettings
                 );
 
                 this.assay.setEndpoint(currentEndpoint);
                 this.assay.setDatabaseVersion(currentDbVersion);
                 this.assay.setDate(new Date());
+                this.assay.setSearchConfiguration(searchSettings);
 
                 // Store results and update metadata...
-                await processedAssayManager.storeProcessingResults(this.assay, pept2ResponseMap, trust);
+                await processedAssayManager.storeProcessingResults(this.assay, pept2ResponseMap, trust, searchSettings);
 
                 return [
                     pept2ResponseMap,

diff --git a/src/logic/filesystem/assay/FileSystemAssayChangeListener.ts b/src/logic/filesystem/assay/FileSystemAssayChangeListener.ts
@@ -64,7 +64,7 @@ export default class FileSystemAssayChangeListener implements ChangeListener<Pro
         await assay.accept(writer);
 
         // noinspection ES6MissingAwait
-        store.dispatch("processAssay", [assay, false]);
+        store.dispatch("processAssay", [assay, false, assay.getSearchConfiguration()]);
     }
 
     private getAssayDirectory(): string {

diff --git a/src/logic/filesystem/assay/processed/ProcessedAssayManager.ts b/src/logic/filesystem/assay/processed/ProcessedAssayManager.ts
@@ -97,7 +97,8 @@ export default class ProcessedAssayManager {
     public async storeProcessingResults(
         assay: ProteomicsAssay,
         pept2Data: ShareableMap<string, PeptideData>,
-        trust: PeptideTrust
+        trust: PeptideTrust,
+        searchSettings: SearchConfiguration
     ) {
         // Delete the metadata that's associated with this assay
         await this.dbManager.performQuery<void>((db: Database) => {
@@ -127,7 +128,7 @@ export default class ProcessedAssayManager {
         });
 
         // Now write the metadata to the database again.
-        const existingConfig = assay.getSearchConfiguration();
+        const existingConfig = searchSettings;
         const searchConfiguration = new SearchConfiguration(
             existingConfig.equateIl,
             existingConfig.filterDuplicates,

diff --git a/src/logic/filesystem/project/FileSystemWatcher.ts b/src/logic/filesystem/project/FileSystemWatcher.ts
@@ -114,7 +114,7 @@ export default class FileSystemWatcher {
                 // it is added to the study.
                 study.addAssay(assay);
                 await store.dispatch("addAssay", assay);
-                store.dispatch("processAssay", [assay, false]);
+                store.dispatch("processAssay", [assay, false, assay.getSearchConfiguration()]);
             }
         } catch (err) {
             this.reportError(err);
@@ -153,7 +153,10 @@ export default class FileSystemWatcher {
             for (const assay of study.getAssays()) {
                 await store.dispatch("addAssay", assay);
                 // noinspection ES6MissingAwait
-                store.dispatch("processAssay", [assay, false]);
+                store.dispatch(
+                    "processAssay",
+                    [assay, false, (assay as ProteomicsAssay).getSearchConfiguration()]
+                );
             }
 
             study.addChangeListener(new FileSystemStudyChangeListener());

diff --git a/src/state/ProjectStore.ts b/src/state/ProjectStore.ts
@@ -1,4 +1,4 @@
-import { Study } from "unipept-web-components";
+import { ProteomicsAssay, Study } from "unipept-web-components";
 import { ActionContext, ActionTree, GetterTree, MutationTree } from "vuex";
 import FileSystemWatcher from "@/logic/filesystem/project/FileSystemWatcher";
 import path from "path";
@@ -102,7 +102,9 @@ const projectActions: ActionTree<ProjectState, any> = {
         for (const study of studies) {
             for (const assay of study.getAssays()) {
                 await store.dispatch("addAssay", assay);
-                store.dispatch("processAssay", [assay, false]);
+                store.dispatch(
+                    "processAssay",
+                    [assay, false, (assay as ProteomicsAssay).getSearchConfiguration()]);
             }
         }