From 4cafa8f41eb76fe1133f1db15fad0342ab248e53 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Fri, 10 Feb 2023 13:39:15 +0100
Subject: [PATCH] Lower the batch size when missed cleavage handling is enabled

---
 package.json                                  |  1 +
 src/logic/Utils.ts                            | 25 +++----------------
 src/logic/application/BootstrapApplication.ts |  5 +++-
 .../analysis/CachedOnlineAnalysisSource.ts    | 16 ++++++------
 yarn.lock                                     |  5 ++++
 5 files changed, 22 insertions(+), 30 deletions(-)

diff --git a/package.json b/package.json
index 6840041f..cbb16a57 100644
--- a/package.json
+++ b/package.json
@@ -26,6 +26,7 @@
         "better-sqlite3": "^8.0.1",
         "check-disk-space": "^3.3.1",
         "chokidar": "^3.5.3",
+        "compare-versions": "^6.0.0-rc.1",
         "core-js": "^3.25.0",
         "dockerode": "^3.3.4",
         "electron": "^21.3.3",
diff --git a/src/logic/Utils.ts b/src/logic/Utils.ts
index 2bc1fbbb..d96a586b 100644
--- a/src/logic/Utils.ts
+++ b/src/logic/Utils.ts
@@ -1,3 +1,5 @@
+import { compareVersions } from "compare-versions";
+
 export default class Utils {
     static isWindows(): boolean {
         return process.platform === "win32";
@@ -19,28 +21,7 @@ export default class Utils {
      * @return True if firstVersion is larger than secondVersion
      */
     static isVersionLargerThan(firstVersion: string, secondVersion: string): boolean {
-        const firstSplitted = firstVersion.split(".").map(x => parseInt(x));
-        const secondSplitted = secondVersion.split(".").map(x => parseInt(x));
-
-        if (firstSplitted.length < secondSplitted.length) {
-            for (let i = 0; i < secondSplitted.length - firstSplitted.length; i++) {
-                firstSplitted.push(0);
-            }
-        } else if (secondSplitted.length < firstSplitted.length) {
-            for (let i = 0; i < firstSplitted.length - secondSplitted.length; i++) {
-                secondSplitted.push(0);
-            }
-        }
-
-        for (let part = 0; part < firstSplitted.length; part++) {
-            if (firstSplitted[part] > secondSplitted[part]) {
-                return true;
-            } else if (firstSplitted[part] < secondSplitted[part]) {
-                return false;
-            }
-        }
-
-        return false;
+        return compareVersions(firstVersion, secondVersion) === 1;
     }
 
     static compareAssays<T>(a: T[], b: T[]): boolean {
diff --git a/src/logic/application/BootstrapApplication.ts b/src/logic/application/BootstrapApplication.ts
index 29a82848..f25dd5c9 100644
--- a/src/logic/application/BootstrapApplication.ts
+++ b/src/logic/application/BootstrapApplication.ts
@@ -1,6 +1,6 @@
 import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
 import Configuration from "@/logic/configuration/Configuration";
-import { NetworkConfiguration, QueueManager } from "unipept-web-components";
+import { NetworkConfiguration, Pept2DataCommunicator, QueueManager } from "unipept-web-components";
 import DockerCommunicator from "@/logic/communication/docker/DockerCommunicator";
 import { Store } from "vuex";
 import ApplicationMigrator from "@/logic/application/ApplicationMigrator";
@@ -20,6 +20,9 @@ export default class BootstrapApplication {
      * Start and load the different components required for the application to function properly.
      */
     public async loadApplicationComponents(): Promise<void> {
+        // Hack to lower the amount of peptides sent at the same time to the server
+        Pept2DataCommunicator.MISSED_CLEAVAGE_BATCH = 5;
+
         await this.runApplicationMigrations();
         const config = await this.initializeConfiguration();
         this.initializeApi(config);
diff --git a/src/logic/communication/analysis/CachedOnlineAnalysisSource.ts b/src/logic/communication/analysis/CachedOnlineAnalysisSource.ts
index fdba3f23..7b06288c 100644
--- a/src/logic/communication/analysis/CachedOnlineAnalysisSource.ts
+++ b/src/logic/communication/analysis/CachedOnlineAnalysisSource.ts
@@ -29,14 +29,16 @@ export default class CachedOnlineAnalysisSource implements AnalysisSource {
     }
 
     public getCommunicationSource() {
+        const pept2DataCommunicator = new CachedPept2DataCommunicator(
+            this.assay,
+            new Pept2DataCommunicator(this.endpoint),
+            this.dbManager,
+            this.projectLocation,
+            this.store
+        );
+
         return new ConfigureableCommunicationSource(
-            new CachedPept2DataCommunicator(
-                this.assay,
-                new Pept2DataCommunicator(this.endpoint),
-                this.dbManager,
-                this.projectLocation,
-                this.store
-            ),
+            pept2DataCommunicator,
             new CachedGoResponseCommunicator(),
             new CachedEcResponseCommunicator(),
             new CachedInterproResponseCommunicator(),
diff --git a/yarn.lock b/yarn.lock
index 33204a81..6fc344c2 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -3215,6 +3215,11 @@ compare-version@^0.1.2:
   resolved "https://registry.yarnpkg.com/compare-version/-/compare-version-0.1.2.tgz#0162ec2d9351f5ddd59a9202cba935366a725080"
   integrity sha512-pJDh5/4wrEnXX/VWRZvruAGHkzKdr46z11OlTPN+VrATlWWhSKewNCJ1futCO5C7eJB3nPMFZA1LeYtcFboZ2A==
 
+compare-versions@^6.0.0-rc.1:
+  version "6.0.0-rc.1"
+  resolved "https://registry.yarnpkg.com/compare-versions/-/compare-versions-6.0.0-rc.1.tgz#93e6beb8767c2375333ee168fa64c28b75ace2c6"
+  integrity sha512-cFhkjbGY1jLFWIV7KegECbfuyYPxSGvgGkdkfM+ibboQDoPwg2FRHm5BSNTOApiauRBzJIQH7qvOJs2sW5ueKQ==
+
 compressible@~2.0.16:
   version "2.0.18"
   resolved "https://registry.yarnpkg.com/compressible/-/compressible-2.0.18.tgz#af53cca6b070d4c3c0750fbd77286a6d7cc46fba"