From cc6b1e0570eea3475a36930b61d425e9b3d74390 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:21:12 +0200
Subject: [PATCH 1/7] Missed cleavage handling always enabled now

---
 src/components/analysis/AnalysisSummary.vue   |   6 +-
 src/components/analysis/CustomTooltip.vue     | 110 +++++++++
 .../analysis/SearchSettingsForm.vue           |  98 ++++++++
 src/components/assay/CreateAssayDialog.vue    |  19 +-
 .../dialogs/SearchConfigurationDialog.vue     | 218 ------------------
 .../navigation-drawers/AssayItem.vue          |   2 +-
 .../navigation-drawers/StudyItem.vue          |   8 -
 .../pages/analysis/AnalysisPage.vue           |   2 -
 .../assay/AssayFileSystemDataReader.ts        |   2 +-
 .../assay/processed/CachedResultsManager.ts   |   2 +-
 .../configuration/SearchConfigManager.ts      |   4 +-
 11 files changed, 226 insertions(+), 245 deletions(-)
 create mode 100644 src/components/analysis/CustomTooltip.vue
 create mode 100644 src/components/analysis/SearchSettingsForm.vue
 delete mode 100644 src/components/dialogs/SearchConfigurationDialog.vue

diff --git a/src/components/analysis/AnalysisSummary.vue b/src/components/analysis/AnalysisSummary.vue
index da0108f2..d2eefe17 100644
--- a/src/components/analysis/AnalysisSummary.vue
+++ b/src/components/analysis/AnalysisSummary.vue
@@ -76,7 +76,7 @@
                             :horizontal="true"
                             :equate-il.sync="equateIl"
                             :filter-duplicates.sync="filterDuplicates"
-                            :missing-cleavage.sync="missedCleavage">
+                            :missing-cleavage="true">
                         </search-settings-form>
 
                         <div class="d-flex justify-center align-center mt-4">
@@ -120,7 +120,6 @@ import {
     ProteomicsAssay,
     CountTable,
     Peptide,
-    SearchSettingsForm,
     SearchConfiguration,
     PeptideTrust,
     Pept2DataCommunicator,
@@ -139,6 +138,7 @@ import AnalysisSourceSelect from "@/components/assay/AnalysisSourceSelect.vue";
 import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
 import CustomDatabase from "@/logic/custom_database/CustomDatabase";
 import ExportResultsButton from "@/components/analysis/ExportResultsButton.vue";
+import SearchSettingsForm from "@/components/analysis/SearchSettingsForm.vue";
 
 @Component({
     components: { PeptideSummaryTable, SearchSettingsForm, ExportResultsButton, Tooltip, AnalysisSourceSelect }
@@ -323,7 +323,7 @@ export default class AnalysisSummary extends Vue {
     }
 
     private update() {
-        const config = new SearchConfiguration(this.equateIl, this.filterDuplicates, this.missedCleavage);
+        const config = new SearchConfiguration(this.equateIl, this.filterDuplicates, true);
         this.assay.setSearchConfiguration(config);
 
         this.assay.setAnalysisSource(this.analysisSource);
diff --git a/src/components/analysis/CustomTooltip.vue b/src/components/analysis/CustomTooltip.vue
new file mode 100644
index 00000000..8bbbf651
--- /dev/null
+++ b/src/components/analysis/CustomTooltip.vue
@@ -0,0 +1,110 @@
+<template>
+  <div
+      class="tooltip-wrapper"
+      @mouseenter="startShowTooltipTimer"
+      @mouseleave="cancelShowTooltipTimer"
+  >
+    <slot></slot>
+    <div
+        v-if="visible"
+        class="custom-tooltip"
+        ref="tooltip"
+        @mouseenter="cancelHideTooltipTimer"
+        @mouseleave="startHideTooltipTimer"
+    >
+      Missed cleavage handling is now always enabled. Because of a change in
+      Unipept's underlying search engine, enabling missed cleavage handling no
+      longer results in a performance penalty. As a result, this configuration
+      option will be removed in a future release. See
+      <a
+          href="https://github.com/unipept/unipept/wiki/Unipept-Next"
+          target="_blank"
+          rel="noopener noreferrer"
+          class="text-white"
+      >this page</a>
+      for more information.
+    </div>
+  </div>
+</template>
+
+<script lang="ts">
+import { Vue, Component } from 'vue-property-decorator';
+
+@Component
+export default class CustomTooltip extends Vue {
+  visible = false;
+  showTooltipTimer: number | null = null;
+  hideTooltipTimer: number | null = null;
+
+  startShowTooltipTimer() {
+    this.cancelHideTooltipTimer();
+    if (this.showTooltipTimer !== null) {
+      clearTimeout(this.showTooltipTimer);
+      this.showTooltipTimer = null;
+    }
+    this.showTooltipTimer = window.setTimeout(() => {
+      this.visible = true;
+    }, 300);
+  }
+
+  cancelShowTooltipTimer() {
+    if (this.showTooltipTimer !== null) {
+      clearTimeout(this.showTooltipTimer);
+      this.showTooltipTimer = null;
+    }
+    this.startHideTooltipTimer();
+  }
+
+  startHideTooltipTimer() {
+    this.cancelHideTooltipTimer();
+    this.hideTooltipTimer = window.setTimeout(() => {
+      this.visible = false;
+    }, 1000);
+  }
+
+  cancelHideTooltipTimer() {
+    if (this.hideTooltipTimer !== null) {
+      clearTimeout(this.hideTooltipTimer);
+      this.hideTooltipTimer = null;
+    }
+  }
+}
+</script>
+
+<style scoped>
+.tooltip-wrapper {
+  position: relative;
+  display: inline-block;
+  overflow: visible;
+}
+
+.custom-tooltip {
+  position: absolute;
+  bottom: 100%;
+  left: 50%;
+  transform: translateX(-50%);
+  background-color: #323232;
+  color: #fff;
+  padding: 8px;
+  border-radius: 4px;
+  box-shadow: 0 2px 10px rgba(0, 0, 0, 0.2);
+  z-index: 1000;
+  margin-bottom: 8px;
+  transition: opacity 0.2s ease-in-out;
+  pointer-events: auto;
+  max-width: 400px;
+  width: max-content;
+  overflow: hidden;
+  white-space: normal;
+  line-height: 1.4;
+}
+
+.custom-tooltip a {
+  color: #1e88e5;
+  text-decoration: underline;
+}
+
+.custom-tooltip a:hover {
+  color: #1565c0;
+}
+</style>
diff --git a/src/components/analysis/SearchSettingsForm.vue b/src/components/analysis/SearchSettingsForm.vue
new file mode 100644
index 00000000..83d31982
--- /dev/null
+++ b/src/components/analysis/SearchSettingsForm.vue
@@ -0,0 +1,98 @@
+<template>
+  <div
+      :class="{
+            'search-settings-form': true,
+            'd-flex': true,
+            'flex-column': !horizontal,
+            'flex-row': horizontal,
+            'justify-space-between': horizontal
+    }">
+    <tooltip message="Equate isoleucine (I) and leucine (L) when matching peptides to UniProt entries.">
+      <v-checkbox :disabled="disabled" v-model="equateIlModel" label="Equate I and L" hide-details class="mt-0">
+        <span slot="label">Equate I and L</span>
+      </v-checkbox>
+    </tooltip>
+    <tooltip message="Remove duplicate peptides from the input before searching.">
+      <v-checkbox :disabled="disabled" v-model="filterDuplicatesModel" hide-details class="mt-0">
+        <span slot="label">Filter duplicate peptides</span>
+      </v-checkbox>
+    </tooltip>
+    <custom-tooltip message="Recombine subpeptides of miscleavages. Enabling this has a serious performance impact!">
+      <v-checkbox disabled input-value="true" hide-details class="mt-0">
+        <span slot="label">Advanced missed cleavage handling</span>
+      </v-checkbox>
+    </custom-tooltip>
+  </div>
+</template>
+
+<script lang="ts">
+import Vue from "vue";
+import Component from "vue-class-component";
+import { Prop, Watch } from "vue-property-decorator";
+import CustomTooltip from "@/components/analysis/CustomTooltip.vue";
+import { Tooltip } from "unipept-web-components"
+
+@Component({
+  components: {
+    CustomTooltip,
+    Tooltip
+  },
+  computed: {
+    equateIlModel: {
+      get() {
+        return this.equateIl;
+      },
+      set(val) {
+        this.equateIlData = val;
+        this.$emit("update:equate-il", val);
+      }
+    },
+    filterDuplicatesModel: {
+      get(): boolean {
+        return this.filterDuplicates;
+      },
+      set(val: boolean) {
+        this.filterDuplicatesData = val;
+        this.$emit("update:filter-duplicates", val);
+      }
+    },
+    missingCleavageModel: {
+      get() {
+        return this.missingCleavage;
+      },
+      set(val) {
+        this.missingCleavageData = val;
+        this.$emit("update:missing-cleavage", val);
+      }
+    }
+  }
+})
+export default class SearchSetingsForm extends Vue {
+  @Prop({ default: false }) disabled!: boolean;
+  @Prop({ default: true }) equateIl!: boolean;
+  @Prop({ default: true }) filterDuplicates!: boolean;
+  @Prop({ default: false }) missingCleavage!: boolean;
+  /**
+   * Show the component in a horizontal or vertical fashion? Set to true to show the different checkboxes on one line.
+   */
+  @Prop({ required: false, default: true })
+  private horizontal: boolean;
+
+  private equateIlData: boolean = this.equateIl;
+  private filterDuplicatesData: boolean = this.filterDuplicates;
+  private missingCleavageData: boolean = this.missingCleavage;
+
+  @Watch("equateIl") onEquateIlChanged() {
+    this.equateIlData = this.equateIl;
+  }
+
+  @Watch("filterDuplicates") onFilterDuplicatesChanged() {
+
+    this.filterDuplicatesData = this.filterDuplicates;
+  }
+
+  @Watch("missingCleavage") onMissingCleavageChanged() {
+    this.missingCleavageData = this.missingCleavage;
+  }
+}
+</script>
diff --git a/src/components/assay/CreateAssayDialog.vue b/src/components/assay/CreateAssayDialog.vue
index ddbf3c18..456e6902 100644
--- a/src/components/assay/CreateAssayDialog.vue
+++ b/src/components/assay/CreateAssayDialog.vue
@@ -110,8 +110,10 @@
                         </v-simple-checkbox>
                     </template>
                     <template v-slot:item.missedCleavage="{ item }">
-                        <v-simple-checkbox v-model="item.searchConfiguration.enableMissingCleavageHandling" color="primary">
-                        </v-simple-checkbox>
+                        <custom-tooltip>
+                            <v-simple-checkbox disabled :value="true" color="primary">
+                            </v-simple-checkbox>
+                        </custom-tooltip>
                     </template>
                     <template v-slot:item.actions="{ item }">
                         <v-tooltip bottom open-delay="500">
@@ -231,6 +233,7 @@ import ConfigurationManager from "@/logic/configuration/ConfigurationManager";
 import AssayFileSystemDataWriter from "@/logic/filesystem/assay/AssayFileSystemDataWriter";
 import CustomDatabase from "@/logic/custom_database/CustomDatabase";
 import ConfirmDeletionDialog from "@/components/dialogs/ConfirmDeletionDialog.vue";
+import CustomTooltip from "@/components/analysis/CustomTooltip.vue";
 
 
 const { dialog } = require("@electron/remote");
@@ -250,7 +253,7 @@ type ProteomicsAssayPlaceholder = {
 }
 
 @Component({
-    components: { ConfirmDeletionDialog, AnalysisSourceSelect }
+    components: { ConfirmDeletionDialog, AnalysisSourceSelect, CustomTooltip }
 })
 export default class CreateAssayDialog extends Vue {
     @Prop({ required: true })
@@ -345,14 +348,12 @@ export default class CreateAssayDialog extends Vue {
     }
 
     get areAllMissedCleavage(): boolean {
-        return this.assayPlaceholders.every(
-            (item: ProteomicsAssayPlaceholder) => item.searchConfiguration.enableMissingCleavageHandling
-        );
+        return true;
     }
 
     set areAllMissedCleavage(value: boolean) {
         for (const item of this.assayPlaceholders) {
-            item.searchConfiguration.enableMissingCleavageHandling = value;
+            item.searchConfiguration.enableMissingCleavageHandling = true;
         }
     }
 
@@ -550,7 +551,7 @@ export default class CreateAssayDialog extends Vue {
             name: this.generateUniqueAssayName("New assay"),
             nameError: "",
             peptides: "",
-            searchConfiguration: new SearchConfiguration(),
+            searchConfiguration: new SearchConfiguration(true, true, true),
             analysisSource: this.renderableSources[0],
             analysisSourceError: "",
             inProgress: false
@@ -577,7 +578,7 @@ export default class CreateAssayDialog extends Vue {
                     name: assayName,
                     nameError: "",
                     peptides: "",
-                    searchConfiguration: new SearchConfiguration(),
+                    searchConfiguration: new SearchConfiguration(true, true, true),
                     analysisSource: this.renderableSources[0],
                     analysisSourceError: "",
                     inProgress: true
diff --git a/src/components/dialogs/SearchConfigurationDialog.vue b/src/components/dialogs/SearchConfigurationDialog.vue
deleted file mode 100644
index 5ebb28eb..00000000
--- a/src/components/dialogs/SearchConfigurationDialog.vue
+++ /dev/null
@@ -1,218 +0,0 @@
-<template>
-    <v-dialog v-model="dialogActive" max-width="900" v-on:click:outside="cancel">
-        <v-card>
-            <v-card-title>
-                Search configuration
-            </v-card-title>
-            <v-card-text>
-                <p>
-                    Please configure the search settings that should be applied to each imported assay. Note that
-                    enabling the <span class="font-italic">advanced missed cleavage handling</span> setting has a
-                    serious performance impact and leads to a slower analysis!
-                </p>
-                <v-data-table
-                    :items="tableItems"
-                    :headers="tableHeaders"
-                    class="searchConfigTable">
-                    <template v-slot:header.equateIl="{ header }">
-                        {{ header.text }}
-                        <div>
-                            <a v-if="areAllEquateIl" @click="areAllEquateIl = false">
-                                Uncheck all
-                            </a>
-                            <a v-else @click="areAllEquateIl = true">
-                                Check all
-                            </a>
-                        </div>
-                    </template>
-                    <template v-slot:header.filterDuplicates="{ header }">
-                        {{ header.text }}
-                        <div>
-                            <a v-if="areAllFilterDuplicate" @click="areAllFilterDuplicate = false">
-                                Uncheck all
-                            </a>
-                            <a v-else @click="areAllFilterDuplicate = true">
-                                Check all
-                            </a>
-                        </div>
-                    </template>
-                    <template v-slot:header.missedCleavage="{ header }">
-                        {{ header.text }}
-                        <div>
-                            <a v-if="areAllMissedCleavage" @click="areAllMissedCleavage = false">
-                                Uncheck all
-                            </a>
-                            <a v-else @click="areAllMissedCleavage = true">
-                                Check all
-                            </a>
-                        </div>
-                    </template>
-                    <template v-slot:item.equateIl="{ item }">
-                        <v-simple-checkbox v-model="item.equateIl" color="primary">
-                        </v-simple-checkbox>
-                    </template>
-                    <template v-slot:item.filterDuplicates="{ item }">
-                        <v-simple-checkbox v-model="item.filterDuplicates" color="primary">
-                        </v-simple-checkbox>
-                    </template>
-                    <template v-slot:item.missedCleavage="{ item }">
-                        <v-simple-checkbox v-model="item.missedCleavage" color="primary">
-                        </v-simple-checkbox>
-                    </template>
-                </v-data-table>
-                <div class="d-flex justify-center mt-4">
-                    <v-btn @click="cancel" class="mr-2">
-                        Cancel
-                    </v-btn>
-                    <v-btn color="primary" @click="setConfigs">
-                        Start analysis
-                    </v-btn>
-                </div>
-            </v-card-text>
-        </v-card>
-    </v-dialog>
-</template>
-
-<script lang="ts">
-import Vue from "vue";
-import Component from "vue-class-component";
-import { Prop, Watch } from "vue-property-decorator";
-import { ProteomicsAssay, SearchSettingsForm, SearchConfiguration  } from "unipept-web-components";
-
-type SearchConfigTableItem = {
-    name: string,
-    equateIl: boolean,
-    filterDuplicates: boolean,
-    missedCleavage: boolean,
-    assay: ProteomicsAssay
-}
-
-@Component({
-    components: {
-        SearchSettingsForm
-    },
-    computed: {
-        areAllEquateIl: {
-            get() {
-                return this.tableItems.every((item: SearchConfigTableItem) => item.equateIl);
-            },
-
-            set(value) {
-                for (const item of this.tableItems) {
-                    item.equateIl = value;
-                }
-            }
-        },
-        areAllFilterDuplicate: {
-            get() {
-                return this.tableItems.every((item: SearchConfigTableItem) => item.filterDuplicates);
-            },
-            set() {
-                const value = !this.areAllFilterDuplicate;
-                for (const item of this.tableItems) {
-                    item.filterDuplicates = value;
-                }
-            }
-        },
-        areAllMissedCleavage: {
-            get() {
-                return this.tableItems.every((item: SearchConfigTableItem) => item.missedCleavage);
-            },
-            set() {
-                const value = !this.areAllMissedCleavage;
-                for (const item of this.tableItems) {
-                    item.missedCleavage = value;
-                }
-            }
-        }
-    }
-})
-export default class SearchConfigurationDialog extends Vue {
-    @Prop({ required: true })
-    private value: boolean;
-    @Prop({ required: true })
-    private assays: ProteomicsAssay[];
-    /**
-     * What function should be executed after the user clicked OK?
-     */
-    @Prop({ required: false, default: async(cancelled: boolean) => {
-        return;
-    } })
-    private callback: (cancelled: boolean) => Promise<void>;
-
-    private dialogActive = false;
-
-    private tableItems: SearchConfigTableItem[] = [];
-    private tableHeaders = [
-        {
-            text: "Assay name",
-            align: "start",
-            sortable: true,
-            value: "name",
-            width: "25%"
-        }, {
-            text: "Equate I/L",
-            align: "center",
-            sortable: false,
-            value: "equateIl",
-            width: "25%"
-        }, {
-            text: "Filter duplicates",
-            align: "center",
-            sortable: false,
-            value: "filterDuplicates",
-            width: "25%"
-        }, {
-            text: "Advanced missed cleavages",
-            align: "center",
-            sortable: false,
-            value: "missedCleavage",
-            width: "25%"
-        }
-    ];
-
-    @Watch("assays", {
-        immediate: true
-    })
-    private onAssaysChanged() {
-        this.tableItems.splice(0, this.tableItems.length);
-        for (const assay of this.assays) {
-            this.tableItems.push({
-                name: assay.getName(),
-                equateIl: true,
-                filterDuplicates: true,
-                missedCleavage: false,
-                assay
-            });
-        }
-    }
-
-    @Watch("value")
-    private async onValueChanged() {
-        this.dialogActive = this.value;
-    }
-
-    private async setConfigs() {
-        for (const item of this.tableItems) {
-            const config = new SearchConfiguration(item.equateIl, item.filterDuplicates, item.missedCleavage);
-            item.assay.setSearchConfiguration(config);
-        }
-        await this.callback(false);
-        this.dialogActive = false;
-        this.$emit("input", this.dialogActive);
-    }
-
-    private async cancel() {
-        await this.callback(true);
-        this.dialogActive = false;
-        this.$emit("input", this.dialogActive);
-    }
-}
-</script>
-
-<style>
-    .searchConfigTable th {
-        vertical-align: baseline;
-        padding-top: 8px;
-    }
-</style>
diff --git a/src/components/navigation-drawers/AssayItem.vue b/src/components/navigation-drawers/AssayItem.vue
index f3176047..e5538b48 100644
--- a/src/components/navigation-drawers/AssayItem.vue
+++ b/src/components/navigation-drawers/AssayItem.vue
@@ -363,7 +363,7 @@ export default class AssayItem extends Vue {
         const searchConfiguration = new SearchConfiguration(
             originalSearchConfig.equateIl,
             originalSearchConfig.filterDuplicates,
-            originalSearchConfig.enableMissingCleavageHandling
+            true
         );
         newAssay.setSearchConfiguration(searchConfiguration);
 
diff --git a/src/components/navigation-drawers/StudyItem.vue b/src/components/navigation-drawers/StudyItem.vue
index 03d70ad1..b52cd399 100644
--- a/src/components/navigation-drawers/StudyItem.vue
+++ b/src/components/navigation-drawers/StudyItem.vue
@@ -91,11 +91,6 @@
                 </div>
             </div>
         </div>
-        <search-configuration-dialog
-            v-model="showSearchConfigDialog"
-            :assays="searchConfigAssays"
-            :callback="searchConfigCallback">
-        </search-configuration-dialog>
         <confirm-deletion-dialog
             v-model="removeConfirmationActive"
             :action="() => removeStudy()"
@@ -123,7 +118,6 @@ import {
 import AssayItem from "./AssayItem.vue";
 import ConfirmDeletionDialog from "@/components/dialogs/ConfirmDeletionDialog.vue";
 import StudyFileSystemRemover from "@/logic/filesystem/study/StudyFileSystemRemover";
-import SearchConfigurationDialog from "@/components/dialogs/SearchConfigurationDialog.vue";
 import BinaryFilesErrorDialog from "@/components/dialogs/BinaryFilesErrorDialog.vue";
 import StudyManager from "@/logic/filesystem/study/StudyManager";
 
@@ -134,7 +128,6 @@ const fs = require("fs").promises;
 @Component({
     components: {
         BinaryFilesErrorDialog,
-        SearchConfigurationDialog,
         ConfirmDeletionDialog,
         CreateDatasetCard,
         Tooltip,
@@ -171,7 +164,6 @@ export default class StudyItem extends Vue {
     private binaryFilesList: string[] = [];
 
     private removeConfirmationActive = false;
-    private showSearchConfigDialog = false;
     private searchConfigCallback: (cancelled: boolean) => Promise<void> = async(cancelled: boolean) => {
         return;
     };
diff --git a/src/components/pages/analysis/AnalysisPage.vue b/src/components/pages/analysis/AnalysisPage.vue
index 72c9de41..7203c467 100644
--- a/src/components/pages/analysis/AnalysisPage.vue
+++ b/src/components/pages/analysis/AnalysisPage.vue
@@ -188,7 +188,6 @@ import {
 import Snake from "@/components/games/Snake.vue";
 import Toolbar from "@/components/navigation-drawers/Toolbar.vue";
 import ProjectExplorer from "@/components/navigation-drawers/ProjectExplorer.vue";
-import SearchConfigurationDialog from "@/components/dialogs/SearchConfigurationDialog.vue";
 import CreateAssayDialog from "@/components/assay/CreateAssayDialog.vue";
 import ProgressReportSummary from "@/components/analysis/ProgressReportSummary.vue";
 import { Watch } from "vue-property-decorator";
@@ -198,7 +197,6 @@ const { app } = require("@electron/remote");
 @Component({
     components: {
         ProgressReportSummary,
-        SearchConfigurationDialog,
         Snake,
         Toolbar,
         ProjectExplorer,
diff --git a/src/logic/filesystem/assay/AssayFileSystemDataReader.ts b/src/logic/filesystem/assay/AssayFileSystemDataReader.ts
index 273cf65c..0fe1176e 100644
--- a/src/logic/filesystem/assay/AssayFileSystemDataReader.ts
+++ b/src/logic/filesystem/assay/AssayFileSystemDataReader.ts
@@ -89,7 +89,7 @@ export default class AssayFileSystemDataReader extends FileSystemAssayVisitor {
                 mpAssay.setDate(metadata.analysisDate);
             }
         } else {
-            mpAssay.setSearchConfiguration(new SearchConfiguration());
+            mpAssay.setSearchConfiguration(new SearchConfiguration(true, true, true));
             mpAssay.setAnalysisSource(
                 new CachedOnlineAnalysisSource(
                     NetworkConfiguration.BASE_URL,
diff --git a/src/logic/filesystem/assay/processed/CachedResultsManager.ts b/src/logic/filesystem/assay/processed/CachedResultsManager.ts
index f4d43be5..a3dab26a 100644
--- a/src/logic/filesystem/assay/processed/CachedResultsManager.ts
+++ b/src/logic/filesystem/assay/processed/CachedResultsManager.ts
@@ -158,7 +158,7 @@ export default class CachedResultsManager {
         const searchConfiguration = new SearchConfiguration(
             existingConfig.equateIl,
             existingConfig.filterDuplicates,
-            existingConfig.enableMissingCleavageHandling
+            true
         );
 
         const searchConfigManager = new SearchConfigManager(this.dbManager);
diff --git a/src/logic/filesystem/configuration/SearchConfigManager.ts b/src/logic/filesystem/configuration/SearchConfigManager.ts
index b2ca4b0f..5abe1669 100644
--- a/src/logic/filesystem/configuration/SearchConfigManager.ts
+++ b/src/logic/filesystem/configuration/SearchConfigManager.ts
@@ -17,7 +17,7 @@ export default class SearchConfigManager {
             return new SearchConfiguration(
                 searchRow.equate_il === 1,
                 searchRow.filter_duplicates === 1,
-                searchRow.missing_cleavage_handling === 1,
+                true,
                 searchRow.id.toString()
             );
         } else {
@@ -43,7 +43,7 @@ export default class SearchConfigManager {
             ).run(
                 config.equateIl ? 1 : 0,
                 config.filterDuplicates ? 1 : 0,
-                config.enableMissingCleavageHandling ? 1 : 0,
+                1,
             );
 
             config.id = info.lastInsertRowid.toString();

From b1099a241cd653f7ce6309e4ccaa0f55f7ae857c Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:25:02 +0200
Subject: [PATCH 2/7] Bump version number to v2.0.2

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index d1445fc4..b39dd1d6 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "unipept-desktop",
-    "version": "2.0.1",
+    "version": "2.0.2",
     "productName": "Unipept Desktop",
     "private": false,
     "author": "Unipept Team (Ghent University)",

From 2fae6fcf32eb5db1eed01f7d513d25b3dc0f8f57 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:30:45 +0200
Subject: [PATCH 3/7] Update macos publish action for missing distutils

---
 .github/workflows/publish_macos.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/publish_macos.yml b/.github/workflows/publish_macos.yml
index e7432c4a..d50006b8 100644
--- a/.github/workflows/publish_macos.yml
+++ b/.github/workflows/publish_macos.yml
@@ -15,6 +15,8 @@ jobs:
       - uses: actions/setup-node@v2
         with:
           node-version: 16
+      - name: Install setuptools for Python
+        run: pip install setuptools
       - name: Install Yarn
         run: npm install --global yarn
       - name: Install dependencies

From ec839c188b339f531ff4f6f54f11d0c9f5749ee8 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:37:00 +0200
Subject: [PATCH 4/7] Try with new setuptools

---
 .github/workflows/publish_macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_macos.yml b/.github/workflows/publish_macos.yml
index d50006b8..cf967782 100644
--- a/.github/workflows/publish_macos.yml
+++ b/.github/workflows/publish_macos.yml
@@ -16,7 +16,7 @@ jobs:
         with:
           node-version: 16
       - name: Install setuptools for Python
-        run: pip install setuptools
+        run: pip install --upgrade setuptools
       - name: Install Yarn
         run: npm install --global yarn
       - name: Install dependencies

From 6812c35ec1d22b4e317959571133fce859f4871b Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:42:06 +0200
Subject: [PATCH 5/7] Try with older Python

---
 .github/workflows/publish_macos.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_macos.yml b/.github/workflows/publish_macos.yml
index cf967782..b03149d3 100644
--- a/.github/workflows/publish_macos.yml
+++ b/.github/workflows/publish_macos.yml
@@ -15,8 +15,8 @@ jobs:
       - uses: actions/setup-node@v2
         with:
           node-version: 16
-      - name: Install setuptools for Python
-        run: pip install --upgrade setuptools
+      - name: Install Python 3.10
+        run: brew install python@3.10 && brew unlink python && brew link --force --overwrite python@3.10
       - name: Install Yarn
         run: npm install --global yarn
       - name: Install dependencies

From b5b495d200e83cf51130e89f0db5d3a4943079d1 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 09:45:15 +0200
Subject: [PATCH 6/7] Try with older macos version

---
 .github/workflows/publish_macos.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/publish_macos.yml b/.github/workflows/publish_macos.yml
index b03149d3..bc38068d 100644
--- a/.github/workflows/publish_macos.yml
+++ b/.github/workflows/publish_macos.yml
@@ -8,15 +8,13 @@ on:
 
 jobs:
   release_macos:
-    runs-on: macos-latest
+    runs-on: macos-12
 
     steps:
       - uses: actions/checkout@v1
       - uses: actions/setup-node@v2
         with:
           node-version: 16
-      - name: Install Python 3.10
-        run: brew install python@3.10 && brew unlink python && brew link --force --overwrite python@3.10
       - name: Install Yarn
         run: npm install --global yarn
       - name: Install dependencies

From d9643b79f4d9cfba3cbdbfca62e501ca6a7d5a0f Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Thu, 8 Aug 2024 11:43:43 +0200
Subject: [PATCH 7/7] Disable code signing on Windows

---
 .github/workflows/publish_windows.yml | 2 --
 vue.config.js                         | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/publish_windows.yml b/.github/workflows/publish_windows.yml
index 775b4b57..59f83fbd 100644
--- a/.github/workflows/publish_windows.yml
+++ b/.github/workflows/publish_windows.yml
@@ -23,5 +23,3 @@ jobs:
         run: yarn run electron:publish
         env:
           GH_TOKEN: ${{ secrets.GH_TOKEN }}
-          CSC_LINK: ${{ secrets.windows_certs }}
-          CSC_KEY_PASSWORD: ${{ secrets.windows_certs_password }}
diff --git a/vue.config.js b/vue.config.js
index f4d97c72..8834c200 100644
--- a/vue.config.js
+++ b/vue.config.js
@@ -48,7 +48,7 @@ module.exports = {
                 },
                 "linux": {
                     "target": "AppImage",
-                },
+                }
             },
         },
     },