Add settings for specifying crap sequences

src/components/pages/SettingsPage.vue

@@ -112,6 +112,55 @@
                                 </v-container>
                             </v-card-text>
                         </v-card>
+                        <h2 class="mx-auto settings-category-title">Global analysis settings</h2>
+                        <v-card>
+                            <v-card-text>
+                                <v-container fluid>
+                                    <v-row>
+                                        <v-col cols="11">
+                                            <div class="settings-title">Exclude (cRAP) sequences?</div>
+                                            <span class="settings-text">
+                                                Use this option if you would like to exclude specific peptides that are
+                                                known to be associated with cRAP-proteins. You can specify exactly which
+                                                protein sequences should be considered using the text area below.
+                                            </span>
+                                        </v-col>
+                                        <v-col cols="1">
+                                            <v-checkbox
+                                                class="float-end"
+                                                v-model="excludeSequences"
+                                            />
+                                        </v-col>
+                                    </v-row>
+                                    <v-row>
+                                        <v-col cols="6">
+                                            <v-textarea
+                                                filled
+                                                v-model="crapSequences"
+                                                :disabled="!excludeSequences"
+                                                clearable
+                                                :rows="8"
+                                            />
+                                        </v-col>
+                                        <v-divider vertical />
+                                        <v-col cols="6">
+                                            <div class="d-flex flex-column align-center">
+                                                <div class="font-weight-bold">
+                                                    Or, import sequences from a FASTA file...
+                                                </div>
+                                                <v-btn
+                                                    class="mt-2"
+                                                    @click="importCrapFasta"
+                                                    :disabled="!excludeSequences"
+                                                >
+                                                    Import from file
+                                                </v-btn>
+                                            </div>
+                                        </v-col>
+                                    </v-row>
+                                </v-container>
+                            </v-card-text>
+                        </v-card>
                         <h2 class="mx-auto settings-category-title">Storage</h2>
                         <v-card>
                             <v-card-text>
@@ -264,6 +313,8 @@ import Rules from "./../validation/Rules";
 import { NetworkConfiguration, NetworkUtils } from "unipept-web-components";
 import DockerCommunicator from "@/logic/communication/docker/DockerCommunicator";
 import Utils from "@/logic/Utils";
+import { promises as fs } from "fs";
+import FastaParser from "./../../logic/filesystem/fasta/FastaParser";
 
 @Component
 export default class SettingsPage extends Vue {
@@ -342,6 +393,25 @@ export default class SettingsPage extends Vue {
         return this.configuration.dockerConfigurationSettings;
     }
 
+    set excludeSequences(val: boolean) {
+        this.configuration.crapFilteringEnabled = val;
+    }
+
+    get excludeSequences(): boolean {
+        return this.configuration.crapFilteringEnabled;
+    }
+
+    set crapSequences(val: string) {
+        if (val == null) {
+            val = "";
+        }
+        this.configuration.crapSequences = val.split("\r?\n");
+    }
+
+    get crapSequences(): string {
+        return this.configuration.crapSequences.join("\n");
+    }
+
     set customDbStorageLocation(value: string) {
         this.configuration.customDbStorageLocation = value;
     }
@@ -439,6 +509,28 @@ export default class SettingsPage extends Vue {
         }
     }
 
+    public async importCrapFasta(): Promise<void> {
+        const { dialog } = require("@electron/remote");
+
+        const chosenPath: Electron.OpenDialogReturnValue | undefined = await dialog.showOpenDialog({
+            properties: ["openFile"],
+            filters: [
+                { name: "FASTA files", extensions: ["fasta"] }
+            ]
+        });
+
+        if (chosenPath && chosenPath.filePaths.length > 0) {
+            const fastaPath = chosenPath.filePaths[0];
+            const fastaContent = await fs.readFile(fastaPath, "utf8");
+
+            // Now, parse the fasta content and extract the protein sequences
+            const fastaParser = new FastaParser();
+            const sequences = fastaParser.extractProteinSequences(fastaContent);
+
+            this.crapSequences = sequences.join("\n");
+        }
+    }
+
     private showError(message: string): void {
         this.errorVisible = true;
         this.errorMessage = message;

src/logic/configuration/Configuration.ts

@@ -7,4 +7,6 @@ export default interface Configuration {
     configurationAppVersion: string;
     // List of custom Unipept endpoints that were provided to this app.
     endpoints: string[];
+    crapFilteringEnabled: boolean;
+    crapSequences: string[];
 }

src/logic/configuration/ConfigurationManager.ts

@@ -36,8 +36,9 @@ export default class ConfigurationManager {
             }
         },
         (config: Configuration) => config.customDbStorageLocation !== "",
-        (config: Configuration) => config.endpoints.every(e => this.isUrl(e))
-    ]
+        (config: Configuration) => config.endpoints.every(e => this.isUrl(e)),
+        (config: Configuration) => Array.isArray(config.crapSequences),
+    ];
 
     private app: App;
 
@@ -69,6 +70,14 @@ export default class ConfigurationManager {
                 data["endpoints"].push(ConfigurationManager.DEFAULT_ENDPOINT);
             }
 
+            if (!data["crapSequences"] || !Array.isArray(data["crapSequences"])) {
+                data["crapSequences"] = [];
+            }
+
+            if (!data["crapFilteringEnabled"]) {
+                data["crapFilteringEnabled"] = false;
+            }
+
             if (!this.isValidConfiguration(data)) {
                 ConfigurationManager.currentConfiguration = await this.getDefaultConfiguration();
                 return ConfigurationManager.currentConfiguration;
@@ -93,7 +102,9 @@ export default class ConfigurationManager {
                 Utils.isWindows() ? DockerCommunicator.WINDOWS_DEFAULT_SETTINGS : DockerCommunicator.UNIX_DEFAULT_SETTINGS,
             customDbStorageLocation: customDbDir,
             configurationAppVersion: this.app.getVersion(),
-            endpoints: ["https://api.unipept.ugent.be/"]
+            endpoints: ["https://api.unipept.ugent.be/"],
+            crapFilteringEnabled: false,
+            crapSequences: []
         }
     }
 

src/logic/filesystem/fasta/FastaParser.ts

@@ -0,0 +1,41 @@
+export default class FastaParser {
+    /**
+     * This function reads in a FASTA string and extracts all protein sequences from this string and returns them as an
+     * array of strings.
+     *
+     * @param fasta
+     */
+    public extractProteinSequences(fasta: string): string[] {
+        // Split the input string into lines
+        const lines = fasta.trim().split("\n");
+
+        // Initialize an empty array to hold the sequences
+        const sequences: string[] = [];
+
+        // Initialize an empty string to hold the current sequence
+        let currentSequence = "";
+
+        // Iterate over each line
+        for (const line of lines) {
+            // If the line starts with '>', it's a description line
+            if (line.startsWith(">")) {
+                // If there's a current sequence, add it to the sequences array
+                if (currentSequence) {
+                    sequences.push(currentSequence);
+                }
+                // Start a new sequence
+                currentSequence = "";
+            } else {
+                // If the line doesn't start with '>', it's a sequence line, so add it to the current sequence
+                currentSequence += line;
+            }
+        }
+
+        // If there's a current sequence at the end, add it to the sequences array
+        if (currentSequence) {
+            sequences.push(currentSequence);
+        }
+
+        return sequences;
+    }
+}

src/logic/filesystem/study/StudyFileSystemDataWriter.ts

@@ -11,7 +11,7 @@ export default class StudyFileSystemDataWriter extends FileSystemStudyVisitor {
     public async visitStudy(study: Study): Promise<void> {
         try {
             // Make study directory if it does not exist yet...
-            await mkdirp(`${this.studyPath}`);
+            await mkdirp(this.studyPath);
 
             await this.dbManager.performQuery<void>((db: Database) => {
                 db.prepare("REPLACE INTO studies (id, name) VALUES (?, ?)").run(study.getId(), study.getName())