Merge pull request #159 from unipept/fix/export-results-not-available

Fix/export results not available

package.json

@@ -1,6 +1,6 @@
 {
   "name": "unipept-desktop",
-  "version": "1.2.2",
+  "version": "1.2.3",
   "private": true,
   "author": "Unipept Team (Ghent University)",
   "description": "A desktop equivalent of unipept.ugent.be. This app aims at high-throughput analysis of metaproteomics samples.",
@@ -53,7 +53,7 @@
     "node-abi": "^2.19.3",
     "regenerator-runtime": "^0.13.3",
     "shared-memory-datastructures": "0.1.9",
-    "unipept-web-components": "^1.5.0",
+    "unipept-web-components": "^1.5.1",
     "uuid": "^7.0.3",
     "vue": "^2.6.12",
     "vue-class-component": "^7.1.0",

src/db/migrations/v3_to_v4.sql

@@ -0,0 +1,4 @@
+/*
+    NOOP since nothing has changed to the database structure itself between these versions, only a change to the
+    encoding of data in the database has been performed.
+ */

src/db/schemas/schema_v4.sql

@@ -0,0 +1,58 @@
+CREATE TABLE studies (
+    id TEXT PRIMARY KEY,
+    name TEXT NOT NULL
+);
+
+CREATE TABLE assays (
+    id TEXT PRIMARY KEY,
+    name TEXT NOT NULL,
+    study_id TEXT NOT NULL,
+    configuration_id INT NOT NULL,
+    /*
+      Endpoint that was last selected for this assay. This endpoint does not necessarily need to be the same as the one
+      selected for the storage_metadata table. This endpoint is only used to detect whether the assay needs to be
+      recomputed or not.
+     */
+    endpoint TEXT,
+    FOREIGN KEY(study_id) REFERENCES studies(id),
+    FOREIGN KEY(configuration_id) REFERENCES search_configuration(id)
+);
+
+CREATE TABLE search_configuration (
+    id INTEGER PRIMARY KEY,
+    equate_il INT NOT NULL,
+    filter_duplicates INT NOT NULL,
+    missing_cleavage_handling INT NOT NULL
+);
+
+CREATE TABLE peptide_trust (
+    assay_id TEXT NOT NULL,
+    missed_peptides TEXT NOT NULL,
+    matched_peptides INT NOT NULL,
+    searched_peptides INT NOT NULL,
+    PRIMARY KEY(assay_id)
+);
+
+CREATE TABLE storage_metadata (
+    assay_id TEXT NOT NULL,
+    configuration_id INT NOT NULL,
+    endpoint TEXT,
+    /*
+       Unique fingerprint hash for the data that has been stored on the hard drive for this specific combination of
+       assay configuration properties.
+    */
+    fingerprint TEXT,
+    /*
+       Hash of the files that are stored on the local filesystem. This hash can be used to verify the integrity of the
+       files containing the offline result data on the filesystem. Value for this column is the concatenation of
+       the hash for both the data buffer and index buffer files.
+    */
+    data_hash TEXT,
+    analysis_date TEXT,
+    PRIMARY KEY(assay_id),
+    FOREIGN KEY(configuration_id) REFERENCES search_configuration(id)
+);
+
+CREATE TABLE database_metadata (
+    application_version TEXT NOT NULL
+);

src/logic/filesystem/BufferUtils.ts

@@ -0,0 +1,14 @@
+export default class BufferUtils {
+    public static bufferToSharedArrayBuffer(buf: Buffer): SharedArrayBuffer {
+        const ab = new SharedArrayBuffer(buf.length);
+        const view = new Uint8Array(ab);
+        for (let i = 0; i < buf.length; ++i) {
+            view[i] = buf[i];
+        }
+        return ab;
+    }
+
+    public static arrayBufferToBuffer(buffer: ArrayBuffer): Buffer {
+        return Buffer.from(buffer);
+    }
+}

src/logic/filesystem/assay/processed/CachedResultsManager.ts

@@ -23,6 +23,7 @@ import SearchConfigManager from "@/logic/filesystem/configuration/SearchConfigMa
 import StorageMetadataManager from "@/logic/filesystem/metadata/StorageMetadataManager";
 import StorageMetadata from "@/logic/filesystem/metadata/StorageMetadata";
 import PeptideTrustManager from "@/logic/filesystem/trust/PeptideTrustManager";
+import BufferUtils from "@/logic/filesystem/BufferUtils";
 
 export default class CachedResultsManager {
     constructor(
@@ -188,19 +189,6 @@ export default class CachedResultsManager {
         }
     }
 
-    private arrayBufferToBuffer(buffer: ArrayBuffer): Buffer {
-        return Buffer.from(buffer);
-    }
-
-    private bufferToSharedArrayBuffer(buf: Buffer): SharedArrayBuffer {
-        const ab = new SharedArrayBuffer(buf.length);
-        const view = new Uint8Array(ab);
-        for (let i = 0; i < buf.length; ++i) {
-            view[i] = buf[i];
-        }
-        return ab;
-    }
-
     /**
      * Write the given assay and the corresponding data to the filesystem.
      *
@@ -239,8 +227,8 @@ export default class CachedResultsManager {
         const dataBufferPath = this.getDataBufferPath(assay);
 
         try {
-            const indexBuffer = this.bufferToSharedArrayBuffer(await fs.readFile(indexBufferPath));
-            const dataBuffer = this.bufferToSharedArrayBuffer(await fs.readFile(dataBufferPath));
+            const indexBuffer = BufferUtils.bufferToSharedArrayBuffer(await fs.readFile(indexBufferPath));
+            const dataBuffer = BufferUtils.bufferToSharedArrayBuffer(await fs.readFile(dataBufferPath));
 
             const output = new ShareableMap<Peptide, PeptideData>(0, 0, new PeptideDataSerializer());
             output.setBuffers(indexBuffer, dataBuffer);

src/logic/filesystem/database/DatabaseManager.ts

@@ -10,6 +10,7 @@ const app = electron.remote.app;
 
 import path from "path";
 import DatabaseMigratorV2ToV3 from "@/logic/filesystem/database/DatabaseMigratorV2ToV3";
+import DatabaseMigratorV3ToV4 from "@/logic/filesystem/database/DatabaseMigratorV3ToV4";
 
 export default class DatabaseManager {
     // Reading and writing large assays to and from the database can easily take longer than 5 seconds, causing
@@ -29,7 +30,8 @@ export default class DatabaseManager {
     private readonly migrations: (() => DatabaseMigrator)[] = [
         () => new DatabaseMigratorV0ToV1(),
         () => new DatabaseMigratorV1ToV2(path.dirname(this.dbLocation)),
-        () => new DatabaseMigratorV2ToV3(path.dirname(this.dbLocation))
+        () => new DatabaseMigratorV2ToV3(path.dirname(this.dbLocation)),
+        () => new DatabaseMigratorV3ToV4(path.dirname(this.dbLocation))
     ];
 
     constructor(
@@ -88,7 +90,6 @@ export default class DatabaseManager {
      */
     private checkAndUpgradeSchema(): void {
         for (let currentSchema: number = this.schemaVersion; currentSchema < Schema.LATEST_VERSION; currentSchema++) {
-            console.log(currentSchema);
             this.migrations[currentSchema]().upgrade(this.db);
             this.db.pragma("user_version = " + (currentSchema + 1));
         }

src/logic/filesystem/database/DatabaseMigratorV2ToV3.ts

@@ -42,8 +42,6 @@ export default class DatabaseMigratorV2ToV3 implements DatabaseMigrator {
             });
         }
 
-        console.log(JSON.stringify(assays));
-
         const studyData = database.prepare(
             "SELECT * FROM studies"
         ).all();