feat(website): add file uploads to revisions

integration-tests/tests/pages/edit.page.ts

@@ -1,9 +1,14 @@
 import { expect, Page } from '@playwright/test';
 import { ReviewPage } from './review.page';
+import { prepareTmpDirForSingleUpload, uploadFilesFromTmpDir } from '../utils/file-upload-helpers';
 
 export class EditPage {
     constructor(private page: Page) {}
 
+    async goto(organism: string, accession: string, version: number) {
+        await this.page.goto(`/${organism}/submission/edit/${accession}/${version}`);
+    }
+
     async discardSequenceFile() {
         await this.page.getByRole('button', { name: 'Discard file' }).click();
     }
@@ -31,4 +36,14 @@ export class EditPage {
         await this.page.waitForURL('**/review', { timeout: 15_000 });
         return new ReviewPage(this.page);
     }
+
+    async uploadExternalFiles(
+        fileId: string,
+        fileContents: Record<string, string>,
+        tmpDir: string,
+    ) {
+        await prepareTmpDirForSingleUpload(fileContents, tmpDir);
+        const fileCount = Object.keys(fileContents).length;
+        await uploadFilesFromTmpDir(this.page, fileId, tmpDir, fileCount);
+    }
 }

integration-tests/tests/pages/revision.page.ts

@@ -1,4 +1,5 @@
 import { expect, type Page } from '@playwright/test';
+import { prepareTmpDirForBulkUpload, uploadFilesFromTmpDir } from '../utils/file-upload-helpers';
 
 /**
  * Page object for the sequence revision page.
@@ -121,7 +122,6 @@ export class RevisionPage {
     async submitRevision() {
         await this.acceptTerms();
         await this.clickSubmit();
-        await this.clickConfirm();
     }
 
     /**
@@ -187,4 +187,17 @@ export class RevisionPage {
 
         await this.submitRevision();
     }
+
+    async uploadExternalFiles(
+        fileId: string,
+        fileContents: Record<string, Record<string, string>>,
+        tmpDir: string,
+    ) {
+        await prepareTmpDirForBulkUpload(fileContents, tmpDir);
+        const fileCount = Object.values(fileContents).reduce(
+            (total, files) => total + Object.keys(files).length,
+            0,
+        );
+        await uploadFilesFromTmpDir(this.page, fileId, tmpDir, fileCount);
+    }
 }

integration-tests/tests/pages/submission.page.ts

@@ -1,10 +1,12 @@
 import { Page } from '@playwright/test';
 import { ReviewPage } from './review.page';
-import fs from 'fs';
-import path from 'path';
 import Papa from 'papaparse';
 import { NavigationPage } from './navigation.page';
-import { clearTmpDir } from '../utils/tmpdir';
+import {
+    prepareTmpDirForBulkUpload,
+    prepareTmpDirForSingleUpload,
+    uploadFilesFromTmpDir,
+} from '../utils/file-upload-helpers';
 
 class SubmissionPage {
     protected page: Page;
@@ -68,17 +70,6 @@ class SubmissionPage {
         await reviewPage.waitForZeroProcessing();
         return reviewPage;
     }
-
-    protected async _uploadFilesFromTmpDir(testId: string, tmpDir: string, fileCount: number) {
-        await this.page.getByRole('heading', { name: 'Extra files' }).scrollIntoViewIfNeeded();
-        // Trigger file upload (don't await) and wait for checkmarks to appear (indicates success)
-        void this.page.getByTestId(testId).setInputFiles(tmpDir);
-        return Promise.all(
-            Array.from({ length: fileCount }, (_, i) =>
-                this.page.getByText('✓').nth(i).waitFor({ state: 'visible' }),
-            ),
-        );
-    }
 }
 
 export class SingleSequenceSubmissionPage extends SubmissionPage {
@@ -140,19 +131,9 @@ export class SingleSequenceSubmissionPage extends SubmissionPage {
         fileContents: Record<string, string>,
         tmpDir: string,
     ) {
-        await this._prepareTmpDirWithFiles(fileContents, tmpDir);
+        await prepareTmpDirForSingleUpload(fileContents, tmpDir);
         const fileCount = Object.keys(fileContents).length;
-        await this._uploadFilesFromTmpDir(fileId, tmpDir, fileCount);
-    }
-
-    private async _prepareTmpDirWithFiles(fileContents: Record<string, string>, tmpDir: string) {
-        await clearTmpDir(tmpDir);
-
-        await Promise.all(
-            Object.entries(fileContents).map(([fileName, fileContent]) =>
-                fs.promises.writeFile(path.join(tmpDir, fileName), fileContent),
-            ),
-        );
+        await uploadFilesFromTmpDir(this.page, fileId, tmpDir, fileCount);
     }
 
     async completeSubmission(
@@ -229,43 +210,16 @@ export class BulkSubmissionPage extends SubmissionPage {
         });
     }
 
-    /**
-     * The given file contents will be stored in a temp dir and then submitted
-     * for the given file ID.
-     * @param fileId For which file ID to upload the files.
-     * @param fileContents A struct: submissionID -> filename -> filecontent.
-     * @param tmpDir The temporary directory to use for storing files.
-     */
     async uploadExternalFiles(
         fileId: string,
         fileContents: Record<string, Record<string, string>>,
         tmpDir: string,
     ) {
-        await this._prepareTmpDirWithFiles(fileContents, tmpDir);
+        await prepareTmpDirForBulkUpload(fileContents, tmpDir);
         const fileCount = Object.values(fileContents).reduce(
             (total, files) => total + Object.keys(files).length,
             0,
         );
-        await this._uploadFilesFromTmpDir(fileId, tmpDir, fileCount);
-    }
-
-    private async _prepareTmpDirWithFiles(
-        fileContents: Record<string, Record<string, string>>,
-        tmpDir: string,
-    ) {
-        await clearTmpDir(tmpDir);
-
-        // Create submission directories and write files
-        const submissionIds = Object.keys(fileContents);
-        await Promise.all(
-            submissionIds.map((submissionId) => fs.promises.mkdir(path.join(tmpDir, submissionId))),
-        );
-        await Promise.all(
-            Object.entries(fileContents).flatMap(([submissionId, files]) => {
-                return Object.entries(files).map(([fileName, fileContent]) =>
-                    fs.promises.writeFile(path.join(tmpDir, submissionId, fileName), fileContent),
-                );
-            }),
-        );
+        await uploadFilesFromTmpDir(this.page, fileId, tmpDir, fileCount);
     }
 }

integration-tests/tests/specs/features/file-sharing.spec.ts

@@ -1,7 +1,13 @@
+import { expect } from '@playwright/test';
 import { test } from '../../fixtures/tmpdir.fixture';
+import { EditPage } from '../../pages/edit.page';
+import { ReviewPage } from '../../pages/review.page';
+import { RevisionPage } from '../../pages/revision.page';
+import { SearchPage } from '../../pages/search.page';
 import { BulkSubmissionPage, SingleSequenceSubmissionPage } from '../../pages/submission.page';
 
 const ORGANISM_NAME = 'Test organism (with files)';
+const ORGANISM_URL_NAME = 'dummy-organism-with-files';
 const RAW_READS = 'raw_reads';
 const METADATA_HEADERS = ['submissionId', 'country', 'date'];
 const COUNTRY_1 = 'Norway';
@@ -88,3 +94,116 @@ test('bulk submit 1 seq with a 35 MB file', async ({ page, groupId, tmpDir }) =>
     const searchPage = await reviewPage.releaseAndGoToReleasedSequences();
     await searchPage.checkFileContentInModal('cell', COUNTRY_1, LARGE_FILE);
 });
+
+const REVISION_METADATA_HEADERS = ['accession', 'submissionId', 'country', 'date'];
+const REVISION_FILES = { 'revised_file.txt': 'This is a revised file.' };
+const REVISION_FILES_2 = { 'another_file.txt': 'Another revised file content.' };
+
+test('bulk revise 2 seqs with files', async ({ page, groupId, tmpDir }) => {
+    test.setTimeout(300_000);
+
+    const timestamp = Date.now();
+    const id1 = `bulk-rev-1-${timestamp}`;
+    const id2 = `bulk-rev-2-${timestamp}`;
+    const revId1 = `bulk-rev-updated-1-${timestamp}`;
+    const revId2 = `bulk-rev-updated-2-${timestamp}`;
+
+    // Step 1: Submit and release 2 sequences
+    const submissionPage = new BulkSubmissionPage(page);
+    await submissionPage.navigateToSubmissionPage(ORGANISM_NAME);
+    await submissionPage.uploadMetadataFile(METADATA_HEADERS, [
+        [id1, COUNTRY_1, '2022-01-01'],
+        [id2, COUNTRY_2, '2022-01-02'],
+    ]);
+    const reviewPage = await submissionPage.submitAndWaitForProcessingDone();
+    const searchPage = await reviewPage.releaseAndGoToReleasedSequences();
+
+    // Get the accessions of the released sequences
+    const accessionVersions = await searchPage.waitForSequencesInSearch(2);
+    const accession1 = accessionVersions.find((av) => av.version === 1)?.accession;
+    const accession2 = accessionVersions.find(
+        (av) => av.version === 1 && av.accession !== accession1,
+    )?.accession;
+    expect(accession1).toBeDefined();
+    expect(accession2).toBeDefined();
+
+    // Step 2: Bulk revise with files
+    const revisionPage = new RevisionPage(page);
+    await revisionPage.goto(ORGANISM_URL_NAME, groupId);
+
+    // Upload revision metadata (with accession column)
+    const revisionMetadata = [
+        [accession1, revId1, COUNTRY_1, '2022-02-01'],
+        [accession2, revId2, COUNTRY_2, '2022-02-02'],
+    ];
+    await page.getByTestId('metadata_file').setInputFiles({
+        name: 'revision_metadata.tsv',
+        mimeType: 'text/plain',
+        buffer: Buffer.from(
+            [
+                REVISION_METADATA_HEADERS.join('\t'),
+                ...revisionMetadata.map((r) => r.join('\t')),
+            ].join('\n'),
+        ),
+    });
+
+    // Upload files for each revision
+    await revisionPage.uploadExternalFiles(
+        RAW_READS,
+        { [revId1]: REVISION_FILES, [revId2]: REVISION_FILES_2 },
+        tmpDir,
+    );
+    await revisionPage.submitRevision();
+
+    // Step 3: Verify in review page and release
+    const reviewPage2 = new ReviewPage(page);
+    await reviewPage2.waitForZeroProcessing();
+    await reviewPage2.releaseValidSequences();
+
+    const searchPage2 = new SearchPage(page);
+    await searchPage2.goToReleasedSequences(ORGANISM_URL_NAME, groupId);
+    await page.goto(page.url() + '?column_submissionId=true');
+
+    // Check that revised sequences have the files
+    await searchPage2.checkFileContentInModal('cell', revId1, REVISION_FILES);
+    await searchPage2.checkFileContentInModal('cell', revId2, REVISION_FILES_2);
+});
+
+test('single revise seq with files via edit page', async ({ page, groupId, tmpDir }) => {
+    test.setTimeout(300_000);
+
+    // Step 1: Submit and release a sequence
+    const submissionPage = new SingleSequenceSubmissionPage(page);
+    await submissionPage.navigateToSubmissionPage(ORGANISM_NAME);
+    await submissionPage.fillSubmissionFormDummyOrganism({
+        submissionId: 'single-rev',
+        country: COUNTRY_1,
+        date: '2023-01-01',
+    });
+    const reviewPage = await submissionPage.submitAndWaitForProcessingDone();
+    const searchPage = await reviewPage.releaseAndGoToReleasedSequences();
+
+    // Step 2: Wait until sequence is available and directly go to revise/edit page
+    const accessionVersions = await searchPage.waitForSequencesInSearch(1);
+    const editPage = new EditPage(page);
+    await editPage.goto(
+        ORGANISM_URL_NAME,
+        accessionVersions[0].accession,
+        accessionVersions[0].version,
+    );
+
+    // Step 3: Upload files in the edit page
+    await editPage.uploadExternalFiles(RAW_READS, REVISION_FILES, tmpDir);
+    const reviewPage2 = await editPage.submitChanges();
+    await reviewPage2.waitForZeroProcessing();
+    await reviewPage2.releaseValidSequences();
+
+    // Step 4: Release and verify files
+    const searchPage2 = new SearchPage(page);
+    await searchPage2.goToReleasedSequences(ORGANISM_URL_NAME, groupId);
+    await searchPage2.checkFileContentInModal(
+        'link',
+        `${accessionVersions[0].accession}.${accessionVersions[0].version + 1}`,
+        REVISION_FILES,
+    );
+});

integration-tests/tests/utils/file-upload-helpers.ts

@@ -0,0 +1,61 @@
+import { Page } from '@playwright/test';
+import fs from 'fs';
+import path from 'path';
+import { clearTmpDir } from './tmpdir';
+
+/**
+ * @param fileContents A struct: submissionID -> filename -> filecontent
+ * @param tmpDir The temporary directory to use for storing files
+ */
+export async function prepareTmpDirForBulkUpload(
+    fileContents: Record<string, Record<string, string>>,
+    tmpDir: string,
+) {
+    await clearTmpDir(tmpDir);
+
+    // Create submission directories and write files
+    const submissionIds = Object.keys(fileContents);
+    await Promise.all(
+        submissionIds.map((submissionId) => fs.promises.mkdir(path.join(tmpDir, submissionId))),
+    );
+    await Promise.all(
+        Object.entries(fileContents).flatMap(([submissionId, files]) => {
+            return Object.entries(files).map(([fileName, fileContent]) =>
+                fs.promises.writeFile(path.join(tmpDir, submissionId, fileName), fileContent),
+            );
+        }),
+    );
+}
+
+/**
+ * @param fileContents A struct: filename -> filecontent
+ * @param tmpDir The temporary directory to use for storing files
+ */
+export async function prepareTmpDirForSingleUpload(
+    fileContents: Record<string, string>,
+    tmpDir: string,
+) {
+    await clearTmpDir(tmpDir);
+
+    await Promise.all(
+        Object.entries(fileContents).map(([fileName, fileContent]) =>
+            fs.promises.writeFile(path.join(tmpDir, fileName), fileContent),
+        ),
+    );
+}
+
+export async function uploadFilesFromTmpDir(
+    page: Page,
+    testId: string,
+    tmpDir: string,
+    fileCount: number,
+) {
+    await page.getByRole('heading', { name: 'Extra files' }).scrollIntoViewIfNeeded();
+    // Trigger file upload (don't await) and wait for checkmarks to appear (indicates success)
+    void page.getByTestId(testId).setInputFiles(tmpDir);
+    return Promise.all(
+        Array.from({ length: fileCount }, (_, i) =>
+            page.getByText('✓').nth(i).waitFor({ state: 'visible' }),
+        ),
+    );
+}