refactor(integration-tests): remove unused methods

integration-tests/tests/pages/CliPage.ts

@@ -210,62 +210,13 @@ export class CliPage {
         );
     }
 
-    /**
-     * Set default organism
-     */
-    async setDefaultOrganism(organism: string): Promise<CliResult> {
-        return this.execute(['organism', 'select', organism]);
-    }
-
-    /**
-     * Set default group
-     */
-    async setDefaultGroup(groupId: number): Promise<CliResult> {
-        return this.execute(['group', 'select', groupId.toString()]);
-    }
-
-    /**
-     * Clear default organism
-     */
-    async clearDefaultOrganism(): Promise<CliResult> {
-        return this.execute(['organism', 'select', '--none']);
-    }
-
-    /**
-     * Clear default group
-     */
-    async clearDefaultGroup(): Promise<CliResult> {
-        return this.execute(['group', 'select', '--none']);
-    }
-
-    /**
-     * Get available organisms
-     */
-    async getAvailableOrganisms(): Promise<CliResult> {
-        return this.execute(['organism', 'list']);
-    }
-
-    /**
-     * Get available groups
-     */
-    async getAvailableGroups(): Promise<CliResult> {
-        return this.execute(['group', 'list']);
-    }
-
     /**
      * Login with username and password
      */
     async login(username: string, password: string): Promise<CliResult> {
         return this.execute(['auth', 'login', '--username', username, '--password', password]);
     }
 
-    /**
-     * Check authentication status
-     */
-    async authStatus(): Promise<CliResult> {
-        return this.execute(['auth', 'status']);
-    }
-
     /**
      * Logout
      */

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/group.page.ts

@@ -166,10 +166,6 @@ export class GroupPage {
         await this.page.getByLabel('Address Line 1').fill(line1);
     }
 
-    async editAddressLine2(line2: string) {
-        await this.page.getByLabel('Address Line 2').fill(line2);
-    }
-
     async editCity(city: string) {
         await this.page.getByLabel('City').fill(city);
     }

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

@@ -137,14 +137,6 @@ export class ReviewPage {
             .toBe(true);
     }
 
-    async navigateToReviewPage() {
-        await this.page.goto('/');
-        await this.navigation.openOrganismNavigation();
-        await this.navigation.selectOrganism('Ebola Sudan');
-        await this.navigation.clickSubmitSequences();
-        await this.page.getByRole('link', { name: "Review Review your group's" }).click();
-    }
-
     async releaseValidSequences() {
         await this.page.getByRole('button', { name: /Release \d+ valid sequence/ }).click();
         await this.page.getByRole('button', { name: 'Release', exact: true }).click();

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.
@@ -14,23 +15,6 @@ export class RevisionPage {
         await this.page.goto(`/${organism}/submission/${groupId}/revise`);
     }
 
-    /**
-     * Navigate to revision page from a sequence details page
-     * Clicks the "Revise this sequence" link
-     */
-    async clickReviseSequenceLink() {
-        // Sometimes clicking revise button doesn't register, so let's wait for sequence viewer to be visible first
-        // See #5447
-        await expect(this.page.getByTestId('fixed-length-text-viewer')).toBeVisible();
-
-        await this.page
-            .getByRole('link', { name: 'Revise this sequence' })
-            .click({ timeout: 15000 });
-        await expect(
-            this.page.getByRole('heading', { name: 'Create new revision from' }),
-        ).toBeVisible();
-    }
-
     /**
      * Upload a sequence file
      */
@@ -55,39 +39,6 @@ export class RevisionPage {
         await expect(this.page.getByTestId('discard_metadata_file')).toBeEnabled();
     }
 
-    /**
-     * Upload a segment file for multi-segment organisms
-     */
-    async uploadSegmentFile(segmentName: string, fileName: string, content: string | Buffer) {
-        await this.page.getByTestId(`${segmentName}_segment_file`).setInputFiles({
-            name: fileName,
-            mimeType: 'text/plain',
-            buffer: typeof content === 'string' ? Buffer.from(content) : content,
-        });
-        await expect(this.page.getByTestId(`discard_${segmentName}_segment_file`)).toBeEnabled();
-    }
-
-    /**
-     * Discard a segment file for multi-segment organisms
-     */
-    async discardSegmentFile(segmentName: string) {
-        await this.page.getByTestId(`discard_${segmentName}_segment_file`).click();
-    }
-
-    /**
-     * Discard the sequence file
-     */
-    async discardSequenceFile() {
-        await this.page.getByTestId('discard_sequence_file').click();
-    }
-
-    /**
-     * Discard the metadata file
-     */
-    async discardMetadataFile() {
-        await this.page.getByTestId('discard_metadata_file').click();
-    }
-
     /**
      * Accept the data submission terms
      */
@@ -107,84 +58,25 @@ export class RevisionPage {
         await this.page.getByRole('button', { name: 'Submit' }).click();
     }
 
-    /**
-     * Click the Confirm button in the confirmation dialog
-     */
-    async clickConfirm() {
-        await this.page.getByRole('button', { name: 'Confirm' }).click();
-    }
-
     /**
      * Complete the full revision submission flow
      * Accepts terms, submits, and confirms
      */
     async submitRevision() {
         await this.acceptTerms();
         await this.clickSubmit();
-        await this.clickConfirm();
     }
 
-    /**
-     * Download metadata template in TSV format
-     */
-    async downloadTsvTemplate() {
-        const downloadPromise = this.page.waitForEvent('download');
-        await this.page.getByText('TSV', { exact: true }).click();
-        return downloadPromise;
-    }
-
-    /**
-     * Download metadata template in XLSX format
-     */
-    async downloadXlsxTemplate() {
-        const downloadPromise = this.page.waitForEvent('download');
-        await this.page.getByText('XLSX', { exact: true }).click();
-        return downloadPromise;
-    }
-
-    /**
-     * High-level helper: Revise a single-segment sequence
-     */
-    async reviseSequence(options: {
-        sequenceFile?: { name: string; content: string | Buffer };
-        metadataFile?: { name: string; content: string | Buffer };
-    }) {
-        if (options.sequenceFile) {
-            await this.uploadSequenceFile(options.sequenceFile.name, options.sequenceFile.content);
-        }
-        if (options.metadataFile) {
-            await this.uploadMetadataFile(options.metadataFile.name, options.metadataFile.content);
-        }
-        await this.submitRevision();
-    }
-
-    /**
-     * High-level helper: Revise a multi-segment sequence
-     */
-    async reviseMultiSegmentSequence(options: {
-        segments?: Record<string, { name: string; content: string | Buffer }>;
-        metadataFile?: { name: string; content: string | Buffer };
-        discardSegments?: string[];
-    }) {
-        // Discard segments first if specified
-        if (options.discardSegments) {
-            for (const segment of options.discardSegments) {
-                await this.discardSegmentFile(segment);
-            }
-        }
-
-        // Upload new segment files
-        if (options.segments) {
-            for (const [segmentName, file] of Object.entries(options.segments)) {
-                await this.uploadSegmentFile(segmentName, file.name, file.content);
-            }
-        }
-
-        // Upload metadata if provided
-        if (options.metadataFile) {
-            await this.uploadMetadataFile(options.metadataFile.name, options.metadataFile.content);
-        }
-
-        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/search.page.ts

@@ -149,14 +149,6 @@ export class SearchPage {
         return accessionVersion;
     }
 
-    getSequencePreviewModal() {
-        return this.page.locator('[data-testid="sequence-preview-modal"]');
-    }
-
-    getHalfScreenPreview() {
-        return this.page.locator('[data-testid="half-screen-preview"]');
-    }
-
     toggleHalfScreenButton() {
         return this.page.locator('[data-testid="toggle-half-screen-button"]');
     }

integration-tests/tests/pages/sequence-detail.page.ts

@@ -26,12 +26,6 @@ export class SequenceDetailPage {
         }
     }
 
-    async selectAlignedTab() {
-        if (await this.alignedTab.isVisible()) {
-            await this.alignedTab.click();
-        }
-    }
-
     async expectSequenceContentVisible(timeout = 10000) {
         await expect(this.page.getByText(/[ACGTN]{20,}/)).toBeVisible({ timeout });
     }
@@ -83,8 +77,4 @@ export class SequenceDetailPage {
         await expect(link).toBeVisible();
         await link.click();
     }
-
-    getPage() {
-        return this.page;
-    }
 }