sequenceserver 3.1.2 → 3.2.0

data/public/js/tests/alignment_exporter.spec.js

@@ -0,0 +1,38 @@
+import AlignmentExporter from '../alignment_exporter';
+
+describe('AlignmentExporter', () => {
+  let exporter;
+
+  beforeEach(() => {
+    exporter = new AlignmentExporter();
+  });
+
+  describe('wrap_string', () => {
+    it('wraps a string to a specified width', () => {
+      const str = 'abcdefghijklmnopqrstuvwxyz';
+      const width = 5;
+      const expected = 'abcde\nfghij\nklmno\npqrst\nuvwxy\nz';
+      expect(exporter.wrap_string(str, width)).toBe(expected);
+    });
+  });
+
+  describe('generate_fasta', () => {
+    it('generates a fasta string from hsps', () => {
+      const hsps = [
+        {
+          query_id: 'query1',
+          qstart: 1,
+          qend: 10,
+          qseq: 'ATGCATGCAT',
+          hit_id: 'hit1',
+          sstart: 1,
+          send: 10,
+          midline: '||||||||||',
+          sseq: 'ATGCATGCAT',
+        },
+      ];
+      const expected = '>query1:1-10\nATGCATGCAT\n>query1:1-10_alignment_hit1:1-10\n||||||||||\n>hit1:1-10\nATGCATGCAT\n';
+      expect(exporter.generate_fasta(hsps)).toBe(expected);
+    });
+  });
+});

data/public/js/tests/cloud_share_modal.spec.js

@@ -0,0 +1,75 @@
+import { render, fireEvent, waitFor } from '@testing-library/react';
+import CloudShareModal, { handleSubmit } from '../cloud_share_modal';
+
+describe('CloudShareModal', () => {
+    let component;
+
+    beforeEach(() => {
+        global.fetch = jest.fn(() =>
+            Promise.resolve({
+                json: () => Promise.resolve({ shareable_url: 'http://test.com' }),
+                ok: true
+            })
+        );
+        component = render(<CloudShareModal querydb="" program="" queryLength="0" />);
+    });
+
+    it('renders without crashing', () => {
+        expect(component).toBeTruthy();
+    });
+
+    it('initial state is correct', () => {
+        const { getByLabelText } = component;
+        const emailInput = getByLabelText('Your Email Address');
+        const tosCheckbox = getByLabelText('I agree to the Terms and Conditions of Service');
+
+        expect(emailInput.value).toBe('');
+        expect(tosCheckbox.checked).toBe(false);
+    });
+
+    it('handles form submission', async () => {
+        const { getByLabelText, getByText, getByDisplayValue } = component;
+
+        // Fill out the form
+        fireEvent.change(getByLabelText(/Your Email Address/i), { target: { value: 'test@test.com' } });
+        fireEvent.click(getByLabelText(/I agree to the/i));
+
+        // Submit the form
+        fireEvent.click(getByText('Submit'));
+
+       // Wait for the loading state to finish
+        await waitFor(() => getByText('Uploading the job to SequenceServer Cloud, please wait...'));
+
+        // Check that the results are displayed
+        await waitFor(() => getByText('Copy to Clipboard'));
+
+        expect(getByDisplayValue(/http:\/\/test.com/i)).toBeTruthy()
+    });
+
+    it('handles form submission errors', async () => {
+        // Override the fetch mock to simulate a server error
+        global.fetch = jest.fn(() =>
+            Promise.resolve({
+                json: () => Promise.resolve({ errors: ['Test error'] }),
+                ok: false
+            })
+        );
+
+        const { getByLabelText, getByText } = component;
+
+        // Fill out the form
+        fireEvent.change(getByLabelText(/Your Email Address/i), { target: { value: 'test@test.com' } });
+        fireEvent.click(getByLabelText(/I agree to the/i));
+
+        // Submit the form
+        fireEvent.click(getByText('Submit'));
+
+        // Wait for the loading state to finish
+        await waitFor(() => getByText('Uploading the job to SequenceServer Cloud, please wait...'));
+
+        // Check that the results are displayed
+        await waitFor(() => getByText('Network response was not ok'));
+
+        expect(getByText(/Network response was not ok/i)).toBeTruthy();
+    });
+});

data/public/js/tests/form.spec.js

@@ -12,7 +12,7 @@ export const setMockJSONResult = (result) => {
     global.$.getJSON = (_, cb) => cb(result);
 };
 
-describe('ADVANCED PARAMETERS', () => {
+describe('PARAMETERS', () => {
     let csrfMetaTag;
 
     beforeEach(() => {

data/public/js/tests/report.spec.js

@@ -1,13 +1,20 @@
 /* eslint-disable no-undef */
 /* eslint-disable no-unused-vars */
 import { render, screen, fireEvent } from '@testing-library/react';
+import { act } from 'react';
 import Report from '../report';
 import Sidebar from '../sidebar';
 import shortResponseJSON from './mock_data/short_response.json';
 import longResponseJSON from './mock_data/long_response.json';
 
 const setMockJSONResult = (result) => {
-    global.$.getJSON = () => ({ complete: jest.fn((callback) => callback(result)) });
+    global.fetch = jest.fn(() =>
+        Promise.resolve({
+            ok: result.status === 200,
+            status: result.status,
+            text: () => Promise.resolve(JSON.stringify(result.responseJSON)),
+        })
+    );
 };
 
 const nextQueryButton = () => screen.queryByRole('button', { name: /next query/i });
@@ -38,19 +45,30 @@ describe('REPORT PAGE', () => {
         expect(screen.getByRole('heading', { name: 'BLAST-ing' })).toBeInTheDocument();
     });
 
-    it('should show error modal if error occurs while fetching queries', () => {
+    it('should show error modal if error occurs while fetching queries', async () => {
         const showErrorModal = jest.fn();
-        setMockJSONResult({ status: 500 });
-        render(<Report showErrorModal={showErrorModal} />);
+
+        setMockJSONResult({ status: 500, responseJSON: { error: "Internal Server Error" }});
+
+        await act(async () => {
+            render(<Report showErrorModal={showErrorModal} />);
+        });
+
         expect(showErrorModal).toHaveBeenCalledTimes(1);
     });
 
-    it('it should render the report page correctly if there\'s a response provided', () => {
+    it('it should render the report page correctly if there\'s a response provided', async () => {
         setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
-        const { container } = render(<Report getCharacterWidth={jest.fn()} />);
-        expect(container.querySelector('#results')).toBeInTheDocument();
 
+        let container;
+        await act(async () => {
+            const result = render(<Report getCharacterWidth={jest.fn()} />);
+            container = result.container;
+        });
+
+        expect(container.querySelector('#results')).toBeInTheDocument();
     });
+
     describe('SIDEBAR', () => {
         it('should render the sidebar component with correct heading', () => {
             setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
@@ -105,23 +123,27 @@ describe('REPORT PAGE', () => {
 
         describe('DOWNLOAD LINKS', () => {
             let container;
-            beforeEach(() => {
+            beforeEach(async () => {
                 setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
-                container = render(<Report getCharacterWidth={jest.fn()}  />).container;
+                await act(async () => {
+                    container = render(<Report getCharacterWidth={jest.fn()}  />).container;
+                });
             });
             describe('ALIGNMENT DOWNLOAD', () => {
                 it('should generate a blob url and filename for downloading alignment of all hits on render', () => {
-                    const alignment_download_link = container.querySelector('.download-alignment-of-all');
-                    const expected_num_hits = container.querySelectorAll('.hit-links input[type="checkbox"]').length;
-                    const file_name = `alignment-${expected_num_hits}_hits.txt`;
-                    expect(alignment_download_link.download).toEqual(file_name);
-                    expect(alignment_download_link.hred).not.toEqual('#');
+                    const alignmentDownloadLink = container.querySelector('.download-alignment-of-all');
+                    const hitLinks = container.querySelectorAll('.hit-links input[type="checkbox"]');
+                    const expectedNumHits = hitLinks.length;
+                    const fileName = `alignment-${expectedNumHits}_hits.txt`;
+                    expect(alignmentDownloadLink.download).toEqual(fileName);
+                    expect(alignmentDownloadLink.href).not.toEqual('#');
                 });
+
                 it('link for downloading alignment of specific number of selected hits should be disabled on initial load', () => {
                     const alignment_download_link = container.querySelector('.download-alignment-of-selected');
                     expect(alignment_download_link.classList.contains('disabled')).toBeTruthy();
-
                 });
+
                 it('should generate a blob url and filename for downloading alignment of specific number of selected hits', () => {
                     const alignment_download_link = container.querySelector('.download-alignment-of-selected');
                     // QUERY ALL HIT LINKS CHECKBOXES

data/public/js/tests/visualisation_helpers.spec.js

@@ -0,0 +1,28 @@
+// Import the necessary functions
+import { tick_formatter, formatNumberUnits } from '../visualisation_helpers';
+
+describe('tick_formatter', () => {
+    test('formats tick for amino_acid sequence', () => {
+        const formatter = tick_formatter(null, 'amino_acid');
+        expect(formatter(1_000)).toBe('1 kaa');
+        expect(formatter(25_286_936)).toBe('25.3 Maa');
+    });
+
+    test('formats tick for nucleic_acid sequence', () => {
+        const formatter = tick_formatter(null, 'nucleic_acid');
+        expect(formatter(1_000)).toBe('1 kbp');
+        expect(formatter(25_965_000)).toBe('26 Mbp');
+    });
+});
+
+describe('formatNumberUnits', () => {
+    test('formats number with units correctly', () => {
+        expect(formatNumberUnits('1.9k')).toBe('1.9 k');
+        expect(formatNumberUnits('1.5k')).toBe('1.5 k');
+    });
+
+    test('rounds up correctly based on threshold', () => {
+        expect(formatNumberUnits('2.95k')).toBe('3 k');
+        expect(formatNumberUnits('2.94k')).toBe('2.9 k');
+    });
+});

data/public/js/visualisation_helpers.js

@@ -1,8 +1,7 @@
 import _ from 'underscore';
-import d3 from 'd3';
+import * as d3 from 'd3';
 export function get_colors_for_evalue(evalue, hits) {
-    var colors = d3.scale
-        .log()
+    var colors = d3.scaleLog()
         .domain([
             d3.min([1e-5, d3.min(hits.map(function (d) {
                 if (parseFloat(d.evalue) === 0.0) return undefined;
@@ -24,40 +23,38 @@ export function toLetters(num) {
     return pow ? toLetters(pow) + out : out;
 }
 
+export function getPrefix(str) {
+    if (str.length === 0) return '';
+
+    var lastChar = str.charAt(str.length - 1);
+    return /[a-zA-Z]/.test(lastChar) ? lastChar : '';
+}
+
 /**
- * Defines how ticks will be formatted.
+* Defines how ticks will be formatted.
  *
  * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.
  *
  * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.
  */
 export function tick_formatter(scale, seq_type) {
-    var ticks = scale.ticks();
-    var prefix = d3.formatPrefix(ticks[ticks.length - 1]);
-    var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
+    const prefix = d3.format('~s')
+    const suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
 
-    var digits = 0;
-    var format;
-    var _ticks;
+    return function (d) {
+        const formatted = prefix(d);
 
-    do {
-        format = d3.format('.' + digits + 'f');
-        _ticks = scale.ticks().map(function (d) {
-            return format(prefix.scale(d));
-        });
-        digits++;
+        return `${formatNumberUnits(formatted)}${suffixes[seq_type]}`;
+    };
+}
 
-    } while (_ticks.length !== _.uniq(_ticks).length);
+export function formatNumberUnits(number) {
+    const suffix = number.replace(/[0-9.]/g, '');
+    const numericPart = parseFloat(number).toFixed(2);
+    // Round to 1 decimal place
+    const rounded = Math.round(numericPart * 10) / 10;
 
-    return function (d) {
-        if (!prefix.symbol || d === scale.domain()[0]) {
-            return (d + ' ' + suffixes[seq_type]);
-        }
-        else {
-            return (format(prefix.scale(d)) +
-                  ' ' + prefix.symbol + suffixes[seq_type]);
-        }
-    };
+    return `${rounded % 1 === 0 ? rounded.toFixed(0) : rounded} ${suffix}`;
 }
 
 export function get_seq_type(algorithm) {
@@ -103,4 +100,4 @@ export function prettify_evalue(evalue) {
         else
             return base;
     }
-}
+}