Merge pull request #657 from Lazy-poet/test-cases

augeas · web-flow · commit ae0765933859 · 2023-08-03T10:05:41.000+01:00
Improve test coverage
diff --git a/public/js/tests/advanced_parameters.spec.js b/public/js/tests/advanced_parameters.spec.js
@@ -0,0 +1,36 @@
+/* eslint-disable no-unused-vars */
+/* eslint-disable no-undef */
+import { render, screen, fireEvent } from '@testing-library/react';
+import { Form } from '../form';
+import { AMINO_ACID_SEQUENCE } from './mock_data/sequences';
+import data from './mock_data/databases.json';
+import userEvent from '@testing-library/user-event';
+import '@testing-library/jest-dom/extend-expect';
+import '@testing-library/react/dont-cleanup-after-each';
+
+export const setMockJSONResult = (result) => {
+    global.$.getJSON = (_, cb) => cb(result);
+};
+describe('ADVANCED PARAMETERS', () => {
+    const getInputElement = () => screen.getByRole('textbox', { name: '' });
+    test('should not render the link to advanced parameters modal if blast algorithm is unknown', () => {
+        setMockJSONResult(data);
+        const {container } =render(<Form onSequenceTypeChanged={() => { }
+        } />);
+        const modalButton = container.querySelector('[data-target="#help"]');
+        expect(modalButton).toBeNull();
+    });
+    test('should render the link to advanced parameters modal if blast algorithm is known', () => {
+        setMockJSONResult(data);
+        const {container } =render(<Form onSequenceTypeChanged={() => { }
+        } />);
+        
+        const inputEl = getInputElement();
+        // populate search and select dbs to determine blast algorithm
+        fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
+        const proteinSelectAllBtn = screen.getByRole('heading', { name: /protein databases/i }).parentElement.querySelector('button');
+        fireEvent.click(proteinSelectAllBtn);
+        const modalButton = container.querySelector('[data-target="#help"]');
+        expect(modalButton).not.toBeNull();
+    });
+});
diff --git a/public/js/tests/mock_data/sequences.js b/public/js/tests/mock_data/sequences.js
@@ -0,0 +1,32 @@
+export const AMINO_ACID_SEQUENCE = `MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+KENKIKEGMKMMGLNDSVF
+>SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+TSYCGP
+`;
+export const NUCLEOTIDE_SEQUENCE = `ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG
+GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT
+CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG
+ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT
+TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA
+TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT
+ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG
+TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT
+TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG
+AAGGAAAATAAGATTAAAGAGGGAATGAAGATGATGGGCTTAAATGATTCTGTGTTT
+>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1
+ATGTCCGCGAATCGATTGAACGTGCTGGTGACCCTGATGCTCGCCGTCGCGCTTCTTGTG
+ACGGAATCAGGAAATGCACAGGTGGATGGCTATCTCCAATTCAACCCAAAGCGATCCGCC
+GTGAGCTCGCCGCAGAAGTATTGCGGCAAAAAGCTTTCTAATGCTCTACAGATAATCTGT
+GATGGCGTGTACAATTCCATGTTTAAGAAGAGTGGTCAAGATTTTCCCCCGCAAAATAAG
+AGACACATAGCACACAGAATAAATGGGAATGAGGAAGAGAGCTTTACTACGTTAAAGTCG
+AATTTTTTAAACTGGTGTGTTGAAGTTTATCATCGTCACTACAGATTCGTTTTTGTTTCA
+GAGATGGAAATGGCCGATTACCCGCTCGCCTATGATATTTCCCCGTATCTTCCGCCGTTC
+CTGTCGCGAGCGAGGGCACGGGGAATGTTAGACGGTCGCTTCGCCGGCAGACGCTACCGA
+AGGGAGTCGCGGGGCATTCACGAGGAGTGTTGCATCAACGGATGTACGATAAACGAATTG
+ACCAGCTACTGCGGCCCC
+`;
diff --git a/public/js/tests/report.spec.js b/public/js/tests/report.spec.js
@@ -25,7 +25,14 @@ const TestSidebar = ({ long }) => {
     />;
 };
 
+const clickCheckboxes = (checkboxes, count) => {
+    Array.from(checkboxes).slice(0, count).forEach((checkbox) => {
+        fireEvent.click(checkbox);
+    });
+};
 describe('REPORT PAGE', () => {
+    global.URL.createObjectURL = jest.fn();//.mockReturnValue('xyz.test');
+    global.setTimeout = (cb) => cb();
     it('should render the report component with initial loading state', () => {
         render(<Report />);
         expect(screen.getByRole('heading', { name: 'BLAST-ing' })).toBeInTheDocument();
@@ -39,7 +46,7 @@ describe('REPORT PAGE', () => {
     });
     it('it should render the report page correctly if there\'s a response provided', () => {
         setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
-        const { container } = render(<Report />);
+        const { container } = render(<Report getCharacterWidth={jest.fn()} />);
         expect(container.querySelector('#results')).toBeInTheDocument();
 
     });
@@ -63,18 +70,18 @@ describe('REPORT PAGE', () => {
         });
 
         describe('LONG QUERIES (>12)', () => {
-
+            let container;
+            beforeEach(() => {
+                container = render(<TestSidebar long />).container;
+            });
             it('should not show navigation links for long queries', () => {
-                const { container } = render(<TestSidebar long />);
                 expect(container.querySelectorAll('a[href^="#Query_"]').length).toBe(0);
             });
             it('should show only next button if on first query ', () => {
-                render(<TestSidebar long />);
                 expect(nextQueryButton()).toBeInTheDocument();
                 expect(previousQueryButton()).not.toBeInTheDocument();
             });
             it('should show both previous and next buttons if not on first query', () => {
-                render(<TestSidebar long />);
                 const nextBtn = nextQueryButton();
                 expect(nextBtn).toBeInTheDocument();
                 fireEvent.click(nextBtn);
@@ -84,7 +91,6 @@ describe('REPORT PAGE', () => {
             });
             it('should show only previous button if on last query', () => {
                 const { queries } = longResponseJSON;
-                render(<TestSidebar long />);
                 expect(nextQueryButton()).toBeInTheDocument();
                 expect(previousQueryButton()).not.toBeInTheDocument();
 
@@ -95,5 +101,55 @@ describe('REPORT PAGE', () => {
                 expect(previousQueryButton()).toBeInTheDocument();
             });
         });
+
+        describe('DOWNLOAD LINKS', () => {
+            let container;
+            beforeEach(() => {
+                setMockJSONResult({ status: 200, responseJSON: shortResponseJSON });
+                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('#');
+                });
+                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
+                    const checkboxes = container.querySelectorAll('.hit-links input[type="checkbox"]');
+                    // SELECT 4 CHECKBOXES
+                    clickCheckboxes(checkboxes, 4);
+                    const file_name = 'alignment-4_hits.txt';
+                    expect(alignment_download_link.textContent).toEqual('Alignment of 4 selected hit(s)');
+                    expect(alignment_download_link.download).toEqual(file_name);
+                });
+            });
+    
+            describe('FASTA DOWNLOAD', () => {
+                let fasta_download_link;
+                beforeEach(() => {
+                    fasta_download_link = container.querySelector('.download-fasta-of-selected');
+                });
+                it('link for downloading fasta of selected number of hits should be disabled on initial load', () => {
+                    expect(fasta_download_link.classList.contains('disabled')).toBeTruthy();
+                });
+    
+                it('link for downloading fasta of specific number of selected hits should be active after selection', () => {
+                    const checkboxes = container.querySelectorAll('.hit-links input[type="checkbox"]');
+                    // SELECT 5 CHECKBOXES
+                    clickCheckboxes(checkboxes, 5);
+                    expect(fasta_download_link.textContent).toEqual('FASTA of 5 selected hit(s)');
+                });
+            });
+        });
     });
+
 });
diff --git a/public/js/tests/search_query.spec.js b/public/js/tests/search_query.spec.js
@@ -3,39 +3,56 @@
 import { render, screen, fireEvent } from '@testing-library/react';
 import { SearchQueryWidget } from '../query';
 import { Form } from '../form';
-import userEvent from '@testing-library/user-event';
+import { AMINO_ACID_SEQUENCE, NUCLEOTIDE_SEQUENCE } from './mock_data/sequences';
 import '@testing-library/jest-dom/extend-expect';
 import '@testing-library/react/dont-cleanup-after-each';
 
-export const AMINO_ACID_SEQUENCE = `MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
-TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
-ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
-KENKIKEGMKMMGLNDSVF
->SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
-MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
-DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
-EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
-TSYCGP
-`;
+let container;
+let inputEl;
+
 describe('SEARCH COMPONENT', () => {
-    const getInputElement = () => screen.getByRole('textbox', { name: '' });
+    beforeEach(() => {
+        container  = render(<Form onSequenceTypeChanged={() => { }
+        } />).container;
+        inputEl = screen.getByRole('textbox', { name: '' });
+    });
+    
     test('should render the search component textarea', () => {
-        render(<SearchQueryWidget onSequenceTypeChanged={() => { }
-        } />);
-        const el = getInputElement();
-        expect(el).toHaveClass('form-control');
+        expect(inputEl).toHaveClass('form-control');
     });
 
     test('clear button should only become visible if textarea is not empty', () => {
-        render(<SearchQueryWidget onSequenceTypeChanged={() => { }
-        } />);
         const getButtonWrapper = () => screen.getByRole('button', { name: /clear query sequence\(s\)\./i }).parentElement;
         expect(getButtonWrapper()).toHaveClass('hidden');
-        const inputEl = getInputElement();
         fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
         expect(getButtonWrapper()).not.toHaveClass('hidden');
         fireEvent.change(inputEl, { target: { value: '' } });
         expect(getButtonWrapper()).toHaveClass('hidden');
+    });
 
+    test('should correctly detect the amino-acid sequence type and show notification', () => {
+        // populate search
+        fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
+        const activeNotification = container.querySelector('.notification.active');
+        expect(activeNotification.id).toBe('protein-sequence-notification');
+        const alertWrapper = activeNotification.children[0];
+        expect(alertWrapper).toHaveTextContent('Detected: amino-acid sequence(s).');
+    });
+
+    test('should correctly detect the nucleotide sequence type and show notification', () => {
+        // populate search
+        fireEvent.change(inputEl, { target: { value: NUCLEOTIDE_SEQUENCE } });
+        const activeNotification = container.querySelector('.notification.active');
+        const alertWrapper = activeNotification.children[0];
+        expect(activeNotification.id).toBe('nucleotide-sequence-notification');
+        expect(alertWrapper).toHaveTextContent('Detected: nucleotide sequence(s).');
+    });
+    
+    test('should correctly detect the mixed sequences and show error notification', () => {
+        fireEvent.change(inputEl, { target: { value: `${NUCLEOTIDE_SEQUENCE}${AMINO_ACID_SEQUENCE}` } });
+        const activeNotification = container.querySelector('.notification.active');
+        expect(activeNotification.id).toBe('mixed-sequence-notification');
+        const alertWrapper = activeNotification.children[0];
+        expect(alertWrapper).toHaveTextContent('Error: mixed nucleotide and amino-acid sequences detected.');
     });
 });
diff --git a/public/js/visualisation_helpers.js b/public/js/visualisation_helpers.js
@@ -1,5 +1,5 @@
 import _ from 'underscore';
-
+import d3 from 'd3';
 export function get_colors_for_evalue(evalue, hits) {
     var colors = d3.scale
         .log()
diff --git a/public/sequenceserver-report.min.js b/public/sequenceserver-report.min.js
diff --git a/public/sequenceserver-search.min.js b/public/sequenceserver-search.min.js
