sequenceserver 3.0.1 → 3.1.1

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Files changed (62) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +2 -2
  3. data/lib/sequenceserver/api_errors.rb +32 -2
  4. data/lib/sequenceserver/blast/job.rb +20 -3
  5. data/lib/sequenceserver/blast/report.rb +74 -86
  6. data/lib/sequenceserver/blast/tasks.rb +38 -0
  7. data/lib/sequenceserver/config.rb +54 -20
  8. data/lib/sequenceserver/makeblastdb.rb +16 -2
  9. data/lib/sequenceserver/report.rb +0 -6
  10. data/lib/sequenceserver/routes.rb +66 -25
  11. data/lib/sequenceserver/sequence.rb +35 -7
  12. data/lib/sequenceserver/server.rb +1 -1
  13. data/lib/sequenceserver/version.rb +1 -1
  14. data/lib/sequenceserver.rb +1 -1
  15. data/public/404.html +1 -1
  16. data/public/css/app.css +121 -0
  17. data/public/css/app.min.css +1 -0
  18. data/public/css/sequenceserver.css +0 -148
  19. data/public/css/sequenceserver.min.css +3 -3
  20. data/public/js/circos.js +2 -2
  21. data/public/js/collapse_preferences.js +37 -0
  22. data/public/js/databases.js +65 -37
  23. data/public/js/databases_tree.js +2 -1
  24. data/public/js/dnd.js +37 -50
  25. data/public/js/download_fasta.js +1 -0
  26. data/public/js/form.js +79 -50
  27. data/public/js/grapher.js +23 -37
  28. data/public/js/hits_overview.js +2 -2
  29. data/public/js/kablammo.js +2 -2
  30. data/public/js/length_distribution.js +3 -3
  31. data/public/js/null_plugins/grapher/histogram.js +25 -0
  32. data/public/js/null_plugins/options.js +3 -0
  33. data/public/js/null_plugins/query_stats.js +11 -0
  34. data/public/js/null_plugins/report_plugins.js +6 -1
  35. data/public/js/null_plugins/search_header_plugin.js +4 -0
  36. data/public/js/options.js +161 -56
  37. data/public/js/query.js +85 -59
  38. data/public/js/report.js +1 -1
  39. data/public/js/search.js +2 -0
  40. data/public/js/search_button.js +67 -56
  41. data/public/js/sidebar.js +10 -1
  42. data/public/js/tests/database.spec.js +5 -5
  43. data/public/js/tests/form.spec.js +98 -0
  44. data/public/js/tests/mock_data/databases.json +5 -5
  45. data/public/js/tests/mocks/circos.js +6 -0
  46. data/public/js/tests/report.spec.js +4 -3
  47. data/public/js/tests/search_query.spec.js +16 -6
  48. data/public/sequenceserver-report.min.js +46 -24
  49. data/public/sequenceserver-search.min.js +57 -13
  50. data/public/sequenceserver_logo.webp +0 -0
  51. data/views/blastn_options.erb +66 -66
  52. data/views/blastp_options.erb +59 -59
  53. data/views/blastx_options.erb +68 -68
  54. data/views/layout.erb +61 -3
  55. data/views/search.erb +33 -38
  56. data/views/search_layout.erb +153 -0
  57. data/views/tblastn_options.erb +57 -57
  58. data/views/tblastx_options.erb +64 -64
  59. metadata +51 -22
  60. data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +0 -345
  61. data/public/SequenceServer_logo.png +0 -0
  62. data/public/js/tests/advanced_parameters.spec.js +0 -36
data/public/js/tests/search_query.spec.js CHANGED
@@ -1,7 +1,6 @@
1
1
  /* eslint-disable no-unused-vars */
2
2
  /* eslint-disable no-undef */
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  import { render, screen, fireEvent } from '@testing-library/react';
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- import { SearchQueryWidget } from '../query';
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  import { Form } from '../form';
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  import { AMINO_ACID_SEQUENCE, NUCLEOTIDE_SEQUENCE, FASTQ_SEQUENCE, FASTA_OF_FASTQ_SEQUENCE } from './mock_data/sequences';
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  import '@testing-library/jest-dom/extend-expect';
@@ -11,14 +10,25 @@ let container;
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  let inputEl;
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  describe('SEARCH COMPONENT', () => {
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+ let csrfMetaTag;
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+
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  beforeEach(() => {
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+ csrfMetaTag = document.createElement('meta');
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+ csrfMetaTag.setAttribute('name', '_csrf');
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+ csrfMetaTag.setAttribute('content', 'test-token');
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+ document.head.appendChild(csrfMetaTag);
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  container = render(<Form onSequenceTypeChanged={() => { }
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  } />).container;
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  inputEl = screen.getByRole('textbox', { name: '' });
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  });
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+ afterEach(() => {
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+ // Remove the CSRF meta tag after each test to clean up
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+ document.head.removeChild(csrfMetaTag);
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+ });
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+
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  test('should render the search component textarea', () => {
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- expect(inputEl).toHaveClass('form-control');
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+ expect(inputEl).toBeInTheDocument();
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  });
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  test('clear button should only become visible if textarea is not empty', () => {
@@ -33,7 +43,7 @@ describe('SEARCH COMPONENT', () => {
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  test('should correctly detect the amino-acid sequence type and show notification', () => {
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  // populate search
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  fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
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- const activeNotification = container.querySelector('.notification.active');
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+ const activeNotification = container.querySelector('[data-role=notification].active');
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  expect(activeNotification.id).toBe('protein-sequence-notification');
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  const alertWrapper = activeNotification.children[0];
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  expect(alertWrapper).toHaveTextContent('Detected: amino-acid sequence(s).');
@@ -42,7 +52,7 @@ describe('SEARCH COMPONENT', () => {
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  test('should correctly detect the nucleotide sequence type and show notification', () => {
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  // populate search
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  fireEvent.change(inputEl, { target: { value: NUCLEOTIDE_SEQUENCE } });
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- const activeNotification = container.querySelector('.notification.active');
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+ const activeNotification = container.querySelector('[data-role=notification].active');
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  const alertWrapper = activeNotification.children[0];
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  expect(activeNotification.id).toBe('nucleotide-sequence-notification');
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  expect(alertWrapper).toHaveTextContent('Detected: nucleotide sequence(s).');
@@ -50,7 +60,7 @@ describe('SEARCH COMPONENT', () => {
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60
 
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  test('should correctly detect the mixed sequences and show error notification', () => {
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  fireEvent.change(inputEl, { target: { value: `${NUCLEOTIDE_SEQUENCE}${AMINO_ACID_SEQUENCE}` } });
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- const activeNotification = container.querySelector('.notification.active');
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+ const activeNotification = container.querySelector('[data-role=notification].active');
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  expect(activeNotification.id).toBe('mixed-sequence-notification');
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  const alertWrapper = activeNotification.children[0];
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  expect(alertWrapper).toHaveTextContent('Error: mixed nucleotide and amino-acid sequences detected.');
@@ -58,7 +68,7 @@ describe('SEARCH COMPONENT', () => {
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68
 
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  test('should correctly detect FASTQ and convert it to FASTA', () => {
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  fireEvent.change(inputEl, { target: { value: FASTQ_SEQUENCE } });
61
- const activeNotification = container.querySelector('.notification.active');
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+ const activeNotification = container.querySelector('[data-role=notification].active');
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  const alertWrapper = activeNotification.children[0];
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  expect(activeNotification.id).toBe('fastq-sequence-notification');
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  expect(alertWrapper).toHaveTextContent('Detected FASTQ and automatically converted to FASTA.');