sequenceserver 2.0.0.beta4 → 2.0.0.rc5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (119) hide show
  1. checksums.yaml +5 -5
  2. data/.dockerignore +1 -0
  3. data/.travis.yml +7 -4
  4. data/AppImage/sequenceserver.sh +5 -0
  5. data/Dockerfile +14 -12
  6. data/bin/sequenceserver +37 -28
  7. data/lib/sequenceserver.rb +35 -7
  8. data/lib/sequenceserver/blast/job.rb +18 -25
  9. data/lib/sequenceserver/blast/report.rb +68 -34
  10. data/lib/sequenceserver/config.rb +1 -1
  11. data/lib/sequenceserver/database.rb +0 -129
  12. data/lib/sequenceserver/makeblastdb.rb +243 -0
  13. data/lib/sequenceserver/routes.rb +28 -2
  14. data/lib/sequenceserver/version.rb +1 -1
  15. data/public/SequenceServer_logo.png +0 -0
  16. data/public/css/grapher.css +8 -15
  17. data/public/css/sequenceserver.css +119 -55
  18. data/public/css/sequenceserver.min.css +3 -3
  19. data/public/js/circos.js +1 -1
  20. data/public/js/download_fasta.js +17 -0
  21. data/public/js/grapher.js +7 -9
  22. data/public/js/hit.js +217 -0
  23. data/public/js/hits_overview.js +12 -13
  24. data/public/js/hsp.js +104 -84
  25. data/public/js/{sequenceserver.js → jquery_world.js} +1 -18
  26. data/public/js/kablammo.js +337 -334
  27. data/public/js/length_distribution.js +1 -1
  28. data/public/js/query.js +147 -0
  29. data/public/js/report.js +216 -836
  30. data/public/js/search.js +194 -192
  31. data/public/js/sequence_modal.js +167 -0
  32. data/public/js/sidebar.js +210 -0
  33. data/public/js/utils.js +2 -19
  34. data/public/js/visualisation_helpers.js +2 -2
  35. data/public/sequenceserver-report.min.js +19 -19
  36. data/public/sequenceserver-search.min.js +11 -11
  37. data/public/vendor/github/twbs/bootstrap@3.3.5/js/bootstrap.js +2 -2
  38. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +15 -15
  39. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +15 -15
  40. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +15 -15
  41. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +15 -15
  42. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +15 -15
  43. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +15 -15
  44. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +15 -15
  45. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +15 -15
  46. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +15 -15
  47. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +6 -6
  48. data/spec/capybara_spec.rb +14 -3
  49. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ndb +0 -0
  50. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  51. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  52. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nos +0 -0
  53. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.not +0 -0
  54. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ntf +0 -0
  55. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nto +0 -0
  56. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pdb +0 -0
  57. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  58. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  59. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pos +0 -0
  60. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pot +0 -0
  61. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.ptf +0 -0
  62. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pto +0 -0
  63. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pdb +0 -0
  64. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  65. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  66. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pos +0 -0
  67. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pot +0 -0
  68. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.ptf +0 -0
  69. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pto +0 -0
  70. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ndb +0 -0
  71. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  72. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  73. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nos +0 -0
  74. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.not +0 -0
  75. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  76. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ntf +0 -0
  77. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nto +0 -0
  78. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +8 -0
  79. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  80. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  81. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  82. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  83. data/spec/database/{sample → v4}/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +0 -0
  84. data/spec/database/{sample → v4}/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
  85. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  86. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +8 -0
  87. data/spec/database/v4/links.rb +23 -0
  88. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
  89. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +1189 -0
  90. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
  91. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  92. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  93. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  94. data/spec/database/{sample → v4}/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +0 -0
  95. data/spec/database/{sample → v4}/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  96. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  97. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +9140 -0
  98. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
  99. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  100. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  101. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
  102. data/spec/database/{sample → v4}/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd +0 -0
  103. data/spec/database/{sample → v4}/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
  104. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
  105. data/spec/database/v4/proteins/uniprot/URL +1 -0
  106. data/spec/database/v4/si_uniprot_idmap.yml +14180 -0
  107. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
  108. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +473 -0
  109. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
  110. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  111. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  112. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  113. data/spec/database/{sample → v4}/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +0 -0
  114. data/spec/database/{sample → v4}/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  115. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  116. data/spec/database_spec.rb +0 -76
  117. data/spec/makeblastdb_spec.rb +121 -0
  118. data/views/layout.erb +5 -1
  119. metadata +75 -15
data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb CHANGED
@@ -84,8 +84,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
84
84
  # download of PNG/SVG file and test that it initiated a file download in a
85
85
  # right format.
86
86
 
87
- page.should have_content('Chord diagram: queries and their top hits')
88
- page.execute_script("$('.circos > .grapher-header > h5').click()")
87
+ page.should have_content('Queries and their top hits: chord diagram')
88
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
89
89
  sleep 1
90
90
 
91
91
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -107,7 +107,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
107
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  # download in a right format.
108
108
 
109
109
  page.should have_content('Length distribution of hits')
110
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
110
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
111
111
  sleep 1
112
112
 
113
113
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -200,8 +200,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
200
200
  # download of PNG/SVG file and test that it initiated a file download in a
201
201
  # right format.
202
202
 
203
- page.should have_content('Chord diagram: queries and their top hits')
204
- page.execute_script("$('.circos > .grapher-header > h5').click()")
203
+ page.should have_content('Queries and their top hits: chord diagram')
204
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
205
205
  sleep 1
206
206
 
207
207
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -221,7 +221,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
221
221
  # download in a right format.
222
222
 
223
223
  page.should have_content('Length distribution of hits')
224
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
224
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
225
225
  sleep 1
226
226
 
227
227
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -314,8 +314,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
314
314
  # download of PNG/SVG file and test that it initiated a file download in a
315
315
  # right format.
316
316
 
317
- page.should have_content('Chord diagram: queries and their top hits')
318
- page.execute_script("$('.circos > .grapher-header > h5').click()")
317
+ page.should have_content('Queries and their top hits: chord diagram')
318
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
319
319
  sleep 1
320
320
 
321
321
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -335,7 +335,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
335
335
  # download in a right format.
336
336
 
337
337
  page.should have_content('Length distribution of hits')
338
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
338
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
339
339
  sleep 1
340
340
 
341
341
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -425,8 +425,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
425
425
  # download of PNG/SVG file and test that it initiated a file download in a
426
426
  # right format.
427
427
 
428
- page.should have_content('Chord diagram: queries and their top hits')
429
- page.execute_script("$('.circos > .grapher-header > h5').click()")
428
+ page.should have_content('Queries and their top hits: chord diagram')
429
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
430
430
  sleep 1
431
431
 
432
432
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -447,7 +447,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
447
447
  # download in a right format.
448
448
 
449
449
  page.should have_content('Length distribution of hits')
450
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
450
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
451
451
  sleep 1
452
452
 
453
453
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -540,8 +540,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
540
540
  # download of PNG/SVG file and test that it initiated a file download in a
541
541
  # right format.
542
542
 
543
- page.should have_content('Chord diagram: queries and their top hits')
544
- page.execute_script("$('.circos > .grapher-header > h5').click()")
543
+ page.should have_content('Queries and their top hits: chord diagram')
544
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
545
545
  sleep 1
546
546
 
547
547
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -562,7 +562,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
562
562
  # download in a right format.
563
563
 
564
564
  page.should have_content('Length distribution of hits')
565
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
565
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
566
566
  sleep 1
567
567
 
568
568
  page.execute_script("$('.export-to-png:eq(1)').click()")
data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb CHANGED
@@ -84,8 +84,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
84
84
  # download of PNG/SVG file and test that it initiated a file download in a
85
85
  # right format.
86
86
 
87
- page.should have_content('Chord diagram: queries and their top hits')
88
- page.execute_script("$('.circos > .grapher-header > h5').click()")
87
+ page.should have_content('Queries and their top hits: chord diagram')
88
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
89
89
  sleep 1
90
90
 
91
91
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -107,7 +107,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
107
107
  # download in a right format.
108
108
 
109
109
  page.should have_content('Length distribution of hits')
110
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
110
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
111
111
  sleep 1
112
112
 
113
113
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -200,8 +200,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
200
200
  # download of PNG/SVG file and test that it initiated a file download in a
201
201
  # right format.
202
202
 
203
- page.should have_content('Chord diagram: queries and their top hits')
204
- page.execute_script("$('.circos > .grapher-header > h5').click()")
203
+ page.should have_content('Queries and their top hits: chord diagram')
204
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
205
205
  sleep 1
206
206
 
207
207
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -221,7 +221,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
221
221
  # download in a right format.
222
222
 
223
223
  page.should have_content('Length distribution of hits')
224
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
224
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
225
225
  sleep 1
226
226
 
227
227
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -314,8 +314,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
314
314
  # download of PNG/SVG file and test that it initiated a file download in a
315
315
  # right format.
316
316
 
317
- page.should have_content('Chord diagram: queries and their top hits')
318
- page.execute_script("$('.circos > .grapher-header > h5').click()")
317
+ page.should have_content('Queries and their top hits: chord diagram')
318
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
319
319
  sleep 1
320
320
 
321
321
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -335,7 +335,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
335
335
  # download in a right format.
336
336
 
337
337
  page.should have_content('Length distribution of hits')
338
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
338
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
339
339
  sleep 1
340
340
 
341
341
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -425,8 +425,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
425
425
  # download of PNG/SVG file and test that it initiated a file download in a
426
426
  # right format.
427
427
 
428
- page.should have_content('Chord diagram: queries and their top hits')
429
- page.execute_script("$('.circos > .grapher-header > h5').click()")
428
+ page.should have_content('Queries and their top hits: chord diagram')
429
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
430
430
  sleep 1
431
431
 
432
432
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -447,7 +447,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
447
447
  # download in a right format.
448
448
 
449
449
  page.should have_content('Length distribution of hits')
450
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
450
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
451
451
  sleep 1
452
452
 
453
453
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -540,8 +540,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
540
540
  # download of PNG/SVG file and test that it initiated a file download in a
541
541
  # right format.
542
542
 
543
- page.should have_content('Chord diagram: queries and their top hits')
544
- page.execute_script("$('.circos > .grapher-header > h5').click()")
543
+ page.should have_content('Queries and their top hits: chord diagram')
544
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
545
545
  sleep 1
546
546
 
547
547
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -562,7 +562,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
562
562
  # download in a right format.
563
563
 
564
564
  page.should have_content('Length distribution of hits')
565
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
565
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
566
566
  sleep 1
567
567
 
568
568
  page.execute_script("$('.export-to-png:eq(1)').click()")
data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb CHANGED
@@ -84,8 +84,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
84
84
  # download of PNG/SVG file and test that it initiated a file download in a
85
85
  # right format.
86
86
 
87
- page.should have_content('Chord diagram: queries and their top hits')
88
- page.execute_script("$('.circos > .grapher-header > h5').click()")
87
+ page.should have_content('Queries and their top hits: chord diagram')
88
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
89
89
  sleep 1
90
90
 
91
91
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -107,7 +107,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
107
107
  # download in a right format.
108
108
 
109
109
  page.should have_content('Length distribution of hits')
110
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
110
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
111
111
  sleep 1
112
112
 
113
113
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -200,8 +200,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
200
200
  # download of PNG/SVG file and test that it initiated a file download in a
201
201
  # right format.
202
202
 
203
- page.should have_content('Chord diagram: queries and their top hits')
204
- page.execute_script("$('.circos > .grapher-header > h5').click()")
203
+ page.should have_content('Queries and their top hits: chord diagram')
204
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
205
205
  sleep 1
206
206
 
207
207
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -221,7 +221,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
221
221
  # download in a right format.
222
222
 
223
223
  page.should have_content('Length distribution of hits')
224
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
224
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
225
225
  sleep 1
226
226
 
227
227
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -314,8 +314,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
314
314
  # download of PNG/SVG file and test that it initiated a file download in a
315
315
  # right format.
316
316
 
317
- page.should have_content('Chord diagram: queries and their top hits')
318
- page.execute_script("$('.circos > .grapher-header > h5').click()")
317
+ page.should have_content('Queries and their top hits: chord diagram')
318
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
319
319
  sleep 1
320
320
 
321
321
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -335,7 +335,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
335
335
  # download in a right format.
336
336
 
337
337
  page.should have_content('Length distribution of hits')
338
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
338
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
339
339
  sleep 1
340
340
 
341
341
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -425,8 +425,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
425
425
  # download of PNG/SVG file and test that it initiated a file download in a
426
426
  # right format.
427
427
 
428
- page.should have_content('Chord diagram: queries and their top hits')
429
- page.execute_script("$('.circos > .grapher-header > h5').click()")
428
+ page.should have_content('Queries and their top hits: chord diagram')
429
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
430
430
  sleep 1
431
431
 
432
432
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -447,7 +447,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
447
447
  # download in a right format.
448
448
 
449
449
  page.should have_content('Length distribution of hits')
450
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
450
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
451
451
  sleep 1
452
452
 
453
453
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -540,8 +540,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
540
540
  # download of PNG/SVG file and test that it initiated a file download in a
541
541
  # right format.
542
542
 
543
- page.should have_content('Chord diagram: queries and their top hits')
544
- page.execute_script("$('.circos > .grapher-header > h5').click()")
543
+ page.should have_content('Queries and their top hits: chord diagram')
544
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
545
545
  sleep 1
546
546
 
547
547
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -562,7 +562,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
562
562
  # download in a right format.
563
563
 
564
564
  page.should have_content('Length distribution of hits')
565
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
565
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
566
566
  sleep 1
567
567
 
568
568
  page.execute_script("$('.export-to-png:eq(1)').click()")
data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb CHANGED
@@ -83,8 +83,8 @@ describe 'report generated from imported XML',type: :feature, js: true do
83
83
  # download of PNG/SVG file and test that it initiated a file download in a
84
84
  # right format.
85
85
 
86
- page.should have_content('Chord diagram: queries and their top hits')
87
- page.execute_script("$('.circos > .grapher-header > h5').click()")
86
+ page.should have_content('Queries and their top hits: chord diagram')
87
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
88
88
  sleep 1
89
89
 
90
90
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -106,7 +106,7 @@ describe 'report generated from imported XML',type: :feature, js: true do
106
106
  # download in a right format.
107
107
 
108
108
  page.should have_content('Length distribution of hits')
109
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
109
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
110
110
  sleep 1
111
111
 
112
112
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -199,8 +199,8 @@ describe 'report generated from imported XML',type: :feature, js: true do
199
199
  # download of PNG/SVG file and test that it initiated a file download in a
200
200
  # right format.
201
201
 
202
- page.should have_content('Chord diagram: queries and their top hits')
203
- page.execute_script("$('.circos > .grapher-header > h5').click()")
202
+ page.should have_content('Queries and their top hits: chord diagram')
203
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
204
204
  sleep 1
205
205
 
206
206
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -220,7 +220,7 @@ describe 'report generated from imported XML',type: :feature, js: true do
220
220
  # download in a right format.
221
221
 
222
222
  page.should have_content('Length distribution of hits')
223
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
223
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
224
224
  sleep 1
225
225
 
226
226
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -313,8 +313,8 @@ describe 'report generated from imported XML',type: :feature, js: true do
313
313
  # download of PNG/SVG file and test that it initiated a file download in a
314
314
  # right format.
315
315
 
316
- page.should have_content('Chord diagram: queries and their top hits')
317
- page.execute_script("$('.circos > .grapher-header > h5').click()")
316
+ page.should have_content('Queries and their top hits: chord diagram')
317
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
318
318
  sleep 1
319
319
 
320
320
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -334,7 +334,7 @@ describe 'report generated from imported XML',type: :feature, js: true do
334
334
  # download in a right format.
335
335
 
336
336
  page.should have_content('Length distribution of hits')
337
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
337
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
338
338
  sleep 1
339
339
 
340
340
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -424,8 +424,8 @@ describe 'report generated from imported XML',type: :feature, js: true do
424
424
  # download of PNG/SVG file and test that it initiated a file download in a
425
425
  # right format.
426
426
 
427
- page.should have_content('Chord diagram: queries and their top hits')
428
- page.execute_script("$('.circos > .grapher-header > h5').click()")
427
+ page.should have_content('Queries and their top hits: chord diagram')
428
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
429
429
  sleep 1
430
430
 
431
431
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -446,7 +446,7 @@ describe 'report generated from imported XML',type: :feature, js: true do
446
446
  # download in a right format.
447
447
 
448
448
  page.should have_content('Length distribution of hits')
449
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
449
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
450
450
  sleep 1
451
451
 
452
452
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -538,8 +538,8 @@ describe 'report generated from imported XML',type: :feature, js: true do
538
538
  # download of PNG/SVG file and test that it initiated a file download in a
539
539
  # right format.
540
540
 
541
- page.should have_content('Chord diagram: queries and their top hits')
542
- page.execute_script("$('.circos > .grapher-header > h5').click()")
541
+ page.should have_content('Queries and their top hits: chord diagram')
542
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
543
543
  sleep 1
544
544
 
545
545
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -560,7 +560,7 @@ describe 'report generated from imported XML',type: :feature, js: true do
560
560
  # download in a right format.
561
561
 
562
562
  page.should have_content('Length distribution of hits')
563
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
563
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
564
564
  sleep 1
565
565
 
566
566
  page.execute_script("$('.export-to-png:eq(1)').click()")
data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb CHANGED
@@ -76,8 +76,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
76
76
  # download of PNG/SVG file and test that it initiated a file download in a
77
77
  # right format.
78
78
 
79
- page.should have_content('Chord diagram: queries and their top hits')
80
- page.execute_script("$('.circos > .grapher-header > h5').click()")
79
+ page.should have_content('Queries and their top hits: chord diagram')
80
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
81
81
  sleep 1
82
82
 
83
83
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -99,7 +99,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
99
99
  # download in a right format.
100
100
 
101
101
  page.should have_content('Length distribution of hits')
102
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
102
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
103
103
  sleep 1
104
104
 
105
105
  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -190,8 +190,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
190
190
  # download of PNG/SVG file and test that it initiated a file download in a
191
191
  # right format.
192
192
 
193
- page.should have_content('Chord diagram: queries and their top hits')
194
- page.execute_script("$('.circos > .grapher-header > h5').click()")
193
+ page.should have_content('Queries and their top hits: chord diagram')
194
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
195
195
  sleep 1
196
196
 
197
197
  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -213,7 +213,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
213
213
  # download in a right format.
214
214
 
215
215
  page.should have_content('Length distribution of hits')
216
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
216
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
217
217
  sleep 1
218
218
 
219
219
  page.execute_script("$('.export-to-png:eq(1)').click()")
data/spec/capybara_spec.rb CHANGED
@@ -1,4 +1,15 @@
1
1
  describe 'a browser', type: :feature, js: true do
2
+ it 'sorts databases alphabetically' do
3
+ visit '/'
4
+ fill_in('sequence', with: nucleotide_query)
5
+
6
+ prot = page.evaluate_script("$('.protein .database').text().trim()")
7
+ prot.should eq("2018-04 Swiss-Prot insecta Sinvicta 2-2-3 prot subset")
8
+
9
+ nucl = page.evaluate_script("$('.nucleotide .database').text().trim()")
10
+ nucl.should eq("Sinvicta 2-2-3 cdna subset Solenopsis invicta gnG subset")
11
+ end
12
+
2
13
  it 'properly controls blast button' do
3
14
  visit '/'
4
15
 
@@ -231,8 +242,8 @@ describe 'a browser', type: :feature, js: true do
231
242
  databases: protein_databases.values_at(0))
232
243
 
233
244
  ## Check that there is a circos vis and unfold it.
234
- page.should have_content('Chord diagram: queries and their top hits')
235
- page.execute_script("$('.circos > .grapher-header > h5').click()")
245
+ page.should have_content('Queries and their top hits: chord diagram')
246
+ page.execute_script("$('.circos > .grapher-header > h4').click()")
236
247
  sleep 1
237
248
 
238
249
  page.execute_script("$('.export-to-svg:eq(0)').click()")
@@ -260,7 +271,7 @@ describe 'a browser', type: :feature, js: true do
260
271
 
261
272
  ## Check that there is a length distribution of hits.
262
273
  page.should have_content('Length distribution of hits')
263
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
274
+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
264
275
  sleep 1
265
276
 
266
277
  page.execute_script("$('.export-to-svg:eq(2)').click()")