sequenceserver 2.0.0.beta4 → 2.0.0.rc5

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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
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  # download of PNG/SVG file and test that it initiated a file download in a
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85
  # right format.
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86
 
87
- page.should have_content('Chord diagram: queries and their top hits')
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- page.execute_script("$('.circos > .grapher-header > h5').click()")
87
+ page.should have_content('Queries and their top hits: chord diagram')
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+ page.execute_script("$('.circos > .grapher-header > h4').click()")
89
89
  sleep 1
90
90
 
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  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -107,7 +107,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
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  # download in a right format.
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  page.should have_content('Length distribution of hits')
110
- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
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+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
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  sleep 1
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  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -200,8 +200,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
200
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  # download of PNG/SVG file and test that it initiated a file download in a
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  # right format.
202
202
 
203
- page.should have_content('Chord diagram: queries and their top hits')
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- page.execute_script("$('.circos > .grapher-header > h5').click()")
203
+ page.should have_content('Queries and their top hits: chord diagram')
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+ page.execute_script("$('.circos > .grapher-header > h4').click()")
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205
  sleep 1
206
206
 
207
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  page.execute_script("$('.export-to-png:eq(0)').click()")
@@ -221,7 +221,7 @@ describe 'report generated from imported XML', type: :feature, js: true do
221
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  # download in a right format.
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223
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  page.should have_content('Length distribution of hits')
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- page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
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+ page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
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225
  sleep 1
226
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227
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  page.execute_script("$('.export-to-png:eq(1)').click()")
@@ -314,8 +314,8 @@ describe 'report generated from imported XML', type: :feature, js: true do
314
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  # download of PNG/SVG file and test that it initiated a file download in a
315
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  # right format.
316
316
 
317
- page.should have_content('Chord diagram: queries and their top hits')
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- page.execute_script("$('.circos > .grapher-header > h5').click()")
317
+ page.should have_content('Queries and their top hits: chord diagram')
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+ page.execute_script("$('.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
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  # 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
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  # 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()")