sequenceserver 2.0.0.beta4 → 2.0.0.rc1

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Files changed (44) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +7 -4
  3. data/AppImage/sequenceserver.sh +5 -0
  4. data/lib/sequenceserver.rb +9 -5
  5. data/lib/sequenceserver/blast/job.rb +7 -24
  6. data/lib/sequenceserver/blast/report.rb +66 -33
  7. data/lib/sequenceserver/routes.rb +28 -2
  8. data/lib/sequenceserver/version.rb +1 -1
  9. data/public/SequenceServer_logo.png +0 -0
  10. data/public/css/grapher.css +8 -15
  11. data/public/css/sequenceserver.css +115 -55
  12. data/public/css/sequenceserver.min.css +3 -3
  13. data/public/js/circos.js +1 -1
  14. data/public/js/download_fasta.js +17 -0
  15. data/public/js/grapher.js +7 -9
  16. data/public/js/hit.js +217 -0
  17. data/public/js/hits_overview.js +12 -13
  18. data/public/js/hsp.js +104 -84
  19. data/public/js/{sequenceserver.js → jquery_world.js} +1 -18
  20. data/public/js/kablammo.js +337 -334
  21. data/public/js/length_distribution.js +1 -1
  22. data/public/js/query.js +147 -0
  23. data/public/js/report.js +203 -830
  24. data/public/js/search.js +176 -169
  25. data/public/js/sequence_modal.js +167 -0
  26. data/public/js/sidebar.js +210 -0
  27. data/public/js/utils.js +2 -19
  28. data/public/js/visualisation_helpers.js +2 -2
  29. data/public/sequenceserver-report.min.js +19 -19
  30. data/public/sequenceserver-search.min.js +11 -11
  31. data/public/vendor/github/twbs/bootstrap@3.3.5/js/bootstrap.js +2 -2
  32. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +5 -5
  33. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +5 -5
  34. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +5 -5
  35. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +5 -5
  36. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +5 -5
  37. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +5 -5
  38. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +5 -5
  39. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +5 -5
  40. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +5 -5
  41. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +2 -2
  42. data/spec/capybara_spec.rb +1 -1
  43. data/views/layout.erb +1 -1
  44. metadata +9 -3
data/spec/capybara_spec.rb CHANGED
@@ -231,7 +231,7 @@ describe 'a browser', type: :feature, js: true do
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  databases: protein_databases.values_at(0))
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  ## Check that there is a circos vis and unfold it.
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- page.should have_content('Chord diagram: queries and their top hits')
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+ page.should have_content('Queries and their top hits: chord diagram')
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  page.execute_script("$('.circos > .grapher-header > h5').click()")
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  sleep 1
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data/views/layout.erb CHANGED
@@ -29,7 +29,7 @@
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  <a
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  class="navbar-brand"
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  href="http://sequenceserver.com" target="_blank">
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- SequenceServer
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+ <img class="logo" src="SequenceServer_logo.png" alt="sequenceserver_logo">
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  <small>
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  <%= SequenceServer::VERSION %>
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  </small>
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: sequenceserver
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  version: !ruby/object:Gem::Version
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- version: 2.0.0.beta4
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+ version: 2.0.0.rc1
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  platform: ruby
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  authors:
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  - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2019-12-13 00:00:00.000000000 Z
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+ date: 2020-03-14 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: json_pure
@@ -292,6 +292,7 @@ files:
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  - lib/sequenceserver/sys.rb
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  - lib/sequenceserver/version.rb
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  - package.json
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+ - public/SequenceServer_logo.png
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  - public/config.js
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  - public/css/fonts.css
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  - public/css/grapher.css
@@ -315,18 +316,23 @@ files:
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  - public/fonts/fontawesome-webfont.woff2
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  - public/js/alignment_exporter.js
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  - public/js/circos.js
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+ - public/js/download_fasta.js
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  - public/js/error_modal.js
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  - public/js/exporter.js
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  - public/js/grapher.js
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+ - public/js/hit.js
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  - public/js/hits_overview.js
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  - public/js/hsp.js
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+ - public/js/jquery_world.js
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  - public/js/kablammo.js
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  - public/js/kablammo/alignment_viewer.js
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  - public/js/length_distribution.js
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+ - public/js/query.js
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  - public/js/report.js
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  - public/js/search.js
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  - public/js/sequence.js
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- - public/js/sequenceserver.js
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+ - public/js/sequence_modal.js
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+ - public/js/sidebar.js
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  - public/js/svgExporter.js
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  - public/js/utils.js
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  - public/js/visualisation_helpers.js