sequenceserver 1.1.0.beta11 → 1.1.0.beta12

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Files changed (30) hide show
  1. checksums.yaml +4 -4
  2. data/.rubocop.yml +14 -9
  3. data/Rakefile +1 -1
  4. data/bin/sequenceserver +79 -89
  5. data/lib/sequenceserver.rb +21 -18
  6. data/lib/sequenceserver/api_errors.rb +10 -11
  7. data/lib/sequenceserver/blast/constants.rb +6 -6
  8. data/lib/sequenceserver/blast/formatter.rb +3 -4
  9. data/lib/sequenceserver/blast/hit.rb +5 -2
  10. data/lib/sequenceserver/blast/hsp.rb +8 -5
  11. data/lib/sequenceserver/blast/job.rb +14 -13
  12. data/lib/sequenceserver/blast/query.rb +5 -3
  13. data/lib/sequenceserver/blast/report.rb +25 -23
  14. data/lib/sequenceserver/config.rb +26 -6
  15. data/lib/sequenceserver/database.rb +4 -3
  16. data/lib/sequenceserver/doctor.rb +22 -22
  17. data/lib/sequenceserver/exceptions.rb +17 -24
  18. data/lib/sequenceserver/job.rb +7 -7
  19. data/lib/sequenceserver/links.rb +11 -12
  20. data/lib/sequenceserver/logger.rb +1 -1
  21. data/lib/sequenceserver/pool.rb +0 -2
  22. data/lib/sequenceserver/report.rb +0 -1
  23. data/lib/sequenceserver/routes.rb +16 -16
  24. data/lib/sequenceserver/sequence.rb +24 -20
  25. data/lib/sequenceserver/server.rb +8 -8
  26. data/lib/sequenceserver/version.rb +1 -1
  27. data/public/js/search.js +2 -12
  28. data/public/sequenceserver-search.min.js +2 -2
  29. data/sequenceserver.gemspec +18 -17
  30. metadata +55 -55
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: sequenceserver
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  version: !ruby/object:Gem::Version
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- version: 1.1.0.beta11
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+ version: 1.1.0.beta12
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  platform: ruby
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  authors:
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  - Anurag Priyam
@@ -11,68 +11,68 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2018-07-10 00:00:00.000000000 Z
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+ date: 2018-09-10 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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- name: sinatra
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+ name: json_pure
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.0'
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+ version: '1.8'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.0.0
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+ version: 1.8.2
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.0'
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+ version: '1.8'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.0.0
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+ version: 1.8.2
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  - !ruby/object:Gem::Dependency
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- name: json_pure
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+ name: ox
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.8'
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+ version: '2.1'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.8.2
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+ version: 2.1.1
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.8'
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+ version: '2.1'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.8.2
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+ version: 2.1.1
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  - !ruby/object:Gem::Dependency
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- name: ox
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+ name: sinatra
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.1'
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+ version: '2.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.1.1
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+ version: 2.0.0
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.1'
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+ version: '2.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.1.1
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+ version: 2.0.0
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  - !ruby/object:Gem::Dependency
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  name: slop
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  requirement: !ruby/object:Gem::Requirement
@@ -94,148 +94,148 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: 3.6.0
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  - !ruby/object:Gem::Dependency
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- name: rake
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+ name: capybara
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '10.3'
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+ version: '2.18'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 10.3.2
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+ version: 2.18.0
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '10.3'
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+ version: '2.18'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 10.3.2
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+ version: 2.18.0
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  - !ruby/object:Gem::Dependency
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- name: rspec
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+ name: codeclimate-test-reporter
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '3.7'
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+ version: '1.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 3.7.0
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+ version: 1.0.8
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '3.7'
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+ version: '1.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 3.7.0
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+ version: 1.0.8
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  - !ruby/object:Gem::Dependency
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- name: capybara
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+ name: rack-test
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.18'
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+ version: '1.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.18.0
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+ version: 1.0.0
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '2.18'
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+ version: '1.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 2.18.0
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+ version: 1.0.0
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  - !ruby/object:Gem::Dependency
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- name: rack-test
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+ name: rake
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.0'
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+ version: '10.3'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 10.3.2
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.0'
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+ version: '10.3'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 10.3.2
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  - !ruby/object:Gem::Dependency
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- name: sauce_whisk
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+ name: rspec
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0.0'
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+ version: '3.7'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.0.19
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+ version: 3.7.0
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0.0'
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+ version: '3.7'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 0.0.19
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+ version: 3.7.0
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  - !ruby/object:Gem::Dependency
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- name: selenium-webdriver
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+ name: sauce_whisk
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '3.11'
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+ version: '0.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 3.11.0
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+ version: 0.0.19
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '3.11'
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+ version: '0.0'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 3.11.0
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+ version: 0.0.19
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  - !ruby/object:Gem::Dependency
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- name: codeclimate-test-reporter
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+ name: selenium-webdriver
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.0'
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+ version: '3.11'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.0.8
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+ version: 3.11.0
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - "~>"
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  - !ruby/object:Gem::Version
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- version: '1.0'
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+ version: '3.11'
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  - - ">="
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  - !ruby/object:Gem::Version
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- version: 1.0.8
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+ version: 3.11.0
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  description: |
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- SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
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- interface for use locally or over the web.
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+ SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
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+ user interface for use locally or over the web.
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  email:
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  - anurag08priyam@gmail.com
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  - b.woodcroft@uq.edu.au
@@ -3825,7 +3825,7 @@ metadata: {}
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  post_install_message: |2+
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  ------------------------------------------------------------------------
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- Thank you for installing SequenceServer :)!
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+ Thank you for installing SequenceServer :)
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  To launch SequenceServer execute 'sequenceserver' from command line.
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