quorum 0.3.3 → 0.4.0

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Files changed (43) hide show
  1. data/Gemfile.lock +42 -48
  2. data/HISTORY.md +11 -0
  3. data/app/assets/javascripts/quorum/quorum.js +8 -5
  4. data/db/migrate/20120807202555_add_gaps_to_blast_reports.rb +8 -0
  5. data/lib/generators/templates/blast.rb +76 -40
  6. data/lib/quorum/version.rb +1 -1
  7. data/quorum.gemspec +6 -7
  8. data/spec/data/fake_seq.txt +2 -0
  9. data/spec/data/nucl_prot_seqs.txt +15 -0
  10. data/spec/data/tmp/test.tgz +0 -0
  11. data/spec/dummy/config/initializers/quorum_initializer.rb +1 -1
  12. data/spec/dummy/config/quorum_settings.yml +5 -9
  13. data/spec/dummy/db/schema.rb +23 -19
  14. data/spec/dummy/quorum/bin/fetch +3 -3
  15. data/spec/dummy/quorum/bin/search +8 -8
  16. data/spec/dummy/quorum/blastdb/test/contigs.fa +13 -0
  17. data/spec/dummy/quorum/blastdb/test/peptides.fa +2 -0
  18. data/spec/dummy/quorum/blastdb/test.nhd +1 -0
  19. data/spec/dummy/quorum/blastdb/test.nhi +0 -0
  20. data/spec/dummy/quorum/blastdb/test.nhr +0 -0
  21. data/spec/dummy/quorum/blastdb/test.nin +0 -0
  22. data/spec/dummy/quorum/blastdb/test.nog +0 -0
  23. data/spec/dummy/quorum/blastdb/test.nsd +1 -0
  24. data/spec/dummy/quorum/blastdb/test.nsi +0 -0
  25. data/spec/dummy/quorum/blastdb/test.nsq +0 -0
  26. data/spec/dummy/quorum/blastdb/test.phd +1 -0
  27. data/spec/dummy/quorum/blastdb/test.phi +0 -0
  28. data/spec/dummy/quorum/blastdb/test.phr +0 -0
  29. data/spec/dummy/quorum/blastdb/test.pin +0 -0
  30. data/spec/dummy/quorum/blastdb/test.pog +0 -0
  31. data/spec/dummy/quorum/blastdb/test.psd +1 -0
  32. data/spec/dummy/quorum/blastdb/test.psi +0 -0
  33. data/spec/dummy/quorum/blastdb/test.psq +0 -0
  34. data/spec/dummy/quorum/lib/fetch_tools/blast_db.rb +6 -6
  35. data/spec/dummy/quorum/lib/logger.rb +4 -4
  36. data/spec/dummy/quorum/lib/search_tools/blast.rb +76 -40
  37. data/spec/dummy/quorum/lib/trollop.rb +4 -4
  38. data/spec/javascripts/fixtures/formatted_sequence.html +1 -1
  39. data/spec/javascripts/quorum_spec.js +8 -6
  40. data/spec/requests/jobs_spec.rb +13 -3
  41. data/spec/spec_helper.rb +0 -4
  42. data/spec/templates/blast_spec.rb +53 -3
  43. metadata +17 -31
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: quorum
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.3
4
+ version: 0.4.0
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,7 +9,7 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-07-19 00:00:00.000000000 Z
12
+ date: 2012-08-10 00:00:00.000000000 Z
13
13
  dependencies:
14
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  - !ruby/object:Gem::Dependency
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15
  name: rails
@@ -66,7 +66,7 @@ dependencies:
66
66
  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.19.0
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+ version: 1.20.0
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -74,7 +74,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.19.0
77
+ version: 1.20.0
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  - !ruby/object:Gem::Dependency
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  name: resque-result
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  requirement: !ruby/object:Gem::Requirement
@@ -98,7 +98,7 @@ dependencies:
98
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  requirements:
99
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  - - ~>
100
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  - !ruby/object:Gem::Version
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- version: 1.0.1
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+ version: 1.1.0
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102
  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -106,7 +106,7 @@ dependencies:
106
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  requirements:
107
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.0.1
109
+ version: 1.1.0
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  - !ruby/object:Gem::Dependency
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  name: mysql2
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  requirement: !ruby/object:Gem::Requirement
@@ -130,7 +130,7 @@ dependencies:
130
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '2.6'
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+ version: '2.11'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -138,7 +138,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '2.6'
141
+ version: '2.11'
142
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  - !ruby/object:Gem::Dependency
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  name: resque_spec
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  requirement: !ruby/object:Gem::Requirement
@@ -146,7 +146,7 @@ dependencies:
146
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '0.8'
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+ version: '0.12'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -154,7 +154,7 @@ dependencies:
154
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '0.8'
157
+ version: '0.12'
158
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  - !ruby/object:Gem::Dependency
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  name: capybara
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  requirement: !ruby/object:Gem::Requirement
@@ -178,7 +178,7 @@ dependencies:
178
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '0.6'
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+ version: '0.8'
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  type: :development
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  prerelease: false
184
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  version_requirements: !ruby/object:Gem::Requirement
@@ -186,9 +186,9 @@ dependencies:
186
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '0.6'
189
+ version: '0.8'
190
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  - !ruby/object:Gem::Dependency
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- name: factory_girl_rails
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+ name: jasmine
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  requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
@@ -203,22 +203,6 @@ dependencies:
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  - - ~>
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  - !ruby/object:Gem::Version
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  version: '1.2'
206
- - !ruby/object:Gem::Dependency
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- name: jasmine
208
- requirement: !ruby/object:Gem::Requirement
209
- none: false
210
- requirements:
211
- - - ~>
212
- - !ruby/object:Gem::Version
213
- version: '1.1'
214
- type: :development
215
- prerelease: false
216
- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
219
- - - ~>
220
- - !ruby/object:Gem::Version
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- version: '1.1'
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206
  description: Flexible bioinformatics search tool.
223
207
  email:
224
208
  - kas@ncgr.org
@@ -295,6 +279,7 @@ files:
295
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  - db/migrate/20111031204922_create_blastp_job_reports.rb
296
280
  - db/migrate/20111031204941_create_tblastn_job_reports.rb
297
281
  - db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
282
+ - db/migrate/20120807202555_add_gaps_to_blast_reports.rb
298
283
  - lib/generators/quorum/images_generator.rb
299
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  - lib/generators/quorum/install_generator.rb
300
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  - lib/generators/quorum/styles_generator.rb
@@ -321,6 +306,7 @@ files:
321
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  - lib/workers/quorum.rb
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  - quorum.gemspec
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  - script/rails
309
+ - spec/data/fake_seq.txt
324
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  - spec/data/nucl_prot_seqs.txt
325
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  - spec/data/nucl_seqs.txt
326
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  - spec/data/nucl_seqs_lower.txt
@@ -440,7 +426,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -91775132015006220
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+ hash: -3860118891920834630
444
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  required_rubygems_version: !ruby/object:Gem::Requirement
445
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  none: false
446
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  requirements:
@@ -449,7 +435,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
449
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  version: '0'
450
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  segments:
451
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  - 0
452
- hash: -91775132015006220
438
+ hash: -3860118891920834630
453
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  requirements: []
454
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  rubyforge_project:
455
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  rubygems_version: 1.8.24