quorum 0.1.0 → 0.2.0

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Files changed (48) hide show
  1. data/Gemfile.lock +82 -74
  2. data/HISTORY.md +9 -0
  3. data/README.rdoc +101 -23
  4. data/app/assets/javascripts/quorum/jobs.js +45 -3
  5. data/app/controllers/quorum/jobs_controller.rb +47 -2
  6. data/app/models/quorum/job.rb +52 -9
  7. data/app/views/quorum/jobs/new.html.erb +7 -6
  8. data/app/views/quorum/jobs/show.html.erb +7 -118
  9. data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +53 -0
  10. data/app/views/quorum/jobs/templates/_blast_template.html.erb +68 -0
  11. data/config/routes.rb +2 -0
  12. data/db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb +8 -0
  13. data/lib/generators/quorum/images_generator.rb +18 -0
  14. data/lib/generators/quorum/install_generator.rb +41 -13
  15. data/lib/generators/templates/README +1 -1
  16. data/lib/generators/templates/blast.rb +18 -7
  17. data/lib/generators/templates/blast_db.rb +106 -0
  18. data/lib/generators/templates/fetch +115 -0
  19. data/lib/generators/templates/quorum_initializer.rb +1 -1
  20. data/lib/generators/templates/quorum_settings.yml +4 -4
  21. data/lib/quorum/helpers.rb +71 -1
  22. data/lib/quorum/version.rb +1 -1
  23. data/lib/quorum.rb +15 -5
  24. data/lib/workers/quorum.rb +12 -2
  25. data/quorum.gemspec +4 -2
  26. data/spec/data/seqs_not_fa.txt +16 -16
  27. data/spec/dummy/config/initializers/quorum_initializer.rb +1 -1
  28. data/spec/dummy/config/initializers/resque.rb +4 -1
  29. data/spec/dummy/config/quorum_settings.yml +4 -4
  30. data/spec/dummy/db/schema.rb +8 -1
  31. data/spec/dummy/quorum/bin/fetch +115 -0
  32. data/spec/dummy/quorum/blastdb/test.nin +0 -0
  33. data/spec/dummy/quorum/blastdb/test.pin +0 -0
  34. data/spec/dummy/quorum/lib/fetch_tools/blast_db.rb +106 -0
  35. data/spec/dummy/quorum/lib/search_tools/blast.rb +18 -7
  36. data/spec/models/job_spec.rb +3 -4
  37. data/spec/quorum_installed_spec.rb +5 -0
  38. data/spec/requests/jobs_spec.rb +14 -1
  39. data/spec/spec_helper.rb +32 -1
  40. data/spec/support/streams.rb +16 -0
  41. data/spec/templates/blast_db_spec.rb +63 -0
  42. data/spec/templates/blast_spec.rb +108 -2
  43. metadata +64 -37
  44. /data/app/assets/images/quorum/{knight_rider.gif → loading.gif} +0 -0
  45. /data/app/views/quorum/jobs/{_blastn_form.html.erb → form/_blastn_form.html.erb} +0 -0
  46. /data/app/views/quorum/jobs/{_blastp_form.html.erb → form/_blastp_form.html.erb} +0 -0
  47. /data/app/views/quorum/jobs/{_blastx_form.html.erb → form/_blastx_form.html.erb} +0 -0
  48. /data/app/views/quorum/jobs/{_tblastn_form.html.erb → form/_tblastn_form.html.erb} +0 -0
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: 0.1.0
4
+ version: 0.2.0
5
5
  prerelease:
6
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  platform: ruby
7
7
  authors:
@@ -9,11 +9,11 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-01-06 00:00:00.000000000Z
12
+ date: 2012-01-20 00:00:00.000000000Z
13
13
  dependencies:
14
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  - !ruby/object:Gem::Dependency
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15
  name: rails
16
- requirement: &18633320 !ruby/object:Gem::Requirement
16
+ requirement: &66807880 !ruby/object:Gem::Requirement
17
17
  none: false
18
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  requirements:
19
19
  - - ~>
@@ -21,10 +21,10 @@ dependencies:
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21
  version: 3.1.0
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  type: :runtime
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23
  prerelease: false
24
- version_requirements: *18633320
24
+ version_requirements: *66807880
25
25
  - !ruby/object:Gem::Dependency
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26
  name: jquery-rails
27
- requirement: &18631940 !ruby/object:Gem::Requirement
27
+ requirement: &66807340 !ruby/object:Gem::Requirement
28
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  none: false
29
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  requirements:
30
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  - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
32
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  version: '0'
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  type: :runtime
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  prerelease: false
35
- version_requirements: *18631940
35
+ version_requirements: *66807340
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  - !ruby/object:Gem::Dependency
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  name: net-ssh
38
- requirement: &18630220 !ruby/object:Gem::Requirement
38
+ requirement: &66806540 !ruby/object:Gem::Requirement
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  none: false
40
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  requirements:
41
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  - - ~>
@@ -43,10 +43,10 @@ dependencies:
43
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  version: 2.2.1
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  type: :runtime
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  prerelease: false
46
- version_requirements: *18630220
46
+ version_requirements: *66806540
47
47
  - !ruby/object:Gem::Dependency
48
48
  name: resque
49
- requirement: &18628400 !ruby/object:Gem::Requirement
49
+ requirement: &66805840 !ruby/object:Gem::Requirement
50
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  none: false
51
51
  requirements:
52
52
  - - ~>
@@ -54,10 +54,21 @@ dependencies:
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  version: 1.19.0
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  type: :runtime
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  prerelease: false
57
- version_requirements: *18628400
57
+ version_requirements: *66805840
58
+ - !ruby/object:Gem::Dependency
59
+ name: resque-result
60
+ requirement: &66805380 !ruby/object:Gem::Requirement
61
+ none: false
62
+ requirements:
63
+ - - ~>
64
+ - !ruby/object:Gem::Version
65
+ version: 1.0.1
66
+ type: :runtime
67
+ prerelease: false
68
+ version_requirements: *66805380
58
69
  - !ruby/object:Gem::Dependency
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  name: bio-blastxmlparser
60
- requirement: &18624440 !ruby/object:Gem::Requirement
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+ requirement: &66804700 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
63
74
  - - ~>
@@ -65,10 +76,10 @@ dependencies:
65
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  version: 1.0.1
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  type: :runtime
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  prerelease: false
68
- version_requirements: *18624440
79
+ version_requirements: *66804700
69
80
  - !ruby/object:Gem::Dependency
70
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  name: mysql2
71
- requirement: &18620600 !ruby/object:Gem::Requirement
82
+ requirement: &66804300 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -76,10 +87,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
79
- version_requirements: *18620600
90
+ version_requirements: *66804300
80
91
  - !ruby/object:Gem::Dependency
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  name: rspec-rails
82
- requirement: &18619380 !ruby/object:Gem::Requirement
93
+ requirement: &66803760 !ruby/object:Gem::Requirement
83
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  none: false
84
95
  requirements:
85
96
  - - ~>
@@ -87,32 +98,43 @@ dependencies:
87
98
  version: '2.6'
88
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  type: :development
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  prerelease: false
90
- version_requirements: *18619380
101
+ version_requirements: *66803760
102
+ - !ruby/object:Gem::Dependency
103
+ name: resque_spec
104
+ requirement: &66803240 !ruby/object:Gem::Requirement
105
+ none: false
106
+ requirements:
107
+ - - ~>
108
+ - !ruby/object:Gem::Version
109
+ version: 0.8.1
110
+ type: :development
111
+ prerelease: false
112
+ version_requirements: *66803240
91
113
  - !ruby/object:Gem::Dependency
92
114
  name: capybara
93
- requirement: &18618260 !ruby/object:Gem::Requirement
115
+ requirement: &66802760 !ruby/object:Gem::Requirement
94
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  none: false
95
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  requirements:
96
- - - ! '>='
118
+ - - ~>
97
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  - !ruby/object:Gem::Version
98
- version: '0'
120
+ version: 1.1.1
99
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  type: :development
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  prerelease: false
101
- version_requirements: *18618260
123
+ version_requirements: *66802760
102
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  - !ruby/object:Gem::Dependency
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  name: database_cleaner
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- requirement: &18617000 !ruby/object:Gem::Requirement
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+ requirement: &66802300 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
107
- - - ! '>='
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+ - - ~>
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  - !ruby/object:Gem::Version
109
- version: '0'
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+ version: 0.6.7
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  type: :development
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  prerelease: false
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- version_requirements: *18617000
134
+ version_requirements: *66802300
113
135
  - !ruby/object:Gem::Dependency
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  name: factory_girl_rails
115
- requirement: &18613860 !ruby/object:Gem::Requirement
137
+ requirement: &66801840 !ruby/object:Gem::Requirement
116
138
  none: false
117
139
  requirements:
118
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  - - ~>
@@ -120,7 +142,7 @@ dependencies:
120
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  version: 1.2.0
121
143
  type: :development
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  prerelease: false
123
- version_requirements: *18613860
145
+ version_requirements: *66801840
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  description: Flexible bioinformatics search tool.
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  email:
126
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  - kas@ncgr.org
@@ -132,12 +154,13 @@ files:
132
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  - .rspec
133
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  - Gemfile
134
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  - Gemfile.lock
157
+ - HISTORY.md
135
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  - MIT-LICENSE
136
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  - README.rdoc
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  - Rakefile
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  - app/assets/images/quorum/.gitkeep
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  - app/assets/images/quorum/bg.png
140
- - app/assets/images/quorum/knight_rider.gif
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+ - app/assets/images/quorum/loading.gif
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  - app/assets/images/quorum/ui-bg_flat_0_aaaaaa_40x100.png
142
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  - app/assets/images/quorum/ui-bg_flat_75_ffffff_40x100.png
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  - app/assets/images/quorum/ui-bg_glass_55_fbf9ee_1x400.png
@@ -170,12 +193,14 @@ files:
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  - app/models/quorum/tblastn_job.rb
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  - app/models/quorum/tblastn_job_report.rb
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  - app/views/layouts/quorum/application.html.erb
173
- - app/views/quorum/jobs/_blastn_form.html.erb
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- - app/views/quorum/jobs/_blastp_form.html.erb
175
- - app/views/quorum/jobs/_blastx_form.html.erb
176
- - app/views/quorum/jobs/_tblastn_form.html.erb
196
+ - app/views/quorum/jobs/form/_blastn_form.html.erb
197
+ - app/views/quorum/jobs/form/_blastp_form.html.erb
198
+ - app/views/quorum/jobs/form/_blastx_form.html.erb
199
+ - app/views/quorum/jobs/form/_tblastn_form.html.erb
177
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  - app/views/quorum/jobs/new.html.erb
178
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  - app/views/quorum/jobs/show.html.erb
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+ - app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb
203
+ - app/views/quorum/jobs/templates/_blast_template.html.erb
179
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  - app/views/shared/_error_messages.html.erb
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  - config/locales/en.yml
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  - config/routes.rb
@@ -188,11 +213,15 @@ files:
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  - db/migrate/20111031204903_create_blastx_job_reports.rb
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  - db/migrate/20111031204922_create_blastp_job_reports.rb
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  - db/migrate/20111031204941_create_tblastn_job_reports.rb
216
+ - db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
217
+ - lib/generators/quorum/images_generator.rb
191
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  - lib/generators/quorum/install_generator.rb
192
219
  - lib/generators/quorum/styles_generator.rb
193
220
  - lib/generators/quorum/views_generator.rb
194
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  - lib/generators/templates/README
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  - lib/generators/templates/blast.rb
223
+ - lib/generators/templates/blast_db.rb
224
+ - lib/generators/templates/fetch
196
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  - lib/generators/templates/logger.rb
197
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  - lib/generators/templates/quorum_initializer.rb
198
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  - lib/generators/templates/quorum_settings.yml
@@ -251,6 +280,7 @@ files:
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  - spec/dummy/public/422.html
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  - spec/dummy/public/500.html
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  - spec/dummy/public/favicon.ico
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+ - spec/dummy/quorum/bin/fetch
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  - spec/dummy/quorum/bin/search
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  - spec/dummy/quorum/blastdb/test.nhd
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  - spec/dummy/quorum/blastdb/test.nhi
@@ -270,6 +300,7 @@ files:
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  - spec/dummy/quorum/blastdb/test.psq
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  - spec/dummy/quorum/blastdb/test/contigs.fa
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  - spec/dummy/quorum/blastdb/test/peptides.fa
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+ - spec/dummy/quorum/lib/fetch_tools/blast_db.rb
273
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  - spec/dummy/quorum/lib/logger.rb
274
305
  - spec/dummy/quorum/lib/search_tools/blast.rb
275
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  - spec/dummy/quorum/lib/trollop.rb
@@ -287,7 +318,9 @@ files:
287
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  - spec/quorum_installed_spec.rb
288
319
  - spec/requests/jobs_spec.rb
289
320
  - spec/spec_helper.rb
321
+ - spec/support/streams.rb
290
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  - spec/tasks/blastdb_rake_spec.rb
323
+ - spec/templates/blast_db_spec.rb
291
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  - spec/templates/blast_spec.rb
292
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  - spec/templates/logger_spec.rb
293
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  - vendor/assets/javascripts/jquery.tipsy.js
@@ -304,18 +337,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
304
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
307
- segments:
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- - 0
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- hash: 1834928333496566984
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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- segments:
317
- - 0
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- hash: 1834928333496566984
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  requirements: []
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  rubyforge_project:
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  rubygems_version: 1.8.10