miga-base 0.2.0.6 → 0.2.0.7

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Files changed (60) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -0
  3. data/LICENSE +201 -0
  4. data/README.md +17 -335
  5. data/Rakefile +31 -0
  6. data/actions/add_result +2 -5
  7. data/actions/add_taxonomy +4 -7
  8. data/actions/create_dataset +5 -6
  9. data/actions/create_project +2 -5
  10. data/actions/daemon +2 -5
  11. data/actions/download_dataset +88 -58
  12. data/actions/find_datasets +36 -38
  13. data/actions/import_datasets +2 -5
  14. data/actions/index_taxonomy +2 -5
  15. data/actions/list_datasets +47 -49
  16. data/actions/list_files +7 -11
  17. data/actions/unlink_dataset +2 -5
  18. data/bin/miga +1 -1
  19. data/lib/miga/common.rb +132 -0
  20. data/lib/miga/daemon.rb +229 -168
  21. data/lib/miga/dataset.rb +354 -277
  22. data/lib/miga/gui.rb +346 -269
  23. data/lib/miga/metadata.rb +115 -71
  24. data/lib/miga/project.rb +361 -259
  25. data/lib/miga/remote_dataset.rb +200 -148
  26. data/lib/miga/result.rb +150 -99
  27. data/lib/miga/tax_index.rb +124 -67
  28. data/lib/miga/taxonomy.rb +129 -100
  29. data/lib/miga/version.rb +57 -0
  30. data/lib/miga.rb +2 -77
  31. data/scripts/_distances_noref_nomulti.bash +2 -0
  32. data/scripts/_distances_ref_nomulti.bash +2 -0
  33. data/scripts/aai_distances.bash +1 -0
  34. data/scripts/ani_distances.bash +1 -0
  35. data/scripts/assembly.bash +1 -0
  36. data/scripts/cds.bash +1 -0
  37. data/scripts/clade_finding.bash +17 -1
  38. data/scripts/distances.bash +1 -0
  39. data/scripts/essential_genes.bash +1 -0
  40. data/scripts/haai_distances.bash +1 -0
  41. data/scripts/init.bash +2 -0
  42. data/scripts/mytaxa.bash +1 -0
  43. data/scripts/mytaxa_scan.bash +1 -0
  44. data/scripts/ogs.bash +1 -0
  45. data/scripts/read_quality.bash +1 -0
  46. data/scripts/ssu.bash +1 -0
  47. data/scripts/subclades.bash +1 -0
  48. data/scripts/trimmed_fasta.bash +1 -0
  49. data/scripts/trimmed_reads.bash +1 -0
  50. data/test/common_test.rb +82 -0
  51. data/test/daemon_test.rb +53 -0
  52. data/test/dataset_test.rb +156 -0
  53. data/test/jruby_gui_test.rb +20 -0
  54. data/test/metadata_test.rb +48 -0
  55. data/test/project_test.rb +54 -0
  56. data/test/remote_dataset_test.rb +41 -0
  57. data/test/tax_index_test.rb +44 -0
  58. data/test/taxonomy_test.rb +36 -0
  59. data/test/test_helper.rb +32 -0
  60. metadata +53 -38
metadata CHANGED
@@ -1,99 +1,99 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
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3
  version: !ruby/object:Gem::Version
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- version: 0.2.0.6
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+ version: 0.2.0.7
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5
  platform: ruby
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6
  authors:
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  - Luis M. Rodriguez-R
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8
  autorequire:
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9
  bindir: bin
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  cert_chain: []
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- date: 2015-12-07 00:00:00.000000000 Z
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+ date: 2016-04-13 00:00:00.000000000 Z
12
12
  dependencies:
13
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  - !ruby/object:Gem::Dependency
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  name: rest-client
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
17
- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.7'
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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:
24
- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.7'
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.3'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.3'
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  - !ruby/object:Gem::Dependency
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  name: daemons
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.2'
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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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51
  requirements:
52
- - - ~>
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+ - - "~>"
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53
  - !ruby/object:Gem::Version
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54
  version: '1.2'
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  - !ruby/object:Gem::Dependency
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  name: json
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.8'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '1.8'
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
73
- - - '>='
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '11'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '11'
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  - !ruby/object:Gem::Dependency
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  name: test-unit
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>='
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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '3'
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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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+ - - "~>"
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  - !ruby/object:Gem::Version
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- version: '0'
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+ version: '3'
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  description: Microbial Genomes Atlas
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  email: lmrodriguezr@gmail.com
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  executables:
@@ -102,7 +102,25 @@ extensions: []
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  extra_rdoc_files:
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  - README.md
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  files:
105
+ - Gemfile
106
+ - LICENSE
107
+ - README.md
108
+ - Rakefile
109
+ - actions/add_result
110
+ - actions/add_taxonomy
111
+ - actions/create_dataset
112
+ - actions/create_project
113
+ - actions/daemon
114
+ - actions/download_dataset
115
+ - actions/find_datasets
116
+ - actions/import_datasets
117
+ - actions/index_taxonomy
118
+ - actions/list_datasets
119
+ - actions/list_files
120
+ - actions/unlink_dataset
121
+ - bin/miga
105
122
  - lib/miga.rb
123
+ - lib/miga/common.rb
106
124
  - lib/miga/daemon.rb
107
125
  - lib/miga/dataset.rb
108
126
  - lib/miga/gui.rb
@@ -112,6 +130,7 @@ files:
112
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  - lib/miga/result.rb
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131
  - lib/miga/tax_index.rb
114
132
  - lib/miga/taxonomy.rb
133
+ - lib/miga/version.rb
115
134
  - scripts/_distances_noref_nomulti.bash
116
135
  - scripts/_distances_ref_nomulti.bash
117
136
  - scripts/aai_distances.bash
@@ -132,53 +151,49 @@ files:
132
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  - scripts/subclades.bash
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  - scripts/trimmed_fasta.bash
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  - scripts/trimmed_reads.bash
154
+ - test/common_test.rb
155
+ - test/daemon_test.rb
156
+ - test/dataset_test.rb
157
+ - test/jruby_gui_test.rb
158
+ - test/metadata_test.rb
159
+ - test/project_test.rb
160
+ - test/remote_dataset_test.rb
161
+ - test/tax_index_test.rb
162
+ - test/taxonomy_test.rb
163
+ - test/test_helper.rb
135
164
  - utils/adapters.fa
136
165
  - utils/mytaxa_scan.R
137
166
  - utils/mytaxa_scan.rb
138
167
  - utils/requirements.txt
139
168
  - utils/subclades-compile.rb
140
169
  - utils/subclades.R
141
- - bin/miga
142
- - actions/add_result
143
- - actions/add_taxonomy
144
- - actions/create_dataset
145
- - actions/create_project
146
- - actions/daemon
147
- - actions/download_dataset
148
- - actions/find_datasets
149
- - actions/import_datasets
150
- - actions/index_taxonomy
151
- - actions/list_datasets
152
- - actions/list_files
153
- - actions/unlink_dataset
154
- - README.md
155
170
  homepage: http://enve-omics.ce.gatech.edu/miga
156
171
  licenses:
157
- - artistic 2.0
172
+ - Artistic-2.0
158
173
  metadata: {}
159
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  post_install_message:
160
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  rdoc_options:
161
176
  - lib
162
177
  - README.md
163
- - --main
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+ - "--main"
164
179
  - README.md
165
- - --title
180
+ - "--title"
166
181
  - MiGA
167
182
  require_paths:
168
183
  - lib
169
184
  required_ruby_version: !ruby/object:Gem::Requirement
170
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  requirements:
171
- - - ~>
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+ - - "~>"
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  - !ruby/object:Gem::Version
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  version: '2.0'
174
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  required_rubygems_version: !ruby/object:Gem::Requirement
175
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  requirements:
176
- - - '>='
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+ - - ">="
177
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
181
- rubygems_version: 2.0.14
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+ rubygems_version: 2.5.1
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197
  signing_key:
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  specification_version: 4
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  summary: MiGA