opentox-ruby 3.0.1 → 3.1.0

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Files changed (20) hide show
  1. data/ChangeLog +8 -0
  2. data/Rakefile +2 -3
  3. data/VERSION +1 -1
  4. data/lib/algorithm.rb +227 -675
  5. data/lib/authorization.rb +10 -8
  6. data/lib/compound.rb +47 -11
  7. data/lib/dataset.rb +50 -2
  8. data/lib/environment.rb +6 -1
  9. data/lib/model.rb +37 -72
  10. data/lib/opentox-ruby.rb +1 -1
  11. data/lib/parser.rb +115 -57
  12. data/lib/r-util.rb +354 -0
  13. data/lib/rest_client_wrapper.rb +1 -1
  14. data/lib/serializer.rb +47 -30
  15. data/lib/stratification.R +201 -0
  16. data/lib/task.rb +5 -1
  17. data/lib/transform.rb +520 -0
  18. data/lib/utils.rb +372 -0
  19. data/lib/validation.rb +52 -6
  20. metadata +413 -428
metadata CHANGED
@@ -1,545 +1,537 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: opentox-ruby
3
- version: !ruby/object:Gem::Version
4
- hash: 5
3
+ version: !ruby/object:Gem::Version
4
+ version: 3.1.0
5
5
  prerelease:
6
- segments:
7
- - 3
8
- - 0
9
- - 1
10
- version: 3.0.1
11
6
  platform: ruby
12
- authors:
7
+ authors:
13
8
  - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
14
9
  autorequire:
15
10
  bindir: bin
16
11
  cert_chain: []
17
-
18
- date: 2011-10-24 00:00:00 +02:00
19
- default_executable:
20
- dependencies:
21
- - !ruby/object:Gem::Dependency
12
+ date: 2012-03-26 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
22
15
  name: sinatra
23
- prerelease: false
24
- requirement: &id001 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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17
  none: false
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- requirements:
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- - - "="
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- - !ruby/object:Gem::Version
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- hash: 19
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- segments:
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- - 1
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- - 2
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- - 6
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+ requirements:
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+ - - '='
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+ - !ruby/object:Gem::Version
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  version: 1.2.6
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22
  type: :runtime
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: emk-sinatra-url-for
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23
  prerelease: false
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- requirement: &id002 !ruby/object:Gem::Requirement
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+ version_requirements: !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: 1.2.6
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+ - !ruby/object:Gem::Dependency
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+ name: emk-sinatra-url-for
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  none: false
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- hash: 21
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- segments:
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+ - !ruby/object:Gem::Version
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  version: 0.2.1
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38
  type: :runtime
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- version_requirements: *id002
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- - !ruby/object:Gem::Dependency
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- name: sinatra-respond_to
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39
  prerelease: false
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- requirement: &id003 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - !ruby/object:Gem::Version
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- name: sinatra-static-assets
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55
  prerelease: false
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- requirement: &id004 !ruby/object:Gem::Requirement
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+ none: false
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- - !ruby/object:Gem::Dependency
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- name: rest-client
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  prerelease: false
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  version: 1.6.1
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- name: rack
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- hash: 25
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- segments:
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- - !ruby/object:Gem::Dependency
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- name: rack-contrib
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  prerelease: false
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+ - !ruby/object:Gem::Dependency
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+ name: rack-contrib
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  none: false
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  version: 1.1.0
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  type: :runtime
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- - !ruby/object:Gem::Dependency
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- name: rack-flash
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  prerelease: false
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- requirement: &id008 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ - !ruby/object:Gem::Version
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+ version: 1.1.0
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+ - !ruby/object:Gem::Dependency
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+ name: rack-flash
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  none: false
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  version: 0.1.1
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- - !ruby/object:Gem::Dependency
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- name: nokogiri
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  prerelease: false
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- requirement: &id009 !ruby/object:Gem::Requirement
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+ none: false
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+ version: 0.1.1
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+ name: nokogiri
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  type: :runtime
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- - !ruby/object:Gem::Dependency
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- name: rubyzip
167
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  prerelease: false
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- requirement: &id010 !ruby/object:Gem::Requirement
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+ version: 1.4.4
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+ - !ruby/object:Gem::Dependency
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+ name: rubyzip
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  none: false
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- - !ruby/object:Gem::Version
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- - 9
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  version: 0.9.4
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166
  type: :runtime
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- version_requirements: *id010
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- - !ruby/object:Gem::Dependency
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- name: roo
183
167
  prerelease: false
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- requirement: &id011 !ruby/object:Gem::Requirement
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+ none: false
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+ - !ruby/object:Gem::Version
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+ version: 0.9.4
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+ name: roo
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  type: :runtime
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- - !ruby/object:Gem::Dependency
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- name: spreadsheet
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- hash: 99
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- - 0
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+ none: false
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+ - !ruby/object:Gem::Version
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  version: 0.6.5.4
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- version_requirements: *id012
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- - !ruby/object:Gem::Dependency
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- name: google-spreadsheet-ruby
216
199
  prerelease: false
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- requirement: &id013 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ - !ruby/object:Gem::Version
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+ - !ruby/object:Gem::Dependency
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+ name: google-spreadsheet-ruby
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- - !ruby/object:Gem::Dependency
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- name: yajl-ruby
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215
  prerelease: false
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+ none: false
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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244
230
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- - !ruby/object:Gem::Dependency
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- name: rinruby
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  prerelease: false
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- requirement: &id015 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ - !ruby/object:Gem::Version
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+ - !ruby/object:Gem::Dependency
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+ name: rinruby
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  none: false
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- - !ruby/object:Gem::Dependency
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- name: ohm
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247
  prerelease: false
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- requirement: &id016 !ruby/object:Gem::Requirement
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276
262
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- - !ruby/object:Gem::Dependency
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280
263
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273
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278
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279
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289
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293
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308
294
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312
295
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305
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309
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324
310
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- - !ruby/object:Gem::Dependency
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328
311
  prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ version: 1.3.4
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+ - !ruby/object:Gem::Dependency
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321
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325
  version: 3.1.1
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326
  type: :runtime
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- - !ruby/object:Gem::Dependency
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- name: akephalos
344
327
  prerelease: false
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341
  version: 0.2.5
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342
  type: :runtime
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- - !ruby/object:Gem::Dependency
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- name: dm-core
360
343
  prerelease: false
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- requirement: &id022 !ruby/object:Gem::Requirement
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353
  none: false
363
- requirements:
364
- - - "="
365
- - !ruby/object:Gem::Version
366
- hash: 19
367
- segments:
368
- - 1
369
- - 1
370
- - 0
354
+ requirements:
355
+ - - '='
356
+ - !ruby/object:Gem::Version
371
357
  version: 1.1.0
372
358
  type: :runtime
373
- version_requirements: *id022
374
- - !ruby/object:Gem::Dependency
375
- name: dm-serializer
376
359
  prerelease: false
377
- requirement: &id023 !ruby/object:Gem::Requirement
360
+ version_requirements: !ruby/object:Gem::Requirement
361
+ none: false
362
+ requirements:
363
+ - - '='
364
+ - !ruby/object:Gem::Version
365
+ version: 1.1.0
366
+ - !ruby/object:Gem::Dependency
367
+ name: dm-serializer
368
+ requirement: !ruby/object:Gem::Requirement
378
369
  none: false
379
- requirements:
380
- - - "="
381
- - !ruby/object:Gem::Version
382
- hash: 19
383
- segments:
384
- - 1
385
- - 1
386
- - 0
370
+ requirements:
371
+ - - '='
372
+ - !ruby/object:Gem::Version
387
373
  version: 1.1.0
388
374
  type: :runtime
389
- version_requirements: *id023
390
- - !ruby/object:Gem::Dependency
391
- name: dm-timestamps
392
375
  prerelease: false
393
- requirement: &id024 !ruby/object:Gem::Requirement
376
+ version_requirements: !ruby/object:Gem::Requirement
377
+ none: false
378
+ requirements:
379
+ - - '='
380
+ - !ruby/object:Gem::Version
381
+ version: 1.1.0
382
+ - !ruby/object:Gem::Dependency
383
+ name: dm-timestamps
384
+ requirement: !ruby/object:Gem::Requirement
394
385
  none: false
395
- requirements:
396
- - - "="
397
- - !ruby/object:Gem::Version
398
- hash: 19
399
- segments:
400
- - 1
401
- - 1
402
- - 0
386
+ requirements:
387
+ - - '='
388
+ - !ruby/object:Gem::Version
403
389
  version: 1.1.0
404
390
  type: :runtime
405
- version_requirements: *id024
406
- - !ruby/object:Gem::Dependency
407
- name: dm-types
408
391
  prerelease: false
409
- requirement: &id025 !ruby/object:Gem::Requirement
392
+ version_requirements: !ruby/object:Gem::Requirement
393
+ none: false
394
+ requirements:
395
+ - - '='
396
+ - !ruby/object:Gem::Version
397
+ version: 1.1.0
398
+ - !ruby/object:Gem::Dependency
399
+ name: dm-types
400
+ requirement: !ruby/object:Gem::Requirement
410
401
  none: false
411
- requirements:
412
- - - "="
413
- - !ruby/object:Gem::Version
414
- hash: 19
415
- segments:
416
- - 1
417
- - 1
418
- - 0
402
+ requirements:
403
+ - - '='
404
+ - !ruby/object:Gem::Version
419
405
  version: 1.1.0
420
406
  type: :runtime
421
- version_requirements: *id025
422
- - !ruby/object:Gem::Dependency
423
- name: dm-migrations
424
407
  prerelease: false
425
- requirement: &id026 !ruby/object:Gem::Requirement
408
+ version_requirements: !ruby/object:Gem::Requirement
409
+ none: false
410
+ requirements:
411
+ - - '='
412
+ - !ruby/object:Gem::Version
413
+ version: 1.1.0
414
+ - !ruby/object:Gem::Dependency
415
+ name: dm-migrations
416
+ requirement: !ruby/object:Gem::Requirement
426
417
  none: false
427
- requirements:
428
- - - "="
429
- - !ruby/object:Gem::Version
430
- hash: 19
431
- segments:
432
- - 1
433
- - 1
434
- - 0
418
+ requirements:
419
+ - - '='
420
+ - !ruby/object:Gem::Version
435
421
  version: 1.1.0
436
422
  type: :runtime
437
- version_requirements: *id026
438
- - !ruby/object:Gem::Dependency
439
- name: dm-validations
440
423
  prerelease: false
441
- requirement: &id027 !ruby/object:Gem::Requirement
424
+ version_requirements: !ruby/object:Gem::Requirement
425
+ none: false
426
+ requirements:
427
+ - - '='
428
+ - !ruby/object:Gem::Version
429
+ version: 1.1.0
430
+ - !ruby/object:Gem::Dependency
431
+ name: dm-validations
432
+ requirement: !ruby/object:Gem::Requirement
442
433
  none: false
443
- requirements:
444
- - - "="
445
- - !ruby/object:Gem::Version
446
- hash: 19
447
- segments:
448
- - 1
449
- - 1
450
- - 0
434
+ requirements:
435
+ - - '='
436
+ - !ruby/object:Gem::Version
451
437
  version: 1.1.0
452
438
  type: :runtime
453
- version_requirements: *id027
454
- - !ruby/object:Gem::Dependency
455
- name: dm-sqlite-adapter
456
439
  prerelease: false
457
- requirement: &id028 !ruby/object:Gem::Requirement
440
+ version_requirements: !ruby/object:Gem::Requirement
441
+ none: false
442
+ requirements:
443
+ - - '='
444
+ - !ruby/object:Gem::Version
445
+ version: 1.1.0
446
+ - !ruby/object:Gem::Dependency
447
+ name: dm-sqlite-adapter
448
+ requirement: !ruby/object:Gem::Requirement
458
449
  none: false
459
- requirements:
460
- - - "="
461
- - !ruby/object:Gem::Version
462
- hash: 19
463
- segments:
464
- - 1
465
- - 1
466
- - 0
450
+ requirements:
451
+ - - '='
452
+ - !ruby/object:Gem::Version
467
453
  version: 1.1.0
468
454
  type: :runtime
469
- version_requirements: *id028
470
- - !ruby/object:Gem::Dependency
471
- name: ruby-plot
472
455
  prerelease: false
473
- requirement: &id029 !ruby/object:Gem::Requirement
456
+ version_requirements: !ruby/object:Gem::Requirement
474
457
  none: false
475
- requirements:
476
- - - "="
477
- - !ruby/object:Gem::Version
478
- hash: 11
479
- segments:
480
- - 0
481
- - 5
482
- - 0
483
- version: 0.5.0
458
+ requirements:
459
+ - - '='
460
+ - !ruby/object:Gem::Version
461
+ version: 1.1.0
462
+ - !ruby/object:Gem::Dependency
463
+ name: ruby-plot
464
+ requirement: !ruby/object:Gem::Requirement
465
+ none: false
466
+ requirements:
467
+ - - '='
468
+ - !ruby/object:Gem::Version
469
+ version: 0.6.0
484
470
  type: :runtime
485
- version_requirements: *id029
486
- - !ruby/object:Gem::Dependency
487
- name: gsl
488
471
  prerelease: false
489
- requirement: &id030 !ruby/object:Gem::Requirement
472
+ version_requirements: !ruby/object:Gem::Requirement
490
473
  none: false
491
- requirements:
492
- - - "="
493
- - !ruby/object:Gem::Version
494
- hash: 33
495
- segments:
496
- - 1
497
- - 14
498
- - 7
474
+ requirements:
475
+ - - '='
476
+ - !ruby/object:Gem::Version
477
+ version: 0.6.0
478
+ - !ruby/object:Gem::Dependency
479
+ name: gsl
480
+ requirement: !ruby/object:Gem::Requirement
481
+ none: false
482
+ requirements:
483
+ - - '='
484
+ - !ruby/object:Gem::Version
499
485
  version: 1.14.7
500
486
  type: :runtime
501
- version_requirements: *id030
502
- - !ruby/object:Gem::Dependency
503
- name: statsample
504
487
  prerelease: false
505
- requirement: &id031 !ruby/object:Gem::Requirement
488
+ version_requirements: !ruby/object:Gem::Requirement
489
+ none: false
490
+ requirements:
491
+ - - '='
492
+ - !ruby/object:Gem::Version
493
+ version: 1.14.7
494
+ - !ruby/object:Gem::Dependency
495
+ name: statsample
496
+ requirement: !ruby/object:Gem::Requirement
506
497
  none: false
507
- requirements:
508
- - - "="
509
- - !ruby/object:Gem::Version
510
- hash: 19
511
- segments:
512
- - 1
513
- - 1
514
- - 0
498
+ requirements:
499
+ - - '='
500
+ - !ruby/object:Gem::Version
515
501
  version: 1.1.0
516
502
  type: :runtime
517
- version_requirements: *id031
518
- - !ruby/object:Gem::Dependency
519
- name: jeweler
520
503
  prerelease: false
521
- requirement: &id032 !ruby/object:Gem::Requirement
504
+ version_requirements: !ruby/object:Gem::Requirement
505
+ none: false
506
+ requirements:
507
+ - - '='
508
+ - !ruby/object:Gem::Version
509
+ version: 1.1.0
510
+ - !ruby/object:Gem::Dependency
511
+ name: jeweler
512
+ requirement: !ruby/object:Gem::Requirement
522
513
  none: false
523
- requirements:
524
- - - ">="
525
- - !ruby/object:Gem::Version
526
- hash: 3
527
- segments:
528
- - 0
529
- version: "0"
514
+ requirements:
515
+ - - ! '>='
516
+ - !ruby/object:Gem::Version
517
+ version: '0'
530
518
  type: :development
531
- version_requirements: *id032
519
+ prerelease: false
520
+ version_requirements: !ruby/object:Gem::Requirement
521
+ none: false
522
+ requirements:
523
+ - - ! '>='
524
+ - !ruby/object:Gem::Version
525
+ version: '0'
532
526
  description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
533
527
  email: helma@in-silico.ch
534
528
  executables: []
535
-
536
529
  extensions: []
537
-
538
- extra_rdoc_files:
530
+ extra_rdoc_files:
539
531
  - ChangeLog
540
532
  - LICENSE
541
533
  - README.markdown
542
- files:
534
+ files:
543
535
  - ChangeLog
544
536
  - LICENSE
545
537
  - README.markdown
@@ -562,47 +554,40 @@ files:
562
554
  - lib/overwrite.rb
563
555
  - lib/parser.rb
564
556
  - lib/policy.rb
557
+ - lib/r-util.rb
565
558
  - lib/rest_client_wrapper.rb
566
559
  - lib/serializer.rb
567
560
  - lib/spork.rb
561
+ - lib/stratification.R
568
562
  - lib/task.rb
569
563
  - lib/templates/default_guest_policy.xml
570
564
  - lib/templates/default_policy.xml
571
565
  - lib/to-html.rb
566
+ - lib/transform.rb
567
+ - lib/utils.rb
572
568
  - lib/validation.rb
573
- has_rdoc: true
574
569
  homepage: http://github.com/opentox/opentox-ruby
575
570
  licenses: []
576
-
577
571
  post_install_message:
578
572
  rdoc_options: []
579
-
580
- require_paths:
573
+ require_paths:
581
574
  - lib
582
- required_ruby_version: !ruby/object:Gem::Requirement
575
+ required_ruby_version: !ruby/object:Gem::Requirement
583
576
  none: false
584
- requirements:
585
- - - ">="
586
- - !ruby/object:Gem::Version
587
- hash: 3
588
- segments:
589
- - 0
590
- version: "0"
591
- required_rubygems_version: !ruby/object:Gem::Requirement
577
+ requirements:
578
+ - - ! '>='
579
+ - !ruby/object:Gem::Version
580
+ version: '0'
581
+ required_rubygems_version: !ruby/object:Gem::Requirement
592
582
  none: false
593
- requirements:
594
- - - ">="
595
- - !ruby/object:Gem::Version
596
- hash: 3
597
- segments:
598
- - 0
599
- version: "0"
583
+ requirements:
584
+ - - ! '>='
585
+ - !ruby/object:Gem::Version
586
+ version: '0'
600
587
  requirements: []
601
-
602
588
  rubyforge_project:
603
- rubygems_version: 1.5.2
589
+ rubygems_version: 1.8.18
604
590
  signing_key:
605
591
  specification_version: 3
606
592
  summary: Ruby wrapper for the OpenTox REST API
607
593
  test_files: []
608
-