sequencescape-client-api 0.3.5

Sign up to get free protection for your applications and to get access to all the features.
Files changed (313) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +7 -0
  3. data/.rspec +1 -0
  4. data/.rvmrc +52 -0
  5. data/.yardoc/checksums +96 -0
  6. data/.yardoc/complete +0 -0
  7. data/.yardoc/object_types +0 -0
  8. data/.yardoc/objects/root.dat +0 -0
  9. data/.yardoc/proxy_types +0 -0
  10. data/Gemfile +4 -0
  11. data/README.markdown +4 -0
  12. data/Rakefile +2 -0
  13. data/doc/Array.html +192 -0
  14. data/doc/BaitLibrary.html +139 -0
  15. data/doc/Hash.html +242 -0
  16. data/doc/NilClass.html +214 -0
  17. data/doc/Sequencescape/Api/Actions/ClassActionHelpers.html +213 -0
  18. data/doc/Sequencescape/Api/Actions/InstanceActionHelpers.html +282 -0
  19. data/doc/Sequencescape/Api/Actions.html +197 -0
  20. data/doc/Sequencescape/Api/Associations/Base/InstanceMethods.html +352 -0
  21. data/doc/Sequencescape/Api/Associations/Base.html +237 -0
  22. data/doc/Sequencescape/Api/Associations/BelongsTo/AssociationProxy.html +332 -0
  23. data/doc/Sequencescape/Api/Associations/BelongsTo/CommonBehaviour/LoadHandler.html +279 -0
  24. data/doc/Sequencescape/Api/Associations/BelongsTo/CommonBehaviour.html +432 -0
  25. data/doc/Sequencescape/Api/Associations/BelongsTo/InlineAssociationProxy.html +173 -0
  26. data/doc/Sequencescape/Api/Associations/BelongsTo.html +212 -0
  27. data/doc/Sequencescape/Api/Associations/HasMany/AssociationProxy.html +366 -0
  28. data/doc/Sequencescape/Api/Associations/HasMany/InlineAssociationProxy.html +529 -0
  29. data/doc/Sequencescape/Api/Associations/HasMany/Json.html +250 -0
  30. data/doc/Sequencescape/Api/Associations/HasMany/Validation/CompositeErrors.html +493 -0
  31. data/doc/Sequencescape/Api/Associations/HasMany/Validation.html +245 -0
  32. data/doc/Sequencescape/Api/Associations/HasMany.html +212 -0
  33. data/doc/Sequencescape/Api/Associations/InstanceMethods/CompositeErrors.html +379 -0
  34. data/doc/Sequencescape/Api/Associations/InstanceMethods.html +496 -0
  35. data/doc/Sequencescape/Api/Associations.html +201 -0
  36. data/doc/Sequencescape/Api/BasicErrorHandling.html +371 -0
  37. data/doc/Sequencescape/Api/Composition/Target.html +262 -0
  38. data/doc/Sequencescape/Api/Composition.html +215 -0
  39. data/doc/Sequencescape/Api/ConnectionFactory/Actions.html +611 -0
  40. data/doc/Sequencescape/Api/ConnectionFactory/Helpers.html +233 -0
  41. data/doc/Sequencescape/Api/ConnectionFactory.html +321 -0
  42. data/doc/Sequencescape/Api/ErrorHandling/TurnOffValidationOfUuidOnlyRecords.html +189 -0
  43. data/doc/Sequencescape/Api/ErrorHandling.html +201 -0
  44. data/doc/Sequencescape/Api/FinderMethods/AllHandler.html +279 -0
  45. data/doc/Sequencescape/Api/FinderMethods/Caching.html +183 -0
  46. data/doc/Sequencescape/Api/FinderMethods/Delegation.html +189 -0
  47. data/doc/Sequencescape/Api/FinderMethods/FindByUuidHandler.html +279 -0
  48. data/doc/Sequencescape/Api/FinderMethods.html +364 -0
  49. data/doc/Sequencescape/Api/GeneralError.html +176 -0
  50. data/doc/Sequencescape/Api/JsonError.html +205 -0
  51. data/doc/Sequencescape/Api/ModifyingHandler.html +359 -0
  52. data/doc/Sequencescape/Api/PageOfResults/UpdateHandler.html +279 -0
  53. data/doc/Sequencescape/Api/PageOfResults.html +611 -0
  54. data/doc/Sequencescape/Api/Rails/ApplicationController.html +207 -0
  55. data/doc/Sequencescape/Api/Rails/Resourced.html +269 -0
  56. data/doc/Sequencescape/Api/Rails.html +117 -0
  57. data/doc/Sequencescape/Api/Resource/ActiveModel.html +287 -0
  58. data/doc/Sequencescape/Api/Resource/Attributes/InstanceMethods.html +272 -0
  59. data/doc/Sequencescape/Api/Resource/Attributes.html +199 -0
  60. data/doc/Sequencescape/Api/Resource/Groups/InstanceMethods.html +378 -0
  61. data/doc/Sequencescape/Api/Resource/Groups/Json.html +112 -0
  62. data/doc/Sequencescape/Api/Resource/Groups/Proxy/InstanceMethods.html +256 -0
  63. data/doc/Sequencescape/Api/Resource/Groups/Proxy.html +177 -0
  64. data/doc/Sequencescape/Api/Resource/Groups.html +270 -0
  65. data/doc/Sequencescape/Api/Resource/InstanceMethods.html +344 -0
  66. data/doc/Sequencescape/Api/Resource/Json/ClassMethods.html +243 -0
  67. data/doc/Sequencescape/Api/Resource/Json/CoercionHandler.html +279 -0
  68. data/doc/Sequencescape/Api/Resource/Json.html +405 -0
  69. data/doc/Sequencescape/Api/Resource/Modifications.html +295 -0
  70. data/doc/Sequencescape/Api/Resource.html +436 -0
  71. data/doc/Sequencescape/Api/ResourceInvalid.html +289 -0
  72. data/doc/Sequencescape/Api/ResourceModelProxy.html +444 -0
  73. data/doc/Sequencescape/Api/Version1.html +218 -0
  74. data/doc/Sequencescape/Api/Version2.html +222 -0
  75. data/doc/Sequencescape/Api.html +704 -0
  76. data/doc/Sequencescape/Asset.html +262 -0
  77. data/doc/Sequencescape/AssetAudit.html +258 -0
  78. data/doc/Sequencescape/AssetGroup.html +258 -0
  79. data/doc/Sequencescape/BaitLibraryLayout.html +258 -0
  80. data/doc/Sequencescape/BarcodePrinter.html +258 -0
  81. data/doc/Sequencescape/BarcodedAsset.html +293 -0
  82. data/doc/Sequencescape/Batch.html +327 -0
  83. data/doc/Sequencescape/Behaviour/Barcoded.html +195 -0
  84. data/doc/Sequencescape/Behaviour/Labeled.html +189 -0
  85. data/doc/Sequencescape/Behaviour/Qced/QcFile.html +244 -0
  86. data/doc/Sequencescape/Behaviour/Qced.html +199 -0
  87. data/doc/Sequencescape/Behaviour/Receptacle/Aliquot.html +258 -0
  88. data/doc/Sequencescape/Behaviour/Receptacle.html +195 -0
  89. data/doc/Sequencescape/Behaviour/StateDriven.html +205 -0
  90. data/doc/Sequencescape/Behaviour.html +130 -0
  91. data/doc/Sequencescape/BulkTransfer.html +258 -0
  92. data/doc/Sequencescape/Comment.html +258 -0
  93. data/doc/Sequencescape/Lane.html +282 -0
  94. data/doc/Sequencescape/LibraryEvent.html +258 -0
  95. data/doc/Sequencescape/LibraryTube.html +322 -0
  96. data/doc/Sequencescape/Lot.html +258 -0
  97. data/doc/Sequencescape/LotType/LotCreator.html +182 -0
  98. data/doc/Sequencescape/LotType.html +268 -0
  99. data/doc/Sequencescape/MultiplexedLibraryTube.html +326 -0
  100. data/doc/Sequencescape/Order.html +338 -0
  101. data/doc/Sequencescape/OrderTemplate/OrderCreator.html +182 -0
  102. data/doc/Sequencescape/OrderTemplate.html +268 -0
  103. data/doc/Sequencescape/Pipeline.html +258 -0
  104. data/doc/Sequencescape/Plate/CommentsCreation.html +184 -0
  105. data/doc/Sequencescape/Plate/CurrentVolumeSubstraction.html +236 -0
  106. data/doc/Sequencescape/Plate/Pooling.html +249 -0
  107. data/doc/Sequencescape/Plate/WellStructure.html +313 -0
  108. data/doc/Sequencescape/Plate.html +446 -0
  109. data/doc/Sequencescape/PlateConversion.html +258 -0
  110. data/doc/Sequencescape/PlateCreation.html +258 -0
  111. data/doc/Sequencescape/PlatePurpose/PlateCreation.html +186 -0
  112. data/doc/Sequencescape/PlatePurpose.html +268 -0
  113. data/doc/Sequencescape/PlateTemplate.html +282 -0
  114. data/doc/Sequencescape/PooledPlateCreation.html +258 -0
  115. data/doc/Sequencescape/Project.html +258 -0
  116. data/doc/Sequencescape/QcDecision.html +258 -0
  117. data/doc/Sequencescape/QcFile.html +327 -0
  118. data/doc/Sequencescape/Qcable.html +258 -0
  119. data/doc/Sequencescape/QcableCreator.html +258 -0
  120. data/doc/Sequencescape/Request.html +258 -0
  121. data/doc/Sequencescape/Robot.html +258 -0
  122. data/doc/Sequencescape/Sample.html +258 -0
  123. data/doc/Sequencescape/SampleTube.html +318 -0
  124. data/doc/Sequencescape/Search/BaseHandler.html +234 -0
  125. data/doc/Sequencescape/Search/MultipleResultHandler.html +276 -0
  126. data/doc/Sequencescape/Search/SingleResultHandler.html +303 -0
  127. data/doc/Sequencescape/Search.html +431 -0
  128. data/doc/Sequencescape/SpecificTubeCreation.html +258 -0
  129. data/doc/Sequencescape/Stamp.html +258 -0
  130. data/doc/Sequencescape/StateChange.html +258 -0
  131. data/doc/Sequencescape/Study.html +258 -0
  132. data/doc/Sequencescape/Submission.html +258 -0
  133. data/doc/Sequencescape/SubmissionPool.html +258 -0
  134. data/doc/Sequencescape/Tag/Group.html +219 -0
  135. data/doc/Sequencescape/Tag.html +149 -0
  136. data/doc/Sequencescape/Tag2Layout.html +258 -0
  137. data/doc/Sequencescape/Tag2LayoutTemplate.html +258 -0
  138. data/doc/Sequencescape/TagGroup.html +258 -0
  139. data/doc/Sequencescape/TagLayout.html +258 -0
  140. data/doc/Sequencescape/TagLayoutTemplate.html +258 -0
  141. data/doc/Sequencescape/Template.html +258 -0
  142. data/doc/Sequencescape/Transfer.html +258 -0
  143. data/doc/Sequencescape/TransferTemplate.html +258 -0
  144. data/doc/Sequencescape/Tube.html +319 -0
  145. data/doc/Sequencescape/TubeCreation.html +258 -0
  146. data/doc/Sequencescape/TubeFromTubeCreation.html +258 -0
  147. data/doc/Sequencescape/TubePurpose/TubeCreation.html +186 -0
  148. data/doc/Sequencescape/TubePurpose.html +268 -0
  149. data/doc/Sequencescape/User.html +258 -0
  150. data/doc/Sequencescape/VolumeUpdate.html +258 -0
  151. data/doc/Sequencescape/Well.html +362 -0
  152. data/doc/Sequencescape.html +121 -0
  153. data/doc/_index.html +1248 -0
  154. data/doc/class_list.html +51 -0
  155. data/doc/css/common.css +1 -0
  156. data/doc/css/full_list.css +58 -0
  157. data/doc/css/style.css +481 -0
  158. data/doc/file.README.html +76 -0
  159. data/doc/file_list.html +56 -0
  160. data/doc/frames.html +17 -0
  161. data/doc/index.html +76 -0
  162. data/doc/js/app.js +243 -0
  163. data/doc/js/full_list.js +216 -0
  164. data/doc/js/jquery.js +4 -0
  165. data/doc/method_list.html +1411 -0
  166. data/doc/top-level-namespace.html +114 -0
  167. data/lib/sequencescape/asset.rb +10 -0
  168. data/lib/sequencescape/asset_audit.rb +7 -0
  169. data/lib/sequencescape/asset_group.rb +9 -0
  170. data/lib/sequencescape/bait_library.rb +14 -0
  171. data/lib/sequencescape/bait_library_layout.rb +9 -0
  172. data/lib/sequencescape/barcode_printer.rb +13 -0
  173. data/lib/sequencescape/barcoded_asset.rb +12 -0
  174. data/lib/sequencescape/batch.rb +24 -0
  175. data/lib/sequencescape/behaviour/barcoded.rb +15 -0
  176. data/lib/sequencescape/behaviour/labeled.rb +14 -0
  177. data/lib/sequencescape/behaviour/qced.rb +31 -0
  178. data/lib/sequencescape/behaviour/receptacle.rb +21 -0
  179. data/lib/sequencescape/behaviour/state_driven.rb +19 -0
  180. data/lib/sequencescape/bulk_transfer.rb +8 -0
  181. data/lib/sequencescape/comment.rb +7 -0
  182. data/lib/sequencescape/custom_metadatum_collection.rb +8 -0
  183. data/lib/sequencescape/lane.rb +8 -0
  184. data/lib/sequencescape/library_event.rb +5 -0
  185. data/lib/sequencescape/library_tube.rb +7 -0
  186. data/lib/sequencescape/locale/en.yml +190 -0
  187. data/lib/sequencescape/lot.rb +11 -0
  188. data/lib/sequencescape/lot_type.rb +20 -0
  189. data/lib/sequencescape/multiplexed_library_tube.rb +6 -0
  190. data/lib/sequencescape/order.rb +13 -0
  191. data/lib/sequencescape/order_template.rb +19 -0
  192. data/lib/sequencescape/pipeline.rb +10 -0
  193. data/lib/sequencescape/plate/pooling.rb +23 -0
  194. data/lib/sequencescape/plate/well_structure.rb +27 -0
  195. data/lib/sequencescape/plate.rb +71 -0
  196. data/lib/sequencescape/plate_conversion.rb +8 -0
  197. data/lib/sequencescape/plate_creation.rb +8 -0
  198. data/lib/sequencescape/plate_purpose.rb +24 -0
  199. data/lib/sequencescape/plate_template.rb +13 -0
  200. data/lib/sequencescape/pooled_plate_creation.rb +8 -0
  201. data/lib/sequencescape/project.rb +11 -0
  202. data/lib/sequencescape/qc_decision.rb +9 -0
  203. data/lib/sequencescape/qc_file.rb +14 -0
  204. data/lib/sequencescape/qcable.rb +17 -0
  205. data/lib/sequencescape/qcable_creator.rb +13 -0
  206. data/lib/sequencescape/request.rb +16 -0
  207. data/lib/sequencescape/robot.rb +5 -0
  208. data/lib/sequencescape/sample.rb +51 -0
  209. data/lib/sequencescape/sample_tube.rb +7 -0
  210. data/lib/sequencescape/search.rb +80 -0
  211. data/lib/sequencescape/specific_tube_creation.rb +8 -0
  212. data/lib/sequencescape/stamp.rb +9 -0
  213. data/lib/sequencescape/state_change.rb +11 -0
  214. data/lib/sequencescape/study.rb +14 -0
  215. data/lib/sequencescape/submission.rb +16 -0
  216. data/lib/sequencescape/submission_pool.rb +7 -0
  217. data/lib/sequencescape/tag.rb +14 -0
  218. data/lib/sequencescape/tag2_layout.rb +10 -0
  219. data/lib/sequencescape/tag2_layout_template.rb +9 -0
  220. data/lib/sequencescape/tag_group.rb +4 -0
  221. data/lib/sequencescape/tag_layout.rb +10 -0
  222. data/lib/sequencescape/tag_layout_template.rb +15 -0
  223. data/lib/sequencescape/template.rb +6 -0
  224. data/lib/sequencescape/transfer.rb +9 -0
  225. data/lib/sequencescape/transfer_request.rb +12 -0
  226. data/lib/sequencescape/transfer_request_collection.rb +8 -0
  227. data/lib/sequencescape/transfer_template.rb +9 -0
  228. data/lib/sequencescape/tube.rb +26 -0
  229. data/lib/sequencescape/tube_creation.rb +8 -0
  230. data/lib/sequencescape/tube_from_tube_creation.rb +8 -0
  231. data/lib/sequencescape/tube_purpose.rb +24 -0
  232. data/lib/sequencescape/user.rb +13 -0
  233. data/lib/sequencescape/volume_update.rb +6 -0
  234. data/lib/sequencescape/well.rb +19 -0
  235. data/lib/sequencescape/work_completion.rb +10 -0
  236. data/lib/sequencescape-api/actions.rb +69 -0
  237. data/lib/sequencescape-api/associations/base/instance_methods.rb +57 -0
  238. data/lib/sequencescape-api/associations/base.rb +15 -0
  239. data/lib/sequencescape-api/associations/belongs_to.rb +127 -0
  240. data/lib/sequencescape-api/associations/has_many/json.rb +10 -0
  241. data/lib/sequencescape-api/associations/has_many/validation.rb +37 -0
  242. data/lib/sequencescape-api/associations/has_many.rb +123 -0
  243. data/lib/sequencescape-api/associations.rb +112 -0
  244. data/lib/sequencescape-api/capabilities.rb +11 -0
  245. data/lib/sequencescape-api/composition.rb +37 -0
  246. data/lib/sequencescape-api/connection_factory/actions.rb +154 -0
  247. data/lib/sequencescape-api/connection_factory/helpers.rb +9 -0
  248. data/lib/sequencescape-api/connection_factory.rb +40 -0
  249. data/lib/sequencescape-api/core.rb +63 -0
  250. data/lib/sequencescape-api/core_ext/array.rb +7 -0
  251. data/lib/sequencescape-api/core_ext/hash.rb +18 -0
  252. data/lib/sequencescape-api/core_ext.rb +2 -0
  253. data/lib/sequencescape-api/error_handling.rb +42 -0
  254. data/lib/sequencescape-api/errors.rb +38 -0
  255. data/lib/sequencescape-api/finder_methods.rb +184 -0
  256. data/lib/sequencescape-api/locale/en.yml +7 -0
  257. data/lib/sequencescape-api/rails.rb +88 -0
  258. data/lib/sequencescape-api/resource/active_model.rb +17 -0
  259. data/lib/sequencescape-api/resource/attribute_groups.rb +94 -0
  260. data/lib/sequencescape-api/resource/attributes.rb +87 -0
  261. data/lib/sequencescape-api/resource/instance_methods.rb +24 -0
  262. data/lib/sequencescape-api/resource/json.rb +114 -0
  263. data/lib/sequencescape-api/resource/modifications.rb +111 -0
  264. data/lib/sequencescape-api/resource.rb +47 -0
  265. data/lib/sequencescape-api/resource_model_proxy.rb +44 -0
  266. data/lib/sequencescape-api/version.rb +5 -0
  267. data/lib/sequencescape-api.rb +16 -0
  268. data/lib/sequencescape.rb +81 -0
  269. data/sequencescape-api.gemspec +32 -0
  270. data/spec/sequencescape-api/associations_spec.rb +95 -0
  271. data/spec/sequencescape-api/contracts/belongs-to-association.txt +14 -0
  272. data/spec/sequencescape-api/contracts/client-fails-authentication.txt +6 -0
  273. data/spec/sequencescape-api/contracts/create-invalid-resource.txt +10 -0
  274. data/spec/sequencescape-api/contracts/create-model-c-has-many-inline-nested.txt +10 -0
  275. data/spec/sequencescape-api/contracts/create-model-c-has-many-inline.txt +10 -0
  276. data/spec/sequencescape-api/contracts/create-model-c-has-many.txt +10 -0
  277. data/spec/sequencescape-api/contracts/create-model-c.txt +11 -0
  278. data/spec/sequencescape-api/contracts/create-via-has-many.txt +9 -0
  279. data/spec/sequencescape-api/contracts/model-a-instance.txt +21 -0
  280. data/spec/sequencescape-api/contracts/model-b-instance.txt +38 -0
  281. data/spec/sequencescape-api/contracts/model-c-instance-created.txt +17 -0
  282. data/spec/sequencescape-api/contracts/model-c-instance-updated.txt +17 -0
  283. data/spec/sequencescape-api/contracts/model-c-instance.txt +28 -0
  284. data/spec/sequencescape-api/contracts/model-c-invalid-attribute.txt +8 -0
  285. data/spec/sequencescape-api/contracts/resource-not-found.txt +6 -0
  286. data/spec/sequencescape-api/contracts/results-page-1.txt +17 -0
  287. data/spec/sequencescape-api/contracts/results-page-2.txt +18 -0
  288. data/spec/sequencescape-api/contracts/results-page-3.txt +17 -0
  289. data/spec/sequencescape-api/contracts/retrieve-belongs-to-association.txt +3 -0
  290. data/spec/sequencescape-api/contracts/retrieve-model.txt +4 -0
  291. data/spec/sequencescape-api/contracts/retrieve-results-page-1.txt +3 -0
  292. data/spec/sequencescape-api/contracts/retrieve-results-page-2.txt +3 -0
  293. data/spec/sequencescape-api/contracts/retrieve-results-page-3.txt +3 -0
  294. data/spec/sequencescape-api/contracts/retrieve-root-with-an-authorised-client.txt +5 -0
  295. data/spec/sequencescape-api/contracts/retrieve-root-with-an-unauthorised-client.txt +4 -0
  296. data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-a-list.txt +4 -0
  297. data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-b-list.txt +4 -0
  298. data/spec/sequencescape-api/contracts/retrieve-unauthorised-model-c-list.txt +4 -0
  299. data/spec/sequencescape-api/contracts/root-response-for-authorised-client.txt +20 -0
  300. data/spec/sequencescape-api/contracts/root-response-for-unauthorised-client.txt +28 -0
  301. data/spec/sequencescape-api/contracts/unauthorised-model-a-list.txt +15 -0
  302. data/spec/sequencescape-api/contracts/unauthorised-model-b-list.txt +14 -0
  303. data/spec/sequencescape-api/contracts/unauthorised-model-c-list.txt +15 -0
  304. data/spec/sequencescape-api/contracts/update-invalid-resource.txt +10 -0
  305. data/spec/sequencescape-api/contracts/update-model-c.txt +11 -0
  306. data/spec/sequencescape-api/finding_methods_spec.rb +34 -0
  307. data/spec/sequencescape-api/modifications_spec.rb +169 -0
  308. data/spec/sequencescape-api/root_spec.rb +58 -0
  309. data/spec/spec_helper.rb +13 -0
  310. data/spec/support/contract_helper.rb +112 -0
  311. data/spec/support/namespaces.rb +67 -0
  312. data/spec/support/shared_examples.rb +12 -0
  313. metadata +540 -0
@@ -0,0 +1,114 @@
1
+ <!DOCTYPE html>
2
+ <html>
3
+ <head>
4
+ <meta charset="utf-8">
5
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
6
+ <title>
7
+ Top Level Namespace
8
+
9
+ &mdash; Documentation by YARD 0.9.5
10
+
11
+ </title>
12
+
13
+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
14
+
15
+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
16
+
17
+ <script type="text/javascript" charset="utf-8">
18
+ pathId = "";
19
+ relpath = '';
20
+ </script>
21
+
22
+
23
+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
24
+
25
+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
26
+
27
+
28
+ </head>
29
+ <body>
30
+ <div class="nav_wrap">
31
+ <iframe id="nav" src="class_list.html"></iframe>
32
+ <div id="resizer"></div>
33
+ </div>
34
+
35
+ <div id="main" tabindex="-1">
36
+ <div id="header">
37
+ <div id="menu">
38
+
39
+ <a href="_index.html">Index</a> &raquo;
40
+
41
+
42
+ <span class="title">Top Level Namespace</span>
43
+
44
+ </div>
45
+
46
+ <div id="search">
47
+
48
+ <a class="full_list_link" id="class_list_link"
49
+ href="class_list.html">
50
+
51
+ <svg width="24" height="24">
52
+ <rect x="0" y="4" width="24" height="4" rx="1" ry="1"></rect>
53
+ <rect x="0" y="12" width="24" height="4" rx="1" ry="1"></rect>
54
+ <rect x="0" y="20" width="24" height="4" rx="1" ry="1"></rect>
55
+ </svg>
56
+ </a>
57
+
58
+ </div>
59
+ <div class="clear"></div>
60
+ </div>
61
+
62
+ <iframe id="search_frame" src="class_list.html"></iframe>
63
+
64
+ <div id="content"><h1>Top Level Namespace
65
+
66
+
67
+
68
+ </h1>
69
+ <div class="box_info">
70
+
71
+
72
+
73
+
74
+
75
+
76
+
77
+
78
+
79
+
80
+
81
+ </div>
82
+
83
+ <h2>Defined Under Namespace</h2>
84
+ <p class="children">
85
+
86
+
87
+ <strong class="modules">Modules:</strong> <span class='object_link'><a href="Sequencescape.html" title="Sequencescape (module)">Sequencescape</a></span>
88
+
89
+
90
+
91
+ <strong class="classes">Classes:</strong> <span class='object_link'><a href="Array.html" title="Array (class)">Array</a></span>, <span class='object_link'><a href="BaitLibrary.html" title="BaitLibrary (class)">BaitLibrary</a></span>, <span class='object_link'><a href="Hash.html" title="Hash (class)">Hash</a></span>, <span class='object_link'><a href="NilClass.html" title="NilClass (class)">NilClass</a></span>
92
+
93
+
94
+ </p>
95
+
96
+
97
+
98
+
99
+
100
+
101
+
102
+
103
+
104
+ </div>
105
+
106
+ <div id="footer">
107
+ Generated on Wed Nov 16 16:31:13 2016 by
108
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
109
+ 0.9.5 (ruby-2.3.0).
110
+ </div>
111
+
112
+ </div>
113
+ </body>
114
+ </html>
@@ -0,0 +1,10 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::Asset < ::Sequencescape::Api::Resource
4
+ attribute_accessor :name
5
+ attribute_accessor :qc_state
6
+
7
+ # TODO: This is a hack for the warehouse that should be removed! The type is always known by the application
8
+ # that is using an asset (actually it comes from request JSON) so it's pointless this being here!
9
+ attribute_accessor :type
10
+ end
@@ -0,0 +1,7 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::AssetAudit < ::Sequencescape::Api::Resource
4
+ belongs_to :asset
5
+
6
+ attribute_accessor :message, :key, :created_by, :asset, :witnessed_by
7
+ end
@@ -0,0 +1,9 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::AssetGroup < ::Sequencescape::Api::Resource
4
+ belongs_to :submission
5
+ belongs_to :study
6
+ has_many :assets
7
+
8
+ attribute_accessor :name
9
+ end
@@ -0,0 +1,14 @@
1
+ class BaitLibrary
2
+ include Sequencescape::Api::Composition::Target
3
+
4
+ attribute_accessor :name
5
+ attribute_accessor :created_at, :updated_at, :conversion => :to_time
6
+
7
+ attribute_group :supplier do
8
+ attribute_accessor :name, :identifier
9
+ end
10
+
11
+ attribute_group :target do
12
+ attribute_accessor :species
13
+ end
14
+ end
@@ -0,0 +1,9 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::BaitLibraryLayout < ::Sequencescape::Api::Resource
4
+ belongs_to :user
5
+ belongs_to :plate, :class_name => 'Plate'
6
+ attribute_reader :layout
7
+
8
+ has_class_create_action(:preview!, :action => :preview)
9
+ end
@@ -0,0 +1,13 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::BarcodePrinter < Sequencescape::Api::Resource
4
+ attribute_reader :name, :active
5
+
6
+ attribute_group :service do
7
+ attribute_reader :url
8
+ end
9
+
10
+ attribute_group :type do
11
+ attribute_reader :name, :layout
12
+ end
13
+ end
@@ -0,0 +1,12 @@
1
+ require 'sequencescape-api/resource'
2
+ require 'sequencescape/asset'
3
+
4
+ class Sequencescape::BarcodedAsset < ::Sequencescape::Asset
5
+ require 'sequencescape/behaviour/barcoded'
6
+ require 'sequencescape/behaviour/qced'
7
+ # Used in transfer to make barcodes easily retrieveable
8
+ include Sequencescape::Behaviour::Barcoded
9
+ include Sequencescape::Behaviour::Qced
10
+
11
+ belongs_to :stock_plate, :class_name => 'Plate'
12
+ end
@@ -0,0 +1,24 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::Batch < ::Sequencescape::Api::Resource
4
+ belongs_to :pipeline
5
+ has_many :requests, :disposition => :inline
6
+ composed_of :user
7
+
8
+ has_update_action :start!, :action => 'start'
9
+ has_update_action :complete!, :action => 'complete'
10
+ has_update_action :release!, :action => 'release'
11
+
12
+ attribute_accessor :state, :production_state, :qc_state, :barcode
13
+
14
+ def self.state_method(name)
15
+ class_eval(%Q{def #{name}? ; state == #{name.to_s.inspect} ; end})
16
+ end
17
+
18
+ state_method(:pending)
19
+ state_method(:started)
20
+ state_method(:completed)
21
+ state_method(:released)
22
+
23
+ validates_presence_of :requests, :allow_blank => false
24
+ end
@@ -0,0 +1,15 @@
1
+ # Anything that can have a barcode is considered to be barcoded!
2
+ module Sequencescape::Behaviour
3
+ module Barcoded
4
+ def self.included(base)
5
+ base.class_eval do
6
+ attribute_group :barcode do
7
+ attribute_accessor :prefix, :number # The pieces that make up a barcode
8
+ attribute_accessor :ean13 # The EAN13 barcode number
9
+ attribute_accessor :two_dimensional # The 2D barcode
10
+ attribute_accessor :type # The type of barcode (or rather barcode printer)
11
+ end
12
+ end
13
+ end
14
+ end
15
+ end
@@ -0,0 +1,14 @@
1
+ # Prefix depends on the submission template used and sumarises the order.
2
+ # Text at the moment is a bit redundant, being the purpose name. However
3
+ # it makes things much easier for cases where we are hashing our objects manually
4
+ module Sequencescape::Behaviour
5
+ module Labeled
6
+ def self.included(base)
7
+ base.class_eval do
8
+ attribute_group :label do
9
+ attribute_accessor :prefix, :text
10
+ end
11
+ end
12
+ end
13
+ end
14
+ end
@@ -0,0 +1,31 @@
1
+ module Sequencescape::Behaviour
2
+ module Qced
3
+
4
+ module QcFile
5
+ def create!(attributes = nil)
6
+ attributes ||= {}
7
+
8
+ new({}, false).tap do |qc_file|
9
+ api.create(actions.create, { 'qc_file' => attributes }, Sequencescape::Api::ModifyingHandler.new(qc_file))
10
+ end
11
+ end
12
+
13
+ def create_from_file!(file, filename)
14
+ attributes ||= {}
15
+
16
+ new({}, false).tap do |qc_file|
17
+ api.create_from_file(actions.create, file, filename, 'sequencescape/qc_file', Sequencescape::Api::ModifyingHandler.new(qc_file))
18
+ end
19
+ end
20
+ end
21
+
22
+ def self.included(base)
23
+ base.class_eval do
24
+ has_many :qc_files do
25
+ include Sequencescape::Behaviour::Qced::QcFile
26
+ end
27
+ end
28
+ end
29
+
30
+ end
31
+ end
@@ -0,0 +1,21 @@
1
+ require 'sequencescape/tag'
2
+ require 'sequencescape/bait_library'
3
+
4
+ module Sequencescape::Behaviour
5
+ module Receptacle
6
+ class Aliquot < Sequencescape::Api::Resource
7
+ belongs_to :sample, :disposition => :inline
8
+ composed_of :tag
9
+ composed_of :tag2, :class_name => 'Tag'
10
+ composed_of :bait_library
11
+
12
+ attribute_accessor :suboptimal
13
+ end
14
+
15
+ def self.included(base)
16
+ base.class_eval do
17
+ has_many :aliquots, :disposition => :inline, :class_name => 'Behaviours::Receptacle::Aliquot'
18
+ end
19
+ end
20
+ end
21
+ end
@@ -0,0 +1,19 @@
1
+ module Sequencescape::Behaviour
2
+ module StateDriven
3
+ def self.included(base)
4
+ base.class_eval do
5
+ attribute_reader :state
6
+
7
+ # Define a few default states
8
+ [ :pending, :started, :passed, :failed, :cancelled, :unknown, :qc_complete ].each do |state|
9
+ line = __LINE__ + 1
10
+ class_eval(%Q{
11
+ def #{state}?
12
+ state == #{state.to_s.inspect}
13
+ end
14
+ }, __FILE__, line)
15
+ end
16
+ end
17
+ end
18
+ end
19
+ end
@@ -0,0 +1,8 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::BulkTransfer < ::Sequencescape::Api::Resource
4
+ belongs_to :user
5
+ has_many :transfers, :class_name => 'Transfer'
6
+
7
+ attribute_accessor :well_transfers
8
+ end
@@ -0,0 +1,7 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::Comment < ::Sequencescape::Api::Resource
4
+
5
+ attribute_accessor :description, :title
6
+
7
+ end
@@ -0,0 +1,8 @@
1
+ require 'sequencescape-api/resource'
2
+
3
+ class Sequencescape::CustomMetadatumCollection < Sequencescape::Api::Resource
4
+ belongs_to :asset
5
+ belongs_to :user
6
+
7
+ attribute_accessor :metadata
8
+ end
@@ -0,0 +1,8 @@
1
+ require 'sequencescape/asset'
2
+ require 'sequencescape/behaviour/receptacle'
3
+
4
+ class Sequencescape::Lane < ::Sequencescape::Asset
5
+ include Sequencescape::Behaviour::Receptacle
6
+
7
+ attribute_accessor :external_release
8
+ end
@@ -0,0 +1,5 @@
1
+ class Sequencescape::LibraryEvent < ::Sequencescape::Api::Resource
2
+ belongs_to :user
3
+ belongs_to :seed, :class_name => 'Plate'
4
+ attribute_accessor :event_type
5
+ end
@@ -0,0 +1,7 @@
1
+ require 'sequencescape/tube'
2
+
3
+ class Sequencescape::LibraryTube < ::Sequencescape::Tube
4
+ has_many :requests
5
+ belongs_to :source_request, :class_name => 'Sequencescape::Request'
6
+ belongs_to :custom_metadatum_collection
7
+ end
@@ -0,0 +1,190 @@
1
+ en:
2
+ activemodel:
3
+ models:
4
+ sequencescape:
5
+ asset: "Asset"
6
+ asset_group: "Asset group"
7
+ batch: "Batch"
8
+ library_tube: "Library tube"
9
+ pipeline: "Pipeline"
10
+ plate: "Plate"
11
+ plate_purpose: "Plate purpose"
12
+ project: "Project"
13
+ sample: "Sample"
14
+ sample_tube: "Sample tube"
15
+ study: "Study"
16
+ submission: "Submission"
17
+ submission_template: "Submission template"
18
+ well: "Well"
19
+
20
+ attributes:
21
+ sequencescape:
22
+ asset: &asset
23
+ name: "Name"
24
+ qc_state: "QC state"
25
+ barcode_prefix: "Barcode prefix"
26
+ barcode: "Barcode"
27
+ two_dimensional_barcode: "2D Barcode"
28
+
29
+ request:
30
+ request_options: &request_options
31
+ read_length: "Read length"
32
+ library_type: "Library type"
33
+ fragment_size_required:
34
+ from: "Fragment size (from)"
35
+ to: "Fragment size (to)"
36
+
37
+ asset_group:
38
+ name: "Name"
39
+ study:
40
+ name: "Study name"
41
+
42
+ batch:
43
+ state: "State"
44
+ production_state: "Production state"
45
+ qc_state: "QC state"
46
+ barcode: "Barcode"
47
+ requests: "Requests"
48
+ user:
49
+ login: "User login"
50
+
51
+ library_tube:
52
+ <<: *asset
53
+ closed: "Closed"
54
+ concentration: "Concentration"
55
+ volume: "Volume"
56
+ scanned_in_date: "Date scanned into the lab"
57
+
58
+ sample:
59
+ name: "Sample name"
60
+
61
+ source_request:
62
+ <<: *request_options
63
+
64
+ tag:
65
+ uuid: "UUID"
66
+ expected_sequence: "Expected sequence"
67
+
68
+ group:
69
+ uuid: "UUID"
70
+ name: "Name"
71
+
72
+ pipeline:
73
+ name: "Name"
74
+
75
+ plate:
76
+ <<: *asset
77
+ size: "Size"
78
+ wells: "Wells"
79
+
80
+ plate_purpose:
81
+ name: "Plate purpose name"
82
+
83
+ plate_purpose:
84
+ name: "Name"
85
+
86
+ project:
87
+ name: "Name"
88
+ approved: "Approval status"
89
+ state: "State"
90
+
91
+ project_manager: "Project manager"
92
+ cost_code: "Cost code"
93
+ funding_comments: "Funding comments"
94
+ collaborators: "Collaborators"
95
+ external_funding_source: "External funding source"
96
+ budget_division: "Budget division"
97
+ budget_cost_centre: "Budget cost centre"
98
+ funding_model: "Funding model"
99
+
100
+ roles: "Roles"
101
+
102
+ sample:
103
+ name: "Name"
104
+ sanger_id: "Sanger sample identifier"
105
+ control: "Control sample"
106
+
107
+ organism: "Organism"
108
+ cohort: "Cohort"
109
+ country_of_origin: "Country of origin"
110
+ geographical_region: "Geographical region"
111
+ ethnicity: "Ethnicity"
112
+ volume: "Volume"
113
+ supplier_plate_id: "Supplier plate identifier"
114
+ mother: "Mother"
115
+ father: "Father"
116
+ replicate: "Replicate"
117
+ gc_content: "GC content level"
118
+ gender: "Gender"
119
+ dna_source: "DNA source"
120
+ public_name: "Public name"
121
+ common_name: "Common name"
122
+ strain_att: "Strain"
123
+ taxon_id: "Taxon identifier"
124
+ ebi_accession_number: "ENA accession number"
125
+ description: "Description"
126
+ sra_hold: "Sample visibility"
127
+ reference_genome: "Reference genome"
128
+
129
+ sample_tube:
130
+ <<: *asset
131
+ closed: "Closed"
132
+ concentration: "Concentration"
133
+ volume: "Volume"
134
+ scanned_in_date: "Date scanned into lab"
135
+
136
+ sample:
137
+ name: "Sample name"
138
+
139
+ study:
140
+ name: "Name"
141
+ ethically_approved: "Ethical approval status"
142
+ state: "State"
143
+ abbreviation: "Abbreviation"
144
+
145
+ type: "Type of study"
146
+ sac_sponsor: "Faculty sponsor"
147
+ reference_genome: "Reference genome"
148
+ accession_number: "ENA accession number"
149
+ description: "Description"
150
+ abstract: "Abstract"
151
+
152
+ contaminated_human_dna: "Contaminated with human DNA"
153
+ contains_human_dna: "Contains human DNA"
154
+ data_release_sort_of_study: "Type of study"
155
+ data_release_strategy: "Release strategy"
156
+
157
+ submission:
158
+ state: "State"
159
+
160
+ # TODO: Wonder how you can deal with nesting of 'name' in these
161
+ study: "Study"
162
+ project: "Project"
163
+ asset_group: "Asset group"
164
+
165
+ assets: "Asset UUIDs"
166
+
167
+ request_types: "Request types"
168
+
169
+ request_options:
170
+ <<: *request_options
171
+ number_of_lanes: "Number of lanes"
172
+
173
+ submission_template:
174
+ name: "Name"
175
+
176
+ well:
177
+ location: "Location on plate"
178
+
179
+ errors:
180
+ models:
181
+ sequencescape:
182
+ request:
183
+ attributes:
184
+ state:
185
+ inclusion: "is not a valid state"
186
+
187
+ study:
188
+ attributes:
189
+ name:
190
+ blank: "can't be blank"