caruby-tissue 1.2.2 → 1.2.3

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Files changed (153) hide show
  1. data/History.txt +4 -0
  2. data/bin/crtdump +11 -3
  3. data/bin/{seed → crtseed} +0 -0
  4. data/conf/annotation/pathology_scg/AdditionalFinding.hbm.xml +19 -0
  5. data/conf/annotation/pathology_scg/BasePathologyAnnotation.hbm.xml +260 -0
  6. data/conf/annotation/pathology_scg/BreastMargin.hbm.xml +21 -0
  7. data/conf/annotation/pathology_scg/BreastMarginInvolved.hbm.xml +15 -0
  8. data/conf/annotation/pathology_scg/BreastMarginUninvolved.hbm.xml +14 -0
  9. data/conf/annotation/pathology_scg/CNSMargin.hbm.xml +19 -0
  10. data/conf/annotation/pathology_scg/CNSMarginLocation.hbm.xml +14 -0
  11. data/conf/annotation/pathology_scg/CarcinomaInSituStatus.hbm.xml +14 -0
  12. data/conf/annotation/pathology_scg/ColorectalLocalExcisionMarginUninvolved.hbm.xml +15 -0
  13. data/conf/annotation/pathology_scg/ColorectalResectedMarginUninvolved.hbm.xml +22 -0
  14. data/conf/annotation/pathology_scg/Cytogenetics.hbm.xml +15 -0
  15. data/conf/annotation/pathology_scg/DeepMelanomaMargin.hbm.xml +16 -0
  16. data/conf/annotation/pathology_scg/Details.hbm.xml +14 -0
  17. data/conf/annotation/pathology_scg/DirectExtensionOfTumor.hbm.xml +14 -0
  18. data/conf/annotation/pathology_scg/DistalMargin.hbm.xml +15 -0
  19. data/conf/annotation/pathology_scg/DistanceFromAnalVerge.hbm.xml +23 -0
  20. data/conf/annotation/pathology_scg/DistantMetastasis.hbm.xml +19 -0
  21. data/conf/annotation/pathology_scg/ExcionalBiopsyMarginUninvolved.hbm.xml +15 -0
  22. data/conf/annotation/pathology_scg/ExcisionalBiopsyColorectalDeepMargin.hbm.xml +15 -0
  23. data/conf/annotation/pathology_scg/ExcisionalBiopsyColorectalLateralOrMucosalMargin.hbm.xml +15 -0
  24. data/conf/annotation/pathology_scg/ExtraprostaticExtension.hbm.xml +20 -0
  25. data/conf/annotation/pathology_scg/ExtraprostaticExtensionTissueSites.hbm.xml +14 -0
  26. data/conf/annotation/pathology_scg/GleasonScore.hbm.xml +16 -0
  27. data/conf/annotation/pathology_scg/HistologicGrade.hbm.xml +16 -0
  28. data/conf/annotation/pathology_scg/HistologicType.hbm.xml +19 -0
  29. data/conf/annotation/pathology_scg/HistologicVariantType.hbm.xml +14 -0
  30. data/conf/annotation/pathology_scg/ImmunoPhenotyping.hbm.xml +16 -0
  31. data/conf/annotation/pathology_scg/Invasion.hbm.xml +16 -0
  32. data/conf/annotation/pathology_scg/KidneyMarginLocation.hbm.xml +15 -0
  33. data/conf/annotation/pathology_scg/KidneyNephrectomyMargin.hbm.xml +19 -0
  34. data/conf/annotation/pathology_scg/LateralMelanomaMargin.hbm.xml +16 -0
  35. data/conf/annotation/pathology_scg/LocalExcisionColorectalDeepMargin.hbm.xml +15 -0
  36. data/conf/annotation/pathology_scg/LocalExcisionColorectalLateralMargin.hbm.xml +20 -0
  37. data/conf/annotation/pathology_scg/LungResectionMargin.hbm.xml +17 -0
  38. data/conf/annotation/pathology_scg/LungResectionMarginsUninvolved.hbm.xml +14 -0
  39. data/conf/annotation/pathology_scg/MacroscopicExtentOfTumor.hbm.xml +14 -0
  40. data/conf/annotation/pathology_scg/MesentricMargin.hbm.xml +15 -0
  41. data/conf/annotation/pathology_scg/MetastasisTissueSite.hbm.xml +15 -0
  42. data/conf/annotation/pathology_scg/Microcalcification.hbm.xml +14 -0
  43. data/conf/annotation/pathology_scg/NottinghamHistologicScore.hbm.xml +17 -0
  44. data/conf/annotation/pathology_scg/OtherResectedOrgans.hbm.xml +15 -0
  45. data/conf/annotation/pathology_scg/PancreasMargin.hbm.xml +20 -0
  46. data/conf/annotation/pathology_scg/PancreasMarginInvolvedByInvasiveCarcinoma.hbm.xml +15 -0
  47. data/conf/annotation/pathology_scg/PancreasMarginUninvolvedByInvasiveCarcinoma.hbm.xml +20 -0
  48. data/conf/annotation/pathology_scg/PathologicalStaging.hbm.xml +16 -0
  49. data/conf/annotation/pathology_scg/PolypConfiguration.hbm.xml +15 -0
  50. data/conf/annotation/pathology_scg/PrimaryTumorStage.hbm.xml +14 -0
  51. data/conf/annotation/pathology_scg/ProstateMarginLocation.hbm.xml +15 -0
  52. data/conf/annotation/pathology_scg/ProximalMargin.hbm.xml +15 -0
  53. data/conf/annotation/pathology_scg/RadialMargin.hbm.xml +15 -0
  54. data/conf/annotation/pathology_scg/RadicalProstatectomyMargin.hbm.xml +20 -0
  55. data/conf/annotation/pathology_scg/RegionalLymphNode.hbm.xml +19 -0
  56. data/conf/annotation/pathology_scg/SatelliteNodule.hbm.xml +14 -0
  57. data/conf/annotation/pathology_scg/SpecimenCollectionGroup.hbm.xml +87 -0
  58. data/conf/annotation/pathology_scg/SpecimenIntegrity.hbm.xml +15 -0
  59. data/conf/annotation/pathology_scg/SpecimenSize.hbm.xml +17 -0
  60. data/conf/annotation/pathology_scg/TissueSide.hbm.xml +14 -0
  61. data/conf/annotation/pathology_scg/TumorSize.hbm.xml +29 -0
  62. data/conf/annotation/pathology_scg/TumorTissueSite.hbm.xml +20 -0
  63. data/conf/annotation/pathology_scg/UninvolvedMelanomaMargin.hbm.xml +15 -0
  64. data/conf/annotation/pathology_specimen/AdditionalFinding.hbm.xml +19 -0
  65. data/conf/annotation/pathology_specimen/AdditionalPathologicFinding.hbm.xml +18 -0
  66. data/conf/annotation/pathology_specimen/Details.hbm.xml +15 -0
  67. data/conf/annotation/pathology_specimen/GleasonScore.hbm.xml +16 -0
  68. data/conf/annotation/pathology_specimen/HistologicGrade.hbm.xml +16 -0
  69. data/conf/annotation/pathology_specimen/HistologicType.hbm.xml +19 -0
  70. data/conf/annotation/pathology_specimen/HistologicVariantType.hbm.xml +14 -0
  71. data/conf/annotation/pathology_specimen/Invasion.hbm.xml +16 -0
  72. data/conf/annotation/pathology_specimen/NottinghamHistologicScore.hbm.xml +17 -0
  73. data/conf/annotation/pathology_specimen/Specimen.hbm.xml +52 -0
  74. data/conf/annotation/pathology_specimen/SpecimenBaseSolidTissuePathologyAnnotation.hbm.xml +73 -0
  75. data/examples/galena/lib/galena/cli/seed.rb +0 -21
  76. data/examples/galena/lib/galena/migration/frozen_shims.rb +6 -5
  77. data/examples/galena/lib/galena/seed/defaults.rb +0 -5
  78. data/{lib → examples/galena/lib}/galena.rb +0 -0
  79. data/lib/catissue/annotation/annotatable.rb +37 -0
  80. data/lib/catissue/annotation/annotatable_class.rb +255 -0
  81. data/lib/catissue/annotation/annotation.rb +49 -0
  82. data/lib/catissue/annotation/annotation_class.rb +277 -0
  83. data/lib/catissue/annotation/annotation_module.rb +77 -0
  84. data/lib/catissue/annotation/hibernate_mapping.rb +46 -0
  85. data/lib/catissue/annotation/proxy.rb +28 -0
  86. data/lib/catissue/annotation/proxy_class.rb +68 -0
  87. data/lib/catissue/cli/migrate.rb +2 -2
  88. data/lib/catissue/cli/smoke.rb +6 -4
  89. data/lib/catissue/database/annotation/annotation_service.rb +75 -61
  90. data/lib/catissue/database/annotation/annotator.rb +17 -76
  91. data/lib/catissue/database/annotation/entity_facade.rb +265 -0
  92. data/lib/catissue/database/annotation/id_generator.rb +62 -0
  93. data/lib/catissue/database/annotation/integration_service.rb +105 -59
  94. data/lib/catissue/database/annotation/reference_writer.rb +150 -0
  95. data/lib/catissue/database/controlled_values.rb +12 -12
  96. data/lib/catissue/database.rb +148 -58
  97. data/lib/catissue/domain/abstract_specimen.rb +40 -14
  98. data/lib/catissue/domain/abstract_specimen_collection_group.rb +1 -3
  99. data/lib/catissue/domain/collection_protocol.rb +13 -5
  100. data/lib/catissue/domain/collection_protocol_event.rb +1 -14
  101. data/lib/catissue/domain/consent_tier_response.rb +2 -0
  102. data/lib/catissue/domain/consent_tier_status.rb +5 -3
  103. data/lib/catissue/domain/container.rb +14 -10
  104. data/lib/catissue/domain/container_position.rb +8 -0
  105. data/lib/catissue/domain/container_type.rb +13 -6
  106. data/lib/catissue/domain/participant.rb +15 -10
  107. data/lib/catissue/domain/site.rb +9 -3
  108. data/lib/catissue/domain/specimen.rb +79 -40
  109. data/lib/catissue/domain/specimen_array.rb +11 -1
  110. data/lib/catissue/domain/specimen_collection_group.rb +79 -41
  111. data/lib/catissue/domain/specimen_event_parameters.rb +5 -8
  112. data/lib/catissue/domain/specimen_position.rb +0 -2
  113. data/lib/catissue/domain/specimen_requirement.rb +1 -1
  114. data/lib/catissue/domain/storage_container.rb +109 -48
  115. data/lib/catissue/domain/storage_type.rb +1 -1
  116. data/lib/catissue/migration/migrator.rb +6 -14
  117. data/lib/catissue/resource.rb +18 -8
  118. data/lib/catissue/util/position.rb +11 -1
  119. data/lib/catissue/util/storable.rb +18 -11
  120. data/lib/catissue/util/storage_type_holder.rb +44 -6
  121. data/lib/catissue/version.rb +1 -1
  122. metadata +86 -35
  123. data/bin/migrate.rb +0 -42
  124. data/bin/seed.rb +0 -43
  125. data/examples/galena/doc/CaTissue/Participant.html +0 -241
  126. data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +0 -190
  127. data/examples/galena/doc/CaTissue/StorageContainer.html +0 -179
  128. data/examples/galena/doc/CaTissue/TissueSpecimen.html +0 -320
  129. data/examples/galena/doc/CaTissue.html +0 -93
  130. data/examples/galena/doc/Galena/Seed/Defaults.html +0 -650
  131. data/examples/galena/doc/Galena/Seed.html +0 -203
  132. data/examples/galena/doc/Galena.html +0 -172
  133. data/examples/galena/doc/_index.html +0 -181
  134. data/examples/galena/doc/class_list.html +0 -36
  135. data/examples/galena/doc/css/common.css +0 -1
  136. data/examples/galena/doc/css/full_list.css +0 -53
  137. data/examples/galena/doc/css/style.css +0 -307
  138. data/examples/galena/doc/file.README.html +0 -153
  139. data/examples/galena/doc/file_list.html +0 -38
  140. data/examples/galena/doc/frames.html +0 -13
  141. data/examples/galena/doc/index.html +0 -153
  142. data/examples/galena/doc/js/app.js +0 -202
  143. data/examples/galena/doc/js/full_list.js +0 -149
  144. data/examples/galena/doc/js/jquery.js +0 -154
  145. data/examples/galena/doc/method_list.html +0 -163
  146. data/examples/galena/doc/top-level-namespace.html +0 -112
  147. data/lib/README.html +0 -33
  148. data/lib/catissue/database/annotation/annotatable_service.rb +0 -25
  149. data/lib/catissue/database/annotation/entity_manager.rb +0 -10
  150. data/lib/galena/cli/seed.rb +0 -43
  151. data/lib/galena/migration/filter_shims.rb +0 -43
  152. data/lib/galena/migration/frozen_shims.rb +0 -53
  153. data/lib/galena/seed/defaults.rb +0 -109
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- Creates the Galena example Defaults singleton and populates the attributes.
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- </p>
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- </div>
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- </div>
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- <div class="tags">
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 34</span>
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-
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- <span class='def def kw'>def</span> <span class='initialize identifier id'>initialize</span>
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- <span class='super super kw'>super</span>
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- <span class='populate identifier id'>populate</span>
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- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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- </div>
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-
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- <div id="instance_attr_details" class="attr_details">
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- <h2>Instance Attribute Details</h2>
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-
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-
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- <span id=""></span>
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- <span id="box_type-instance_method"></span>
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- <div class="method_details first">
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- <p class="signature first" id="box_type-instance_method">
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-
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- - (<tt>Object</tt>) <strong>box_type</strong> <span class="extras">(readonly)</span>
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-
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-
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-
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- </p><div class="docstring">
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- <div class="discussion">
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- <p>
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- Returns the value of attribute box_type
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- </p>
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-
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- </div>
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- </div>
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- <div class="tags">
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-
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- <tr>
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- <td>
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- <pre class="lines">
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- 31
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- 33</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
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-
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- <span class='def def kw'>def</span> <span class='box_type identifier id'>box_type</span>
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- <span class='@box_type ivar id'>@box_type</span>
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- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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-
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- <span id=""></span>
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- <span id="freezer_type-instance_method"></span>
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- <div class="method_details ">
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- <p class="signature " id="freezer_type-instance_method">
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-
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- - (<tt>Object</tt>) <strong>freezer_type</strong> <span class="extras">(readonly)</span>
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-
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-
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- </p><div class="docstring">
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- <div class="discussion">
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- <p>
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- Returns the value of attribute freezer_type
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- </p>
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- </div>
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- </div>
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- <div class="tags">
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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- 31
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- 32
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- 33</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
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-
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- <span class='def def kw'>def</span> <span class='freezer_type identifier id'>freezer_type</span>
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- <span class='@freezer_type ivar id'>@freezer_type</span>
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- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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-
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- <span id=""></span>
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- <span id="hospital-instance_method"></span>
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- <div class="method_details ">
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- <p class="signature " id="hospital-instance_method">
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-
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- - (<tt>Object</tt>) <strong>hospital</strong> <span class="extras">(readonly)</span>
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-
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-
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-
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- </p><div class="docstring">
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- <div class="discussion">
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- <p>
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- Returns the value of attribute hospital
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- </p>
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-
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-
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- </div>
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- </div>
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- <div class="tags">
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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-
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- 31
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- 32
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- 33</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
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-
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- <span class='def def kw'>def</span> <span class='hospital identifier id'>hospital</span>
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- <span class='@hospital ivar id'>@hospital</span>
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- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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-
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- <span id=""></span>
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- <span id="protocol-instance_method"></span>
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- <div class="method_details ">
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- <p class="signature " id="protocol-instance_method">
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-
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- - (<tt>Object</tt>) <strong>protocol</strong> <span class="extras">(readonly)</span>
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-
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-
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-
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- </p><div class="docstring">
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- <div class="discussion">
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- <p>
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- Returns the value of attribute protocol
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- </p>
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- </div>
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- </div>
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- <div class="tags">
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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-
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- 31
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- 32
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- 33</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
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-
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- <span class='def def kw'>def</span> <span class='protocol identifier id'>protocol</span>
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- <span class='@protocol ivar id'>@protocol</span>
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- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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-
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- <span id=""></span>
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- <span id="tissue_bank-instance_method"></span>
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- <div class="method_details ">
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- <p class="signature " id="tissue_bank-instance_method">
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-
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- - (<tt>Object</tt>) <strong>tissue_bank</strong> <span class="extras">(readonly)</span>
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-
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-
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-
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- </p><div class="docstring">
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- <div class="discussion">
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- <p>
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- Returns the value of attribute tissue_bank
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- </p>
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-
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-
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- </div>
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- </div>
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- <div class="tags">
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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-
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- 31
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- 32
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- 33</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
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-
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- <span class='def def kw'>def</span> <span class='tissue_bank identifier id'>tissue_bank</span>
578
- <span class='@tissue_bank ivar id'>@tissue_bank</span>
579
- <span class='end end kw'>end</span>
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- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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- </div>
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-
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-
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- <div id="instance_method_details" class="method_details_list">
590
- <h2>Instance Method Details</h2>
591
-
592
-
593
- <div class="method_details first">
594
- <p class="signature first" id="ensure_exists-instance_method">
595
-
596
- - (<tt>Object</tt>) <strong>ensure_exists</strong>
597
-
598
-
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-
600
- </p><div class="docstring">
601
- <div class="discussion">
602
- <p>
603
- Creates the Galena example administrative objects as necessary.
604
- </p>
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-
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-
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- </div>
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- </div>
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- <div class="tags">
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-
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- </div><table class="source_code">
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- <tr>
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- <td>
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- <pre class="lines">
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-
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-
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- 40
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- 41
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- 42
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- 43
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- 44
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- 45</pre>
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- </td>
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- <td>
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- <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 40</span>
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-
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- <span class='def def kw'>def</span> <span class='ensure_exists identifier id'>ensure_exists</span>
628
- <span class='@protocol ivar id'>@protocol</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
629
- <span class='@hospital ivar id'>@hospital</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
630
- <span class='@surgeon ivar id'>@surgeon</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
631
- <span class='@box ivar id'>@box</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
632
- <span class='end end kw'>end</span>
633
- </pre>
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- </td>
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- </tr>
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- </table>
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- </div>
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-
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- </div>
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-
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- </div>
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-
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- <div id="footer">
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- Generated on Tue Nov 30 11:09:43 2010 by
645
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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- 0.6.1 (ruby-1.8.6).
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- </div>
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- </body>
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- </html>