caruby-tissue 1.2.1 → 1.2.2

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Files changed (64) hide show
  1. data/History.txt +4 -0
  2. data/LICENSE +1 -1
  3. data/README.md +79 -30
  4. data/bin/crtmigrate +2 -2
  5. data/{examples/galena/bin → bin}/migrate.rb +0 -0
  6. data/bin/seed +26 -0
  7. data/bin/seed.rb +43 -0
  8. data/conf/extract/simple_fields.yaml +4 -0
  9. data/conf/migration/filter_fields.yaml +7 -0
  10. data/{examples/galena/conf → conf}/migration/filter_migration.yaml +0 -0
  11. data/conf/migration/frozen_fields.yaml +11 -0
  12. data/{examples/galena/conf → conf}/migration/frozen_migration.yaml +0 -0
  13. data/conf/migration/general_fields.yaml +44 -0
  14. data/{examples/galena/conf → conf}/migration/general_migration.yaml +0 -0
  15. data/conf/migration/simple_fields.yaml +30 -0
  16. data/{examples/galena/conf → conf}/migration/simple_migration.yaml +0 -0
  17. data/{examples/galena/conf → conf}/migration/small_fields.yaml +0 -0
  18. data/{examples/galena/conf → conf}/migration/small_migration.yaml +0 -0
  19. data/examples/galena/README.md +46 -6
  20. data/examples/galena/bin/seed +26 -0
  21. data/examples/galena/conf/migration/frozen_fields.yaml +1 -0
  22. data/examples/galena/conf/migration/general_fields.yaml +2 -0
  23. data/examples/galena/data/filter.csv +1 -1
  24. data/examples/galena/data/frozen.csv +1 -1
  25. data/examples/galena/data/general.csv +1 -1
  26. data/examples/galena/doc/CaTissue.html +2 -2
  27. data/examples/galena/doc/CaTissue/Participant.html +1 -1
  28. data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +1 -1
  29. data/examples/galena/doc/CaTissue/StorageContainer.html +6 -6
  30. data/examples/galena/doc/CaTissue/TissueSpecimen.html +1 -1
  31. data/examples/galena/doc/Galena.html +4 -122
  32. data/examples/galena/doc/Galena/Seed.html +1 -1
  33. data/examples/galena/doc/Galena/Seed/Defaults.html +28 -24
  34. data/examples/galena/doc/_index.html +1 -8
  35. data/examples/galena/doc/class_list.html +1 -1
  36. data/examples/galena/doc/file.README.html +52 -7
  37. data/examples/galena/doc/index.html +52 -7
  38. data/examples/galena/doc/method_list.html +9 -25
  39. data/examples/galena/doc/top-level-namespace.html +1 -1
  40. data/examples/galena/lib/galena/migration/frozen_shims.rb +4 -15
  41. data/examples/galena/lib/galena/seed/defaults.rb +16 -4
  42. data/{examples/galena/lib → lib}/README.html +0 -0
  43. data/lib/catissue/cli/command.rb +6 -9
  44. data/lib/catissue/cli/migrate.rb +11 -10
  45. data/lib/catissue/cli/smoke.rb +5 -5
  46. data/lib/catissue/database.rb +31 -8
  47. data/lib/catissue/domain/abstract_specimen.rb +1 -1
  48. data/lib/catissue/domain/collection_protocol.rb +29 -13
  49. data/lib/catissue/domain/participant_medical_identifier.rb +1 -1
  50. data/lib/catissue/domain/site.rb +3 -0
  51. data/lib/catissue/domain/specimen.rb +17 -14
  52. data/lib/catissue/domain/specimen_collection_group.rb +2 -5
  53. data/lib/catissue/extract/delta.rb +2 -6
  54. data/lib/catissue/migration/migrator.rb +6 -0
  55. data/lib/catissue/resource.rb +5 -2
  56. data/lib/catissue/util/log.rb +3 -3
  57. data/lib/catissue/version.rb +1 -1
  58. data/{examples/galena/lib → lib}/galena.rb +0 -0
  59. data/{examples/galena/bin → lib/galena/cli}/seed.rb +1 -1
  60. data/lib/galena/migration/filter_shims.rb +43 -0
  61. data/lib/galena/migration/frozen_shims.rb +53 -0
  62. data/lib/galena/seed/defaults.rb +109 -0
  63. metadata +27 -17
  64. data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html +0 -181
metadata CHANGED
@@ -10,33 +10,40 @@ executables:
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  - crtsmoke
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  version: !ruby/object:Gem::Version
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  prerelease: false
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- version: 1.2.1
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+ version: 1.2.2
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  segments:
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  - 1
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  - 2
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- - 1
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+ - 2
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  post_install_message:
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- date: 2010-09-30 07:00:00 +00:00
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+ date: 2010-11-30 08:00:00 +00:00
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  files:
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  - bin/crtdump
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  - bin/crtexample
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  - bin/crtextract
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  - bin/crtmigrate
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  - bin/crtsmoke
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+ - bin/migrate.rb
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+ - bin/seed
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+ - bin/seed.rb
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+ - conf/extract/simple_fields.yaml
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+ - conf/migration/filter_fields.yaml
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+ - conf/migration/filter_migration.yaml
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+ - conf/migration/frozen_fields.yaml
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+ - conf/migration/frozen_migration.yaml
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+ - conf/migration/general_fields.yaml
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+ - conf/migration/general_migration.yaml
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+ - conf/migration/simple_fields.yaml
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+ - conf/migration/simple_migration.yaml
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+ - conf/migration/small_fields.yaml
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+ - conf/migration/small_migration.yaml
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  - examples/galena/README.md
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- - examples/galena/bin/migrate.rb
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- - examples/galena/bin/seed.rb
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+ - examples/galena/bin/seed
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  - examples/galena/conf/extract/simple_fields.yaml
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  - examples/galena/conf/migration/filter_fields.yaml
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- - examples/galena/conf/migration/filter_migration.yaml
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  - examples/galena/conf/migration/frozen_fields.yaml
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- - examples/galena/conf/migration/frozen_migration.yaml
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  - examples/galena/conf/migration/general_fields.yaml
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- - examples/galena/conf/migration/general_migration.yaml
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  - examples/galena/conf/migration/simple_fields.yaml
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- - examples/galena/conf/migration/simple_migration.yaml
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- - examples/galena/conf/migration/small_fields.yaml
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- - examples/galena/conf/migration/small_migration.yaml
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  - examples/galena/data/filter.csv
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  - examples/galena/data/frozen.csv
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  - examples/galena/data/general.csv
@@ -53,7 +60,6 @@ files:
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  - examples/galena/doc/index.html
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  - examples/galena/doc/method_list.html
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  - examples/galena/doc/top-level-namespace.html
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- - examples/galena/doc/CaTissue/CollectionProtocolRegistration.html
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  - examples/galena/doc/CaTissue/Participant.html
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  - examples/galena/doc/CaTissue/SpecimenCollectionGroup.html
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  - examples/galena/doc/CaTissue/StorageContainer.html
@@ -66,13 +72,13 @@ files:
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  - examples/galena/doc/js/app.js
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  - examples/galena/doc/js/full_list.js
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  - examples/galena/doc/js/jquery.js
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- - examples/galena/lib/galena.rb
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- - examples/galena/lib/README.html
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  - examples/galena/lib/galena/cli/seed.rb
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  - examples/galena/lib/galena/migration/filter_shims.rb
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  - examples/galena/lib/galena/migration/frozen_shims.rb
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  - examples/galena/lib/galena/seed/defaults.rb
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  - lib/catissue.rb
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+ - lib/galena.rb
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+ - lib/README.html
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  - lib/catissue/database.rb
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  - lib/catissue/resource.rb
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  - lib/catissue/version.rb
@@ -146,6 +152,10 @@ files:
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  - lib/catissue/util/position.rb
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  - lib/catissue/util/storable.rb
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  - lib/catissue/util/storage_type_holder.rb
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+ - lib/galena/cli/seed.rb
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+ - lib/galena/migration/filter_shims.rb
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+ - lib/galena/migration/frozen_shims.rb
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+ - lib/galena/seed/defaults.rb
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  - History.txt
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  - LEGAL
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  - LICENSE
@@ -157,13 +167,13 @@ signing_key:
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  cert_chain: []
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  name: caruby-tissue
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- has_rdoc: catissue
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+ has_rdoc: yard
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  platform: ruby
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  summary: Ruby facade for caTissue.
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  default_executable:
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  bindir: bin
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- licenses: []
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-
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+ licenses:
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+ - MIT
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html DELETED
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- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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- <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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- <head>
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- <meta name="Content-Type" content="text/html; charset=utf-8" />
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- <title>Class: CaTissue::CollectionProtocolRegistration</title>
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- <link rel="stylesheet" href="../css/style.css" type="text/css" media="screen" charset="utf-8" />
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- <link rel="stylesheet" href="../css/common.css" type="text/css" media="screen" charset="utf-8" />
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- <script type="text/javascript" charset="utf-8">
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- relpath = '..';
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- if (relpath != '') relpath += '/';
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- </script>
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- <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
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- </head>
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- <body>
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- <script type="text/javascript" charset="utf-8">
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- if (window.top.frames.main) document.body.className = 'frames';
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- </script>
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-
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- <div id="header">
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- <div id="menu">
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-
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- <a href="../_index.html">Index (C)</a> &raquo;
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- <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
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- &raquo;
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- <span class="title">CollectionProtocolRegistration</span>
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- </div>
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- <div id="search">
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- <a id="class_list_link" href="#">Class List</a>
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- <a id="method_list_link" href="#">Method List</a>
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- <a id ="file_list_link" href="#">File List</a>
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- </div>
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- <div class="clear"></div>
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- </div>
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- <iframe id="search_frame"></iframe>
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-
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- <div id="content"><h1>Class: CaTissue::CollectionProtocolRegistration
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-
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- </h1>
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- <dl class="box">
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- <dt class="r1">Inherits:</dt>
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- <dd class="r1">
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- <span class="inheritName">Object</span>
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-
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- <ul class="fullTree">
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- <li>Object</li>
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-
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- <li class="next">CaTissue::CollectionProtocolRegistration</li>
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- </ul>
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- <a href="#" class="inheritanceTree">show all</a>
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- </dd>
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- <dt class="r2 last">Defined in:</dt>
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- <dd class="r2 last">examples/galena/lib/galena/migration/frozen_shims.rb</dd>
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-
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- </dl>
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- <div class="clear"></div>
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- <h2>
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- Instance Method Summary
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- <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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- </h2>
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- <ul class="summary">
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- <li class="public ">
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- <span class="summary_signature">
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- <a href="#migrate-instance_method" title="#migrate (instance method)">- (Object) <strong>migrate</strong>(row, migrated) </a>
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- Sets this CPR&#8217;s protocol to the pre-defined
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- Galena::Migration::Defaults#protocol.
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- </p>
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- </div></span>
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- <p class="signature first" id="migrate-instance_method">
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- - (<tt>Object</tt>) <strong>migrate</strong>(row, migrated)
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- <span class='def def kw'>def</span> <span class='migrate identifier id'>migrate</span><span class='lparen token'>(</span><span class='row identifier id'>row</span><span class='comma token'>,</span> <span class='migrated identifier id'>migrated</span><span class='rparen token'>)</span>
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- <span class='self self kw'>self</span><span class='dot token'>.</span><span class='protocol identifier id'>protocol</span> <span class='assign token'>=</span> <span class='Galena constant id'>Galena</span><span class='colon2 op'>::</span><span class='Seed constant id'>Seed</span><span class='dot token'>.</span><span class='defaults identifier id'>defaults</span><span class='dot token'>.</span><span class='protocol identifier id'>protocol</span>
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- Generated on Tue Nov 23 11:38:43 2010 by
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- <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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- </html>