caruby-tissue 1.2.1

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Files changed (133) hide show
  1. data/History.txt +4 -0
  2. data/LEGAL +5 -0
  3. data/LICENSE +22 -0
  4. data/README.md +44 -0
  5. data/bin/crtdump +31 -0
  6. data/bin/crtexample +18 -0
  7. data/bin/crtextract +47 -0
  8. data/bin/crtmigrate +17 -0
  9. data/bin/crtsmoke +27 -0
  10. data/examples/galena/README.md +53 -0
  11. data/examples/galena/bin/migrate.rb +42 -0
  12. data/examples/galena/bin/seed.rb +43 -0
  13. data/examples/galena/conf/extract/simple_fields.yaml +4 -0
  14. data/examples/galena/conf/migration/filter_fields.yaml +7 -0
  15. data/examples/galena/conf/migration/filter_migration.yaml +9 -0
  16. data/examples/galena/conf/migration/frozen_fields.yaml +11 -0
  17. data/examples/galena/conf/migration/frozen_migration.yaml +9 -0
  18. data/examples/galena/conf/migration/general_fields.yaml +42 -0
  19. data/examples/galena/conf/migration/general_migration.yaml +9 -0
  20. data/examples/galena/conf/migration/simple_fields.yaml +30 -0
  21. data/examples/galena/conf/migration/simple_migration.yaml +7 -0
  22. data/examples/galena/conf/migration/small_fields.yaml +24 -0
  23. data/examples/galena/conf/migration/small_migration.yaml +9 -0
  24. data/examples/galena/data/filter.csv +1 -0
  25. data/examples/galena/data/frozen.csv +1 -0
  26. data/examples/galena/data/general.csv +1 -0
  27. data/examples/galena/data/minimal.csv +1 -0
  28. data/examples/galena/data/simple.csv +1 -0
  29. data/examples/galena/data/small.csv +1 -0
  30. data/examples/galena/doc/CaTissue.html +93 -0
  31. data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html +181 -0
  32. data/examples/galena/doc/CaTissue/Participant.html +241 -0
  33. data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +190 -0
  34. data/examples/galena/doc/CaTissue/StorageContainer.html +179 -0
  35. data/examples/galena/doc/CaTissue/TissueSpecimen.html +320 -0
  36. data/examples/galena/doc/Galena.html +290 -0
  37. data/examples/galena/doc/Galena/Seed.html +203 -0
  38. data/examples/galena/doc/Galena/Seed/Defaults.html +646 -0
  39. data/examples/galena/doc/_index.html +188 -0
  40. data/examples/galena/doc/class_list.html +36 -0
  41. data/examples/galena/doc/css/common.css +1 -0
  42. data/examples/galena/doc/css/full_list.css +53 -0
  43. data/examples/galena/doc/css/style.css +307 -0
  44. data/examples/galena/doc/file.README.html +108 -0
  45. data/examples/galena/doc/file_list.html +38 -0
  46. data/examples/galena/doc/frames.html +13 -0
  47. data/examples/galena/doc/index.html +108 -0
  48. data/examples/galena/doc/js/app.js +202 -0
  49. data/examples/galena/doc/js/full_list.js +149 -0
  50. data/examples/galena/doc/js/jquery.js +154 -0
  51. data/examples/galena/doc/method_list.html +179 -0
  52. data/examples/galena/doc/top-level-namespace.html +112 -0
  53. data/examples/galena/lib/README.html +33 -0
  54. data/examples/galena/lib/galena.rb +8 -0
  55. data/examples/galena/lib/galena/cli/seed.rb +43 -0
  56. data/examples/galena/lib/galena/migration/filter_shims.rb +43 -0
  57. data/examples/galena/lib/galena/migration/frozen_shims.rb +54 -0
  58. data/examples/galena/lib/galena/seed/defaults.rb +97 -0
  59. data/lib/catissue.rb +26 -0
  60. data/lib/catissue/cli/command.rb +51 -0
  61. data/lib/catissue/cli/example.rb +31 -0
  62. data/lib/catissue/cli/migrate.rb +60 -0
  63. data/lib/catissue/cli/smoke.rb +45 -0
  64. data/lib/catissue/database.rb +451 -0
  65. data/lib/catissue/database/annotation/annotatable_service.rb +25 -0
  66. data/lib/catissue/database/annotation/annotation_service.rb +79 -0
  67. data/lib/catissue/database/annotation/annotator.rb +84 -0
  68. data/lib/catissue/database/annotation/entity_manager.rb +10 -0
  69. data/lib/catissue/database/annotation/integration_service.rb +87 -0
  70. data/lib/catissue/database/controlled_value_finder.rb +43 -0
  71. data/lib/catissue/database/controlled_values.rb +162 -0
  72. data/lib/catissue/domain/abstract_domain_object.rb +8 -0
  73. data/lib/catissue/domain/abstract_position.rb +22 -0
  74. data/lib/catissue/domain/abstract_specimen.rb +288 -0
  75. data/lib/catissue/domain/abstract_specimen_collection_group.rb +25 -0
  76. data/lib/catissue/domain/address.rb +13 -0
  77. data/lib/catissue/domain/cancer_research_group.rb +11 -0
  78. data/lib/catissue/domain/capacity.rb +34 -0
  79. data/lib/catissue/domain/check_in_check_out_event_parameter.rb +19 -0
  80. data/lib/catissue/domain/collection_event_parameters.rb +13 -0
  81. data/lib/catissue/domain/collection_protocol.rb +177 -0
  82. data/lib/catissue/domain/collection_protocol_event.rb +108 -0
  83. data/lib/catissue/domain/collection_protocol_registration.rb +108 -0
  84. data/lib/catissue/domain/consent_tier_response.rb +13 -0
  85. data/lib/catissue/domain/consent_tier_status.rb +29 -0
  86. data/lib/catissue/domain/container.rb +234 -0
  87. data/lib/catissue/domain/container_position.rb +21 -0
  88. data/lib/catissue/domain/container_type.rb +131 -0
  89. data/lib/catissue/domain/department.rb +13 -0
  90. data/lib/catissue/domain/disposal_event_parameters.rb +13 -0
  91. data/lib/catissue/domain/embedded_event_parameters.rb +10 -0
  92. data/lib/catissue/domain/external_identifier.rb +22 -0
  93. data/lib/catissue/domain/frozen_event_parameters.rb +10 -0
  94. data/lib/catissue/domain/institution.rb +13 -0
  95. data/lib/catissue/domain/new_specimen_array_order_item.rb +35 -0
  96. data/lib/catissue/domain/order_details.rb +25 -0
  97. data/lib/catissue/domain/participant.rb +138 -0
  98. data/lib/catissue/domain/participant_medical_identifier.rb +38 -0
  99. data/lib/catissue/domain/password.rb +11 -0
  100. data/lib/catissue/domain/race.rb +11 -0
  101. data/lib/catissue/domain/received_event_parameters.rb +25 -0
  102. data/lib/catissue/domain/scg_event_parameters.rb +11 -0
  103. data/lib/catissue/domain/site.rb +30 -0
  104. data/lib/catissue/domain/specimen.rb +456 -0
  105. data/lib/catissue/domain/specimen_array.rb +47 -0
  106. data/lib/catissue/domain/specimen_array_content.rb +19 -0
  107. data/lib/catissue/domain/specimen_array_type.rb +20 -0
  108. data/lib/catissue/domain/specimen_characteristics.rb +20 -0
  109. data/lib/catissue/domain/specimen_collection_group.rb +412 -0
  110. data/lib/catissue/domain/specimen_event_parameters.rb +111 -0
  111. data/lib/catissue/domain/specimen_position.rb +38 -0
  112. data/lib/catissue/domain/specimen_protocol.rb +34 -0
  113. data/lib/catissue/domain/specimen_requirement.rb +143 -0
  114. data/lib/catissue/domain/storage_container.rb +204 -0
  115. data/lib/catissue/domain/storage_type.rb +82 -0
  116. data/lib/catissue/domain/transfer_event_parameters.rb +53 -0
  117. data/lib/catissue/domain/user.rb +100 -0
  118. data/lib/catissue/extract/command.rb +31 -0
  119. data/lib/catissue/extract/delta.rb +62 -0
  120. data/lib/catissue/extract/extractor.rb +99 -0
  121. data/lib/catissue/migration/migrator.rb +101 -0
  122. data/lib/catissue/migration/shims.rb +108 -0
  123. data/lib/catissue/migration/uniquify.rb +111 -0
  124. data/lib/catissue/resource.rb +84 -0
  125. data/lib/catissue/util/controlled_value.rb +29 -0
  126. data/lib/catissue/util/location.rb +116 -0
  127. data/lib/catissue/util/log.rb +30 -0
  128. data/lib/catissue/util/person.rb +31 -0
  129. data/lib/catissue/util/position.rb +54 -0
  130. data/lib/catissue/util/storable.rb +34 -0
  131. data/lib/catissue/util/storage_type_holder.rb +30 -0
  132. data/lib/catissue/version.rb +7 -0
  133. metadata +212 -0
data/examples/galena/doc/file.README.html ADDED
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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>Documentation by YARD 0.6.1</title>
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+ <link rel="stylesheet" href="css/style.css" type="text/css" media="screen" charset="utf-8" />
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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" title="Index">Index</a> &raquo;
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+ <span class="title">File: README</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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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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+
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><div id='filecontents'><h1>Galena caRuby Tissue example</h1>
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+
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+ <h2>Synopsis</h2>
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+
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+ <p>This directory contains the caRuby Tissue example for the hypothetical Galena Cancer Center.
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+ The example files are a useful template for building your own migrator.</p>
50
+
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+ <p>The Galena example demonstrates how to load the content of a custom tissue bank into caTissue.
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+ The use cases illustrate several common migration impediments:</p>
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+
54
+ <ul>
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+ <li>Different terminology than caTissue</li>
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+ <li>Different associations than caTissue</li>
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+ <li>Incomplete input for caTissue</li>
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+ <li>Denormalized input</li>
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+ <li>Inconsistent input</li>
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+ <li>Input data scrubbing</li>
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+ <li>Aliquot inference</li>
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+ <li>Pre-defined caTissue protocol</li>
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+ </ul>
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+
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+
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+ <h2>Setup</h2>
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+
68
+ <ol>
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+ <li><p>Run the <code>crtexample --list</code> command to display the Galena example location.</p></li>
70
+ <li><p>Copy the example into a location of your choosing.</p></li>
71
+ <li><p>Configure a caTissue client to connect to a test caTissue instance, as described in the
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+ caTissue Technical Guide.</p></li>
73
+ <li><p>Define the caRuby Tissue access property file as described in
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+ <a href="FAQ">http://caruby.tenderapp.com/faqs/getting-started/tissue_config</a>.</p></li>
75
+ </ol>
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+
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+
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+ <h2>Migration</h2>
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+
80
+ <p>The example migration input data resides in the <code>data</code> directory.
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+ Each CSV input file holds one row for each specimen.</p>
82
+
83
+ <p>Each example has a field mapping configuration in the <code>conf/migration</code> directory.
84
+ For example, the <code>simple.csv</code> input file is migrated into caTissue using the
85
+ <code>simple_migration.yaml</code> configuration file.</p>
86
+
87
+ <p>Migrate the Galena <code>simple</code> example as follows:</p>
88
+
89
+ <ol>
90
+ <li><p>Open a console in the copied Galena example location.</p></li>
91
+ <li><p>Run the following:</p>
92
+
93
+ <p> crtmigrate --file conf/migration/simple.yaml data/simple.yaml</p></li>
94
+ <li><p>Check the test database and verify that a there is a collection protocol
95
+ named `Galena CP.</p></li>
96
+ </ol>
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+
98
+
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+ <p>The other examples are run in a similar manner.</p></div></div>
100
+
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+ <div id="footer">
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+ Generated on Tue Nov 23 11:38:42 2010 by
103
+ <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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+
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+ </body>
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+ </html>
data/examples/galena/doc/file_list.html ADDED
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+ <a target="_self" href="class_list.html">Classes</a> |
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data/examples/galena/doc/index.html ADDED
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <head>
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+ <meta name="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Documentation by YARD 0.6.1</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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+ relpath = '';
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+ if (relpath != '') relpath += '/';
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+ </script>
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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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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="_index.html" title="Index">Index</a> &raquo;
27
+ <span class="title">File: README</span>
28
+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+
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+ <div id="search">
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+ <a id="class_list_link" href="#">Class List</a>
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37
+ </div>
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+
39
+ <div class="clear"></div>
40
+ </div>
41
+
42
+ <iframe id="search_frame"></iframe>
43
+
44
+ <div id="content"><div id='filecontents'><h1>Galena caRuby Tissue example</h1>
45
+
46
+ <h2>Synopsis</h2>
47
+
48
+ <p>This directory contains the caRuby Tissue example for the hypothetical Galena Cancer Center.
49
+ The example files are a useful template for building your own migrator.</p>
50
+
51
+ <p>The Galena example demonstrates how to load the content of a custom tissue bank into caTissue.
52
+ The use cases illustrate several common migration impediments:</p>
53
+
54
+ <ul>
55
+ <li>Different terminology than caTissue</li>
56
+ <li>Different associations than caTissue</li>
57
+ <li>Incomplete input for caTissue</li>
58
+ <li>Denormalized input</li>
59
+ <li>Inconsistent input</li>
60
+ <li>Input data scrubbing</li>
61
+ <li>Aliquot inference</li>
62
+ <li>Pre-defined caTissue protocol</li>
63
+ </ul>
64
+
65
+
66
+ <h2>Setup</h2>
67
+
68
+ <ol>
69
+ <li><p>Run the <code>crtexample --list</code> command to display the Galena example location.</p></li>
70
+ <li><p>Copy the example into a location of your choosing.</p></li>
71
+ <li><p>Configure a caTissue client to connect to a test caTissue instance, as described in the
72
+ caTissue Technical Guide.</p></li>
73
+ <li><p>Define the caRuby Tissue access property file as described in
74
+ <a href="FAQ">http://caruby.tenderapp.com/faqs/getting-started/tissue_config</a>.</p></li>
75
+ </ol>
76
+
77
+
78
+ <h2>Migration</h2>
79
+
80
+ <p>The example migration input data resides in the <code>data</code> directory.
81
+ Each CSV input file holds one row for each specimen.</p>
82
+
83
+ <p>Each example has a field mapping configuration in the <code>conf/migration</code> directory.
84
+ For example, the <code>simple.csv</code> input file is migrated into caTissue using the
85
+ <code>simple_migration.yaml</code> configuration file.</p>
86
+
87
+ <p>Migrate the Galena <code>simple</code> example as follows:</p>
88
+
89
+ <ol>
90
+ <li><p>Open a console in the copied Galena example location.</p></li>
91
+ <li><p>Run the following:</p>
92
+
93
+ <p> crtmigrate --file conf/migration/simple.yaml data/simple.yaml</p></li>
94
+ <li><p>Check the test database and verify that a there is a collection protocol
95
+ named `Galena CP.</p></li>
96
+ </ol>
97
+
98
+
99
+ <p>The other examples are run in a similar manner.</p></div></div>
100
+
101
+ <div id="footer">
102
+ Generated on Tue Nov 23 11:38:42 2010 by
103
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
104
+ 0.6.1 (ruby-1.8.6).
105
+ </div>
106
+
107
+ </body>
108
+ </html>
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+ $('.inheritanceTree').toggle(function() {
33
+ tHeight = $(this).parent().prev().height();
34
+ $(this).parent().toggleClass('showAll');
35
+ $(this).text("(hide)");
36
+ $(this).parent().prev().height($(this).parent().height());
37
+ },
38
+ function() {
39
+ $(this).parent().toggleClass('showAll');
40
+ $(this).parent().prev().height(tHeight);
41
+ $(this).text("show all")
42
+ });
43
+ }
44
+
45
+ function fixBoxInfoHeights() {
46
+ $('dl.box dd.r1, dl.box dd.r2').each(function() {
47
+ $(this).prev().height($(this).height());
48
+ });
49
+ }
50
+
51
+ function searchFrameLinks() {
52
+ $('#method_list_link').click(function() {
53
+ toggleSearchFrame(this, relpath + 'method_list.html');
54
+ });
55
+
56
+ $('#class_list_link').click(function() {
57
+ toggleSearchFrame(this, relpath + 'class_list.html');
58
+ });
59
+
60
+ $('#file_list_link').click(function() {
61
+ toggleSearchFrame(this, relpath + 'file_list.html');
62
+ });
63
+ }
64
+
65
+ function toggleSearchFrame(id, link) {
66
+ var frame = $('#search_frame');
67
+ $('#search a').removeClass('active').addClass('inactive');
68
+ if (frame.attr('src') == link && frame.css('display') != "none") {
69
+ frame.slideUp(100);
70
+ $('#search a').removeClass('active inactive');
71
+ }
72
+ else {
73
+ $(id).addClass('active').removeClass('inactive');
74
+ frame.attr('src', link).slideDown(100);
75
+ }
76
+ }
77
+
78
+ function linkSummaries() {
79
+ $('.summary_signature').click(function() {
80
+ document.location = $(this).find('a').attr('href');
81
+ });
82
+ }
83
+
84
+ function framesInit() {
85
+ if (window.top.frames.main) {
86
+ document.body.className = 'frames';
87
+ $('#menu .noframes a').attr('href', document.location);
88
+ $('html head title', window.parent.document).text($('html head title').text());
89
+ }
90
+ }
91
+
92
+ function keyboardShortcuts() {
93
+ if (window.top.frames.main) return;
94
+ $(document).keypress(function(evt) {
95
+ if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
96
+ if (evt.originalTarget.nodeName == "INPUT" ||
97
+ evt.originalTarget.nodeName == "TEXTAREA") return;
98
+ switch (evt.charCode) {
99
+ case 67: case 99: $('#class_list_link').click(); break; // 'c'
100
+ case 77: case 109: $('#method_list_link').click(); break; // 'm'
101
+ case 70: case 102: $('#file_list_link').click(); break; // 'f'
102
+ }
103
+ });
104
+ }
105
+
106
+ function summaryToggle() {
107
+ $('.summary_toggle').click(function() {
108
+ localStorage.summaryCollapsed = $(this).text();
109
+ $(this).text($(this).text() == "collapse" ? "expand" : "collapse");
110
+ var next = $(this).parent().parent().next();
111
+ if (next.hasClass('compact')) {
112
+ next.toggle();
113
+ next.next().toggle();
114
+ }
115
+ else if (next.hasClass('summary')) {
116
+ var list = $('<ul class="summary compact" />');
117
+ list.html(next.html());
118
+ list.find('.summary_desc, .note').remove();
119
+ list.find('a').each(function() {
120
+ $(this).html($(this).find('strong').html());
121
+ $(this).parent().html($(this)[0].outerHTML);
122
+ });
123
+ next.before(list);
124
+ next.toggle();
125
+ }
126
+ return false;
127
+ });
128
+ if (localStorage) {
129
+ if (localStorage.summaryCollapsed == "collapse") $('.summary_toggle').click();
130
+ else localStorage.summaryCollapsed = "expand";
131
+ }
132
+ }
133
+
134
+ function fixOutsideWorldLinks() {
135
+ $('a').each(function() {
136
+ if (window.location.host != this.host) this.target = '_parent';
137
+ });
138
+ }
139
+
140
+ function generateTOC() {
141
+ if ($('#filecontents').length == 0) return;
142
+ var _toc = $('<ol class="top"></ol>');
143
+ var show = false;
144
+ var toc = _toc;
145
+ var counter = 0;
146
+ var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
147
+ if ($('#filecontents h1').length > 1) tags.unshift('h1');
148
+ for (i in tags) { tags[i] = '#filecontents ' + tags[i] }
149
+ var lastTag = parseInt(tags[0][1]);
150
+ $(tags.join(', ')).each(function() {
151
+ if (this.id == "filecontents") return;
152
+ show = true;
153
+ var thisTag = parseInt(this.tagName[1]);
154
+ if (this.id.length == 0) {
155
+ var proposedId = $(this).text().replace(/[^a-z0-9:'"\.()=-]/ig, '_');
156
+ if ($('#' + proposedId).length > 0) proposedId += counter++;
157
+ this.id = proposedId;
158
+ }
159
+ if (thisTag > lastTag) {
160
+ for (var i = 0; i < thisTag - lastTag; i++) {
161
+ var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
162
+ }
163
+ }
164
+ if (thisTag < lastTag) {
165
+ for (var i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
166
+ }
167
+ toc.append('<li><a href="#' + this.id + '">' + $(this).text() + '</a></li>');
168
+ lastTag = thisTag;
169
+ });
170
+ if (!show) return;
171
+ html = '<div id="toc"><p class="title"><a class="hide_toc" href="#"><strong>Table of Contents</strong></a> <small>(<a href="#" class="float_toc">left</a>)</small></p></div>';
172
+ $('#content').prepend(html);
173
+ $('#toc').append(_toc);
174
+ $('#toc .hide_toc').toggle(function() {
175
+ $('#toc .top').slideUp('fast');
176
+ $('#toc').toggleClass('hidden');
177
+ $('#toc .title small').toggle();
178
+ }, function() {
179
+ $('#toc .top').slideDown('fast');
180
+ $('#toc').toggleClass('hidden');
181
+ $('#toc .title small').toggle();
182
+ });
183
+ $('#toc .float_toc').toggle(function() {
184
+ $(this).text('float');
185
+ $('#toc').toggleClass('nofloat');
186
+ }, function() {
187
+ $(this).text('left')
188
+ $('#toc').toggleClass('nofloat');
189
+ });
190
+ }
191
+
192
+ $(framesInit);
193
+ $(createSourceLinks);
194
+ $(createDefineLinks);
195
+ $(createFullTreeLinks);
196
+ $(fixBoxInfoHeights);
197
+ $(searchFrameLinks);
198
+ $(linkSummaries);
199
+ $(keyboardShortcuts);
200
+ $(summaryToggle);
201
+ $(fixOutsideWorldLinks);
202
+ $(generateTOC);