caruby-core 1.4.1

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  1. data/History.txt +4 -0
  2. data/LEGAL +5 -0
  3. data/LICENSE +22 -0
  4. data/README.md +51 -0
  5. data/doc/website/css/site.css +1 -5
  6. data/doc/website/images/avatar.png +0 -0
  7. data/doc/website/images/favicon.ico +0 -0
  8. data/doc/website/images/logo.png +0 -0
  9. data/doc/website/index.html +82 -0
  10. data/doc/website/install.html +87 -0
  11. data/doc/website/quick_start.html +87 -0
  12. data/doc/website/tissue.html +85 -0
  13. data/doc/website/uom.html +10 -0
  14. data/lib/caruby.rb +3 -0
  15. data/lib/caruby/active_support/README.txt +2 -0
  16. data/lib/caruby/active_support/core_ext/string.rb +7 -0
  17. data/lib/caruby/active_support/core_ext/string/inflections.rb +167 -0
  18. data/lib/caruby/active_support/inflections.rb +55 -0
  19. data/lib/caruby/active_support/inflector.rb +398 -0
  20. data/lib/caruby/cli/application.rb +36 -0
  21. data/lib/caruby/cli/command.rb +169 -0
  22. data/lib/caruby/csv/csv_mapper.rb +157 -0
  23. data/lib/caruby/csv/csvio.rb +185 -0
  24. data/lib/caruby/database.rb +252 -0
  25. data/lib/caruby/database/fetched_matcher.rb +66 -0
  26. data/lib/caruby/database/persistable.rb +432 -0
  27. data/lib/caruby/database/persistence_service.rb +162 -0
  28. data/lib/caruby/database/reader.rb +599 -0
  29. data/lib/caruby/database/saved_merger.rb +131 -0
  30. data/lib/caruby/database/search_template_builder.rb +59 -0
  31. data/lib/caruby/database/sql_executor.rb +75 -0
  32. data/lib/caruby/database/store_template_builder.rb +200 -0
  33. data/lib/caruby/database/writer.rb +469 -0
  34. data/lib/caruby/domain/annotatable.rb +25 -0
  35. data/lib/caruby/domain/annotation.rb +23 -0
  36. data/lib/caruby/domain/attribute_metadata.rb +447 -0
  37. data/lib/caruby/domain/java_attribute_metadata.rb +160 -0
  38. data/lib/caruby/domain/merge.rb +91 -0
  39. data/lib/caruby/domain/properties.rb +95 -0
  40. data/lib/caruby/domain/reference_visitor.rb +289 -0
  41. data/lib/caruby/domain/resource_attributes.rb +528 -0
  42. data/lib/caruby/domain/resource_dependency.rb +205 -0
  43. data/lib/caruby/domain/resource_introspection.rb +159 -0
  44. data/lib/caruby/domain/resource_metadata.rb +117 -0
  45. data/lib/caruby/domain/resource_module.rb +285 -0
  46. data/lib/caruby/domain/uniquify.rb +38 -0
  47. data/lib/caruby/import/annotatable_class.rb +28 -0
  48. data/lib/caruby/import/annotation_class.rb +27 -0
  49. data/lib/caruby/import/annotation_module.rb +67 -0
  50. data/lib/caruby/import/java.rb +338 -0
  51. data/lib/caruby/migration/migratable.rb +167 -0
  52. data/lib/caruby/migration/migrator.rb +533 -0
  53. data/lib/caruby/migration/resource.rb +8 -0
  54. data/lib/caruby/migration/resource_module.rb +11 -0
  55. data/lib/caruby/migration/uniquify.rb +20 -0
  56. data/lib/caruby/resource.rb +969 -0
  57. data/lib/caruby/util/attribute_path.rb +46 -0
  58. data/lib/caruby/util/cache.rb +53 -0
  59. data/lib/caruby/util/class.rb +99 -0
  60. data/lib/caruby/util/collection.rb +1053 -0
  61. data/lib/caruby/util/controlled_value.rb +35 -0
  62. data/lib/caruby/util/coordinate.rb +75 -0
  63. data/lib/caruby/util/domain_extent.rb +49 -0
  64. data/lib/caruby/util/file_separator.rb +65 -0
  65. data/lib/caruby/util/inflector.rb +20 -0
  66. data/lib/caruby/util/log.rb +95 -0
  67. data/lib/caruby/util/math.rb +12 -0
  68. data/lib/caruby/util/merge.rb +59 -0
  69. data/lib/caruby/util/module.rb +34 -0
  70. data/lib/caruby/util/options.rb +92 -0
  71. data/lib/caruby/util/partial_order.rb +36 -0
  72. data/lib/caruby/util/person.rb +119 -0
  73. data/lib/caruby/util/pretty_print.rb +184 -0
  74. data/lib/caruby/util/properties.rb +112 -0
  75. data/lib/caruby/util/stopwatch.rb +66 -0
  76. data/lib/caruby/util/topological_sync_enumerator.rb +53 -0
  77. data/lib/caruby/util/transitive_closure.rb +45 -0
  78. data/lib/caruby/util/tree.rb +48 -0
  79. data/lib/caruby/util/trie.rb +37 -0
  80. data/lib/caruby/util/uniquifier.rb +30 -0
  81. data/lib/caruby/util/validation.rb +48 -0
  82. data/lib/caruby/util/version.rb +56 -0
  83. data/lib/caruby/util/visitor.rb +351 -0
  84. data/lib/caruby/util/weak_hash.rb +36 -0
  85. data/lib/caruby/version.rb +3 -0
  86. metadata +186 -0
data/History.txt ADDED
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+ === 1.4.1 / 2010-11-23
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+
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+ * Initial public release
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+
data/LEGAL ADDED
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+ LEGAL NOTICE INFORMATION
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+ ------------------------
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+
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+ All the files in this distribution are covered under either the MIT
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+ license (see the file LICENSE).
data/LICENSE ADDED
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+ Copyright (c) 2010 Oregon Health & Science University Knight Cancer Institute
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+
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+ Permission is hereby granted, free of charge, to any person
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+ obtaining a copy of this software and associated documentation
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+ files (the "Software"), to deal in the Software without
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+ restriction, including without limitation the rights to use,
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+ copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the
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+ Software is furnished to do so, subject to the following
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+ conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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+ OTHER DEALINGS IN THE SOFTWARE.
data/README.md ADDED
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+ caRuby: Simplifying caBIG(TM)
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+ =============================
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+
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+ **Home**: [http://caruby.rubyforge.com](http://caruby.rubyforge.com)
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+ **Git**: [http://github.com/caruby/core](http://github.com/caruby/core)
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+ **Author**: OHSU Knight Cancer Institute
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+ **Copyright**: 2010
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+ **License**: MIT License
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+ **Latest Version**: 1.4.1
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+ **Release Date**: November 23rd 2010
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+
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+ Synopsis
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+ --------
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+
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+ caRuby presents a JRuby facade that simplifies interaction with caBIG applications.
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+
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+ Feature List
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+ ------------
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+
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+ 1. caCORE API wrapper.
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+
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+ 2. Resolves persistence dependencies.
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+
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+ 3. Enforces inverse association integrity.
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+
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+ 4. Run-time declaration of defaults.
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+
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+ 5. Client-side create validation.
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+
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+ Installing
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+ ----------
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+ caRuby is installed automatically when an application gem, e.g. caruby-tissue,
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+ is installed.
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+
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+ Usage
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+ -----
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+
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+ See the project [http://caruby.rubyforge.com](Home) Page for usage examples.
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+
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+ Changelog
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+ ---------
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+
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+ - **November 23, 2010**: 1.4.1 release
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+ - Initial public release
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+
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+ Copyright
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+ ---------
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+
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+ caRuby © 2010 by [Oregon Health & Science University](mailto:loneyf@ohsu.edu).
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+ caRuby is licensed under the MIT license. Please see the LICENSE and LEGAL
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+ files for more information.
data/doc/website/css/site.css ADDED
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+
- ---------------------------------------------- */
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- ---------------------------------------------- */
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- ---------------------------------------------- */
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- ---------------------------------------------- */
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- ----------------------------------------------- */
data/doc/website/images/avatar.png ADDED
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data/doc/website/index.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
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+ <head>
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+ <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
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+ <meta name="author" content="Fred Loney, OHSU" />
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+ <meta name="keywords" content="caRuby, caBIG, caSmall, Ruby, JRuby" />
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+ <meta name="description" content="caRuby landing page." />
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+ <meta name="robots" content="all" />
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+ <title>caRuby: caBIG Simplified</title>
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+
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+ <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
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+ <script type="text/javascript"></script>
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+
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+ <style type="text/css" title="currentStyle" media="screen">
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+ @import "/css/site.css";
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+ </style>
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+ <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
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+ <link rel="Shortcut Icon" href="images/favicon.ico" />
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+ </head>
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+
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+ <body id="caruby">
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+
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+ <div id="container">
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+ <div id="head">
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+ <h1><a href="index.html">caRuby:</a></h1>
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+ <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
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+ <ul>
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+ <li><span class="currentPage">Home</li>
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+ <li><a href='quick_start.html'><em>Quick Start</em></a></li>
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+ <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
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+ <li><a href='http://github.com/caruby'>Source</a></li>
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+ <li><a href='/about.html'>About</a></li>
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+ </ul>
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+ <img src="images/logo.png"/>
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+ </div>
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+
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+ <div id="features">
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+ <h3>Features</h3>
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+ <ul>
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+ <li><a href="/api.html">API</a></li>
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+ <li><a href="/tissue.html">Tissue</a></li>
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+ <li><a href="/migrator.html">Migrator</a></li>
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+ <li><a href="/casmall.html">caSmall</a></li>
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+ </ul>
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+ </div>
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+
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+ <div id="supportingText">
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+ <h3>Overview</h3>
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+ <p>
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+ caRuby simplifies interaction with <a href="http://cabig.nci.nih.gov">caBIG&reg;</a> application
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+ services. caRuby presents a <a href="http://jruby.org">JRuby</a> caBIG fa&ccedil;ade that
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+ supports the following uses:
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+ <ul>
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+ <li>Migration from legacy systems</li>
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+ <li>Incremental update from source applications</li>
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+ <li>Extract from a caBIG database</li>
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+ <li>Utility administrative tasks</li>
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+ <li>Workflow data transformations</li>
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+ <li>Lightweight web services</li>
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+ <li>Site-specific user interfaces</li>
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+ </ul>
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+ </p>
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+ <h3>Getting Started</h3>
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+ <p>
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+ <ol>
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+ <li>Peruse the <strong>Features</strong> to see what caRuby offers.</li>
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+ <li>Follow the <a href='/quick_start.html'>Quick Start</a> instructions to install caRuby.</li>
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+ <li>Consult the <a href='/faq.html'>FAQ</a> for usage tips.</li>
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+ <li>Visit caRuby <a href='http://caruby.tenderapp.com/'>Support</a> if you run into a problem.</li>
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+ <li><a href='/contribute.html'>Contribute</a> a solution if you're feeling ambitious!</li>
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+ <li><a href='mailto:caruby.org@gmail.com'>Let us know</a> what you think.</li>
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+ </ol>
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+ </p>
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+
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+ <div id="footer">
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+ </div>
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+ </div>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/website/install.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
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+ <head>
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+ <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
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+ <meta name="author" content="Fred Loney, OHSU" />
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+ <meta name="keywords" content="caRuby" />
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+ <meta name="description" content="caRuby Quick Start page." />
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+ <meta name="robots" content="all" />
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+ <title>caRuby: Installation</title>
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+
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+ <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
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+ <script type="text/javascript"></script>
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+
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+ <style type="text/css" title="currentStyle" media="screen">
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+ @import "/css/site.css";
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+ </style>
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+ <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
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+ <link rel="Shortcut Icon" href="images/favicon.ico" />
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+ </head>
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+
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+ <body id="quick_start">
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+
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+ <div id="container">
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+ <div id="head">
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+ <h1><a href="index.html">caRuby:</a></h1>
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+ <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
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+ <ul>
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+ <li><a href="/index.html">Home</a></li>
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+ <li><span class="currentPage"><em>Quick Start</em></li>
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+ <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
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+ <li><a href='http://github.com/caruby'>Source</a></li>
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+ <li><a href='/about.html'>About</a></li>
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+ </ul>
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+ <img src="images/logo.png"/>
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+ </div>
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+
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+ <div id="features">
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+ <h3>Features</h3>
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+ <ul>
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+ <li><a href="/api.html">API</a></li>
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+ <li><a href="/tissue.html">Tissue</a></li>
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+ <li><a href="/migrator.html">Migrator</a></li>
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+ <li><a href="/casmall.html">caSmall</a></li>
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+ </ul>
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+ </div>
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+
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+ <div id="supportingText">
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+ <p>
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+ Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
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+ Once you've installed <a href="http://jruby.org">JRuby</a> and the target caBIG application API, installing a caRuby gem is done with a one-line
52
+ command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
53
+ Set up a caRuby environment as follows:
54
+ <ol>
55
+ <li>Install the target caBIG application Java API client.
56
+ Consult the caBIG application Technical Guide for details, available from the caBIG application
57
+ <a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
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+ </li>
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+ <li>Install <a href="http://jruby.org">JRuby</a>.</li>
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+ <li>Open a command console and enter the following:
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+ <pre>
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+ gem install rubygems
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+ </pre>
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+ </li>
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+ </ol>
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+ </p>
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+ <p>
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+ The preceding steps set up a standard JRuby environment. Now the desired caRuby gem is installed using the <code>gem install</code> command, e.g.:
69
+ <pre>
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+ gem install caruby-tissue
71
+ </pre>
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+ </p>
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+ <p>
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+ and updated using the <code>gem update</code> command, e.g.:
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+ <pre>
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+ gem update caruby-tissue
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+ </pre>
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+ </p>
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+ <p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
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+ </p>
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+ <div id="footer">
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+ </div>
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+ </div>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/website/quick_start.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
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+ <head>
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+ <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
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+ <meta name="author" content="Fred Loney, OHSU" />
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+ <meta name="keywords" content="caRuby" />
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+ <meta name="description" content="caRuby Quick Start page." />
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+ <meta name="robots" content="all" />
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+ <title>caRuby: Quick Start</title>
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+
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+ <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
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+ <script type="text/javascript"></script>
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+
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+ <style type="text/css" title="currentStyle" media="screen">
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+ @import "/css/site.css";
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+ </style>
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+ <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
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+ <link rel="Shortcut Icon" href="images/favicon.ico" />
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+ </head>
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+
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+ <body id="quick_start">
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+
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+ <div id="container">
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+ <div id="head">
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+ <h1><a href="index.html">caRuby:</a></h1>
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+ <h2><a href="http://cabig.nci.nih.gov">caBIG&reg;</a> Simplified</h2>
28
+ <ul>
29
+ <li><a href="/index.html">Home</a></li>
30
+ <li><span class="currentPage"><em>Quick Start</em></li>
31
+ <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
32
+ <li><a href='http://github.com/caruby'>Source</a></li>
33
+ <li><a href='/about.html'>About</a></li>
34
+ </ul>
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+ <img src="images/logo.png"/>
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+ </div>
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+
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+ <div id="features">
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+ <h3>Features</h3>
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+ <ul>
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+ <li><a href="/api.html">API</a></li>
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+ <li><a href="/tissue.html">Tissue</a></li>
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+ <li><a href="/migrator.html">Migrator</a></li>
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+ <li><a href="/casmall.html">caSmall</a></li>
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+ </ul>
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+ </div>
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+
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+ <div id="supportingText">
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+ <p>
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+ Each caRuby <a href="/components.html">component</a> is packaged as a standard Ruby <a href="http://docs.rubygems.org/shelf/index">gem</a>.
51
+ Once you've installed <a href="http://jruby.org">JRuby</a> and the target caBIG application API, installing a caRuby gem is done with a one-line
52
+ command. caRuby runs on any on any workstation or server that supports the target caBIG application Java API.
53
+ Set up a caRuby environment as follows:
54
+ <ol>
55
+ <li>Install the target caBIG application Java API client.
56
+ Consult the caBIG application Technical Guide for details, available from the caBIG application
57
+ <a href="https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Knowledge_Center_Index">Knowledge Center</a>.
58
+ </li>
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+ <li>Install <a href="http://jruby.org">JRuby</a>.</li>
60
+ <li>Open a command console and enter the following:
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+ <pre>
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+ gem install rubygems
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+ </pre>
64
+ </li>
65
+ </ol>
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+ </p>
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+ <p>
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+ The preceding steps set up a standard JRuby environment. Now the desired caRuby gem is installed using the <code>gem install</code> command, e.g.:
69
+ <pre>
70
+ gem install caruby-tissue
71
+ </pre>
72
+ </p>
73
+ <p>
74
+ and updated using the <code>gem update</code> command, e.g.:
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+ <pre>
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+ gem update caruby-tissue
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+ </pre>
78
+ </p>
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+ <p>The caRuby gem is now ready for use. Consult the gem <a href="/documentation.html">documentation</a> for usage and examples.
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+ </p>
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+ <div id="footer">
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+ </div>
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+ </div>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/website/tissue.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
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+ <head>
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+ <meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
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+ <meta name="author" content="Fred Loney, OHSU" />
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+ <meta name="keywords" content="caRuby, caTissue" />
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+ <meta name="description" content="caRuby Tissue page." />
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+ <meta name="robots" content="all" />
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+ <title>caRuby: Quick Start</title>
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+
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+ <!-- to correct the unsightly Flash of Unstyled Content. http://www.bluerobot.com/web/css/fouc.asp -->
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+ <script type="text/javascript"></script>
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+
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+ <style type="text/css" title="currentStyle" media="screen">
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+ @import "/css/site.css";
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+ </style>
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+ <link rel='stylesheet' href='css/site.css' type='text/css' media="screen, projection">
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+ <link rel="Shortcut Icon" href="images/favicon.ico" />
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+ </head>
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+
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+ <body id="tissue">
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+
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+ <div id="container">
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+ <div id="head">
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+ <h1><a href="index.html">caRuby:</a></h1>
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+ <h2>Tissue</h2>
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+ <ul>
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+ <li><a href='quick_start.html'><em>Quick Start</em></a></li>
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+ <li><a href='faq.html'>FAQ</a></li>
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+ <li><a href='http://caruby.tenderapp.com/'>Help</a></li>
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+ <li><a href='contribute.html'>Contribute</a></li>
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+ <li><a href='about.html'>About</a></li>
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+ </ul>
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+ <img src="images/logo.png"/>
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+ </div>
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+
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+ <div id="supportingText">
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+ <p>
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+ The caRuby Tissue component applies the caRuby facade to the
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+ <a href="https://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/CaTissue_Suite">caTissue</a>
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+ application. This offers the following features:
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+ <ul>
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+ <li>flexible server interaction</li>
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+ <li>data migration and extraction</li>
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+ <li>a foundation for a <a href="casmall.html">caSmall</a> framework</li>
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+ </ul>
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+ </p>
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+ <p>
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+ Since the caRuby Tissue component is built on the caTissue API, all of the caTissue business logic applies.
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+ In addition, caRuby augments the API as follows:
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+ <ul>
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+ <li>supplies default attribute values</li>
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+ <li>validates mandatory attributes before submission to caTissue</li>
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+ <li>validates additional attributes which are permitted by the caTissue API but corrupt the database</li>
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+ <li>migrates an input CSV record to a caTissue object based on one simple configuration file</li>
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+ <li>validates migration input diagnosis and tissue site permissible values</li>
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+ <li>optionally maps diagnosis and tissue site migration input values to caTissue permissible values</li>
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+ <li>determines how to save the caTissue object based on the caTissue object model</li>
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+ <li>finds referenced objects based on secondary keys and alternative search strategies</li>
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+ <li>creates whatever needs to be created in the required order based on the data model associations</li>
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+ <li>works around caCORE and caTissue bugs and traps</li>
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+ <li>provides helper methods for common tasks, e.g. aliquoting</li>
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+ </ul>
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+ </p>
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+ <p>
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+ The sole configuration is the migration mapping file and a small caTissue server access properties file.
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+ The defaults and other metadata are defined in Ruby declarations rather than a configuration.
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+ These declarations express basic model characteristics, and are expected to be stable and sufficient for most uses.
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+ They can, however, be modified in small Ruby shim files.
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+ Special-purpose migration code can be added in the shim files as well, as described in the
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+ <a href='shims.html'>Shims</a> description.
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+ </p>
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+ <p>
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+ There is almost no class-specific caRuby business logic code similar to that found in caTissue.
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+ Rather, there are basic design patterns driven by the model characteristics defined in the Ruby declarations.
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+ </p>
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+ <div id="footer">
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+ </div>
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+ </div>
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+ </div>
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+
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+ </body>
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+ </html>
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+