RubyGems - caruby-tissue - Versions diffs - 1.2.2 → 1.2.3 - Mend

caruby-tissue 1.2.2 → 1.2.3

Files changed (153) hide show

data/bin/migrate.rb DELETED Viewed

@@ -1,42 +0,0 @@
-#!/usr/bin/env jruby
-#
-# == Synopsis
-#
-# catissue-migrate-galena: migrates the Galena example to caTissue
-#
-# == Usage
-#
-# catissue-migrate-galena.rb [options] file
-#
-# See catissue-migrate.rb for the argments
-#
-# == License
-#
-# This program is licensed under the terms of the +LEGAL+ file in
-# the source distribution.
-# Load the caruby-tissue gem.
-require 'rubygems'
-begin
-  gem 'caruby-tissue'
-rescue LoadError
-  # if the gem is not available, then try a local source
-  $:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
-end
-# Add the example library to the Ruby class load path.
-$:.unshift File.join(File.dirname(__FILE__), '..', 'examples', 'galena', 'lib')
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-# Load the caRuby classes.
-require 'catissue'
-require 'catissue/migration/command'
-require 'galena/seed/defaults'
-# Seed the database, if necessary.
-Galena.seed
-# Migrate the example input using the command line arguments.
-CaTissue::CLI::Migrate.new.start

data/bin/seed.rb DELETED Viewed

@@ -1,43 +0,0 @@
-#!/usr/bin/env jruby
-#
-# crtseed-galena: seeds the Galena example administrative objects in the database
-#
-# == Usage
-#
-# catissue-seed-galena.rb [options] file
-#
-# --help, -h:
-# print this help message and exit
-#
-# --log file, -l file:
-# log file (default ./log/migration.log)
-#
-# --debug, -d:
-# print debug messages to log (optional)
-#
-# == License
-#
-# This program is licensed under the terms of the +LEGAL+ file in
-# the source distribution.
-# load the required gems
-require 'rubygems'
-begin
-  gem 'caruby-tissue'
-rescue LoadError
-  # if the gem is not available, then try a local source
-  $:.unshift File.join(File.dirname(__FILE__), '..', '..', '..', 'lib')
-end
-# add the Galena lib to the path
-$:.unshift File.join(File.dirname(__FILE__), '..', 'lib')
-# the default log file
-DEF_LOG_FILE = 'log/migration.log'
-require 'catissue'
-require 'catissue/cli/command'
-require 'galena/seed/defaults'
-CaTissue::Command.new.start { Galena::Seed.defaults.ensure_exists }

data/examples/galena/doc/CaTissue/Participant.html DELETED Viewed

@@ -1,241 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta name="Content-Type" content="text/html; charset=utf-8" />
-<title>Class: CaTissue::Participant</title>
-<link rel="stylesheet" href="../css/style.css" type="text/css" media="screen" charset="utf-8" />
-<link rel="stylesheet" href="../css/common.css" type="text/css" media="screen" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  relpath = '..';
-  if (relpath != '') relpath += '/';
-</script>
-<script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
-<script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
-  </head>
-  <body>
-    <script type="text/javascript" charset="utf-8">
-      if (window.top.frames.main) document.body.className = 'frames';
-    </script>
-    <div id="header">
-      <div id="menu">
-    <a href="../_index.html">Index (P)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
-     &raquo;
-    <span class="title">Participant</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-  <a id="class_list_link" href="#">Class List</a>
-  <a id="method_list_link" href="#">Method List</a>
-  <a id ="file_list_link" href="#">File List</a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: CaTissue::Participant
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">CaTissue::Participant</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">examples/galena/lib/galena/migration/filter_shims.rb</dd>
-</dl>
-<div class="clear"></div>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#migrate_first_name-instance_method" title="#migrate_first_name (instance method)">- (Object) <strong>migrate_first_name</strong>(value, row) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'><p>
-Extracts the Participant first name from the <tt>Initials</tt> input field.
-</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#migrate_last_name-instance_method" title="#migrate_last_name (instance method)">- (Object) <strong>migrate_last_name</strong>(value, row) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'><p>
-Extracts the Participant last name from the <tt>Initials</tt> input field.
-</p>
-</div></span>
-</li>
-    </ul>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <p class="signature first" id="migrate_first_name-instance_method">
-    - (<tt>Object</tt>) <strong>migrate_first_name</strong>(value, row)
-</p><div class="docstring">
-  <div class="discussion">
-    <p>
-Extracts the Participant first name from the <tt>Initials</tt> input field.
-</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-10
-11
-12</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/filter_shims.rb', line 10</span>
-<span class='def def kw'>def</span> <span class='migrate_first_name identifier id'>migrate_first_name</span><span class='lparen token'>(</span><span class='value identifier id'>value</span><span class='comma token'>,</span> <span class='row identifier id'>row</span><span class='rparen token'>)</span>
-  <span class='self self kw'>self</span><span class='dot token'>.</span><span class='first_name identifier id'>first_name</span> <span class='assign token'>=</span> <span class='value identifier id'>value</span><span class='lbrack token'>[</span><span class='integer val'>0</span><span class='comma token'>,</span> <span class='integer val'>1</span><span class='rbrack token'>]</span>
-<span class='end end kw'>end</span>
-</pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <p class="signature " id="migrate_last_name-instance_method">
-    - (<tt>Object</tt>) <strong>migrate_last_name</strong>(value, row)
-</p><div class="docstring">
-  <div class="discussion">
-    <p>
-Extracts the Participant last name from the <tt>Initials</tt> input field.
-</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-15
-16
-17</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/filter_shims.rb', line 15</span>
-<span class='def def kw'>def</span> <span class='migrate_last_name identifier id'>migrate_last_name</span><span class='lparen token'>(</span><span class='value identifier id'>value</span><span class='comma token'>,</span> <span class='row identifier id'>row</span><span class='rparen token'>)</span>
-  <span class='self self kw'>self</span><span class='dot token'>.</span><span class='last_name identifier id'>last_name</span> <span class='assign token'>=</span> <span class='value identifier id'>value</span><span class='lbrack token'>[</span><span class='integer val'>-1</span><span class='comma token'>,</span> <span class='integer val'>1</span><span class='rbrack token'>]</span>
-<span class='end end kw'>end</span>
-</pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Tue Nov 30 11:09:42 2010 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.6.1 (ruby-1.8.6).
-</div>
-  </body>
-</html>

data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html DELETED Viewed

@@ -1,190 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta name="Content-Type" content="text/html; charset=utf-8" />
-<title>Class: CaTissue::SpecimenCollectionGroup</title>
-<link rel="stylesheet" href="../css/style.css" type="text/css" media="screen" charset="utf-8" />
-<link rel="stylesheet" href="../css/common.css" type="text/css" media="screen" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  relpath = '..';
-  if (relpath != '') relpath += '/';
-</script>
-<script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
-<script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
-  </head>
-  <body>
-    <script type="text/javascript" charset="utf-8">
-      if (window.top.frames.main) document.body.className = 'frames';
-    </script>
-    <div id="header">
-      <div id="menu">
-    <a href="../_index.html">Index (S)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
-     &raquo;
-    <span class="title">SpecimenCollectionGroup</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-  <a id="class_list_link" href="#">Class List</a>
-  <a id="method_list_link" href="#">Method List</a>
-  <a id ="file_list_link" href="#">File List</a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: CaTissue::SpecimenCollectionGroup
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">CaTissue::SpecimenCollectionGroup</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">examples/galena/lib/galena/migration/filter_shims.rb</dd>
-</dl>
-<div class="clear"></div>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#migration_valid%3F-instance_method" title="#migration_valid? (instance method)">- (Boolean) <strong>migration_valid?</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'><p>
-Returns whether this SCG has a SPN.
-</p>
-</div></span>
-</li>
-    </ul>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <p class="signature first" id="migration_valid?-instance_method">
-    - (<tt>Boolean</tt>) <strong>migration_valid?</strong>
-</p><div class="docstring">
-  <div class="discussion">
-    <p>
-Returns whether this SCG has a SPN.
-</p>
-  </div>
-</div>
-<div class="tags">
-  <h3>Returns:</h3>
-<ul class="return">
-    <li>
-        <span class='type'>(<tt>Boolean</tt>)</span>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-39
-40
-41</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/filter_shims.rb', line 39</span>
-<span class='def def kw'>def</span> <span class='migration_valid? fid id'>migration_valid?</span>
-  <span class='surgical_pathology_number identifier id'>surgical_pathology_number</span>
-<span class='end end kw'>end</span>
-</pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Tue Nov 30 11:09:43 2010 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.6.1 (ruby-1.8.6).
-</div>
-  </body>
-</html>

data/examples/galena/doc/CaTissue/StorageContainer.html DELETED Viewed

@@ -1,179 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta name="Content-Type" content="text/html; charset=utf-8" />
-<title>Class: CaTissue::StorageContainer</title>
-<link rel="stylesheet" href="../css/style.css" type="text/css" media="screen" charset="utf-8" />
-<link rel="stylesheet" href="../css/common.css" type="text/css" media="screen" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  relpath = '..';
-  if (relpath != '') relpath += '/';
-</script>
-<script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
-<script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
-  </head>
-  <body>
-    <script type="text/javascript" charset="utf-8">
-      if (window.top.frames.main) document.body.className = 'frames';
-    </script>
-    <div id="header">
-      <div id="menu">
-    <a href="../_index.html">Index (S)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
-     &raquo;
-    <span class="title">StorageContainer</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-  <a id="class_list_link" href="#">Class List</a>
-  <a id="method_list_link" href="#">Method List</a>
-  <a id ="file_list_link" href="#">File List</a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: CaTissue::StorageContainer
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">CaTissue::StorageContainer</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">examples/galena/lib/galena/migration/frozen_shims.rb</dd>
-</dl>
-<div class="clear"></div>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#migrate-instance_method" title="#migrate (instance method)">- (Object) <strong>migrate</strong>(row, migrated) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'><p>
-Creates the migrated box in the database, if necessary.
-</p>
-</div></span>
-</li>
-    </ul>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <p class="signature first" id="migrate-instance_method">
-    - (<tt>Object</tt>) <strong>migrate</strong>(row, migrated)
-</p><div class="docstring">
-  <div class="discussion">
-    <p>
-Creates the migrated box in the database, if necessary.
-</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-22
-23
-24
-25</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/frozen_shims.rb', line 22</span>
-<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>
-  <span class='super super kw'>super</span>
-  <span class='find identifier id'>find</span> <span class='or or kw'>or</span> <span class='create_box identifier id'>create_box</span>
-<span class='end end kw'>end</span>
-</pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Tue Nov 30 11:09:43 2010 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.6.1 (ruby-1.8.6).
-</div>
-  </body>
-</html>