RubyGems - caruby-tissue - Versions diffs - 1.2.1 - Mend

caruby-tissue 1.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (133) hide show

data/History.txt +4 -0
data/LEGAL +5 -0
data/LICENSE +22 -0
data/README.md +44 -0
data/bin/crtdump +31 -0
data/bin/crtexample +18 -0
data/bin/crtextract +47 -0
data/bin/crtmigrate +17 -0
data/bin/crtsmoke +27 -0
data/examples/galena/README.md +53 -0
data/examples/galena/bin/migrate.rb +42 -0
data/examples/galena/bin/seed.rb +43 -0
data/examples/galena/conf/extract/simple_fields.yaml +4 -0
data/examples/galena/conf/migration/filter_fields.yaml +7 -0
data/examples/galena/conf/migration/filter_migration.yaml +9 -0
data/examples/galena/conf/migration/frozen_fields.yaml +11 -0
data/examples/galena/conf/migration/frozen_migration.yaml +9 -0
data/examples/galena/conf/migration/general_fields.yaml +42 -0
data/examples/galena/conf/migration/general_migration.yaml +9 -0
data/examples/galena/conf/migration/simple_fields.yaml +30 -0
data/examples/galena/conf/migration/simple_migration.yaml +7 -0
data/examples/galena/conf/migration/small_fields.yaml +24 -0
data/examples/galena/conf/migration/small_migration.yaml +9 -0
data/examples/galena/data/filter.csv +1 -0
data/examples/galena/data/frozen.csv +1 -0
data/examples/galena/data/general.csv +1 -0
data/examples/galena/data/minimal.csv +1 -0
data/examples/galena/data/simple.csv +1 -0
data/examples/galena/data/small.csv +1 -0
data/examples/galena/doc/CaTissue.html +93 -0
data/examples/galena/doc/CaTissue/CollectionProtocolRegistration.html +181 -0
data/examples/galena/doc/CaTissue/Participant.html +241 -0
data/examples/galena/doc/CaTissue/SpecimenCollectionGroup.html +190 -0
data/examples/galena/doc/CaTissue/StorageContainer.html +179 -0
data/examples/galena/doc/CaTissue/TissueSpecimen.html +320 -0
data/examples/galena/doc/Galena.html +290 -0
data/examples/galena/doc/Galena/Seed.html +203 -0
data/examples/galena/doc/Galena/Seed/Defaults.html +646 -0
data/examples/galena/doc/_index.html +188 -0
data/examples/galena/doc/class_list.html +36 -0
data/examples/galena/doc/css/common.css +1 -0
data/examples/galena/doc/css/full_list.css +53 -0
data/examples/galena/doc/css/style.css +307 -0
data/examples/galena/doc/file.README.html +108 -0
data/examples/galena/doc/file_list.html +38 -0
data/examples/galena/doc/frames.html +13 -0
data/examples/galena/doc/index.html +108 -0
data/examples/galena/doc/js/app.js +202 -0
data/examples/galena/doc/js/full_list.js +149 -0
data/examples/galena/doc/js/jquery.js +154 -0
data/examples/galena/doc/method_list.html +179 -0
data/examples/galena/doc/top-level-namespace.html +112 -0
data/examples/galena/lib/README.html +33 -0
data/examples/galena/lib/galena.rb +8 -0
data/examples/galena/lib/galena/cli/seed.rb +43 -0
data/examples/galena/lib/galena/migration/filter_shims.rb +43 -0
data/examples/galena/lib/galena/migration/frozen_shims.rb +54 -0
data/examples/galena/lib/galena/seed/defaults.rb +97 -0
data/lib/catissue.rb +26 -0
data/lib/catissue/cli/command.rb +51 -0
data/lib/catissue/cli/example.rb +31 -0
data/lib/catissue/cli/migrate.rb +60 -0
data/lib/catissue/cli/smoke.rb +45 -0
data/lib/catissue/database.rb +451 -0
data/lib/catissue/database/annotation/annotatable_service.rb +25 -0
data/lib/catissue/database/annotation/annotation_service.rb +79 -0
data/lib/catissue/database/annotation/annotator.rb +84 -0
data/lib/catissue/database/annotation/entity_manager.rb +10 -0
data/lib/catissue/database/annotation/integration_service.rb +87 -0
data/lib/catissue/database/controlled_value_finder.rb +43 -0
data/lib/catissue/database/controlled_values.rb +162 -0
data/lib/catissue/domain/abstract_domain_object.rb +8 -0
data/lib/catissue/domain/abstract_position.rb +22 -0
data/lib/catissue/domain/abstract_specimen.rb +288 -0
data/lib/catissue/domain/abstract_specimen_collection_group.rb +25 -0
data/lib/catissue/domain/address.rb +13 -0
data/lib/catissue/domain/cancer_research_group.rb +11 -0
data/lib/catissue/domain/capacity.rb +34 -0
data/lib/catissue/domain/check_in_check_out_event_parameter.rb +19 -0
data/lib/catissue/domain/collection_event_parameters.rb +13 -0
data/lib/catissue/domain/collection_protocol.rb +177 -0
data/lib/catissue/domain/collection_protocol_event.rb +108 -0
data/lib/catissue/domain/collection_protocol_registration.rb +108 -0
data/lib/catissue/domain/consent_tier_response.rb +13 -0
data/lib/catissue/domain/consent_tier_status.rb +29 -0
data/lib/catissue/domain/container.rb +234 -0
data/lib/catissue/domain/container_position.rb +21 -0
data/lib/catissue/domain/container_type.rb +131 -0
data/lib/catissue/domain/department.rb +13 -0
data/lib/catissue/domain/disposal_event_parameters.rb +13 -0
data/lib/catissue/domain/embedded_event_parameters.rb +10 -0
data/lib/catissue/domain/external_identifier.rb +22 -0
data/lib/catissue/domain/frozen_event_parameters.rb +10 -0
data/lib/catissue/domain/institution.rb +13 -0
data/lib/catissue/domain/new_specimen_array_order_item.rb +35 -0
data/lib/catissue/domain/order_details.rb +25 -0
data/lib/catissue/domain/participant.rb +138 -0
data/lib/catissue/domain/participant_medical_identifier.rb +38 -0
data/lib/catissue/domain/password.rb +11 -0
data/lib/catissue/domain/race.rb +11 -0
data/lib/catissue/domain/received_event_parameters.rb +25 -0
data/lib/catissue/domain/scg_event_parameters.rb +11 -0
data/lib/catissue/domain/site.rb +30 -0
data/lib/catissue/domain/specimen.rb +456 -0
data/lib/catissue/domain/specimen_array.rb +47 -0
data/lib/catissue/domain/specimen_array_content.rb +19 -0
data/lib/catissue/domain/specimen_array_type.rb +20 -0
data/lib/catissue/domain/specimen_characteristics.rb +20 -0
data/lib/catissue/domain/specimen_collection_group.rb +412 -0
data/lib/catissue/domain/specimen_event_parameters.rb +111 -0
data/lib/catissue/domain/specimen_position.rb +38 -0
data/lib/catissue/domain/specimen_protocol.rb +34 -0
data/lib/catissue/domain/specimen_requirement.rb +143 -0
data/lib/catissue/domain/storage_container.rb +204 -0
data/lib/catissue/domain/storage_type.rb +82 -0
data/lib/catissue/domain/transfer_event_parameters.rb +53 -0
data/lib/catissue/domain/user.rb +100 -0
data/lib/catissue/extract/command.rb +31 -0
data/lib/catissue/extract/delta.rb +62 -0
data/lib/catissue/extract/extractor.rb +99 -0
data/lib/catissue/migration/migrator.rb +101 -0
data/lib/catissue/migration/shims.rb +108 -0
data/lib/catissue/migration/uniquify.rb +111 -0
data/lib/catissue/resource.rb +84 -0
data/lib/catissue/util/controlled_value.rb +29 -0
data/lib/catissue/util/location.rb +116 -0
data/lib/catissue/util/log.rb +30 -0
data/lib/catissue/util/person.rb +31 -0
data/lib/catissue/util/position.rb +54 -0
data/lib/catissue/util/storable.rb +34 -0
data/lib/catissue/util/storage_type_holder.rb +30 -0
data/lib/catissue/version.rb +7 -0
metadata +212 -0

data/examples/galena/doc/Galena/Seed/Defaults.html ADDED Viewed

@@ -0,0 +1,646 @@
+<!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: Galena::Seed::Defaults</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 (D)</a> &raquo;
+    <span class='title'><span class='object_link'><a href="../../Galena.html" title="Galena (module)">Galena</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../Seed.html" title="Galena::Seed (module)">Seed</a></span></span>
+     &raquo;
+    <span class="title">Defaults</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: Galena::Seed::Defaults
+</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">Galena::Seed::Defaults</li>
+        </ul>
+        <a href="#" class="inheritanceTree">show all</a>
+      </dd>
+      <dt class="r2">Includes:</dt>
+      <dd class="r2">Singleton</dd>
+    <dt class="r1 last">Defined in:</dt>
+    <dd class="r1 last">examples/galena/lib/galena/seed/defaults.rb</dd>
+</dl>
+<div class="clear"></div>
+<h2>Overview</h2><div class="docstring">
+  <div class="discussion">
+    <p>
+Pre-defined Galena example administrative objects. If the Galena example is
+already set up in the caTissue database, then the default object secondary
+key attributes can be used as a CaRuby::Persistable#find template to
+retrieve the existing objects. Otherwise, the Defaults attributes can be
+created by calling CaRuby::Persistable#create.
+</p>
+<p>
+In a real-world use case, the administrative objects are typically built in
+the UI before-hand. In that case, it is only necessary to define the object
+secondary key rather than content, e.g.:
+</p>
+<pre class="code">
+  <span class='pcl identifier id'>pcl</span> <span class='assign token'>=</span> <span class='CaTissue constant id'>CaTissue</span><span class='colon2 op'>::</span><span class='CollectionProtocol constant id'>CollectionProtocol</span><span class='dot token'>.</span><span class='new identifier id'>new</span><span class='lparen token'>(</span><span class='symbol val'>:short_title</span> <span class='assign token'>=</span><span class='gt op'>&gt;</span> <span class='string val'>'Galena CP'</span><span class='rparen token'>)</span>
+</pre>
+<p>
+The complete definitions are included in this method for convenience in
+order to seed the example in a test database.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div>
+  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
+  <ul class="summary">
+      <li class="public ">
+  <span class="summary_signature">
+      <a href="#box_type-instance_method" title="#box_type (instance method)">- (Object) <strong>box_type</strong> </a>
+  </span>
+    <span class="note title readonly">readonly</span>
+    <span class="summary_desc"><div class='inline'><p>
+Returns the value of attribute box_type.
+</p>
+</div></span>
+</li>
+      <li class="public ">
+  <span class="summary_signature">
+      <a href="#freezer_type-instance_method" title="#freezer_type (instance method)">- (Object) <strong>freezer_type</strong> </a>
+  </span>
+    <span class="note title readonly">readonly</span>
+    <span class="summary_desc"><div class='inline'><p>
+Returns the value of attribute freezer_type.
+</p>
+</div></span>
+</li>
+      <li class="public ">
+  <span class="summary_signature">
+      <a href="#hospital-instance_method" title="#hospital (instance method)">- (Object) <strong>hospital</strong> </a>
+  </span>
+    <span class="note title readonly">readonly</span>
+    <span class="summary_desc"><div class='inline'><p>
+Returns the value of attribute hospital.
+</p>
+</div></span>
+</li>
+      <li class="public ">
+  <span class="summary_signature">
+      <a href="#protocol-instance_method" title="#protocol (instance method)">- (Object) <strong>protocol</strong> </a>
+  </span>
+    <span class="note title readonly">readonly</span>
+    <span class="summary_desc"><div class='inline'><p>
+Returns the value of attribute protocol.
+</p>
+</div></span>
+</li>
+      <li class="public ">
+  <span class="summary_signature">
+      <a href="#tissue_bank-instance_method" title="#tissue_bank (instance method)">- (Object) <strong>tissue_bank</strong> </a>
+  </span>
+    <span class="note title readonly">readonly</span>
+    <span class="summary_desc"><div class='inline'><p>
+Returns the value of attribute tissue_bank.
+</p>
+</div></span>
+</li>
+  </ul>
+    <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="#ensure_exists-instance_method" title="#ensure_exists (instance method)">- (Object) <strong>ensure_exists</strong> </a>
+  </span>
+    <span class="summary_desc"><div class='inline'><p>
+Creates the Galena example administrative objects as necessary.
+</p>
+</div></span>
+</li>
+        <li class="public ">
+  <span class="summary_signature">
+      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Defaults) <strong>initialize</strong> </a>
+  </span>
+    <span class="note title constructor">constructor</span>
+    <span class="summary_desc"><div class='inline'><p>
+Creates the Galena example Defaults singleton and populates the attributes.
+</p>
+</div></span>
+</li>
+    </ul>
+  <div id="constructor_details" class="method_details_list">
+  <h2>Constructor Details</h2>
+    <div class="method_details first">
+  <p class="signature first" id="initialize-instance_method">
+    - (<tt><span class='object_link'><a href="" title="Galena::Seed::Defaults (class)">Defaults</a></span></tt>) <strong>initialize</strong>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Creates the Galena example Defaults singleton and populates the attributes.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+33
+34
+35
+36</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 33</span>
+<span class='def def kw'>def</span> <span class='initialize identifier id'>initialize</span>
+  <span class='super super kw'>super</span>
+  <span class='populate identifier id'>populate</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+</div>
+  <div id="instance_attr_details" class="attr_details">
+    <h2>Instance Attribute Details</h2>
+      <span id=""></span>
+      <span id="box_type-instance_method"></span>
+      <div class="method_details first">
+  <p class="signature first" id="box_type-instance_method">
+    - (<tt>Object</tt>) <strong>box_type</strong>  <span class="extras">(readonly)</span>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Returns the value of attribute box_type
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+30
+31
+32</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+<span class='def def kw'>def</span> <span class='box_type identifier id'>box_type</span>
+  <span class='@box_type ivar id'>@box_type</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <span id=""></span>
+      <span id="freezer_type-instance_method"></span>
+      <div class="method_details ">
+  <p class="signature " id="freezer_type-instance_method">
+    - (<tt>Object</tt>) <strong>freezer_type</strong>  <span class="extras">(readonly)</span>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Returns the value of attribute freezer_type
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+30
+31
+32</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+<span class='def def kw'>def</span> <span class='freezer_type identifier id'>freezer_type</span>
+  <span class='@freezer_type ivar id'>@freezer_type</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <span id=""></span>
+      <span id="hospital-instance_method"></span>
+      <div class="method_details ">
+  <p class="signature " id="hospital-instance_method">
+    - (<tt>Object</tt>) <strong>hospital</strong>  <span class="extras">(readonly)</span>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Returns the value of attribute hospital
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+30
+31
+32</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+<span class='def def kw'>def</span> <span class='hospital identifier id'>hospital</span>
+  <span class='@hospital ivar id'>@hospital</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <span id=""></span>
+      <span id="protocol-instance_method"></span>
+      <div class="method_details ">
+  <p class="signature " id="protocol-instance_method">
+    - (<tt>Object</tt>) <strong>protocol</strong>  <span class="extras">(readonly)</span>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Returns the value of attribute protocol
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+30
+31
+32</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+<span class='def def kw'>def</span> <span class='protocol identifier id'>protocol</span>
+  <span class='@protocol ivar id'>@protocol</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <span id=""></span>
+      <span id="tissue_bank-instance_method"></span>
+      <div class="method_details ">
+  <p class="signature " id="tissue_bank-instance_method">
+    - (<tt>Object</tt>) <strong>tissue_bank</strong>  <span class="extras">(readonly)</span>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Returns the value of attribute tissue_bank
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+30
+31
+32</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+<span class='def def kw'>def</span> <span class='tissue_bank identifier id'>tissue_bank</span>
+  <span class='@tissue_bank ivar id'>@tissue_bank</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+  </div>
+  <div id="instance_method_details" class="method_details_list">
+    <h2>Instance Method Details</h2>
+      <div class="method_details first">
+  <p class="signature first" id="ensure_exists-instance_method">
+    - (<tt>Object</tt>) <strong>ensure_exists</strong>
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Creates the Galena example administrative objects as necessary.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+39
+40
+41
+42
+43</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 39</span>
+<span class='def def kw'>def</span> <span class='ensure_exists identifier id'>ensure_exists</span>
+  <span class='@protocol ivar id'>@protocol</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
+  <span class='@hospital ivar id'>@hospital</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
+  <span class='@freezer_type ivar id'>@freezer_type</span><span class='dot token'>.</span><span class='find identifier id'>find</span><span class='lparen token'>(</span><span class='symbol val'>:create</span><span class='rparen token'>)</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+  </div>
+</div>
+    <div id="footer">
+  Generated on Tue Nov 23 11:38:43 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>