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/CaTissue/SpecimenCollectionGroup.html ADDED Viewed

@@ -0,0 +1,190 @@
+<!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 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>

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

@@ -0,0 +1,179 @@
+<!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">
+32
+33
+34
+35</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/frozen_shims.rb', line 32</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 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>

data/examples/galena/doc/CaTissue/TissueSpecimen.html ADDED Viewed

@@ -0,0 +1,320 @@
+<!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::TissueSpecimen</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 (T)</a> &raquo;
+    <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
+     &raquo;
+    <span class="title">TissueSpecimen</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::TissueSpecimen
+</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::TissueSpecimen</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<span class="defines">,<br />
+  examples/galena/lib/galena/migration/frozen_shims.rb</span>
+</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>
+Sets the specimen type to <tt>Frozen Tissue</tt>.
+</p>
+</div></span>
+</li>
+        <li class="public ">
+  <span class="summary_signature">
+      <a href="#migrate_initial_quantity-instance_method" title="#migrate_initial_quantity (instance method)">- (Object) <strong>migrate_initial_quantity</strong>(value, row) </a>
+  </span>
+    <span class="summary_desc"><div class='inline'><p>
+Parses the source field as a UOM::Measurement if it is a string.
+</p>
+</div></span>
+</li>
+        <li class="public ">
+  <span class="summary_signature">
+      <a href="#migrate_specimen_type-instance_method" title="#migrate_specimen_type (instance method)">- (Object) <strong>migrate_specimen_type</strong>(value, row) </a>
+  </span>
+    <span class="summary_desc"><div class='inline'><p>
+Transforms the <tt>Frozen?</tt> flag input field to the caTissue specimen
+type <tt>Frozen Tissue</tt> value.
+</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>
+Sets the specimen type to <tt>Frozen Tissue</tt>.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+12
+13
+14
+15</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/frozen_shims.rb', line 12</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='self self kw'>self</span><span class='dot token'>.</span><span class='specimen_type identifier id'>specimen_type</span> <span class='assign token'>=</span> <span class='string val'>'Frozen Tissue'</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <div class="method_details ">
+  <p class="signature " id="migrate_initial_quantity-instance_method">
+    - (<tt>Object</tt>) <strong>migrate_initial_quantity</strong>(value, row)
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Parses the source field as a UOM::Measurement if it is a string.
+Otherwises, returns the source value.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+28
+29
+30
+31
+32
+33
+34</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/filter_shims.rb', line 28</span>
+<span class='def def kw'>def</span> <span class='migrate_initial_quantity identifier id'>migrate_initial_quantity</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='comment val'># if value is not a string, then use it as is</span>
+  <span class='return return kw'>return</span> <span class='value identifier id'>value</span> <span class='unless unless_mod kw'>unless</span> <span class='value identifier id'>value</span><span class='dot token'>.</span><span class='is_a? fid id'>is_a?</span><span class='lparen token'>(</span><span class='String constant id'>String</span><span class='rparen token'>)</span>
+  <span class='comment val'># the value has a unit qualifier; parse the measurement.</span>
+  <span class='comment val'># the unit is normalized to the Specimen standard unit.</span>
+  <span class='value identifier id'>value</span><span class='dot token'>.</span><span class='to_measurement_quantity identifier id'>to_measurement_quantity</span><span class='lparen token'>(</span><span class='standard_unit identifier id'>standard_unit</span><span class='rparen token'>)</span>
+<span class='end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+      <div class="method_details ">
+  <p class="signature " id="migrate_specimen_type-instance_method">
+    - (<tt>Object</tt>) <strong>migrate_specimen_type</strong>(value, row)
+</p><div class="docstring">
+  <div class="discussion">
+    <p>
+Transforms the <tt>Frozen?</tt> flag input field to the caTissue specimen
+type <tt>Frozen Tissue</tt> value.
+</p>
+  </div>
+</div>
+<div class="tags">
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+22
+23
+24</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/filter_shims.rb', line 22</span>
+<span class='def def kw'>def</span> <span class='migrate_specimen_type identifier id'>migrate_specimen_type</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='string val'>'Frozen Tissue'</span> <span class='if if_mod kw'>if</span> <span class='value identifier id'>value</span> <span class='match op'>=~</span> <span class='regexp val'>/TRUE/i</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>