caruby-tissue 1.2.1 → 1.2.2

data/examples/galena/conf/migration/general_fields.yaml

@@ -29,6 +29,8 @@ Diagnosis: SpecimenCollectionGroup.clinical_diagnosis
 
 Anatomic Site: SpecimenCharacteristics.tissue_site
 
+Development: TissueSpecimen.pathological_status
+
 Label: TissueSpecimen.label
 
 Type: TissueSpecimen.specimen_type

data/examples/galena/data/filter.csv

@@ -1 +1 @@
-Protocol,MRN,Initials,Frozen?,SPN,Collection Date,Quantity
+Protocol,MRN,Initials,Frozen?,SPN,Collection Date,Quantity

data/examples/galena/data/frozen.csv

@@ -1 +1 @@
-MRN,SPN,Collection Date,Quantity,Box,X,Y
+Protocol,MRN,SPN,Collection Date,Quantity,Box,X,Y

data/examples/galena/data/general.csv

@@ -1 +1 @@
-Protocol,Collection Site,MRN,First Name,Last Name,PPI,SPN,Collection Point,Receiver,Received Timestamp,Collector,Collected Timestamp,Diagnosis,Anatomic Site,Label,Type,Quantity,Box,X,Y
+Protocol,Collection Site,MRN,First Name,Last Name,PPI,SPN,Collection Point,Receiver,Received Timestamp,Collector,Collected Timestamp,Diagnosis,Anatomic Site,Development,Label,Type,Quantity,Box,X,Y

data/examples/galena/doc/CaTissue.html

@@ -72,7 +72,7 @@
     
    
     
-      <strong class="classes">Classes:</strong> <span class='object_link'><a href="CaTissue/CollectionProtocolRegistration.html" title="CaTissue::CollectionProtocolRegistration (class)">CollectionProtocolRegistration</a></span>, <span class='object_link'><a href="CaTissue/Participant.html" title="CaTissue::Participant (class)">Participant</a></span>, <span class='object_link'><a href="CaTissue/SpecimenCollectionGroup.html" title="CaTissue::SpecimenCollectionGroup (class)">SpecimenCollectionGroup</a></span>, <span class='object_link'><a href="CaTissue/StorageContainer.html" title="CaTissue::StorageContainer (class)">StorageContainer</a></span>, <span class='object_link'><a href="CaTissue/TissueSpecimen.html" title="CaTissue::TissueSpecimen (class)">TissueSpecimen</a></span>
+      <strong class="classes">Classes:</strong> <span class='object_link'><a href="CaTissue/Participant.html" title="CaTissue::Participant (class)">Participant</a></span>, <span class='object_link'><a href="CaTissue/SpecimenCollectionGroup.html" title="CaTissue::SpecimenCollectionGroup (class)">SpecimenCollectionGroup</a></span>, <span class='object_link'><a href="CaTissue/StorageContainer.html" title="CaTissue::StorageContainer (class)">StorageContainer</a></span>, <span class='object_link'><a href="CaTissue/TissueSpecimen.html" title="CaTissue::TissueSpecimen (class)">TissueSpecimen</a></span>
     
   
 </p>
@@ -84,7 +84,7 @@
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

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

@@ -232,7 +232,7 @@ Extracts the Participant last name from the <tt>Initials</tt> input field.
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

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

@@ -181,7 +181,7 @@ Returns whether this SCG has a SPN.
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

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

@@ -147,13 +147,13 @@ Creates the migrated box in the database, if necessary.
       <pre class="lines">
 
 
-32
-33
-34
-35</pre>
+22
+23
+24
+25</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/migration/frozen_shims.rb', line 32</span>
+      <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>
@@ -170,7 +170,7 @@ Creates the migrated box in the database, if necessary.
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

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

@@ -311,7 +311,7 @@ type <tt>Frozen Tissue</tt> value.
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

data/examples/galena/doc/Galena.html

@@ -59,25 +59,12 @@
   
   
     <dt class="r1 last">Defined in:</dt>
-    <dd class="r1 last">examples/galena/lib/galena.rb<span class="defines">,<br />
-  examples/galena/lib/galena/seed/defaults.rb</span>
-</dd>
+    <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>
-The caRuby Tissue Galena example module.
-</p>
-
-
-  </div>
-</div>
-<div class="tags">
-  
-</div><h2>Defined Under Namespace</h2>
+<h2>Defined Under Namespace</h2>
 <p class="children">
    
     
@@ -101,30 +88,6 @@ The caRuby Tissue Galena example module.
         <li class="public ">
   <span class="summary_signature">
     
-      <a href="#resource-class_method" title="resource (class method)">+ (String<sup>?</sup>) <strong>resource</strong>(path) </a>
-    
-
-    
-  </span>
-  
-  
-  
-  
-  
-  
-
-  
-    <span class="summary_desc"><div class='inline'><p>
-The file in this gem which matches the given path.
-</p>
-</div></span>
-  
-</li>
-
-      
-        <li class="public ">
-  <span class="summary_signature">
-    
       <a href="#seed-class_method" title="seed (class method)">+ (Object) <strong>seed</strong> </a>
     
 
@@ -156,88 +119,7 @@ Creates the <span class='object_link'><a href="Galena/Seed/Defaults.html" title=
     
     
       <div class="method_details first">
-  <p class="signature first" id="resource-class_method">
-  
-    + (<tt>String</tt><sup>?</sup>) <strong>resource</strong>(path) 
-  
-
-  
-</p><div class="docstring">
-  <div class="discussion">
-    <p>
-The file in this gem which matches the given path
-</p>
-
-
-  </div>
-</div>
-<div class="tags">
-  <h3>Parameters:</h3>
-<ul class="param">
-  
-    <li>
-      
-        <span class='type'>(<tt>String</tt>)</span>
-      
-      
-        <span class='name'>the</span>
-      
-      
-      
-        &mdash;
-        <div class='inline'><p>
-path (without wildcards) of the desired file relative to the gem root
-directory
-</p>
-</div>
-      
-    </li>
-  
-</ul>
-<h3>Returns:</h3>
-<ul class="return">
-  
-    <li>
-      
-        <span class='type'>(<tt>String</tt>, <tt>nil</tt>)</span>
-      
-      
-      
-      
-        &mdash;
-        <div class='inline'><p>
-the file in this gem which matches the given path
-</p>
-</div>
-      
-    </li>
-  
-</ul>
-
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-
-
-5
-6
-7</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena.rb', line 5</span>
-
-<span class='def def kw'>def</span> <span class='self self kw'>self</span><span class='dot token'>.</span><span class='resource identifier id'>resource</span><span class='lparen token'>(</span><span class='path identifier id'>path</span><span class='rparen token'>)</span>
-  <span class='File constant id'>File</span><span class='dot token'>.</span><span class='expand_path identifier id'>expand_path</span><span class='lparen token'>(</span><span class='File constant id'>File</span><span class='dot token'>.</span><span class='join identifier id'>join</span><span class='lparen token'>(</span><span class='File constant id'>File</span><span class='dot token'>.</span><span class='dirname identifier id'>dirname</span><span class='lparen token'>(</span><span class='__FILE__ __file__ kw'>__FILE__</span><span class='rparen token'>)</span><span class='comma token'>,</span> <span class='string val'>'..'</span><span class='comma token'>,</span> <span class='path identifier id'>path</span><span class='rparen token'>)</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="seed-class_method">
+  <p class="signature first" id="seed-class_method">
   
     + (<tt>Object</tt>) <strong>seed</strong> 
   
@@ -281,7 +163,7 @@ Creates the <span class='object_link'><a href="Galena/Seed/Defaults.html" title=
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

data/examples/galena/doc/Galena/Seed.html

@@ -194,7 +194,7 @@ the defaults instance
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:42 2010 by 
+  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>

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

@@ -102,7 +102,9 @@ secondary key rather than content, e.g.:
 </pre>
 <p>
 The complete definitions are included in this method for convenience in
-order to seed the example in a test database.
+order to seed the example in a test database. A real-world migration might
+find it useful to create a similar defaults file in order to rapidly seed
+an empty test or staging database.
 </p>
 
 
@@ -343,13 +345,13 @@ Creates the Galena example Defaults singleton and populates the attributes.
       <pre class="lines">
 
 
-33
 34
 35
-36</pre>
+36
+37</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 33</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 34</span>
 
 <span class='def def kw'>def</span> <span class='initialize identifier id'>initialize</span>
   <span class='super super kw'>super</span>
@@ -393,12 +395,12 @@ Returns the value of attribute box_type
       <pre class="lines">
 
 
-30
 31
-32</pre>
+32
+33</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</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>
@@ -436,12 +438,12 @@ Returns the value of attribute freezer_type
       <pre class="lines">
 
 
-30
 31
-32</pre>
+32
+33</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</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>
@@ -479,12 +481,12 @@ Returns the value of attribute hospital
       <pre class="lines">
 
 
-30
 31
-32</pre>
+32
+33</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
 
 <span class='def def kw'>def</span> <span class='hospital identifier id'>hospital</span>
   <span class='@hospital ivar id'>@hospital</span>
@@ -522,12 +524,12 @@ Returns the value of attribute protocol
       <pre class="lines">
 
 
-30
 31
-32</pre>
+32
+33</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</span>
 
 <span class='def def kw'>def</span> <span class='protocol identifier id'>protocol</span>
   <span class='@protocol ivar id'>@protocol</span>
@@ -565,12 +567,12 @@ Returns the value of attribute tissue_bank
       <pre class="lines">
 
 
-30
 31
-32</pre>
+32
+33</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 30</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 31</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>
@@ -612,19 +614,21 @@ Creates the Galena example administrative objects as necessary.
       <pre class="lines">
 
 
-39
 40
 41
 42
-43</pre>
+43
+44
+45</pre>
     </td>
     <td>
-      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 39</span>
+      <pre class="code"><span class="info file"># File 'examples/galena/lib/galena/seed/defaults.rb', line 40</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='@surgeon ivar id'>@surgeon</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='@box ivar id'>@box</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>
@@ -637,7 +641,7 @@ Creates the Galena example administrative objects as necessary.
 </div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:43 2010 by 
+  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>

data/examples/galena/doc/_index.html

@@ -76,13 +76,6 @@
                   
                 </li>
               
-                <li>
-                  <span class='object_link'><a href="CaTissue/CollectionProtocolRegistration.html" title="CaTissue::CollectionProtocolRegistration (class)">CollectionProtocolRegistration</a></span> 
-                  
-                    <small>(CaTissue)</small>
-                  
-                </li>
-              
             </ul>
           </ul>
         
@@ -179,7 +172,7 @@
 </div></div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:42 2010 by 
+  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>

data/examples/galena/doc/class_list.html

@@ -27,7 +27,7 @@
 
       <ul id="full_list" class="class">
         <li><span class='object_link'><a href="top-level-namespace.html" title=" (root)">Top Level Namespace</a></span></li>
-<li><a class='toggle'></a> <span class='object_link'><a href="CaTissue.html" title="CaTissue (module)">CaTissue</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><span class='object_link'><a href="CaTissue/CollectionProtocolRegistration.html" title="CaTissue::CollectionProtocolRegistration (class)">CollectionProtocolRegistration</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/Participant.html" title="CaTissue::Participant (class)">Participant</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/SpecimenCollectionGroup.html" title="CaTissue::SpecimenCollectionGroup (class)">SpecimenCollectionGroup</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/StorageContainer.html" title="CaTissue::StorageContainer (class)">StorageContainer</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/TissueSpecimen.html" title="CaTissue::TissueSpecimen (class)">TissueSpecimen</a></span> &lt; Object<small class='search_info'>CaTissue</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Galena.html" title="Galena (module)">Galena</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Galena/Seed.html" title="Galena::Seed (module)">Seed</a></span><small class='search_info'>Galena</small></li><ul><li><span class='object_link'><a href="Galena/Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Defaults</a></span> &lt; Object<small class='search_info'>Galena::Seed</small></li></ul></ul>
+<li><a class='toggle'></a> <span class='object_link'><a href="CaTissue.html" title="CaTissue (module)">CaTissue</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><span class='object_link'><a href="CaTissue/Participant.html" title="CaTissue::Participant (class)">Participant</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/SpecimenCollectionGroup.html" title="CaTissue::SpecimenCollectionGroup (class)">SpecimenCollectionGroup</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/StorageContainer.html" title="CaTissue::StorageContainer (class)">StorageContainer</a></span> &lt; Object<small class='search_info'>CaTissue</small></li><li><span class='object_link'><a href="CaTissue/TissueSpecimen.html" title="CaTissue::TissueSpecimen (class)">TissueSpecimen</a></span> &lt; Object<small class='search_info'>CaTissue</small></li></ul><li><a class='toggle'></a> <span class='object_link'><a href="Galena.html" title="Galena (module)">Galena</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Galena/Seed.html" title="Galena::Seed (module)">Seed</a></span><small class='search_info'>Galena</small></li><ul><li><span class='object_link'><a href="Galena/Seed/Defaults.html" title="Galena::Seed::Defaults (class)">Defaults</a></span> &lt; Object<small class='search_info'>Galena::Seed</small></li></ul></ul>
 
       </ul>
     </div>

data/examples/galena/doc/file.README.html

@@ -70,8 +70,8 @@ The use cases illustrate several common migration impediments:</p>
 <li><p>Copy the example into a location of your choosing.</p></li>
 <li><p>Configure a caTissue client to connect to a test caTissue instance, as described in the
 caTissue Technical Guide.</p></li>
-<li><p>Define the caRuby Tissue access property file as described in
-<a href="FAQ">http://caruby.tenderapp.com/faqs/getting-started/tissue_config</a>.</p></li>
+<li><p>Define the caRuby Tissue access property file as described in the configuration
+<a href="how-do-i-configure-caruby-to-work-with-catissue">FAQ</a>.</p></li>
 </ol>
 
 
@@ -90,16 +90,61 @@ For example, the <code>simple.csv</code> input file is migrated into caTissue us
 <li><p>Open a console in the copied Galena example location.</p></li>
 <li><p>Run the following:</p>
 
-<p>   crtmigrate --file conf/migration/simple.yaml data/simple.yaml</p></li>
-<li><p>Check the test database and verify that a there is a collection protocol
-named `Galena CP.</p></li>
+<p>   bin/seed</p>
+
+<p>This command initializes the administrative objects in the Galena test database,
+including the Galena collection protocol, site, cancer center, tissue bank and coordinator.</p></li>
+<li><p>Run the following:</p>
+
+<p>   crtmigrate --target TissueSpecimen --mapping conf/migration/simple_fields.yaml data/simple.csv</p>
+
+<p>This command migrates the CSV record in the <code>simple.csv</code> input file into a caTissue
+<code>TissueSpecimen</code> based on the <code>simple_fields.yaml</code> mapping file.
+The command will take a couple of minutes to finish, since the less information
+you provide caRuby the more it works to fill in the missing bits. In the meantime,
+peruse the configuration and data files to see which data are migrated and
+where this data ends up in caTissue.</p></li>
+<li><p>Open the caTissue application on the test server and verify the content of the
+Galena CP collection protocol.</p></li>
 </ol>
 
 
-<p>The other examples are run in a similar manner.</p></div></div>
+<p>The other examples are run in a similar manner. Each example demonstrates different
+features of the caRuby Migration utility as follows:</p>
+
+<ul>
+<li>simple - a good starting point with limited input fields</li>
+<li>minimal - the fewest possible input fields without writing custom Ruby shim code</li>
+<li>general - lots of input fields, no custom Ruby code</li>
+<li>filter - a smattering of custom Ruby shim code to convert input values to caTissue values</li>
+<li>frozen - an example demonstrating how to import storage locations</li>
+</ul>
+
+
+<p>Try running an example with the <code>--debug</code> flag and look at the <code>log/migration.log</code> file to see
+what caRuby is up to behind the scenes (hint: a lot!).</p>
+
+<h2>Input data</h2>
+
+<p>The sample Galena Tissue Bank CSV input files hold one row for each specimen.
+Common fields are as follows:</p>
+
+<ul>
+<li>MRN - Patient Medical Record Number</li>
+<li>Initials - Patient name initials</li>
+<li>Frozen? - Flag indicating whether the specimen is frozen</li>
+<li>SPN - Surgical Pathology Number</li>
+<li>Collection Date - Date the specimen was acquired by the tissue bank</li>
+<li>Received Date - Date the specimen was donated by the participant</li>
+<li>Quantity - Amount collected</li>
+<li>Box - Tissue storage container</li>
+<li>X - the tissue box column</li>
+<li>Y - the tissue box row</li>
+</ul>
+</div></div>
     
     <div id="footer">
-  Generated on Tue Nov 23 11:38:42 2010 by 
+  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>