caruby-tissue 1.2.1

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

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+#
+# This is the Galena general example migration configuration file.
+#
+
+# The field heading => CaTissue mapping file.
+mapping: examples/galena/conf/migration/general_fields.yaml
+
+# The migration target class for each record.
+target: TissueSpecimen

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

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+# This is the Galena simple example migration field mapping file.
+# Each entry is in the format:
+#   heading: paths
+# The heading is the CSV file label in the leading heading record.
+# The paths is a comma-separated list of CaTissue domain object attribute paths specifying
+# how the CSV heading maps to a CaTissue attribute value. Each attribute path is in the format:
+#   class.attribute[.attribute]
+# where class is a CaTissue class and attribute is a Ruby accessor method defined in the CaTissue class.
+# The accessor method can be one of the following:
+# * a Java property name, e.g. lastName
+# * the pre-defined Rubyized underscore form of the Java property, e.g. last_name
+
+# The collection protocol title for the specimen
+Protocol: CollectionProtocol.short_title
+
+# The input MRN field is used for the PMI MRN, CPR PPI and Participant last name.
+# Since the migration source is for a single collection site, the MRN is unique within the protocol.
+# The simple input does not have a Participant name field. It is a useful practice to set the caTissue
+# name to some value, since caTissue uses the name for display and sorting. For want of a better
+# value, the name is set to the MRN.
+MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
+
+# The input SPN field is the SCG SPN value.
+SPN: SpecimenCollectionGroup.surgical_pathology_number
+
+# The input Collection Date is the Specimen received timestamp.
+Collection Date: ReceivedEventParameters.timestamp
+
+# The input Quantity is the target Specimen initial quantity.
+Quantity: Specimen.initial_quantity

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

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+# This is the Galena simple example migration configuration file.
+
+# The field heading => CaTissue mapping file.
+mapping: examples/galena/conf/migration/simple_fields.yaml
+
+# The migration target class for each record.
+target: TissueSpecimen

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

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+# This is the Galena example tiny migration field mapping file.
+# This example input has all of the fields necessary to create a specimen.
+# The example does not use a shim.
+
+# The collection protocol title for the specimen
+Protocol: CollectionProtocol.short_title
+
+# The input MRN field is used for the PMI MRN, CPR PPI and Participant last name
+MRN: ParticipantMedicalIdentifier.medical_record_number, Participant.last_name
+
+# The input SPN field is the SCG SPN value
+SPN: SpecimenCollectionGroup.surgical_pathology_number
+
+# The date the specimen was received
+Received Date: ReceivedEventParameters.timestamp
+
+# The specimen label
+Label: TissueSpecimen.label
+
+# The type of the specimen
+Type: TissueSpecimen.specimen_type
+
+# The specimen amount
+Quantity: TissueSpecimen.initial_quantity

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

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+#
+# This is the Galena tiny example migration configuration file.
+#
+
+# The field heading => CaTissue mapping file.
+mapping: examples/galena/conf/migration/tiny_fields.yaml
+
+# The migration target class for each record.
+target: TissueSpecimen

data/examples/galena/data/filter.csv

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+Protocol,MRN,Initials,Frozen?,SPN,Collection Date,Quantity

data/examples/galena/data/frozen.csv

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+MRN,SPN,Collection Date,Quantity,Box,X,Y

data/examples/galena/data/general.csv

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+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

data/examples/galena/data/minimal.csv

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+Protocol,PPI,Label,Received Date

data/examples/galena/data/simple.csv

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+Protocol,MRN,SPN,Collection Date,Quantity

data/examples/galena/data/small.csv

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+Protocol,MRN,SPN,Label,Received Date,Type,Quantity

data/examples/galena/doc/CaTissue.html

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+<!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>Module: CaTissue</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 (C)</a> &raquo; 
+    
+    
+    <span class="title">CaTissue</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>Module: CaTissue
+  
+  
+  
+</h1>
+
+<dl class="box">
+  
+  
+    
+  
+    
+  
+  
+  
+    <dt class="r1 last">Defined in:</dt>
+    <dd class="r1 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>Defined Under Namespace</h2>
+<p class="children">
+   
+    
+   
+    
+      <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>
+    
+  
+</p>
+
+
+
+
+
+</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/CollectionProtocolRegistration.html

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+<!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::CollectionProtocolRegistration</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 (C)</a> &raquo; 
+    <span class='title'><span class='object_link'><a href="../CaTissue.html" title="CaTissue (module)">CaTissue</a></span></span>
+     &raquo; 
+    <span class="title">CollectionProtocolRegistration</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::CollectionProtocolRegistration
+  
+  
+  
+</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::CollectionProtocolRegistration</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>
+Sets this CPR&#8217;s protocol to the pre-defined
+Galena::Migration::Defaults#protocol.
+</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 this CPR&#8217;s protocol to the pre-defined
+Galena::Migration::Defaults#protocol.
+</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='self self kw'>self</span><span class='dot token'>.</span><span class='protocol identifier id'>protocol</span> <span class='assign token'>=</span> <span class='Galena constant id'>Galena</span><span class='colon2 op'>::</span><span class='Seed constant id'>Seed</span><span class='dot token'>.</span><span class='defaults identifier id'>defaults</span><span class='dot token'>.</span><span class='protocol identifier id'>protocol</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/Participant.html

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+<!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 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>