caruby-tissue 1.2.2 → 1.2.3

data/examples/galena/doc/css/style.css

@@ -1,307 +0,0 @@
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-

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

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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-  
-    <a href="_index.html" title="Index">Index</a> &raquo; 
-    <span class="title">File: README</span>
-  
-  
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
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-  <a id="class_list_link" href="#">Class List</a>
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-  <a id ="file_list_link" href="#">File List</a>
-</div>
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-    </div>
-    
-    <iframe id="search_frame"></iframe>
-    
-    <div id="content"><div id='filecontents'><h1>Galena caRuby Tissue example</h1>
-
-<h2>Synopsis</h2>
-
-<p>This directory contains the caRuby Tissue example for the hypothetical Galena Cancer Center.
-The example files are a useful template for building your own migrator.</p>
-
-<p>The Galena example demonstrates how to load the content of a custom tissue bank into caTissue.
-The use cases illustrate several common migration impediments:</p>
-
-<ul>
-<li>Different terminology than caTissue</li>
-<li>Different associations than caTissue</li>
-<li>Incomplete input for caTissue</li>
-<li>Denormalized input</li>
-<li>Inconsistent input</li>
-<li>Input data scrubbing</li>
-<li>Aliquot inference</li>
-<li>Pre-defined caTissue protocol</li>
-</ul>
-
-
-<h2>Setup</h2>
-
-<ol>
-<li><p>Run the <code>crtexample --list</code> command to display the Galena example location.</p></li>
-<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 the configuration
-<a href="how-do-i-configure-caruby-to-work-with-catissue">FAQ</a>.</p></li>
-</ol>
-
-
-<h2>Migration</h2>
-
-<p>The example migration input data resides in the <code>data</code> directory.
-Each CSV input file holds one row for each specimen.</p>
-
-<p>Each example has a field mapping configuration in the <code>conf/migration</code> directory.
-For example, the <code>simple.csv</code> input file is migrated into caTissue using the
-<code>simple_migration.yaml</code> configuration file.</p>
-
-<p>Migrate the Galena <code>simple</code> example as follows:</p>
-
-<ol>
-<li><p>Open a console in the copied Galena example location.</p></li>
-<li><p>Run the following:</p>
-
-<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. 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 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/file_list.html

@@ -1,38 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-    <script type="text/javascript" charset="utf-8">
-      if (window.top.frames.main) {
-        document.getElementById('base_target').target = 'main';
-        document.body.className = 'frames';
-      }
-    </script>
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-
-      <ul id="full_list" class="files">
-        
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-  
-
-      </ul>
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-  </body>
-</html>
-

data/examples/galena/doc/frames.html

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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
-	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
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-  <frame name="main" src="index.html" />
-</frameset>
-</html>

data/examples/galena/doc/index.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>Documentation by YARD 0.6.1</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" />
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-</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>
-
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-    <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" title="Index">Index</a> &raquo; 
-    <span class="title">File: README</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"><div id='filecontents'><h1>Galena caRuby Tissue example</h1>
-
-<h2>Synopsis</h2>
-
-<p>This directory contains the caRuby Tissue example for the hypothetical Galena Cancer Center.
-The example files are a useful template for building your own migrator.</p>
-
-<p>The Galena example demonstrates how to load the content of a custom tissue bank into caTissue.
-The use cases illustrate several common migration impediments:</p>
-
-<ul>
-<li>Different terminology than caTissue</li>
-<li>Different associations than caTissue</li>
-<li>Incomplete input for caTissue</li>
-<li>Denormalized input</li>
-<li>Inconsistent input</li>
-<li>Input data scrubbing</li>
-<li>Aliquot inference</li>
-<li>Pre-defined caTissue protocol</li>
-</ul>
-
-
-<h2>Setup</h2>
-
-<ol>
-<li><p>Run the <code>crtexample --list</code> command to display the Galena example location.</p></li>
-<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 the configuration
-<a href="how-do-i-configure-caruby-to-work-with-catissue">FAQ</a>.</p></li>
-</ol>
-
-
-<h2>Migration</h2>
-
-<p>The example migration input data resides in the <code>data</code> directory.
-Each CSV input file holds one row for each specimen.</p>
-
-<p>Each example has a field mapping configuration in the <code>conf/migration</code> directory.
-For example, the <code>simple.csv</code> input file is migrated into caTissue using the
-<code>simple_migration.yaml</code> configuration file.</p>
-
-<p>Migrate the Galena <code>simple</code> example as follows:</p>
-
-<ol>
-<li><p>Open a console in the copied Galena example location.</p></li>
-<li><p>Run the following:</p>
-
-<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. 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 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>