immunoscore_results_aggregator 0.0.3
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.
- data/.gitignore +4 -0
- data/Gemfile +14 -0
- data/Gemfile.lock +47 -0
- data/README.md +54 -0
- data/Rakefile +2 -0
- data/bin/immunoscore_cli.rb +76 -0
- data/config.rb +14 -0
- data/data_struct.rb +280 -0
- data/docs/aggregator.html +200 -0
- data/docs/analyzer.html +1121 -0
- data/docs/data_struct.html +504 -0
- data/docs/database_connection.html +93 -0
- data/docs/docco.css +506 -0
- data/docs/exporter.html +216 -0
- data/docs/immunoscore_results_loader.html +485 -0
- data/docs/public/fonts/aller-bold.eot +0 -0
- data/docs/public/fonts/aller-bold.ttf +0 -0
- data/docs/public/fonts/aller-bold.woff +0 -0
- data/docs/public/fonts/aller-light.eot +0 -0
- data/docs/public/fonts/aller-light.ttf +0 -0
- data/docs/public/fonts/aller-light.woff +0 -0
- data/docs/public/fonts/novecento-bold.eot +0 -0
- data/docs/public/fonts/novecento-bold.ttf +0 -0
- data/docs/public/fonts/novecento-bold.woff +0 -0
- data/docs/public/stylesheets/normalize.css +375 -0
- data/docs/semicolon_cleaner.html +231 -0
- data/immunoscore_results_aggregator.gemspec +32 -0
- data/immunoscore_results_aggregator.rb +9 -0
- data/lib/analyzer.rb +664 -0
- data/lib/data_struct.rb +280 -0
- data/lib/database_connection.rb +4 -0
- data/lib/exporter.rb +76 -0
- data/lib/immunoscore_results_aggregator/version.rb +3 -0
- data/lib/immunoscore_results_loader.rb +218 -0
- data/lib/mongo_aggregator.rb +106 -0
- data/lib/semicolon_cleaner.rb +68 -0
- data/license.txt +21 -0
- metadata +243 -0
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<h1>data_struct.rb</h1>
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<p>Copyright (c) 2014, Carlo B. Bifulco. All rights reserved.</p>
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require_relative <span class="hljs-string">"analyzer"</span>
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require_relative <span class="hljs-string">"immunoscore_results_loader"</span>
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require_relative <span class="hljs-string">"database_connection"</span></pre></div></div>
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<p>module Show
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def show file_path=self.path
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tf=Tempfile.new [“temp”,File.extname(file_path)]
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tf.write (File.read file_path)
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tf.close
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puts “#{tf.path}”
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fork do
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<code>open #{tf.path}</code></p>
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<pre><code><span class="hljs-keyword">end</span>
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puts <span class="hljs-constant">Process</span>.waitall
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tf.unlink
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</code></pre><p> end
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<h2 id="enables-all-mongo-classes-listed-below-to-have-instances-capable-their-own-cd-quicly">Enables all Mongo classes listed below to have instances capable their own CD quicly</h2>
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<div class="content"><div class='highlight'><pre><span class="hljs-class"><span class="hljs-keyword">module</span> <span class="hljs-title">CdIncluder</span></span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>get_cd
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puts <span class="hljs-keyword">self</span>.cd_type
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<span class="hljs-keyword">if</span> (<span class="hljs-keyword">self</span>.cd_type <span class="hljs-keyword">and</span> <span class="hljs-keyword">self</span>.case_n) != <span class="hljs-keyword">nil</span>
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cd= <span class="hljs-constant">Cd</span>.get(<span class="hljs-keyword">self</span>.cd_type, <span class="hljs-keyword">self</span>.case_n)
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<span class="hljs-keyword">end</span>
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puts cd
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<span class="hljs-keyword">if</span> cd
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<span class="hljs-keyword">self</span>.cd=cd
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<span class="hljs-keyword">self</span>.save
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<span class="hljs-keyword">end</span></pre></div></div>
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<h2 id="enables-loading-and-showing-of-binary-datatsets">enables loading and showing of binary datatsets</h2>
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<div class="content"><div class='highlight'><pre><span class="hljs-class"><span class="hljs-keyword">module</span> <span class="hljs-title">BinManager</span></span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>show graphic_data=<span class="hljs-keyword">self</span>.data_load
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tf.close
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fork <span class="hljs-keyword">do</span>
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`open <span class="hljs-comment">#{tf.path}`</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">ImmunoScoreResults</span></span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
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safe
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timestamps!
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many <span class="hljs-symbol">:cd</span>
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key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span><span class="hljs-keyword">self</span>.get case_n
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<span class="hljs-keyword">self</span>.find_by_case_n(case_n) <span class="hljs-keyword">or</span> <span class="hljs-keyword">self</span>.create(<span class="hljs-symbol">:case_n=>case_n</span>)
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<span class="hljs-keyword">end</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Cd</span></span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
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safe
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timestamps!
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belongs_to <span class="hljs-symbol">:immuno_score_results</span>
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key <span class="hljs-symbol">:cd_type</span>, <span class="hljs-constant">String</span>
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key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
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many <span class="hljs-symbol">:ct_tile</span>
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many <span class="hljs-symbol">:im_tile</span>
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many <span class="hljs-symbol">:statistic</span>
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many <span class="hljs-symbol">:classification</span>
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many <span class="hljs-symbol">:original</span>
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many <span class="hljs-symbol">:density</span>
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many <span class="hljs-symbol">:histogram</span></pre></div></div>
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<p>either get a brand new cd with its own Immunoscore Results instance of find a preexisting one</p>
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<div class="content"><div class='highlight'><pre> <span class="hljs-function"><span class="hljs-keyword">def</span> </span><span class="hljs-keyword">self</span>.get cd_type, case_n
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<span class="hljs-keyword">self</span>.find_by_cd_type_and_case_n(cd_type,case_n) <span class="hljs-keyword">or</span> <span class="hljs-keyword">self</span>.create(<span class="hljs-symbol">:case_n=>case_n</span>,
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<span class="hljs-symbol">:cd_type=>cd_type</span>,
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<span class="hljs-symbol">:immuno_score_results_id=>ImmunoScoreResults</span>.get(case_n)._id)
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<span class="hljs-keyword">end</span></pre></div></div>
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<p>{:cd=>”CD3”,
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:path=>
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“/Volumes/LaCie/patient 1-5/patient 1-5/results/RS_SM02-2576-A4_CD3_2013-11-01 16_52_41.image_0000006553/View_Exports
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:tile=>”CT2”,
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:case_n=>”SM02-2576-A4”,
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:type=>:ct_tile}}</p>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
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extend <span class="hljs-constant">ClassDataUtilities</span>
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safe
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belongs_to <span class="hljs-symbol">:cd</span>
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key <span class="hljs-symbol">:path</span>, <span class="hljs-constant">String</span>
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key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
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key <span class="hljs-symbol">:cd_type</span>, <span class="hljs-constant">String</span>
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key <span class="hljs-symbol">:data_load</span>, <span class="hljs-constant">Binary</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">BinManager</span>
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<span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Original</span></span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
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<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
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<span class="hljs-keyword">end</span></pre></div></div>
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<a class="pilcrow" href="#section-9">¶</a>
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<p>{:case=>”RS_SM02-2576-A4_CD3_2013-11-01 16_52_41.image_0000006553”,
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:path=>
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“/Volumes/LaCie/patient 1-5/patient 1-5/results/RS_SM02-2576-A4_CD3_2013-11-01 16_52_41.image_0000006553/Statistic_Exports/RS_SM02-2576-A4_CD3_2013-11-01 16_52_41.image_0000006553_Statistics.csv”,
|
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:cd=>”CD3”,
|
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:type=>:statistics}</p>
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<div class="content"><div class='highlight'><pre>
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|
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<span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Statistic</span></span>
|
|
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|
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<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
|
|
361
|
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<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
|
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362
|
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<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
|
|
363
|
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<span class="hljs-keyword">include</span> <span class="hljs-constant">BinManager</span>
|
|
364
|
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extend <span class="hljs-constant">ClassDataUtilities</span>
|
|
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|
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safe
|
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|
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timestamps!
|
|
367
|
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belongs_to <span class="hljs-symbol">:cd</span>
|
|
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|
+
key <span class="hljs-symbol">:path</span>, <span class="hljs-constant">String</span>
|
|
369
|
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key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
|
|
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key <span class="hljs-symbol">:cd_type</span>, <span class="hljs-constant">String</span>
|
|
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|
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key <span class="hljs-symbol">:data_load</span>, <span class="hljs-constant">Binary</span>
|
|
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|
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before_save <span class="hljs-symbol">:load_bin</span>
|
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|
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<span class="hljs-keyword">end</span></pre></div></div>
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</li>
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<li id="section-10">
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|
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<div class="annotation">
|
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380
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|
|
381
|
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<div class="pilwrap ">
|
|
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|
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<a class="pilcrow" href="#section-10">¶</a>
|
|
383
|
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</div>
|
|
384
|
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<p>{:path=>
|
|
385
|
+
“/Volumes/LaCie/patient 1-5/patient 1-5/results/RS_SM02-2576-A4_CD3_2013-11-01 16_52_41.image_0000006553/View_Exports
|
|
386
|
+
:case=>”SM02-2576-A4”,
|
|
387
|
+
:new_old=>”old”,
|
|
388
|
+
:cd=>”CD3”,
|
|
389
|
+
:type=>”density”}</p>
|
|
390
|
+
|
|
391
|
+
</div>
|
|
392
|
+
|
|
393
|
+
<div class="content"><div class='highlight'><pre><span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Density</span></span>
|
|
394
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
|
|
395
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
|
|
396
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
|
|
397
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">BinManager</span>
|
|
398
|
+
extend <span class="hljs-constant">ClassDataUtilities</span>
|
|
399
|
+
safe
|
|
400
|
+
timestamps!
|
|
401
|
+
belongs_to <span class="hljs-symbol">:cd</span>
|
|
402
|
+
key <span class="hljs-symbol">:path</span>, <span class="hljs-constant">String</span>
|
|
403
|
+
key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
|
|
404
|
+
key <span class="hljs-symbol">:cd_type</span>, <span class="hljs-constant">String</span>
|
|
405
|
+
key <span class="hljs-symbol">:new_old</span>, <span class="hljs-constant">String</span>
|
|
406
|
+
key <span class="hljs-symbol">:data_load</span>, <span class="hljs-constant">Binary</span>
|
|
407
|
+
before_save <span class="hljs-symbol">:load_bin</span>
|
|
408
|
+
<span class="hljs-keyword">end</span></pre></div></div>
|
|
409
|
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|
|
410
|
+
</li>
|
|
411
|
+
|
|
412
|
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|
|
413
|
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<li id="section-11">
|
|
414
|
+
<div class="annotation">
|
|
415
|
+
|
|
416
|
+
<div class="pilwrap ">
|
|
417
|
+
<a class="pilcrow" href="#section-11">¶</a>
|
|
418
|
+
</div>
|
|
419
|
+
<p>{:path=>
|
|
420
|
+
“/Volumes/LaCie/patient 1-5/patient 1-5/results/RS_SM02-2366-A5_CD8_2013-11-01 16_55_57.image_0000006556/View_Exports
|
|
421
|
+
:case=>”SM02-2366-A5”,
|
|
422
|
+
:type=>:histogram,
|
|
423
|
+
:cd=>”CD8”}</p>
|
|
424
|
+
|
|
425
|
+
</div>
|
|
426
|
+
|
|
427
|
+
<div class="content"><div class='highlight'><pre><span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Histogram</span></span>
|
|
428
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
|
|
429
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
|
|
430
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
|
|
431
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">BinManager</span>
|
|
432
|
+
extend <span class="hljs-constant">ClassDataUtilities</span>
|
|
433
|
+
safe
|
|
434
|
+
timestamps!
|
|
435
|
+
belongs_to <span class="hljs-symbol">:cd</span>
|
|
436
|
+
key <span class="hljs-symbol">:path</span>, <span class="hljs-constant">String</span>
|
|
437
|
+
key <span class="hljs-symbol">:case_n</span>, <span class="hljs-constant">String</span>
|
|
438
|
+
key <span class="hljs-symbol">:cd_type</span>, <span class="hljs-constant">String</span>
|
|
439
|
+
key <span class="hljs-symbol">:data_load</span>, <span class="hljs-constant">Binary</span>
|
|
440
|
+
before_save <span class="hljs-symbol">:load_bin</span>
|
|
441
|
+
<span class="hljs-keyword">end</span>
|
|
442
|
+
|
|
443
|
+
|
|
444
|
+
<span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">Test</span></span>
|
|
445
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">MongoMapper::Document</span>
|
|
446
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">DataUtilities</span>
|
|
447
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">CdIncluder</span>
|
|
448
|
+
<span class="hljs-keyword">include</span> <span class="hljs-constant">BinManager</span>
|
|
449
|
+
extend <span class="hljs-constant">ClassDataUtilities</span>
|
|
450
|
+
|
|
451
|
+
key <span class="hljs-symbol">:path</span>, <span class="hljs-constant">String</span>
|
|
452
|
+
|
|
453
|
+
key <span class="hljs-symbol">:data_load</span>, <span class="hljs-constant">Binary</span>
|
|
454
|
+
before_save <span class="hljs-symbol">:load_bin</span>
|
|
455
|
+
|
|
456
|
+
|
|
457
|
+
<span class="hljs-keyword">end</span></pre></div></div>
|
|
458
|
+
|
|
459
|
+
</li>
|
|
460
|
+
|
|
461
|
+
|
|
462
|
+
<li id="section-12">
|
|
463
|
+
<div class="annotation">
|
|
464
|
+
|
|
465
|
+
<div class="pilwrap ">
|
|
466
|
+
<a class="pilcrow" href="#section-12">¶</a>
|
|
467
|
+
</div>
|
|
468
|
+
<h2 id="mapping-from-definiens-file-type-to-proper-database-entity">mapping from definiens file type to proper database entity</h2>
|
|
469
|
+
|
|
470
|
+
</div>
|
|
471
|
+
|
|
472
|
+
<div class="content"><div class='highlight'><pre><span class="hljs-constant">JSON_CLASS_MAPPER</span>={<span class="hljs-symbol">:ct_tile=>CtTile</span>,
|
|
473
|
+
<span class="hljs-symbol">:im_tile=>ImTile</span>,
|
|
474
|
+
<span class="hljs-symbol">:classification=>Classification</span>,
|
|
475
|
+
<span class="hljs-symbol">:original=>Original</span>,
|
|
476
|
+
<span class="hljs-symbol">:statistic=>Statistic</span>,
|
|
477
|
+
<span class="hljs-symbol">:density=>Density</span>,
|
|
478
|
+
<span class="hljs-symbol">:histogram=>Histogram</span>}</pre></div></div>
|
|
479
|
+
|
|
480
|
+
</li>
|
|
481
|
+
|
|
482
|
+
|
|
483
|
+
<li id="section-13">
|
|
484
|
+
<div class="annotation">
|
|
485
|
+
|
|
486
|
+
<div class="pilwrap ">
|
|
487
|
+
<a class="pilcrow" href="#section-13">¶</a>
|
|
488
|
+
</div>
|
|
489
|
+
<h2 id="resets-all-databases">resets all databases</h2>
|
|
490
|
+
|
|
491
|
+
</div>
|
|
492
|
+
|
|
493
|
+
<div class="content"><div class='highlight'><pre><span class="hljs-function"><span class="hljs-keyword">def</span> </span>mm_clean_all
|
|
494
|
+
[<span class="hljs-constant">ImmunoScoreResults</span>, <span class="hljs-constant">Cd</span>, <span class="hljs-constant">Histogram</span>, <span class="hljs-constant">Density</span>, <span class="hljs-constant">Statistic</span>, <span class="hljs-constant">Original</span>, <span class="hljs-constant">Classification</span>, <span class="hljs-constant">ImTile</span>, <span class="hljs-constant">CtTile</span>].each <span class="hljs-keyword">do</span> |mm_class|
|
|
495
|
+
mm_class.delete_all
|
|
496
|
+
<span class="hljs-keyword">end</span>
|
|
497
|
+
<span class="hljs-keyword">end</span></pre></div></div>
|
|
498
|
+
|
|
499
|
+
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|
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500
|
+
|
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501
|
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|
|
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|
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|
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|
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<a class="source" href="database_connection.html">
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database_connection.rb
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</a>
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<a class="source" href="immunoscore_results_loader.html">
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immunoscore_results_loader.rb
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</a>
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mongo_aggregator.rb
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</a>
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semicolon_cleaner.rb
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</a>
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<ul class="sections">
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<h1>database_connection.rb</h1>
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<a class="pilcrow" href="#section-1">¶</a>
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</div>
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<h2 id="specify-database-name-dynamic-based-on-dir-location-in-path">Specify Database name; dynamic based on dir location in path</h2>
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<div class="content"><div class='highlight'><pre><span class="hljs-constant">DATABASE_NAME</span>= (<span class="hljs-constant">YAML</span>.load_file(<span class="hljs-string">"./config.yaml"</span>)[<span class="hljs-string">"database_name"</span>] <span class="hljs-keyword">or</span> (<span class="hljs-constant">File</span>.basename <span class="hljs-constant">File</span>.absolute_path <span class="hljs-string">"."</span>))
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<span class="hljs-constant">MongoMapper</span>.database = <span class="hljs-constant">DATABASE_NAME</span></pre></div></div>
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