immunoscore_results_aggregator 0.0.3
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- 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
data/docs/exporter.html
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analyzer.rb
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cli.rb
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exporter.rb
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immunoscore_results_loader.rb
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mongo_aggregator.rb
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<h1>exporter.rb</h1>
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<p>Copyright (c) 2014, Carlo B. Bifulco. All rights reserved.</p>
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</div>
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<div class="content"><div class='highlight'><pre>
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<span class="hljs-keyword">require</span> <span class="hljs-string">"csv"</span>
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require_relative <span class="hljs-string">"analyzer"</span>
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require_relative <span class="hljs-string">"data_struct"</span>
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require_relative <span class="hljs-string">"immunoscore_results_loader"</span></pre></div></div>
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<a class="pilcrow" href="#section-2">¶</a>
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</div>
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<h2 id="where-all-export-from-definiens-go">Where all export from Definiens go</h2>
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<div class="content"><div class='highlight'><pre><span class="hljs-constant">EXPORT_DIR</span>=<span class="hljs-constant">YAML</span>.load_file(<span class="hljs-string">"config.yaml"</span>)[<span class="hljs-string">"export_dir"</span>] <span class="hljs-keyword">or</span> <span class="hljs-string">"./results_export"</span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>export_clean_all
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`rm -rf <span class="hljs-comment">#{EXPORT_DIR}/*`</span>
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<span class="hljs-keyword">end</span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>cd3? file_path
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<span class="hljs-keyword">not</span> (file_path !~ <span class="hljs-regexp">/_CD3_/</span>)
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<span class="hljs-keyword">end</span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>cd8? file_path
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<span class="hljs-keyword">not</span> (file_path !~ <span class="hljs-regexp">/_CD8_/</span>)
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<span class="hljs-keyword">end</span>
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<span class="hljs-function"><span class="hljs-keyword">def</span> </span>export_file case_dir,file_path
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<span class="hljs-keyword">if</span> cd8? file_path
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<span class="hljs-constant">Dir</span>.mkdir(case_dir+<span class="hljs-string">"/CD8"</span>) <span class="hljs-keyword">unless</span> <span class="hljs-constant">Dir</span>.exist?(case_dir+<span class="hljs-string">"/CD8"</span>)
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fh=<span class="hljs-constant">File</span>.new(case_dir+<span class="hljs-string">"/CD8/"</span>+<span class="hljs-constant">File</span>.basename(file_path),<span class="hljs-string">"w"</span>)
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<span class="hljs-keyword">else</span>
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<span class="hljs-constant">Dir</span>.mkdir(case_dir+<span class="hljs-string">"/CD3"</span>) <span class="hljs-keyword">unless</span> <span class="hljs-constant">Dir</span>.exist?(case_dir+<span class="hljs-string">"/CD3"</span>)
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fh=<span class="hljs-constant">File</span>.new(case_dir+<span class="hljs-string">"/CD3/"</span>+<span class="hljs-constant">File</span>.basename(file_path),<span class="hljs-string">"w"</span>)
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<span class="hljs-keyword">end</span>
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<span class="hljs-keyword">end</span></pre></div></div>
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<p>exports novel directory structure with only relevant files</p>
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<div class="content"><div class='highlight'><pre><span class="hljs-function"><span class="hljs-keyword">def</span> </span>export_mongo</pre></div></div>
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<p>defined in immunoscore_results_loader</p>
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<div class="content"><div class='highlight'><pre> <span class="hljs-constant">JSON_CLASS_MAPPER</span>.values.each <span class="hljs-keyword">do</span> |mm_class|
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mm_class.all.each <span class="hljs-keyword">do</span> |mm_object|
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puts <span class="hljs-string">"<span class="hljs-subst">#{mm_object}</span>: <span class="hljs-subst">#{mm_object[<span class="hljs-symbol">:case_n</span>]}</span>"</span>
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<span class="hljs-keyword">next</span> <span class="hljs-keyword">unless</span> mm_object[<span class="hljs-symbol">:case_n</span>] != <span class="hljs-keyword">nil</span>
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case_dir=(<span class="hljs-constant">EXPORT_DIR</span>+<span class="hljs-string">"/"</span>+ mm_object[<span class="hljs-symbol">:case_n</span>])
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<span class="hljs-constant">Dir</span>.mkdir case_dir <span class="hljs-keyword">unless</span> <span class="hljs-constant">Dir</span>.exist?(case_dir)
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fh=export_file case_dir, mm_object[<span class="hljs-symbol">:path</span>]
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fh.write(mm_object[<span class="hljs-symbol">:data_load</span>])
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fh.close
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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-function"><span class="hljs-keyword">def</span> </span>make_html reporting_order=[
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<span class="hljs-symbol">:histogram</span>,
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<span class="hljs-symbol">:original</span>,
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<span class="hljs-symbol">:density</span>,
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<span class="hljs-symbol">:ct_tile</span>,
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<span class="hljs-symbol">:im_tile</span>,
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<span class="hljs-symbol">:statistic</span>,
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<span class="hljs-symbol">:classification</span>]
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all_cases=[]
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<span class="hljs-constant">ImmunoScoreResults</span>.all.each <span class="hljs-keyword">do</span> |i|
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case_summary=[]
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i.cd.sort.each <span class="hljs-keyword">do</span> |slide_cd|
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reporting_order.each <span class="hljs-keyword">do</span> |feature|
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slide_cd.public_send(feature).sort!{|a,b| a.path<=>b.path}.each <span class="hljs-keyword">do</span> |report|</pre></div></div>
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<p>binding.pry</p>
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<div class="content"><div class='highlight'><pre> case_summary<< report[<span class="hljs-symbol">: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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all_cases << case_summary
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<span class="hljs-keyword">end</span>
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all_cases
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<span class="hljs-keyword">end</span></pre></div></div>
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