immunoscore_results_aggregator 0.0.3

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Files changed (38) hide show
  1. data/.gitignore +4 -0
  2. data/Gemfile +14 -0
  3. data/Gemfile.lock +47 -0
  4. data/README.md +54 -0
  5. data/Rakefile +2 -0
  6. data/bin/immunoscore_cli.rb +76 -0
  7. data/config.rb +14 -0
  8. data/data_struct.rb +280 -0
  9. data/docs/aggregator.html +200 -0
  10. data/docs/analyzer.html +1121 -0
  11. data/docs/data_struct.html +504 -0
  12. data/docs/database_connection.html +93 -0
  13. data/docs/docco.css +506 -0
  14. data/docs/exporter.html +216 -0
  15. data/docs/immunoscore_results_loader.html +485 -0
  16. data/docs/public/fonts/aller-bold.eot +0 -0
  17. data/docs/public/fonts/aller-bold.ttf +0 -0
  18. data/docs/public/fonts/aller-bold.woff +0 -0
  19. data/docs/public/fonts/aller-light.eot +0 -0
  20. data/docs/public/fonts/aller-light.ttf +0 -0
  21. data/docs/public/fonts/aller-light.woff +0 -0
  22. data/docs/public/fonts/novecento-bold.eot +0 -0
  23. data/docs/public/fonts/novecento-bold.ttf +0 -0
  24. data/docs/public/fonts/novecento-bold.woff +0 -0
  25. data/docs/public/stylesheets/normalize.css +375 -0
  26. data/docs/semicolon_cleaner.html +231 -0
  27. data/immunoscore_results_aggregator.gemspec +32 -0
  28. data/immunoscore_results_aggregator.rb +9 -0
  29. data/lib/analyzer.rb +664 -0
  30. data/lib/data_struct.rb +280 -0
  31. data/lib/database_connection.rb +4 -0
  32. data/lib/exporter.rb +76 -0
  33. data/lib/immunoscore_results_aggregator/version.rb +3 -0
  34. data/lib/immunoscore_results_loader.rb +218 -0
  35. data/lib/mongo_aggregator.rb +106 -0
  36. data/lib/semicolon_cleaner.rb +68 -0
  37. data/license.txt +21 -0
  38. metadata +243 -0
data/docs/aggregator.html ADDED
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <title>aggregator.rb</title>
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+ <meta http-equiv="content-type" content="text/html; charset=UTF-8">
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+ <meta name="viewport" content="width=device-width, target-densitydpi=160dpi, initial-scale=1.0; maximum-scale=1.0; user-scalable=0;">
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+ <link rel="stylesheet" media="all" href="docco.css" />
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+ </head>
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+ <body>
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+ <div id="container">
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+ <div id="background"></div>
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+
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+ <ul id="jump_to">
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+ <li>
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+ <a class="large" href="javascript:void(0);">Jump To &hellip;</a>
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+ <a class="small" href="javascript:void(0);">+</a>
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+ <div id="jump_wrapper">
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+ <div id="jump_page">
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+
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+
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+ <a class="source" href="aggregator.html">
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+ aggregator.rb
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+ </a>
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+
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+
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+ <a class="source" href="analyzer.html">
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+ analyzer.rb
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+ </a>
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+
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+
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+ <a class="source" href="data_struct.html">
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+ data_struct.rb
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+ </a>
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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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+
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+
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+ <a class="source" href="exporter.html">
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+ exporter.rb
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+ </a>
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+
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+
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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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+
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+
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+ <a class="source" href="semicolon_cleaner.html">
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+ semicolon_cleaner.rb
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+ </a>
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+
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+ </div>
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+ </li>
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+ </ul>
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+
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+ <ul class="sections">
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+
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+ <li id="title">
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+ <div class="annotation">
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+ <h1>aggregator.rb</h1>
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+ </div>
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+ </li>
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+
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+
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+
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+ <li id="section-1">
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+ <div class="annotation">
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+
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+ <div class="pilwrap ">
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+ <a class="pilcrow" href="#section-1">&#182;</a>
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+ </div>
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+ <p>Copyright (c) 2014, Carlo B. Bifulco. All rights reserved.</p>
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+
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+ </div>
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+
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+ <div class="content"><div class='highlight'><pre>
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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>
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+
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+
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+
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+ <span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">StatResults</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">include</span> <span class="hljs-constant">BinManager</span>
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+ extend <span class="hljs-constant">ClassDataUtilities</span>
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+ safe
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+ timestamps!
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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">:file_name</span>, <span class="hljs-constant">String</span>
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+ key <span class="hljs-symbol">:tissue_detection_threshold</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:brown_threshold</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:mean_brown</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:median_brown</span>, <span class="hljs-constant">Float</span>
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+ key <span class="hljs-symbol">:sd_brown</span>, <span class="hljs-constant">Float</span>
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+ key <span class="hljs-symbol">:minimum_brown</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:maximum_brown</span>, <span class="hljs-constant">Float</span>
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+ key <span class="hljs-symbol">:mean_3_most_infiltrated_ct</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:mean_3_most_infiltrated_im</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:density_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:area_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:number_of_cells_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_mean_3_most_infiltrated_ct</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_ct_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_ct_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_ct_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_ct_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_ct_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_mean_3_most_infiltrated_im</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_im_tile_1</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_im_tile_2</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_im_tile_3</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_im_tile_4</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_density_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_area_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ key <span class="hljs-symbol">:old_number_of_cells_im_tile_5</span>, <span class="hljs-constant">Integer</span>
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+ <span class="hljs-keyword">end</span>
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+
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+ <span class="hljs-function"><span class="hljs-keyword">def</span> </span>write_stats_csv file_path
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+ csv_array=[]&lt;&lt; <span class="hljs-constant">Statistic</span>.all[<span class="hljs-number">0</span>].data_load.to_s.split(<span class="hljs-string">"\n"</span>)[<span class="hljs-number">0</span>]</pre></div></div>
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+
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+ </li>
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+
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+
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+ <li id="section-2">
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+ <div class="annotation">
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+
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+ <div class="pilwrap ">
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+ <a class="pilcrow" href="#section-2">&#182;</a>
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+ </div>
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+ <h2 id="stat-results-will-contain-all-datasets-in-an-csv-format">Stat Results will contain all datasets in an csv format</h2>
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+
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+ </div>
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+
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+ <div class="content"><div class='highlight'><pre> <span class="hljs-constant">Statistic</span>.all.each <span class="hljs-keyword">do</span> |stat_entry|
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+ csv_array&lt;&lt;stat_entry.data_load.to_s.split(<span class="hljs-string">"\n"</span>)[<span class="hljs-number">1</span>]
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+ <span class="hljs-keyword">end</span>
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+ csv_array
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+ fh=<span class="hljs-constant">File</span>.new(file_path,<span class="hljs-string">"w"</span>)
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+ csv_array.each{|l| fh.write(l+<span class="hljs-string">"\n"</span>)}
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+ fh.close
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+ <span class="hljs-keyword">end</span></pre></div></div>
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+
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+ </li>
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+
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+ </ul>
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+ </div>
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+ </body>
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+ </html>