immunoscore_results_aggregator 0.0.3

data/docs/public/stylesheets/normalize.css

@@ -0,0 +1,375 @@
+/*! normalize.css v2.0.1 | MIT License | git.io/normalize */
+
+/* ==========================================================================
+   HTML5 display definitions
+   ========================================================================== */
+
+/*
+ * Corrects `block` display not defined in IE 8/9.
+ */
+
+article,
+aside,
+details,
+figcaption,
+figure,
+footer,
+header,
+hgroup,
+nav,
+section,
+summary {
+    display: block;
+}
+
+/*
+ * Corrects `inline-block` display not defined in IE 8/9.
+ */
+
+audio,
+canvas,
+video {
+    display: inline-block;
+}
+
+/*
+ * Prevents modern browsers from displaying `audio` without controls.
+ * Remove excess height in iOS 5 devices.
+ */
+
+audio:not([controls]) {
+    display: none;
+    height: 0;
+}
+
+/*
+ * Addresses styling for `hidden` attribute not present in IE 8/9.
+ */
+
+[hidden] {
+    display: none;
+}
+
+/* ==========================================================================
+   Base
+   ========================================================================== */
+
+/*
+ * 1. Sets default font family to sans-serif.
+ * 2. Prevents iOS text size adjust after orientation change, without disabling
+ *    user zoom.
+ */
+
+html {
+    font-family: sans-serif; /* 1 */
+    -webkit-text-size-adjust: 100%; /* 2 */
+    -ms-text-size-adjust: 100%; /* 2 */
+}
+
+/*
+ * Removes default margin.
+ */
+
+body {
+    margin: 0;
+}
+
+/* ==========================================================================
+   Links
+   ========================================================================== */
+
+/*
+ * Addresses `outline` inconsistency between Chrome and other browsers.
+ */
+
+a:focus {
+    outline: thin dotted;
+}
+
+/*
+ * Improves readability when focused and also mouse hovered in all browsers.
+ */
+
+a:active,
+a:hover {
+    outline: 0;
+}
+
+/* ==========================================================================
+   Typography
+   ========================================================================== */
+
+/*
+ * Addresses `h1` font sizes within `section` and `article` in Firefox 4+,
+ * Safari 5, and Chrome.
+ */
+
+h1 {
+    font-size: 2em;
+}
+
+/*
+ * Addresses styling not present in IE 8/9, Safari 5, and Chrome.
+ */
+
+abbr[title] {
+    border-bottom: 1px dotted;
+}
+
+/*
+ * Addresses style set to `bolder` in Firefox 4+, Safari 5, and Chrome.
+ */
+
+b,
+strong {
+    font-weight: bold;
+}
+
+/*
+ * Addresses styling not present in Safari 5 and Chrome.
+ */
+
+dfn {
+    font-style: italic;
+}
+
+/*
+ * Addresses styling not present in IE 8/9.
+ */
+
+mark {
+    background: #ff0;
+    color: #000;
+}
+
+
+/*
+ * Corrects font family set oddly in Safari 5 and Chrome.
+ */
+
+code,
+kbd,
+pre,
+samp {
+    font-family: monospace, serif;
+    font-size: 1em;
+}
+
+/*
+ * Improves readability of pre-formatted text in all browsers.
+ */
+
+pre {
+    white-space: pre;
+    white-space: pre-wrap;
+    word-wrap: break-word;
+}
+
+/*
+ * Sets consistent quote types.
+ */
+
+q {
+    quotes: "\201C" "\201D" "\2018" "\2019";
+}
+
+/*
+ * Addresses inconsistent and variable font size in all browsers.
+ */
+
+small {
+    font-size: 80%;
+}
+
+/*
+ * Prevents `sub` and `sup` affecting `line-height` in all browsers.
+ */
+
+sub,
+sup {
+    font-size: 75%;
+    line-height: 0;
+    position: relative;
+    vertical-align: baseline;
+}
+
+sup {
+    top: -0.5em;
+}
+
+sub {
+    bottom: -0.25em;
+}
+
+/* ==========================================================================
+   Embedded content
+   ========================================================================== */
+
+/*
+ * Removes border when inside `a` element in IE 8/9.
+ */
+
+img {
+    border: 0;
+}
+
+/*
+ * Corrects overflow displayed oddly in IE 9.
+ */
+
+svg:not(:root) {
+    overflow: hidden;
+}
+
+/* ==========================================================================
+   Figures
+   ========================================================================== */
+
+/*
+ * Addresses margin not present in IE 8/9 and Safari 5.
+ */
+
+figure {
+    margin: 0;
+}
+
+/* ==========================================================================
+   Forms
+   ========================================================================== */
+
+/*
+ * Define consistent border, margin, and padding.
+ */
+
+fieldset {
+    border: 1px solid #c0c0c0;
+    margin: 0 2px;
+    padding: 0.35em 0.625em 0.75em;
+}
+
+/*
+ * 1. Corrects color not being inherited in IE 8/9.
+ * 2. Remove padding so people aren't caught out if they zero out fieldsets.
+ */
+
+legend {
+    border: 0; /* 1 */
+    padding: 0; /* 2 */
+}
+
+/*
+ * 1. Corrects font family not being inherited in all browsers.
+ * 2. Corrects font size not being inherited in all browsers.
+ * 3. Addresses margins set differently in Firefox 4+, Safari 5, and Chrome
+ */
+
+button,
+input,
+select,
+textarea {
+    font-family: inherit; /* 1 */
+    font-size: 100%; /* 2 */
+    margin: 0; /* 3 */
+}
+
+/*
+ * Addresses Firefox 4+ setting `line-height` on `input` using `!important` in
+ * the UA stylesheet.
+ */
+
+button,
+input {
+    line-height: normal;
+}
+
+/*
+ * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
+ *    and `video` controls.
+ * 2. Corrects inability to style clickable `input` types in iOS.
+ * 3. Improves usability and consistency of cursor style between image-type
+ *    `input` and others.
+ */
+
+button,
+html input[type="button"], /* 1 */
+input[type="reset"],
+input[type="submit"] {
+    -webkit-appearance: button; /* 2 */
+    cursor: pointer; /* 3 */
+}
+
+/*
+ * Re-set default cursor for disabled elements.
+ */
+
+button[disabled],
+input[disabled] {
+    cursor: default;
+}
+
+/*
+ * 1. Addresses box sizing set to `content-box` in IE 8/9.
+ * 2. Removes excess padding in IE 8/9.
+ */
+
+input[type="checkbox"],
+input[type="radio"] {
+    box-sizing: border-box; /* 1 */
+    padding: 0; /* 2 */
+}
+
+/*
+ * 1. Addresses `appearance` set to `searchfield` in Safari 5 and Chrome.
+ * 2. Addresses `box-sizing` set to `border-box` in Safari 5 and Chrome
+ *    (include `-moz` to future-proof).
+ */
+
+input[type="search"] {
+    -webkit-appearance: textfield; /* 1 */
+    -moz-box-sizing: content-box;
+    -webkit-box-sizing: content-box; /* 2 */
+    box-sizing: content-box;
+}
+
+/*
+ * Removes inner padding and search cancel button in Safari 5 and Chrome
+ * on OS X.
+ */
+
+input[type="search"]::-webkit-search-cancel-button,
+input[type="search"]::-webkit-search-decoration {
+    -webkit-appearance: none;
+}
+
+/*
+ * Removes inner padding and border in Firefox 4+.
+ */
+
+button::-moz-focus-inner,
+input::-moz-focus-inner {
+    border: 0;
+    padding: 0;
+}
+
+/*
+ * 1. Removes default vertical scrollbar in IE 8/9.
+ * 2. Improves readability and alignment in all browsers.
+ */
+
+textarea {
+    overflow: auto; /* 1 */
+    vertical-align: top; /* 2 */
+}
+
+/* ==========================================================================
+   Tables
+   ========================================================================== */
+
+/*
+ * Remove most spacing between table cells.
+ */
+
+table {
+    border-collapse: collapse;
+    border-spacing: 0;
+}

data/docs/semicolon_cleaner.html

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+<!DOCTYPE html>
+
+<html>
+<head>
+  <title>semicolon_cleaner.rb</title>
+  <meta http-equiv="content-type" content="text/html; charset=UTF-8">
+  <meta name="viewport" content="width=device-width, target-densitydpi=160dpi, initial-scale=1.0; maximum-scale=1.0; user-scalable=0;">
+  <link rel="stylesheet" media="all" href="docco.css" />
+</head>
+<body>
+  <div id="container">
+    <div id="background"></div>
+    
+      <ul id="jump_to">
+        <li>
+          <a class="large" href="javascript:void(0);">Jump To &hellip;</a>
+          <a class="small" href="javascript:void(0);">+</a>
+          <div id="jump_wrapper">
+          <div id="jump_page">
+            
+              
+              <a class="source" href="analyzer.html">
+                analyzer.rb
+              </a>
+            
+              
+              <a class="source" href="cli.html">
+                cli.rb
+              </a>
+            
+              
+              <a class="source" href="data_struct.html">
+                data_struct.rb
+              </a>
+            
+              
+              <a class="source" href="database_connection.html">
+                database_connection.rb
+              </a>
+            
+              
+              <a class="source" href="exporter.html">
+                exporter.rb
+              </a>
+            
+              
+              <a class="source" href="immunoscore_results_loader.html">
+                immunoscore_results_loader.rb
+              </a>
+            
+              
+              <a class="source" href="mongo_aggregator.html">
+                mongo_aggregator.rb
+              </a>
+            
+              
+              <a class="source" href="semicolon_cleaner.html">
+                semicolon_cleaner.rb
+              </a>
+            
+          </div>
+        </li>
+      </ul>
+    
+    <ul class="sections">
+        
+          <li id="title">
+              <div class="annotation">
+                  <h1>semicolon_cleaner.rb</h1>
+              </div>
+          </li>
+        
+        
+        
+        <li id="section-1">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-1">&#182;</a>
+              </div>
+              <p>Copyright (c) 2014, Carlo B. Bifulco. All rights reserved.</p>
+
+            </div>
+            
+        </li>
+        
+        
+        <li id="section-2">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-2">&#182;</a>
+              </div>
+              <h2 id="cleaning-of-the-definines-semicolon-junk">Cleaning of the Definines semicolon junk</h2>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre><span class="hljs-class"><span class="hljs-keyword">class</span> <span class="hljs-title">DefinensCSV</span></span>
+
+  <span class="hljs-function"><span class="hljs-keyword">def</span> </span>initialize file_path
+    <span class="hljs-variable">@file_path</span>=file_path
+    <span class="hljs-variable">@text</span>=<span class="hljs-constant">File</span>.read <span class="hljs-variable">@file_path</span></pre></div></div>
+            
+        </li>
+        
+        
+        <li id="section-3">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-3">&#182;</a>
+              </div>
+              <p>puts @text.encode(“UTF-8”)
+clean utf not sure why</p>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre>    _digest_utf</pre></div></div>
+            
+        </li>
+        
+        
+        <li id="section-4">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-4">&#182;</a>
+              </div>
+              <p>header_line</p>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre>    csv=<span class="hljs-constant">CSV</span>.read(<span class="hljs-variable">@file_path</span>)
+    <span class="hljs-keyword">if</span> (csv <span class="hljs-keyword">and</span> csv.count !=<span class="hljs-number">0</span>)
+      puts <span class="hljs-variable">@file_path</span>
+      header=csv[<span class="hljs-number">0</span>][<span class="hljs-number">0</span>]
+      <span class="hljs-keyword">if</span> header.count(<span class="hljs-string">";"</span>)&gt;header.count(<span class="hljs-string">","</span>) <span class="hljs-keyword">then</span> _parse_semicolon <span class="hljs-keyword">end</span>
+    <span class="hljs-keyword">end</span></pre></div></div>
+            
+        </li>
+        
+        
+        <li id="section-5">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-5">&#182;</a>
+              </div>
+              <p>parse_semicolon</p>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre>  <span class="hljs-keyword">end</span>
+
+
+  <span class="hljs-function"><span class="hljs-keyword">def</span> </span>_digest_utf
+    text=<span class="hljs-constant">File</span>.read <span class="hljs-variable">@file_path</span>
+    text=text.encode(<span class="hljs-string">"UTF-16BE"</span>, <span class="hljs-symbol">:invalid=&gt;</span><span class="hljs-symbol">:replace</span>, <span class="hljs-symbol">:replace=&gt;<span class="hljs-string">"?"</span></span>).encode(<span class="hljs-string">"UTF-8"</span>)
+    fh=<span class="hljs-constant">File</span>.new <span class="hljs-variable">@file_path</span>, <span class="hljs-string">"w"</span>
+    fh.write text
+    fh.close
+    <span class="hljs-keyword">self</span>
+  <span class="hljs-keyword">end</span></pre></div></div>
+            
+        </li>
+        
+        
+        <li id="section-6">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-6">&#182;</a>
+              </div>
+              <p>replaces ; from definins csv with ,</p>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre>  <span class="hljs-function"><span class="hljs-keyword">def</span> </span>_parse_semicolon</pre></div></div>
+            
+        </li>
+        
+        
+        <li id="section-7">
+            <div class="annotation">
+              
+              <div class="pilwrap ">
+                <a class="pilcrow" href="#section-7">&#182;</a>
+              </div>
+              <p>puts “removing semicolons”</p>
+
+            </div>
+            
+            <div class="content"><div class='highlight'><pre>    c=<span class="hljs-constant">CSV</span>.table <span class="hljs-variable">@file_path</span>, <span class="hljs-symbol">:col_sep=&gt;</span> <span class="hljs-string">";"</span>
+    fh=<span class="hljs-constant">File</span>.new <span class="hljs-variable">@file_path</span>, <span class="hljs-string">"w"</span>
+    fh.write c.to_csv
+    fh.close
+    <span class="hljs-keyword">self</span>
+  <span class="hljs-keyword">end</span>
+
+  <span class="hljs-function"><span class="hljs-keyword">def</span> </span>table
+    c=<span class="hljs-constant">CSV</span>.table <span class="hljs-variable">@file_path</span>
+  <span class="hljs-keyword">end</span>
+
+  <span class="hljs-function"><span class="hljs-keyword">def</span> </span>get_dictionary
+    table =<span class="hljs-keyword">self</span>.table
+    dictionary={}
+    table.headers.each <span class="hljs-keyword">do</span> |h|
+      dictionary[h]=table[h][<span class="hljs-number">0</span>] <span class="hljs-keyword">if</span> table[h]
+    <span class="hljs-keyword">end</span>
+    dictionary
+  <span class="hljs-keyword">end</span>
+<span class="hljs-keyword">end</span>
+
+
+<span class="hljs-function"><span class="hljs-keyword">def</span> </span>csv_clean_all match_pattern=<span class="hljs-string">"*.csv"</span>, root_directory_path=<span class="hljs-constant">BASE_DIR</span>
+  csv_matches=<span class="hljs-constant">Dir</span>.glob <span class="hljs-string">"<span class="hljs-subst">#{<span class="hljs-constant">File</span>.absolute_path root_directory_path}</span>/**/<span class="hljs-subst">#{match_pattern}</span>"</span>
+  csv_matches.each <span class="hljs-keyword">do</span> |cm|
+    <span class="hljs-keyword">begin</span>
+      <span class="hljs-constant">DefinensCSV</span>.new cm
+    <span class="hljs-keyword">rescue</span>
+      puts <span class="hljs-string">"FAILED on <span class="hljs-subst">#{cm}</span>"</span>
+    <span class="hljs-keyword">end</span>
+  <span class="hljs-keyword">end</span>
+<span class="hljs-keyword">end</span></pre></div></div>
+            
+        </li>
+        
+    </ul>
+  </div>
+</body>
+</html>

data/immunoscore_results_aggregator.gemspec

@@ -0,0 +1,32 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'immunoscore_results_aggregator/version'
+
+Gem::Specification.new do |s|
+  s.name        = 'immunoscore_results_aggregator'
+  s.version     = '0.0.3'
+  s.date        = '2014-10-01'
+  s.add_runtime_dependency "bson_ext"
+  s.add_runtime_dependency 'mongo_mapper'
+  s.add_runtime_dependency "bson_ext"
+  s.add_runtime_dependency 'gibberish'
+  s.add_runtime_dependency 'bicrypt'
+  s.add_runtime_dependency 'chronic'
+  s.add_runtime_dependency "thor"
+  s.add_runtime_dependency 'mm-versionable'
+  s.summary     = "immunoscore_results_aggregator"
+  s.description = "immunoscore_results_aggregator"
+  s.license       = "MIT"
+  s.authors     = ["Carlo Bifulco"]
+  s.email       = 'carlobif@gmail.com'
+  s.files       = `git ls-files -z`.split("\x0")
+  s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  s.homepage    =
+    'https://github.com/carlobifulco/immunoscore_results'
+  s.require_paths = ["lib"]
+  s.license       = 'MIT'
+  s.add_development_dependency "bundler", "~> 1.6"
+  s.add_development_dependency "rake"
+end
+

data/immunoscore_results_aggregator.rb

@@ -0,0 +1,9 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+
+require "immunoscore_results_loader"
+require "mongo_aggregator"
+require "exporter"
+require_relative "config.rb"