andersjacobsen-mirmaid_mir2disease 0.0.0 → 0.1.0

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Files changed (48) hide show
  1. data/MIT-LICENSE +20 -0
  2. data/Rakefile +46 -0
  3. data/VERSION +1 -0
  4. data/app/controllers/m2d_disease_links_controller.rb +44 -0
  5. data/app/controllers/m2d_diseases_controller.rb +44 -0
  6. data/app/models/m2d_disease.rb +22 -0
  7. data/app/models/m2d_disease_link.rb +27 -0
  8. data/app/views/m2d_disease_links/_list_for_mature.html.erb +21 -0
  9. data/app/views/m2d_disease_links/_m2d_disease_link.html.erb +9 -0
  10. data/app/views/m2d_disease_links/index.html.erb +18 -0
  11. data/app/views/m2d_disease_links/show.html.erb +21 -0
  12. data/app/views/m2d_diseases/_m2d_disease.html.erb +4 -0
  13. data/app/views/m2d_diseases/index.html.erb +20 -0
  14. data/app/views/m2d_diseases/show.html.erb +25 -0
  15. data/config/routes.rb +12 -0
  16. data/data/mir2dis.txt +2568 -0
  17. data/init.rb +7 -0
  18. data/install.rb +1 -0
  19. data/lib/mir2disease.rb +1 -0
  20. data/mirmaid_mir2disease.gemspec +87 -0
  21. data/mirmaid_models.rb +9 -0
  22. data/rdoc/classes/M2dDisease.html +140 -0
  23. data/rdoc/classes/M2dDiseaseLink.html +119 -0
  24. data/rdoc/classes/M2dDiseaseLinksController.html +170 -0
  25. data/rdoc/classes/M2dDiseasesController.html +170 -0
  26. data/rdoc/created.rid +1 -0
  27. data/rdoc/css/main.css +191 -0
  28. data/rdoc/css/panel.css +383 -0
  29. data/rdoc/css/reset.css +53 -0
  30. data/rdoc/files/README.html +78 -0
  31. data/rdoc/files/app/controllers/m2d_disease_links_controller_rb.html +66 -0
  32. data/rdoc/files/app/controllers/m2d_diseases_controller_rb.html +66 -0
  33. data/rdoc/files/app/models/m2d_disease_link_rb.html +85 -0
  34. data/rdoc/files/app/models/m2d_disease_rb.html +77 -0
  35. data/rdoc/files/lib/mir2disease_rb.html +64 -0
  36. data/rdoc/i/arrows.png +0 -0
  37. data/rdoc/i/results_bg.png +0 -0
  38. data/rdoc/i/tree_bg.png +0 -0
  39. data/rdoc/index.html +14 -0
  40. data/rdoc/js/jquery-1.3.2.min.js +19 -0
  41. data/rdoc/js/main.js +34 -0
  42. data/rdoc/js/searchdoc.js +620 -0
  43. data/rdoc/panel/index.html +71 -0
  44. data/rdoc/panel/search_index.js +1 -0
  45. data/rdoc/panel/tree.js +1 -0
  46. data/tasks/mir2disease_tasks.rake +115 -0
  47. data/uninstall.rb +1 -0
  48. metadata +51 -2
data/rdoc/panel/index.html ADDED
@@ -0,0 +1,71 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
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+ "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
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+ <head>
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+ <title>layout</title>
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+ <link rel="stylesheet" href="../css/reset.css" type="text/css" media="screen" charset="utf-8" />
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+ <link rel="stylesheet" href="../css/panel.css" type="text/css" media="screen" charset="utf-8" />
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+ <script src="search_index.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="tree.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/jquery-1.3.2.min.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="../js/searchdoc.js" type="text/javascript" charset="utf-8"></script>
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+ <script type="text/javascript" charset="utf-8">
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+ //<![CDATA[
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+ function placeholder() {
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+ if (jQuery.browser.safari) return;
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+ $('#search-label').click(function() {
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+ $('#search').focus();
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+ $('#search-label').hide();
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+ });
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+
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+ $('#search').focus(function() {
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+ $('#search-label').hide();
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+ });
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+ $('#search').blur(function() {
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+ this.value == '' && $('#search-label').show()
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+ });
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+
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+ $('#search')[0].value == '' && $('#search-label').show();
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+ }
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+ $(function() {
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+ placeholder();
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+ var panel = new Searchdoc.Panel($('#panel'), search_data, tree, top.frames[1]);
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+ $('#search').focus();
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+
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+ var s = window.parent.location.search.match(/\?q=(.*)$/);
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+ if (s) {
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+ s = decodeURIComponent(s[1]).replace(/\+/g, ' ');
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+ if (s.length > 0)
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+ {
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+ $('#search').val(s);
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+ panel.search(s, true);
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+ }
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+ }
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+ })
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+ //]]>
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+ </script>
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+ </head>
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+ <body>
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+ <div class="panel panel_tree" id="panel">
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+ <div class="header">
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+ <div>
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+ <label for="search" id="search-label" style="display: none">Search</label>
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+ <table>
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+ <tr><td>
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+ <input type="Search" placeholder="Search" autosave="searchdoc" results="10" id="search" autocomplete="off"/>
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+ </td></tr>
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+ </table></div>
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+ </div>
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+ <div class="tree">
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+ <ul>
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+ </ul>
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+ </div>
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+ <div class="result">
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+ <ul>
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+ </ul>
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+ </div>
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+ </div>
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+ </body>
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+ </html>
data/rdoc/panel/search_index.js ADDED
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+ var search_data = {"index":{"info":[["M2dDisease","app\/models\/m2d_disease.rb","classes\/M2dDisease.html"," < ActiveRecord::Base","== Schema Information Table name: m2d_diseases id :integer not null, primary key doid :integer",1],["M2dDiseaseLink","app\/models\/m2d_disease_link.rb","classes\/M2dDiseaseLink.html"," < ActiveRecord::Base","== Schema Information Table name: m2d_disease_links id :integer not null, primary",1],["M2dDiseaseLinksController","app\/controllers\/m2d_disease_links_controller.rb","classes\/M2dDiseaseLinksController.html"," < ApplicationController","",1],["M2dDiseasesController","app\/controllers\/m2d_diseases_controller.rb","classes\/M2dDiseasesController.html"," < ApplicationController","",1],["find_rest","M2dDisease","classes\/M2dDisease.html#M000004","(id)","",2],["find_rest","M2dDiseaseLink","classes\/M2dDiseaseLink.html#M000006","(id)","",2],["index","M2dDiseaseLinksController","classes\/M2dDiseaseLinksController.html#M000000","()","GET \/m2d_disease_links GET \/m2d_disease_links.xml ",2],["index","M2dDiseasesController","classes\/M2dDiseasesController.html#M000001","()","GET \/m2d_diseases GET \/m2d_diseases.xml ",2],["show","M2dDiseaseLinksController","classes\/M2dDiseaseLinksController.html#M000002","()","GET \/m2d_disease_links\/1 GET \/m2d_disease_links\/1.xml ",2],["show","M2dDiseasesController","classes\/M2dDiseasesController.html#M000003","()","GET \/m2d_diseases\/1 GET \/m2d_diseases\/1.xml ",2],["to_param","M2dDisease","classes\/M2dDisease.html#M000005","()","",2],["README","files\/README.html","files\/README.html","","Mir2disease =========== Introduction goes here. Example ======= Example goes here. Copyright (c)",3],["m2d_disease_links_controller.rb","files\/app\/controllers\/m2d_disease_links_controller_rb.html","files\/app\/controllers\/m2d_disease_links_controller_rb.html","","",3],["m2d_diseases_controller.rb","files\/app\/controllers\/m2d_diseases_controller_rb.html","files\/app\/controllers\/m2d_diseases_controller_rb.html","","",3],["m2d_disease.rb","files\/app\/models\/m2d_disease_rb.html","files\/app\/models\/m2d_disease_rb.html","","== Schema Information Table name: m2d_diseases id :integer not null, primary key doid :integer",3],["m2d_disease_link.rb","files\/app\/models\/m2d_disease_link_rb.html","files\/app\/models\/m2d_disease_link_rb.html","","== Schema Information Table name: m2d_disease_links id :integer not null, primary",3],["mir2disease.rb","files\/lib\/mir2disease_rb.html","files\/lib\/mir2disease_rb.html","","Mir2disease ",3]],"searchIndex":["m2ddisease","m2ddiseaselink","m2ddiseaselinkscontroller","m2ddiseasescontroller","find_rest()","find_rest()","index()","index()","show()","show()","to_param()","readme","m2d_disease_links_controller.rb","m2d_diseases_controller.rb","m2d_disease.rb","m2d_disease_link.rb","mir2disease.rb"],"longSearchIndex":["m2d_disease.rb","m2d_disease_link.rb","m2d_disease_links_controller.rb","m2d_diseases_controller.rb","m2ddisease","m2ddiseaselink","m2ddiseaselinkscontroller","m2ddiseasescontroller","m2ddiseaselinkscontroller","m2ddiseasescontroller","m2ddisease","files\/readme.html","files\/app\/controllers\/m2d_disease_links_controller_rb.html","files\/app\/controllers\/m2d_diseases_controller_rb.html","files\/app\/models\/m2d_disease_rb.html","files\/app\/models\/m2d_disease_link_rb.html","files\/lib\/mir2disease_rb.html"]}}
data/rdoc/panel/tree.js ADDED
@@ -0,0 +1 @@
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+ var tree = [["M2dDisease","classes\/M2dDisease.html"," < ActiveRecord::Base",[]],["M2dDiseaseLink","classes\/M2dDiseaseLink.html"," < ActiveRecord::Base",[]],["M2dDiseaseLinksController","classes\/M2dDiseaseLinksController.html"," < ApplicationController",[]],["M2dDiseasesController","classes\/M2dDiseasesController.html"," < ApplicationController",[]]]
data/tasks/mir2disease_tasks.rake ADDED
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+ require 'progressbar'
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+ require 'activerecord'
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+ require 'pp'
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+
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+ plugin_root = File.join(File.dirname(__FILE__), "..")
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+ app_root = File.join(plugin_root, "..", "..", "..")
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+ datafile = plugin_root+"/data/mir2dis.txt"
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+
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+
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+ # gene.diseases
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+ # disease.genes
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+ # disease.mirnas
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+ # mirna.diseases
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+
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+ namespace :mir2disease do
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+
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+ desc "create plugin schema"
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+ task :create_schema => :environment do
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+
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+ conn = ActiveRecord::Base.connection
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+
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+ conn.create_table(:m2d_diseases) do |t|
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+ t.column :doid, :integer
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+ t.column :name, :string
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+ end
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+
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+ conn.create_table(:m2d_disease_links) do |t|
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+ t.column :mature_id, :integer
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+ t.column :m2d_disease_id, :integer
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+ t.column :mirna, :string
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+ t.column :expression, :string
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+ t.column :method, :string
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+ t.column :description, :text
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+ t.column :year, :integer
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+ t.column :pmid, :integer
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+ t.column :causal, :string
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+ t.column :genes, :string
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+ end
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+
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+ #indexes
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+ conn.add_index :m2d_diseases, :doid, :unique => true
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+ conn.add_index :m2d_disease_links, :mature_id
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+ conn.add_index :m2d_disease_links, :m2d_disease_id
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+
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+ end
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+
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+ desc "drop plugin schema"
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+ task :drop_schema => :environment do
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+ conn = ActiveRecord::Base.connection
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+ conn.drop_table(:m2d_diseases)
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+ conn.drop_table(:m2d_disease_links)
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+ end
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+
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+ desc "load plugin"
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+ task :load => ['mir2disease:create_schema','mir2disease:load_data']
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+
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+ desc "reset plugin"
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+ task :reset => ['mir2disease:drop_schema','mir2disease:load']
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+
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+ desc "load mir2disease data"
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+ task :load_data => :environment do
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+
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+ rows = IO.readlines(datafile)
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+
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+ col = Hash.new()
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+ rows.shift.split("\t").each_with_index{|h,idx| col[h.chomp.strip] = idx}
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+ # miRNA DOID Disease Expression Method Description target tarbase Years PMID Causal
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+
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+ #pbar = ProgressBar.new("loading",rows.size)
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+ rows.each_with_index do |row,idx|
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+ # split and remove newline, whitespace and plings
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+ r = row.split("\t").map{|x| x.chomp.strip.gsub(/^"/,'').gsub(/"$/,'')}
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+ if r.select{|x| x!=""}.size != col.size
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+ puts "warning : data row #{idx+2} has wrong number of fields : #{r.select{|x| x!=''}.size}"
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+ next
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+ end
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+
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+ # look up miRNA
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+ mats = Mature.find_best_by_name(r[col['miRNA']])
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+
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+ if mats.nil? or mats.empty?
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+ puts ("warning : could not match '" + r[col['miRNA']]+ "'")
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+ next
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+ end
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+
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+ # look up disease - create if new
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+
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+ disease = M2dDisease.find_or_create_by_doid(r[col['DOID']].to_i) {|d| d.name = r[col['Disease']]}
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+ next if disease.nil?
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+
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+ # create disease link
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+ mats.each do |mat|
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+ dl = M2dDiseaseLink.new()
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+ dl.mirna = r[col['miRNA']]
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+ dl.expression = r[col['Expression']]
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+ dl.method = r[col['Method']]
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+ dl.description = r[col['Description']].toutf8
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+ dl.year = r[col['Years']].to_i
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+ dl.pmid = r[col['PMID']].to_i
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+ dl.causal = r[col['Causal']]
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+ dl.genes = r[col['target']].toutf8
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+ dl.m2d_disease = disease
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+ dl.mature = mat
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+ dl.save
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+ end
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+
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+ #pbar.inc
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+ end
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+ #pbar.finish
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+
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+
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+ end
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+
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+ end
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+
data/uninstall.rb ADDED
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+ # Uninstall hook code here
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: andersjacobsen-mirmaid_mir2disease
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3
  version: !ruby/object:Gem::Version
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- version: 0.0.0
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+ version: 0.1.0
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5
  platform: ruby
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  authors:
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  - Anders Jacobsen
@@ -13,7 +13,7 @@ date: 2009-07-01 00:00:00 -07:00
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  default_executable:
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  dependencies: []
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- description:
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+ description: TODO
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  email: andersmbj@gmail.com
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  executables: []
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@@ -22,7 +22,56 @@ extensions: []
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  extra_rdoc_files:
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  - README
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  files:
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+ - MIT-LICENSE
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26
  - README
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+ - Rakefile
28
+ - VERSION
29
+ - app/controllers/m2d_disease_links_controller.rb
30
+ - app/controllers/m2d_diseases_controller.rb
31
+ - app/models/m2d_disease.rb
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+ - app/models/m2d_disease_link.rb
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+ - app/views/m2d_disease_links/_list_for_mature.html.erb
34
+ - app/views/m2d_disease_links/_m2d_disease_link.html.erb
35
+ - app/views/m2d_disease_links/index.html.erb
36
+ - app/views/m2d_disease_links/show.html.erb
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+ - app/views/m2d_diseases/_m2d_disease.html.erb
38
+ - app/views/m2d_diseases/index.html.erb
39
+ - app/views/m2d_diseases/show.html.erb
40
+ - config/routes.rb
41
+ - data/mir2dis.txt
42
+ - init.rb
43
+ - install.rb
44
+ - lib/mir2disease.rb
45
+ - mirmaid_mir2disease.gemspec
46
+ - mirmaid_models.rb
47
+ - rdoc/classes/M2dDisease.html
48
+ - rdoc/classes/M2dDiseaseLink.html
49
+ - rdoc/classes/M2dDiseaseLinksController.html
50
+ - rdoc/classes/M2dDiseasesController.html
51
+ - rdoc/created.rid
52
+ - rdoc/css/main.css
53
+ - rdoc/css/panel.css
54
+ - rdoc/css/reset.css
55
+ - rdoc/files/README.html
56
+ - rdoc/files/app/controllers/m2d_disease_links_controller_rb.html
57
+ - rdoc/files/app/controllers/m2d_diseases_controller_rb.html
58
+ - rdoc/files/app/models/m2d_disease_link_rb.html
59
+ - rdoc/files/app/models/m2d_disease_rb.html
60
+ - rdoc/files/lib/mir2disease_rb.html
61
+ - rdoc/i/arrows.png
62
+ - rdoc/i/results_bg.png
63
+ - rdoc/i/tree_bg.png
64
+ - rdoc/index.html
65
+ - rdoc/js/jquery-1.3.2.min.js
66
+ - rdoc/js/main.js
67
+ - rdoc/js/searchdoc.js
68
+ - rdoc/panel/index.html
69
+ - rdoc/panel/search_index.js
70
+ - rdoc/panel/tree.js
71
+ - tasks/mir2disease_tasks.rake
72
+ - test/mir2disease_test.rb
73
+ - test/test_helper.rb
74
+ - uninstall.rb
26
75
  has_rdoc: true
27
76
  homepage: http://github.com/andersjacobsen/mirmaid_mir2disease
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77
  post_install_message: