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class DownloadTrials
  require 'rubygems'

  def self.download_trials
    agent = WWW::Mechanize.new
    file = agent.get("http://clinicaltrials.gov/search?term=%22banana%22&studyxml=true")
    file.save_as(File.dirname(__FILE__) + '/../tmp/trials.zip')
  end 
end

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# test/unit/import_trials_test.rb
def test_import
  search_string = "search string"
  inst_name = "institution name"

  Trial.expects(:create_trials_from_xml).with(DownloadTrials::OUTPUT_DIRECTORY, inst_name)                                                                        
  ImportTrials.import(inst_name, search_string)
end 

# test/unit/trial_test.rb

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580) Error:
test: SporeUnit should require unique value for name. (SporeUnitTest):
ArgumentError: wrong number of arguments (1 for 0)
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:102:in `sum'
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:102:in `instance_method_already_implemented?'
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:72:in `define_attribute_methods'
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:71:in `each'
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:71:in `define_attribute_methods'
    /var/projects/beno/dfhcc_informatics/vendor/rails/activerecord/lib/active_record/attribute_methods.rb:242:in `method_missing'
    /var/projects/beno/dfhcc_informatics/vendor/gems/thoughtbot-shoulda-2.0.5/lib/shoulda/ac

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class Array
  # Split an array into 10 pieces, yield 1/10th and the other 9/10ths.  Do this 10 times, returning a distinct
  # (no overlaps) 1/10th slice each time.
  def iterate_by_tenths(&block)
    self.each_slice((self.length / 10).ceil) do |tenth|
      yield(tenth, self - tenth)
    end
  end
end

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class ClassifyPublications


  # TODO: test corpus should be confirmed AND rejected items; would require a classifyable object

  # Results:
  #
  # (Testing done with 10-fold cross-validation on 31k citations)
  #
  # Training on title and abstract, classifying on title = 90.8% accuracy

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# imports institutions from a filemaker exported xml file
require File.dirname(__FILE__) + '/../../config/environment'
require 'rubygems'
require 'hpricot'

# this establishes a mapping between column names in the 
# exported filemaker xml and the variable names we'll be using in rails
COLUMN_MAP = { 
 "institution_key" => :institution_key,
 "institution_name" => :institution_name,

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  def show
    if (@trial.closed? || @trial.nonrelevant?) && !is_admin?
      render 'admin_only'
    else
      respond_to do |format|
        format.html
        format.xml { render :xml => @trial.to_xml(:include => [:topics, :contacts, :investigators, :institutions]) }
      end 
    end 
  end 

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bjo@dhcp-172-24-115-72:~$ ssh -v ben@railsstage
OpenSSH_5.1p1, OpenSSL 0.9.7l 28 Sep 2006
debug1: Reading configuration data /etc/ssh_config
debug1: Connecting to railsstage [172.24.115.131] port 22.
debug1: Connection established.
debug1: identity file /Users/bjo/.ssh/identity type -1
debug1: identity file /Users/bjo/.ssh/id_rsa type -1
debug1: identity file /Users/bjo/.ssh/id_dsa type 2
debug1: Remote protocol version 2.0, remote software version OpenSSH_5.2
debug1: match: OpenSSH_5.2 pat OpenSSH*

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  ##
  # Delete a (key, value) pair.
  #
  # ==== Example
  #  t = Trie.new.insert("a", 1).insert("a", 2)
  #  t.delete_pair("a", 1)  # t now only contains the second value
  #
  def delete_pair(key, value)
    key = key.split('') if key.is_a?(String)
    if key.empty?

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require 'rbconfig'
require 'find'
require 'ftools'

include Config

# this was adapted from rdoc's install.rb by ways of Log4r

$sitedir = CONFIG["sitelibdir"]
unless $sitedir