summaryrefslogtreecommitdiff
path: root/lib/overwrite.rb
blob: 31d30c99d9c3ec745630facd83f419874a3ce8d0 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
require "base64"
class Object
  # An object is blank if it's false, empty, or a whitespace string.
  # For example, "", "   ", +nil+, [], and {} are all blank.
  def blank?
    respond_to?(:empty?) ? empty? : !self
  end

  def numeric?
    true if Float(self) rescue false
  end

  # Returns dimension of nested arrays
  def dimension
    self.class == Array ? 1 + self[0].dimension : 0
  end
end

class Numeric
  def percent_of(n)
    self.to_f / n.to_f * 100.0
  end
end

class Float
  # round to n significant digits
  # http://stackoverflow.com/questions/8382619/how-to-round-a-float-to-a-specified-number-of-significant-digits-in-ruby
  def signif(n)
    Float("%.#{n}g" % self)
  end

  # converts -10 logarithmized values back
  def delog10
    10**(-1*self)
  end
end

module Enumerable
  # @return [Array] only the duplicates of an enumerable
  def duplicates
    inject({}) {|h,v| h[v]=h[v].to_i+1; h}.reject{|k,v| v==1}.keys
  end
  # http://stackoverflow.com/questions/2562256/find-most-common-string-in-an-array
  Enumerable.class_eval do
    def mode
      group_by do |e|
        e
      end.values.max_by(&:size).first
    end
  end
end

class String
  # @return [String] converts camel-case to underscore-case (OpenTox::SuperModel -> open_tox/super_model)
  def underscore
    self.gsub(/::/, '/').
    gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
    gsub(/([a-z\d])([A-Z])/,'\1_\2').
    tr("-", "_").
    downcase
  end

  # convert strings to boolean values
  # @return [TrueClass,FalseClass] true or false
  def to_boolean
    return true if self == true || self =~ (/(true|t|yes|y|1)$/i)
    return false if self == false || self.nil? || self =~ (/(false|f|no|n|0)$/i)
    bad_request_error "invalid value for Boolean: \"#{self}\""
  end

end

class File
  # @return [String] mime_type including charset using linux cmd command
  def mime_type
    `file -ib '#{self.path}'`.chomp
  end
end

class Array

  # Sum up the size of single arrays in an array of arrays
  # @param [Array] Array of arrays
  # @return [Integer] Sum of size of array elements
  def sum_size
    self.inject(0) { |s,a|
      if a.respond_to?('size')
        s+=a.size
      else
        internal_server_error "No size available: #{a.inspect}"
      end
    }
  end

  # For symbolic features
  # @param [Array] Array to test.
  # @return [Boolean] Whether the array has just one unique value.
  def zero_variance?
    return self.uniq.size == 1
  end

  def median
    sorted = self.sort
    len = sorted.length
    (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0
  end

  def mean
    self.compact.inject{ |sum, el| sum + el }.to_f / self.compact.size
  end

  def sample_variance
    m = self.mean
    sum = self.compact.inject(0){|accum, i| accum +(i-m)**2 }
    sum/(self.compact.length - 1).to_f
  end

  def standard_deviation
    Math.sqrt(self.sample_variance)
  end

  def for_R
    if self.first.is_a?(String) 
      #"\"#{self.collect{|v| v.sub('[','').sub(']','')}.join(" ")}\"" # quote and remove square brackets
      "NA"
    else
      self.median
    end
  end

  def collect_with_index
    result = []
    self.each_with_index do |elt, idx|
      result << yield(elt, idx)
    end
    result
  end
end

module URI

  def self.ssl? uri
    URI.parse(uri).instance_of? URI::HTTPS
  end

  # @return [Boolean] checks if resource exists by making a HEAD-request
  def self.accessible?(uri)
    parsed_uri = URI.parse(uri + (OpenTox::RestClientWrapper.subjectid ? "?subjectid=#{CGI.escape OpenTox::RestClientWrapper.subjectid}" : ""))
    http_code = URI.task?(uri) ? 600 : 400
    http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
    unless (URI.ssl? uri) == true
      http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
      request = Net::HTTP::Head.new(parsed_uri.request_uri)
      http.request(request).code.to_i < http_code
    else
      http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
      http.use_ssl = true
      http.verify_mode = OpenSSL::SSL::VERIFY_NONE
      request = Net::HTTP::Head.new(parsed_uri.request_uri)
      http.request(request).code.to_i < http_code
    end
  rescue
    false
  end

  def self.valid? uri
    u = URI.parse(uri)
    u.scheme!=nil and u.host!=nil
  rescue URI::InvalidURIError
    false
  end

  def self.task? uri
    uri =~ /task/ and URI.valid? uri
  end

end