Module: PubliSci::RDFParser

Included in:
DataSet::ORM::DataCube, DataSet::ORM::DataCube, Dataset::DataCube, Metadata::Generator, PubliSci::Readers::Base, Writers::Base
Defined in:
lib/publisci/parser.rb

Instance Method Summary collapse

Instance Method Details

#add_node(n, str = "") ⇒ Object 



147
148
149
150
151
152
153
154
155
156
157
158
 
# File 'lib/publisci/parser.rb', line 147

def add_node(n,str="")

  raise "need index or identifier to generate blank nodes" unless n
  raise "need base string or blank string for blank node" unless str.is_a? String
  if str["node"]
    ret = str[0..-2] + "/#{n}" + ">"
    ret
    # str[0..-2] + "/#{n}" + ">"
  else
    "<node/#{n}>"
  end
end

#bnode_value(obj, node_index, node_str, options) ⇒ Object 



173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
 
# File 'lib/publisci/parser.rb', line 173

def bnode_value(obj, node_index, node_str, options)
  # TODO - Implement proper recursion
  # TODO - check if object is "a" (rdf:type) => or convert rdf:type to "a"
  str = ""
  subnodes = []
  if obj.is_a?(Array) # && obj.size == 2
    if obj.size == 2
      if obj[0].is_a?(String)
        if is_complex?(obj[1])
          str << "#{to_resource(obj[0])} #{add_node(node_index,node_str)} . \n"
          subnodes << encode_value(obj[1], options, node_index, node_str)
        else
          str << "#{to_resource(obj[0])} #{encode_value(obj[1], options, node_index, node_str)} "
        end
      elsif obj[0].is_a?(Array) && obj[1].is_a?(Array)
        newnode = add_node(0,node_str)
        v1 = bnode_value(obj[0], 0, node_str, options)
        v2 = bnode_value(obj[1], 1, node_str, options)

        if v1.is_a? Array
          subnodes << v1
          v1 = nil
        end

        if v2.is_a? Array
          subnodes << v2
          v2 = nil
        end

        if v1
          str << "#{v1} ;"
        end

        str << "\n#{v2} .\n" if v2
      end
    elsif obj.all?{|ent| ent.is_a? Array}
      obj.each{|ent|
        bn = bnode_value(ent,node_index,node_str,options)
        if bn.is_a? String
          str << bn + "\n"
        else
          str << bn[0] + "\n"
          subnodes << bn[1]
        end
      }
    end
  else
    raise "Invalid Structured value: #{obj}"
  end

  if subnodes.size > 0
    [str, subnodes.flatten].flatten
  else
    str
  end
end

#encode_value(obj, options = {}, node_index = nil, node_str = "") ⇒ Object 



160
161
162
163
164
165
166
167
168
169
170
171
 
# File 'lib/publisci/parser.rb', line 160

def encode_value(obj,options={}, node_index=nil, node_str = "")
  if RDF::Resource(obj).valid?
    to_resource(obj,options)
  elsif obj && obj.is_a?(String) && (obj[0]=="<" && obj[-1] = ">")
    obj
  elsif obj.is_a?(Array)
    node_str = add_node(node_index,node_str)
    ["#{node_str}" ] + [bnode_value(obj, node_index, node_str, options)]
  else
    to_literal(obj,options)
  end
end

#get_ary(query_results, method = 'to_s') ⇒ Object 



50
51
52
53
54
55
56
57
58
59
60
 
# File 'lib/publisci/parser.rb', line 50

def get_ary(query_results,method='to_s')
  query_results.map{|solution|
    solution.to_a.map{|entry|
      if entry.last.respond_to? method
        entry.last.send(method)
      else
        entry.last.to_s
      end
    }
  }
end

#get_hashes(query_results, method = nil) ⇒ Object 



62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
 
# File 'lib/publisci/parser.rb', line 62

def get_hashes(query_results,method=nil)
  arr=[]
  query_results.map{|solution|
    h={}
    solution.map{|element|
      if method && element[1].respond_to?(method)
        h[element[0]] = element[1].send(method)
      else
        h[element[0]] = element[1]
      end
    }
    arr << h
  }
  arr
end

#is_complex?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


143
144
145
 
# File 'lib/publisci/parser.rb', line 143

def is_complex?(obj)
  obj.is_a? Array
end

#is_uri?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


4
5
6
 
# File 'lib/publisci/parser.rb', line 4

def is_uri?(obj)
  RDF::Resource(obj).valid?
end

#load_string(string, repo = RDF::Repository.new) ⇒ Object 



41
42
43
44
45
46
47
48
 
# File 'lib/publisci/parser.rb', line 41

def load_string(string,repo=RDF::Repository.new)
  f = Tempfile.new('repo')
  f.write(string)
  f.close
  repo.load(f.path, :format => :ttl)
  f.unlink
  repo
end

#observation_hash(query_results, shorten_uris = false, method = 'to_s') ⇒ Object 



78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
 
# File 'lib/publisci/parser.rb', line 78

def observation_hash(query_results,shorten_uris=false,method='to_s')
  h={}
  query_results.map{|sol|
    (h[sol[:observation].to_s] ||= {})[sol[:property].to_s] = sol[:value].to_s
  }

  if shorten_uris
    newh= {}
    h.map{|k,v|
      newh[strip_uri(k)] ||= {}
      v.map{|kk,vv|
        newh[strip_uri(k)][strip_uri(kk)] = strip_uri(vv)
      }
    }
    newh
  else
    h
  end
end

#sanitize(array) ⇒ Object 



8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
 
# File 'lib/publisci/parser.rb', line 8

def sanitize(array)
  #remove spaces and other special characters
  array = Array(array)
  processed = []
  array.map{|entry|
    if entry.is_a? String
      if is_uri? entry
        processed << entry.gsub(/[\s]/,'_')
      else
        processed << entry.gsub(/[\s]/,'_')
      end
    else
      processed << entry
    end
  }
  processed
end

#sanitize_hash(h) ⇒ Object 



26
27
28
29
30
31
32
33
34
35
36
37
38
39
 
# File 'lib/publisci/parser.rb', line 26

def sanitize_hash(h)
  mappings = {}
  h.keys.map{|k|
    if(k.is_a? String)
      mappings[k] = k.gsub(' ','_')
    end
  }

  h.keys.map{|k|
    h[mappings[k]] = h.delete(k) if mappings[k]
  }

  h
end

#strip_prefixes(string) ⇒ Object 



261
262
263
 
# File 'lib/publisci/parser.rb', line 261

def strip_prefixes(string)
  string.to_s.split(':').last
end

#strip_uri(uri) ⇒ Object 



255
256
257
258
259
 
# File 'lib/publisci/parser.rb', line 255

def strip_uri(uri)
  uri = uri.to_s.dup
  uri[-1] = '' if uri[-1] == '>'
  uri.to_s.split('/').last.split('#').last
end

#to_literal(obj, options = {}) ⇒ Object 



124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
 
# File 'lib/publisci/parser.rb', line 124

def to_literal(obj, options={})
  if obj.is_a? String
    # Depressing that there's no more elegant way to check if a string is
    # a number...
    if val = Integer(obj) rescue nil
      val
    elsif val = Float(obj) rescue nil
      val
    else
      '"'+obj+'"'
    end
  elsif obj == nil && options[:encode_nulls]
    #TODO decide the right way to handle missing values, since RDF has no null
    'rdf:nil'
  else
    obj
  end
end

#to_resource(obj, options = {}) ⇒ Object 



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
 
# File 'lib/publisci/parser.rb', line 98

def to_resource(obj, options={})
  if obj.is_a? String

    if is_uri? obj
      obj = RDF::Resource(obj).to_base unless obj[/\w+:\w/]
    else

      #TODO decide the right way to handle missing values, since RDF has no null
      #probably throw an error here since a missing resource is a bigger problem
      obj = "rdf:nil" if obj.empty?
      obj=  obj.to_s.gsub(' ','_')
    end

    obj
    #TODO  remove special characters (faster) as well (eg '?')

  elsif obj == nil && options[:encode_nulls]
    'rdf:nil'
  elsif obj.is_a? Numeric
    #resources cannot be referred to purely by integer (?)
    "n"+obj.to_s
  else
    obj
  end
end

#turtle_indent(turtle_str) ⇒ Object 



230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
 
# File 'lib/publisci/parser.rb', line 230

def turtle_indent(turtle_str)
  tabs = 0
  turtle_str.split("\n").map{|str|
    case str[-1]
      when "."
        last_tabs = tabs
        tabs = 0
        ("  " * last_tabs) + str
      when ";"
        last_tabs = tabs
        tabs = 1 if tabs == 0
        ("  " * last_tabs) + str
      else
        last_tabs = tabs
        if str.size < 2
          tabs = 0
        else
          tabs += 1
        end
        ("  " * last_tabs) + str
    end
  }.join("\n")

end