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
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
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
|
module OpenTox
class Dataset
include Owl
#attr_accessor :model
def initialize
super
end
# find or create a new compound and return the resource
def find_or_create_compound(uri)
compound = @model.subject(DC["identifier"], uri)
if compound.nil?
compound = @model.create_resource
@model.add compound, RDF['type'], OT["Compound"]
@model.add compound, DC["identifier"], uri
end
compound
end
# find or create a new feature and return the resource
def find_or_create_feature(f)
feature = @model.subject(DC["title"], f[:name].to_s)
if feature.nil?
feature = @model.create_resource
@model.add feature, RDF['type'], OT["Feature"]
@model.add feature, DC["identifier"], File.join("feature",feature.to_s.gsub(/[()]/,'')) # relative uri as we don know the final uri
@model.add feature, DC["title"], f[:name].to_s
@model.add feature, OT['hasSource'], f[:source].to_s if f[:source]
end
feature
end
# find or create a new value and return the resource
def find_or_create_value(v)
value = @model.subject OT["value"], v.to_s
if value.nil?
value = @model.create_resource
@model.add value, RDF['type'], OT["FeatureValue"]
@model.add value, OT["value"], v.to_s
end
value
end
def tuple?(t)
statements = []
has_tuple = true
t.each do |name,v|
feature = self.find_or_create_feature(:name => name)
value = self.find_or_create_value(v)
tuple = @model.subject(feature,value)
has_tuple = false if tuple.nil?
statements << [tuple,feature,value]
end
tuples_found = statements.collect{|s| s[0]}.uniq
has_tuple = false unless tuples_found.size == 1
has_tuple
end
def create_tuple(t)
tuple = @model.create_resource
@model.add tuple, RDF['type'], OT["Tuple"]
t.each do |name,value|
feature = self.find_or_create_feature(:name => name)
value = self.find_or_create_value(value)
pair = @model.create_resource
@model.add tuple, OT['tuple'], pair
@model.add pair, OT['feature'], feature
@model.add pair, OT['value'], value
end
tuple
end
def find_or_create_tuple(t)
if self.tuple?(t)
t
else
self.create_tuple(t)
end
end
def add_data_entry(compound,feature,value)
data_entry = @model.create_resource
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
@model.add data_entry, OT['feature'], feature
@model.add data_entry, OT['values'], value
end
def self.create(data, content_type = 'application/rdf+xml')
uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
dataset = Dataset.new
dataset.read uri.to_s
dataset
end
def self.find(uri)
begin
RestClient.get uri # check if the resource is available
dataset = Dataset.new
dataset.read uri.to_s
dataset
rescue
nil
end
end
def features
end
def feature_values(uri)
features = {}
feature = @model.subject(DC["identifier"],uri)
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compound = @model.object(compound_node, DC["identifier"]).to_s.sub(/^\[(.*)\]$/,'\1')
features[compound] = [] unless features[compound]
@model.subjects(OT['compound'], compound_node).each do |data_entry|
if feature == @model.object(data_entry, OT['feature'])
values_node = @model.object(data_entry, OT['values'])
@model.find(values_node, OT['value'], nil) do |s,p,value|
case value.to_s
when "true"
features[compound] << true
when "false"
features[compound] << false
else
features[compound] << value.to_s
end
end
end
end
end
features
end
def tuples
tuples = []
@model.subjects(RDF['type'], OT["Tuple"]).each do |t|
tuple = {}
compounds = []
@model.subjects(OT['values'], t).each do |data_entry|
compound_node = @model.object(data_entry,OT['compound'])
compounds << @model.object(compound_node, DC["identifier"]).to_s
end
@model.find(t, OT['tuple'],nil) do |s,p,pair|
feature_node = @model.object(pair, OT['feature'])
feature_name = @model.object(feature_node, DC['title']).to_s
value_node = @model.object(pair, OT['value'])
value = @model.object(value_node, OT['value']).to_s
value = value.to_f if value.match(/^[\d\.]+$/)
tuple[feature_name.to_sym] = value
end
tuple[:compounds] = compounds
tuples << tuple
end
tuples
end
def tuple(compound_uri)
compound_node = @model.subject(DC["identifier"],compound_uri)
#puts compound_uri
@model.subjects(OT['compound'], compound_node).each do |data_entry|
values_node = @model.object(data_entry, OT['values'])
@model.find(values_node, OT['tuple'], nil) do |s,p,tuple|
@model.find(tuple, OT['feature'], nil) do |s,p,feature|
name = @model.object(feature,DC['title']).to_s
#puts name
end
end
#puts values_node
end
end
def compounds
compounds = []
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compounds << @model.object(compound_node, DC["identifier"])#.to_s.sub(/^\[(.*)\]$/,'\1')
end
compounds
end
# Delete a dataset
def delete
RestClient.delete @uri
end
def save
RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s
end
end
end
# def tanimoto(dataset)
# RestClient.get(File.join(@uri,'tanimoto',dataset.path))
# end
#
# def weighted_tanimoto(dataset)
# RestClient.get(File.join(@uri,'weighted_tanimoto',dataset.path))
# end
=begin
def data_entries
data = {}
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compound = @model.object(compound_node, DC["identifier"]).to_s#.sub(/^\[(.*)\]$/,'\1')
#compound = OpenTox::Compound.new(:inchi => compound).smiles
data[compound] = [] unless data[compound]
#puts compound
@model.subjects(OT['compound'], compound_node).each do |data_entry|
feature_node = @model.object(data_entry, OT['feature'])
feature = @model.object(feature_node, DC["identifier"]).to_s
values_node = @model.object(data_entry, OT['values'])
type = @model.object(values_node,RDF['type']).to_s
case type
when /FeatureValue/
@model.find(values_node, OT['value'], nil) do |s,p,value|
case value.to_s
when "true"
data[compound] << {feature => true}
when "false"
data[compound] << {feature => false}
else
data[compound] << {feature => value.to_s}
end
end
when /Tuple/ # this is really slow
t = {}
@model.find(values_node, OT['tuple'], nil) do |s,p,tuple|
@model.find(tuple, OT['feature'], nil) do |s,p,feature|
@name = @model.object(feature,DC['title']).to_s
end
@model.find(tuple, OT['value'], nil) do |s,p,value|
v = @model.object(value,OT['value']).to_s
t[@name] = v
#print @name + ": "
#puts v
end
end
data[compound] << t
end
end
end
data
end
=end
|
