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
|
module OpenTox
class Dataset
include Owl
def initialize
super
end
# create/add to entry from uris or Redland::Resources
def add(compound,feature,value)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
values = @model.create_resource
@model.add data_entry, OT['values'], values
@model.add values, RDF['type'], OT['FeatureValue']
@model.add values, OT['feature'], feature
@model.add values, OT['value'], value.to_s
end
def add_tuple(compound,tuple)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
@model.add data_entry, OT['values'], tuple
end
def create_tuple(feature,t)
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
tuple = @model.create_resource
@model.add tuple, RDF['type'], OT["Tuple"]
@model.add tuple, OT['feature'], feature
t.each do |name,value|
f = self.find_or_create_feature name unless name.class == Redland::Resource
complex_value = @model.create_resource
feature = self.find_or_create_feature(name)
@model.add tuple, OT['complexValue'], complex_value
@model.add complex_value, RDF['type'], OT["FeatureValue"]
@model.add complex_value, OT['feature'], f
@model.add complex_value, OT['value'], value.to_s
end
tuple
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(uri)
feature = @model.subject(DC["identifier"], uri)
if feature.nil?
feature = @model.create_resource
@model.add feature, RDF['type'], OT["Feature"]
@model.add feature, DC["identifier"], uri
@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
@model.add feature, DC['source'], uri
end
feature
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)
dataset = Dataset.new
data = `curl "#{uri}"`
#data = RestClient.get uri, :accept => 'application/rdf+xml' # unclear why this does not work for complex uris, Dataset.find works from irb
dataset.rdf = data
dataset
end
def features
features = []
@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
features << @model.object(feature_node, DC["identifier"])#
end
features
end
def data
data = {}
@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
compound_node = @model.object(data_entry, OT['compound'])
compound_uri = @model.object(compound_node, DC['identifier']).to_s
@model.find(data_entry, OT['values'], nil) do |s,p,values|
feature_node = @model.object values, OT['feature']
feature_uri = @model.object(feature_node, DC['identifier']).to_s.sub(/\^\^.*$/,'') # remove XML datatype
type = @model.object(values, RDF['type'])
if type == OT['FeatureValue']
value = @model.object(values, OT['value']).to_s
case value.to_s
when TRUE_REGEXP # defined in environment.rb
value = true
when FALSE_REGEXP # defined in environment.rb
value = false
else
LOGGER.warn compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
value = nil
end
data[compound_uri] = {} unless data[compound_uri]
data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
data[compound_uri][feature_uri] << value unless value.nil?
elsif type == OT['Tuple']
entry = {}
data[compound_uri] = {} unless data[compound_uri]
data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
name_node = @model.object complex_value, OT['feature']
name = @model.object(name_node, DC['title']).to_s
value = @model.object(complex_value, OT['value']).to_s
v = value.sub(/\^\^.*$/,'') # remove XML datatype
v = v.to_f if v.match(/^[\.|\d]+$/) # guess numeric datatype
entry[name] = v
end
data[compound_uri][feature_uri] << entry
end
end
end
data
end
def compounds
compounds = []
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compounds << @model.object(compound_node, DC["identifier"]).to_s
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
def to_yaml
{
:uri => self.uri,
:opentox_class => self.owl_class,
:title => self.title,
:source => self.source,
:identifier => self.identifier,
:compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')},
:features => self.features.collect{|f| f.to_s },
:data => self.data
}.to_yaml
end
end
end
|