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
|
module OpenTox
module Model
class Generic
MODEL_ATTRIBS = [:uri, :title, :creator, :date, :format, :predictedVariables, :independentVariables, :dependentVariables, :trainingDataset, :algorithm]
MODEL_ATTRIBS.each{ |a| attr_accessor(a) }
def self.find(uri)
owl = OpenTox::Owl.from_uri(uri, "Model")
return self.new(owl)
end
def self.to_rdf(model)
owl = OpenTox::Owl.create 'Model', model.uri
(MODEL_ATTRIBS - [:uri]).each do |a|
owl.set(a.to_s,model.send(a.to_s))
end
owl.rdf
end
protected
def initialize(owl)
[:date, :creator, :title, :format, :algorithm, :dependentVariables,
:independentVariables, :predictedVariables, :trainingDataset].each do |a|
self.send("#{a.to_s}=".to_sym, owl.get(a.to_s))
end
@uri = owl.uri
if ENV['RACK_ENV'] =~ /test|debug/
begin
raise "uri invalid" unless Utils.is_uri?(@uri)
raise "no algorithm" unless @algorithm and @algorithm.size>0
raise "no dependent variables" unless @dependentVariables and @dependentVariables.size>0
raise "no indenpendent variables" unless @independentVariables
raise "no predicted variables" unless @predictedVariables and @predictedVariables.size>0
rescue => ex
RestClientWrapper.raise_uri_error "invalid model: '"+ex.message+"'\n"+self.to_yaml+"\n",@uri.to_s
end
end
end
end
class PredictionModel < Generic
def self.build( algorithm_uri, algorithm_params )
if algorithm_uri =~ /ambit2/
LOGGER.warn "Ambit hack, replacing 'prediction_feature' with 'target'"
algorithm_params[:target] = algorithm_params[:prediction_feature]
algorithm_params.delete(:prediction_feature)
end
LOGGER.debug "Build model, algorithm_uri:"+algorithm_uri.to_s+", algorithm_parms: "+algorithm_params.inspect.to_s
uri = OpenTox::RestClientWrapper.post(algorithm_uri,algorithm_params).to_s
LOGGER.debug "Build model done: "+uri.to_s
RestClientWrapper.raise_uri_error("Invalid build model result: '"+uri.to_s+"'", algorithm_uri, algorithm_params ) unless Utils.model_uri?(uri)
return PredictionModel.find(uri)
end
def predict_dataset( dataset_uri )
LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
uri = RestClientWrapper.post(@uri, {:dataset_uri=>dataset_uri})
RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
uri
end
def classification?
#HACK replace with request to ontology server
if @title =~ /lazar classification/
return true
elsif @uri =~/ntua/ and @title =~ /mlr/
return false
elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
return false
elsif @uri =~/ambit2/ and @title =~ /pKa/
return false
elsif @uri =~/majority/
return (@uri =~ /class/) != nil
else
raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
end
end
end
class Lazar < Generic
attr_accessor :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features
def initialize
@source = "http://github.com/helma/opentox-model"
@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
@features = []
@effects = {}
@activities = {}
@p_values = {}
@fingerprints = {}
end
def save
@features.uniq!
resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(self.to_yaml, :content_type => "text/x-yaml").chomp.to_s
end
def self.find_all
RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
end
=begin
# Predict a compound
def predict(compound)
# nicht absichern??
resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(:compound_uri => compound.uri)
end
def self.base_uri
File.join @@config[:services]["opentox-model"],'lazar'
end
def self.create(data)
resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.post(data, :content_type => "text/x-yaml").chomp.to_s
end
def delete
resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
resource.delete
#RestClient.delete @uri if @uri
#RestClient.delete model.task_uri if model.task_uri
end
# def self.create(task)
# @uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri)
# end
# def yaml=(data)
# RestClient.put(@@uri, data, :content_type => "text/x-yaml").to_s
# end
def endpoint
YAML.load(RestClient.get(uri))[:endpoint]
end
def algorithm=(algorithm)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['algorithm'], Redland::Uri.new(algorithm) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(algorithm), RDF['type'], OT['Algorithm']
end
def trainingDataset=(trainingDataset)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(trainingDataset), RDF['type'], OT['Dataset']
end
def dependentVariables=(dependentVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['dependentVariables'], Redland::Uri.new(dependentVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(dependentVariables), RDF['type'], OT['Feature']
end
def independentVariables=(independentVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['independentVariables'], Redland::Uri.new(independentVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(independentVariables), RDF['type'], OT['Feature']
end
def predictedVariables=(predictedVariables)
me = @model.subject(RDF['type'],OT[self.owl_class])
@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
end
=end
end
end
end
|
