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
|
class Lazar < Model
attr_accessor :prediction_dataset
def classify(compound_uri,prediction)
prediction.title += " lazar classification"
lazar = YAML.load self.yaml
compound = OpenTox::Compound.new(:uri => compound_uri)
compound_matches = compound.match lazar.features
conf = 0.0
similarities = {}
classification = nil
lazar.fingerprints.each do |uri,matches|
sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values)
if sim > 0.3
similarities[uri] = sim
lazar.activities[uri].each do |act|
case act.to_s
when 'true'
conf += OpenTox::Utils.gauss(sim)
when 'false'
conf -= OpenTox::Utils.gauss(sim)
end
end
end
end
conf = conf/similarities.size
if conf > 0.0
classification = true
elsif conf < 0.0
classification = false
end
if (classification != nil)
feature_uri = lazar.dependent_variable + "_lazar_classification"
prediction.compounds << compound_uri
prediction.features << feature_uri
prediction.data[compound_uri] = [] unless prediction.data[compound_uri]
tuple = {
:classification => classification,
:confidence => conf,
:similarities => similarities,
:features => compound_matches
}
prediction.data[compound_uri] << {feature_uri => tuple}
end
end
def database_activity?(compound_uri,prediction)
# find database activities
lazar = YAML.load self.yaml
db_activities = lazar.activities[compound_uri]
if db_activities
prediction.source = lazar.activity_dataset_uri
feature_uri = lazar.dependent_variable
prediction.compounds << compound_uri
prediction.features << feature_uri
prediction.data[compound_uri] = [] unless prediction.data[compound_uri]
db_activities.each do |act|
prediction.data[compound_uri] << {feature_uri => act}
end
true
else
false
end
end
def to_owl
data = YAML.load(yaml)
owl = OpenTox::Owl.new 'Model', uri
owl.source = "http://github.com/helma/opentox-model"
#owl.algorithm = data.algorithm
owl.dependentVariable = data.activity_dataset_uri
owl.independentVariables = data.feature_dataset_uri
owl.rdf
end
end
get '/:id/?' do
model = Lazar.get(params[:id])
halt 404, "Model #{uri} not found." unless model
accept = request.env['HTTP_ACCEPT']
accept = "application/rdf+xml" if accept == '*/*' or accept =~ /html/ or accept == '' or accept.nil?
case accept
when "application/rdf+xml"
response['Content-Type'] = 'application/rdf+xml'
model.to_owl
when /yaml/
response['Content-Type'] = 'application/x-yaml'
model.yaml
else
halt 400, "Unsupported MIME type '#{accept}'"
end
end
post '/?' do # create model
halt 400, "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/yaml/)
model = Lazar.new
model.save
model.uri = url_for("/#{model.id}", :full)
model.yaml = request.env["rack.input"].read
model.save
model.uri
end
post '/:id/?' do # create prediction
lazar = Lazar.get(params[:id])
halt 404, "Model #{params[:id]} does not exist." unless lazar
halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
prediction = OpenTox::Dataset.new
prediction.source = lazar.uri
prediction.title = URI.decode YAML.load(lazar.yaml).dependent_variable.split(/#/).last
if compound_uri
lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction)
LOGGER.debug prediction.to_yaml
case request.env['HTTP_ACCEPT']
when /yaml/
prediction.to_yaml
when 'application/rdf+xml'
prediction.to_owl
else
halt 404, "Content type #{request.env['HTTP_ACCEPT']} not available."
end
elsif dataset_uri
task = OpenTox::Task.create
pid = Spork.spork(:logger => LOGGER) do
task.started
task = OpenTox::Task.create
input_dataset = OpenTox::Dataset.find(dataset_uri)
input_dataset.compounds.each do |compound_uri|
lazar.classify(compound_uri) unless lazar.database_activity?(compound_uri)
end
uri = lazar.prediction_dataset.save
task.completed(uri)
end
task.pid = pid
LOGGER.debug "Task PID: " + pid.to_s
#status 303
response['Content-Type'] = 'text/uri-list'
task.uri + "\n"
end
end
|
