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
|
require "lib/validation_db.rb"
# = Reports::ValidationDB
#
# connects directly to the validation db, overwirte with restclient calls
# if reports/reach reports are seperated from validation someday
#
class Reports::ValidationDB
def same_service?(uri)
self_uri = URI.parse($url_provider.url)
val_uri = URI.parse(uri)
self_uri.host == val_uri.host && self_uri.port == val_uri.port
end
def resolve_cv_uris(validation_uris, identifier, subjectid)
res = {}
count = 0
validation_uris.each do |u|
if u.to_s =~ /.*\/crossvalidation\/[0-9]+/
cv = nil
cv_id = u.split("/")[-1].to_i
val_uris = nil
if same_service?u
raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+u.to_s if
AA_SERVER and !OpenTox::Authorization.authorized?(u,"GET",subjectid)
cv = Validation::Crossvalidation.get( cv_id )
raise OpenTox::NotFoundError.new "crossvalidation with id "+cv_id.to_s+" not found" unless cv
raise OpenTox::BadRequestError.new("crossvalidation with id '"+cv_id.to_s+"' not finished") unless cv.finished
#res += Validation::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.validation_uri.to_s}
val_uris = Validation::Validation.find( :crossvalidation_id => cv_id, :validation_type => "crossvalidation" ).collect{|v| v.validation_uri.to_s}
else
val_base_uri = u.gsub(/\/crossvalidation\/[0-9]+/,"")
val_uris = OpenTox::RestClientWrapper.get( val_base_uri+"?crossvalidation_id="+cv_id.to_s+"&validation_type=crossvalidation", {:subjectid => subjectid, :accept => "text/uri-list" }).split("\n")
end
val_uris.each do |v_uri|
res[v_uri] = identifier ? identifier[count] : nil
end
else
res[u.to_s] = identifier ? identifier[count] : nil
end
count += 1
end
res
end
def init_validation(validation, uri, filter_params, subjectid)
raise OpenTox::BadRequestError.new "not a validation uri: "+uri.to_s unless uri =~ /\/[0-9]+$/
validation_id = uri.split("/")[-1]
raise OpenTox::BadRequestError.new "invalid validation id "+validation_id.to_s unless validation_id!=nil and
(validation_id.to_i > 0 || validation_id.to_s=="0" )
v = nil
if same_service? uri
raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+uri.to_s if
AA_SERVER and !OpenTox::Authorization.authorized?(uri,"GET",subjectid)
v = Validation::Validation.get(validation_id)
else
v = YAML::load(OpenTox::RestClientWrapper.get uri, {:subjectid=>subjectid, :accept=>"application/serialize"})
end
v.filter_predictions(filter_params[:min_confidence], filter_params[:min_num_predictions], filter_params[:max_num_predictions]) if
filter_params
raise OpenTox::NotFoundError.new "validation with id "+validation_id.to_s+" not found" unless v
raise OpenTox::BadRequestError.new "validation with id "+validation_id.to_s+" is not finished yet" unless v.finished
(Validation::VAL_PROPS + Validation::VAL_CV_PROPS).each do |p|
validation.send("#{p.to_s}=".to_sym, v.send(p))
end
# set uris manually, in case external validation is used
validation.validation_uri = uri
validation.crossvalidation_uri = uri.gsub(/\/[0-9]+/,"")+"/crossvalidation/"+validation.crossvalidation_id if validation.crossvalidation_id!=nil
{:classification_statistics => Validation::VAL_CLASS_PROPS,
:regression_statistics => Validation::VAL_REGR_PROPS}.each do |subset_name,subset_props|
subset = v.send(subset_name)
subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
end
end
def init_validation_from_cv_statistics( validation, cv_uri, filter_params, subjectid )
raise OpenTox::BadRequestError.new "not a crossvalidation uri: "+cv_uri.to_s unless cv_uri.uri? and cv_uri =~ /crossvalidation.*\/[0-9]+$/
if same_service?cv_uri
cv_id = cv_uri.split("/")[-1]
raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+cv_uri.to_s if
AA_SERVER and !OpenTox::Authorization.authorized?(cv_uri,"GET",subjectid)
cv = Validation::Crossvalidation.get(cv_id)
raise OpenTox::NotFoundError.new "crossvalidation with id "+crossvalidation_id.to_s+" not found" unless cv
raise OpenTox::BadRequestError.new "crossvalidation with id "+crossvalidation_id.to_s+" is not finished yet" unless cv.finished
v = Validation::Validation.from_cv_statistics(cv_id, subjectid)
else
cv = YAML::load(OpenTox::RestClientWrapper.get cv_uri, {:subjectid=>subjectid, :accept=>"application/serialize"})
v = YAML::load(OpenTox::RestClientWrapper.get cv_uri+"/statistics", {:subjectid=>subjectid, :accept=>"application/serialize"})
end
v.filter_predictions(filter_params[:min_confidence], filter_params[:min_num_predictions], filter_params[:max_num_predictions]) if
filter_params
(Validation::VAL_PROPS + Validation::VAL_CV_PROPS).each do |p|
validation.send("#{p.to_s}=".to_sym, v.send(p))
end
{:classification_statistics => Validation::VAL_CLASS_PROPS,
:regression_statistics => Validation::VAL_REGR_PROPS}.each do |subset_name,subset_props|
subset = v.send(subset_name)
subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
end
#cv props
Validation::CROSS_VAL_PROPS.each do |p|
validation.send("#{p.to_s}=".to_sym, cv.send(p.to_s))
end
validation.crossvalidation_uri = cv_uri
validation.validation_uri = cv_uri+"/statistics"
end
def init_cv(validation, subjectid)
cv = nil
if same_service?validation.crossvalidation_uri
cv = Validation::Crossvalidation.get(validation.crossvalidation_id)
raise OpenTox::BadRequestError.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv
else
cv = YAML::load(OpenTox::RestClientWrapper.get validation.crossvalidation_uri, {:subjectid=>subjectid, :accept=>"application/serialize"})
end
Validation::CROSS_VAL_PROPS.each do |p|
validation.send("#{p.to_s}=".to_sym, cv.send(p.to_s))
end
end
def get_predictions(validation, filter_params, subjectid, task)
# we need compound info, cannot reuse stored prediction data
data = Lib::PredictionData.create( validation.feature_type, validation.test_dataset_uri,
validation.test_target_dataset_uri, validation.prediction_feature, validation.prediction_dataset_uri,
validation.predicted_variable, validation.predicted_confidence, subjectid, task )
data = Lib::PredictionData.filter_data( data.data, data.compounds,
filter_params[:min_confidence], filter_params[:min_num_predictions], filter_params[:max_num_predictions] ) if filter_params!=nil
Lib::OTPredictions.new( data.data, data.compounds )
end
def get_accept_values( validation, subjectid=nil )
# PENDING So far, one has to load the whole dataset to get the accept_value from ambit
test_target_dataset = validation.test_target_dataset_uri
test_target_dataset = validation.test_dataset_uri unless test_target_dataset
d = Lib::DatasetCache.find( test_target_dataset, subjectid )
raise "cannot get test target dataset for accept values, dataset: "+test_target_dataset.to_s unless d
accept_values = d.accept_values(validation.prediction_feature)
raise "cannot get accept values from dataset "+test_target_dataset.to_s+" for feature "+
validation.prediction_feature+":\n"+d.features[validation.prediction_feature].to_yaml unless accept_values!=nil
accept_values
end
def feature_type( validation, subjectid=nil )
OpenTox::Model::Generic.new(validation.model_uri).feature_type(subjectid)
#get_model(validation).classification?
end
def predicted_variable(validation, subjectid=nil)
raise "cannot derive model depended props for merged validations" if Lib::MergeObjects.merged?(validation)
model = OpenTox::Model::Generic.find(validation.model_uri, subjectid)
raise OpenTox::NotFoundError.new "model not found '"+validation.model_uri+"'" unless model
model.predicted_variable(subjectid)
end
def predicted_confidence(validation, subjectid=nil)
raise "cannot derive model depended props for merged validations" if Lib::MergeObjects.merged?(validation)
model = OpenTox::Model::Generic.find(validation.model_uri, subjectid)
raise OpenTox::NotFoundError.new "model not found '"+validation.model_uri+"'" unless model
model.predicted_confidence(subjectid)
end
# private
# def get_model(validation)
# raise "cannot derive model depended props for merged validations" if Lib::MergeObjects.merged?(validation)
# model = @model_store[validation.model_uri]
# unless model
# model = OpenTox::Model::PredictionModel.find(validation.model_uri)
# raise "model not found '"+validation.model_uri+"'" unless validation.model_uri && model
# @model_store[validation.model_uri] = model
# end
# return model
# end
end
|
