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
250
251
252
253
254
255
256
|
[ 'rubygems', 'sinatra', 'sinatra/url_for', 'active_record', 'ar-extensions', 'opentox-ruby-api-wrapper' ].each do |lib|
require lib
end
require 'validation/validation_service.rb'
require 'lib/merge.rb'
get '/crossvalidation/?' do
LOGGER.info "list all crossvalidations"
content_type "text/uri-list"
params.each{ |k,v| halt 400,"no crossvalidation-attribute: "+k.to_s unless Validation::Crossvalidation.column_names.include?(k.gsub(/_like$/,"")) }
Validation::Crossvalidation.find(:all, :conditions => params).collect{ |d| url_for("/crossvalidation/", :full) + d.id.to_s }.join("\n")
end
post '/crossvalidation/loo/?' do
halt 500, "not yet implemented"
end
get '/crossvalidation/loo/?' do
halt 400, "GET operation not supported, use POST for performing a loo-crossvalidation, see "+url_for("/crossvalidation", :full)+" for crossvalidation results"
end
get '/crossvalidation/:id' do
LOGGER.info "get crossvalidation with id "+params[:id].to_s
begin
crossvalidation = Validation::Crossvalidation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Crossvalidation '#{params[:id]}' not found."
end
case request.env['HTTP_ACCEPT'].to_s
when "application/rdf+xml"
content_type "application/rdf+xml"
result = crossvalidation.to_rdf
when /application\/x-yaml|\*\/\*|/ # matches 'text/x-yaml', '*/*', ''
content_type "application/x-yaml"
result = crossvalidation.to_yaml
else
halt 400, "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported."
end
result
end
delete '/crossvalidation/:id/?' do
LOGGER.info "delete crossvalidation with id "+params[:id].to_s
content_type "text/plain"
begin
crossvalidation = Validation::Crossvalidation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Crossvalidation '#{params[:id]}' not found."
end
Validation::Crossvalidation.delete(params[:id])
end
get '/crossvalidation/:id/validations' do
LOGGER.info "get all validations for crossvalidation with id "+params[:id].to_s
begin
crossvalidation = Validation::Crossvalidation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Crossvalidation '#{params[:id]}' not found."
end
content_type "text/uri-list"
Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ).collect{ |v| v.validation_uri.to_s }.join("\n")+"\n"
end
get '/crossvalidation/:id/statistics' do
LOGGER.info "get merged validation-result for crossvalidation with id "+params[:id].to_s
begin
crossvalidation = Validation::Crossvalidation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Crossvalidation '#{params[:id]}' not found."
end
Lib::MergeObjects.register_merge_attributes( Validation::Validation,
Lib::VAL_MERGE_AVG,Lib::VAL_MERGE_SUM,Lib::VAL_MERGE_GENERAL-[:validation_uri]) unless
Lib::MergeObjects.merge_attributes_registered?(Validation::Validation)
v = Lib::MergeObjects.merge_array_objects( Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ) )
v.validation_uri = nil
v.created_at = nil
v.id = nil
content_type "application/x-yaml"
v.to_yaml
end
post '/crossvalidation/?' do
content_type "text/uri-list"
task_uri = OpenTox::Task.as_task do
LOGGER.info "creating crossvalidation "+params.inspect
halt 400, "dataset_uri missing" unless params[:dataset_uri]
halt 400, "algorithm_uri missing" unless params[:algorithm_uri]
halt 400, "prediction_feature missing" unless params[:prediction_feature]
halt 400, "illegal param-value num_folds: '"+params[:num_folds].to_s+"', must be integer >1" unless params[:num_folds]==nil or
params[:num_folds].to_i>1
cv_params = { :dataset_uri => params[:dataset_uri],
:algorithm_uri => params[:algorithm_uri] }
[ :num_folds, :random_seed, :stratified ].each{ |sym| cv_params[sym] = params[sym] if params[sym] }
cv = Validation::Crossvalidation.new cv_params
cv.create_cv_datasets( params[:prediction_feature] )
cv.perform_cv( params[:algorithm_params])
content_type "text/uri-list"
cv.crossvalidation_uri
end
halt 202,task_uri
end
get '/training_test_split' do
halt 400, "GET operation not supported, use POST to perform a training_test_split, see "+url_for("/", :full)+" for validation results"
end
get '/?' do
LOGGER.info "list all validations"
content_type "text/uri-list"
params.each{ |k,v| halt 400,"no validation-attribute: "+k.to_s unless Validation::Validation.column_names.include?(k.gsub(/_like$/,"")) }
Validation::Validation.find(:all, :conditions => params).collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
end
get '/:id' do
LOGGER.info "get validation with id "+params[:id].to_s+" '"+request.env['HTTP_ACCEPT'].to_s+"'"
begin
validation = Validation::Validation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Validation '#{params[:id]}' not found."
end
case request.env['HTTP_ACCEPT'].to_s
when "application/rdf+xml"
content_type "application/rdf+xml"
result = validation.to_rdf
when /application\/x-yaml|\*\/\*|^$/ # matches 'application/x-yaml', '*/*', ''
content_type "application/x-yaml"
result = validation.to_yaml
else
halt 400, "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\" and \"application/x-yaml\"."
end
result
end
post '/?' do
content_type "text/uri-list"
task_uri = OpenTox::Task.as_task do |task|
LOGGER.info "creating validation "+params.inspect
if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri]
v = Validation::Validation.new :model_uri => params[:model_uri],
:test_dataset_uri => params[:test_dataset_uri],
:test_target_dataset_uri => params[:test_target_dataset_uri],
:prediction_feature => params[:prediction_feature]
v.validate_model
elsif params[:algorithm_uri] and params[:training_dataset_uri] and params[:test_dataset_uri] and params[:prediction_feature] and !params[:model_uri]
v = Validation::Validation.new :algorithm_uri => params[:algorithm_uri],
:training_dataset_uri => params[:training_dataset_uri],
:test_dataset_uri => params[:test_dataset_uri],
:test_target_dataset_uri => params[:test_target_dataset_uri],
:prediction_feature => params[:prediction_feature]
v.validate_algorithm( params[:algorithm_params])
else
halt 400, "illegal parameter combination for validation, use either\n"+
"* model_uri, test_dataset_uri\n"+
"* algorithm_uri, training_dataset_uri, test_dataset_uri, prediction_feature\n"+
"params given: "+params.inspect
end
content_type "text/uri-list"
v.validation_uri
end
halt 202,task_uri
end
post '/training_test_split' do
content_type "text/uri-list"
task_uri = OpenTox::Task.as_task do
LOGGER.info "creating training test split "+params.inspect
halt 400, "dataset_uri missing" unless params[:dataset_uri]
halt 400, "algorithm_uri missing" unless params[:algorithm_uri]
halt 400, "prediction_feature missing" unless params[:prediction_feature]
params.merge!(Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], params[:split_ratio], params[:random_seed]))
v = Validation::Validation.new :training_dataset_uri => params[:training_dataset_uri],
:test_dataset_uri => params[:test_dataset_uri],
:test_target_dataset_uri => params[:dataset_uri],
:prediction_feature => params[:prediction_feature],
:algorithm_uri => params[:algorithm_uri]
v.validate_algorithm( params[:algorithm_params])
content_type "text/uri-list"
v.validation_uri
end
halt 202,task_uri
end
post '/plain_training_test_split' do
LOGGER.info "creating pure training test split "+params.inspect
halt 400, "dataset_uri missing" unless params[:dataset_uri]
result = Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], params[:split_ratio], params[:random_seed])
content_type "text/uri-list"
result[:training_dataset_uri]+"\n"+result[:test_dataset_uri]+"\n"
end
post '/validate_datasets' do
content_type "text/uri-list"
task_uri = OpenTox::Task.as_task do
LOGGER.info "validating values "+params.inspect
halt 400, "test_dataset_uri missing" unless params[:test_dataset_uri]
halt 400, "prediction_datset_uri missing" unless params[:prediction_dataset_uri]
if params[:model_uri]
v = Validation::Validation.new params
v.compute_validation_stats_with_model()
else
halt 400, "please specify 'model_uri' or 'prediction_feature'" unless params[:prediction_feature]
halt 400, "please specify 'model_uri' or 'predicted_feature'" unless params[:predicted_feature]
halt 400, "please specify 'model_uri' or set either 'classification' or 'regression' flag" unless
params[:classification] or params[:regression]
predicted_feature = params.delete("predicted_feature")
clazz = params.delete("classification")!=nil
regr = params.delete("regression")!=nil
v = Validation::Validation.new params
v.compute_validation_stats((clazz and !regr),predicted_feature)
end
content_type "text/uri-list"
v.validation_uri
end
halt 202,task_uri
end
get '/:id/:attribute' do
LOGGER.info "access validation attribute "+params.inspect
begin
validation = Validation::Validation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Validation '#{params[:id]}' not found."
end
begin
raise unless validation.attribute_loaded?(params[:attribute])
rescue
halt 400, "Not a validation attribute: "+params[:attribute].to_s
end
content_type "text/plain"
return validation.send(params[:attribute])
end
delete '/:id' do
LOGGER.info "delete validation with id "+params[:id].to_s
begin
validation = Validation::Validation.find(params[:id])
rescue ActiveRecord::RecordNotFound => ex
halt 404, "Validation '#{params[:id]}' not found."
end
content_type "text/plain"
Validation::Validation.delete(params[:id])
end
|
