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
|
require 'ohm'
#require 'redis/objects'
#@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
class ToxCreateModel < Ohm::Model
#include Redis::Objects
#include DataMapper::Resource
#attribute :id
attribute :name
attribute :warnings
attribute :error_messages
attribute :type
attribute :status
attribute :created_at
attribute :task_uri
attribute :uri
attribute :training_dataset
attribute :feature_dataset
#attributey :validation_task_uri
attribute :validation_uri
#attributey :validation_report_task_uri
attribute :validation_report_uri
#attributey :validation_qmrf_task_uri
attribute :validation_qmrf_uri
attribute :nr_compounds
attribute :nr_predictions
attribute :true_positives
attribute :false_positives
attribute :true_negatives
attribute :false_negatives
attribute :correct_predictions
attribute :weighted_area_under_roc
attribute :sensitivity
attribute :specificity
attribute :r_square
attribute :root_mean_squared_error
attribute :mean_absolute_error
attribute :web_uri
attr_accessor :subjectid
@subjectid = nil
#after :save, :check_policy
=begin
attr_accessor :id, :name, :warnings, :error_messages, :type, :status, :created_at, :task_uri, :uri, :training_dataset, :feature_dataset, :validation_task_uri, :validation_uri, :validation_report_task_uri, :validation_report_uri, :validation_qmrf_task_uri, :validation_qmrf_uri, :nr_compounds, :nr_predictions, :true_positives, :false_positives, :true_negatives, :false_negatives, :correct_predictions, :weighted_area_under_roc, :sensitivity, :specificity, :r_square, :root_mean_squared_error, :mean_absolute_error, :web_uri
def self.all
end
def self.get(id)
end
def self.create(params)
@id = @@redis.incr "toxcreate"
params.each { |k,v| @@redis.hset "toxcreate:#{@id}", k, v }
self.get(@id)
end
def update(params)
end
def method_missing
begin
rescue
raise "Unknown method"
end
end
attr_accessor :subjectid
@subjectid = nil
after :save, :check_policy
def status
#begin
RestClient.get(File.join(@task_uri, 'hasStatus')).body
#rescue
# "Service offline"
#end
end
=end
def validation_status
begin
RestClient.get(File.join(@validation_task_uri, 'hasStatus')).body
rescue
"Service offline"
end
end
def validation_report_status
begin
RestClient.get(File.join(@validation_report_task_uri, 'hasStatus')).body
rescue
"Service offline"
end
end
def validation_qmrf_status
begin
RestClient.get(File.join(@validation_qmrf_task_uri, 'hasStatus')).body
rescue
"Service offline"
end
end
def algorithm
begin
RestClient.get(File.join(@uri, 'algorithm')).body
rescue
""
end
end
def training_dataset
begin
RestClient.get(File.join(@uri, 'trainingDataset')).body
rescue
""
end
end
def feature_dataset
begin
RestClient.get(File.join(@uri, 'feature_dataset')).body
rescue
""
end
end
=begin
def process
LOGGER.debug self.to_yaml
if @uri.nil? and status == "Completed"
#update :uri => RestClient.get(File.join(@task_uri, 'resultURI')).body
#lazar = YAML.load(RestClient.get(@uri, :accept => "application/x-yaml").body)
elsif @validation_uri.nil? and validation_status == "Completed"
begin
#update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
#LOGGER.debug "Validation URI: #{@validation_uri}"
#update :validation_report_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
#LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
#update :validation_qmrf_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).body
#LOGGER.debug "QMRF Report Task URI: #{@validation_qmrf_task_uri}"
uri = File.join(@validation_uri, 'statistics')
yaml = RestClient.get(uri).body
v = YAML.load(yaml)
case type
when "classification"
tp=0; tn=0; fp=0; fn=0; n=0
v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
tp = cell[:confusion_matrix_value]
n += tp
elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
tn = cell[:confusion_matrix_value]
n += tn
elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
fn = cell[:confusion_matrix_value]
n += fn
elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
fp = cell[:confusion_matrix_value]
n += fp
end
end
update :nr_predictions => n
update :true_positives => tp
update :false_positives => fp
update :true_negatives => tn
update :false_negatives => fn
update :correct_predictions => 100*(tp+tn).to_f/n
update :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f
update :sensitivity => tp.to_f/(tp+fn)
update :specificity => tn.to_f/(tn+fp)
when "regression"
update :nr_predictions => v[:num_instances] - v[:num_unpredicted]
update :r_square => v[:regression_statistics][:r_square]
update :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error]
update :mean_absolute_error => v[:regression_statistics][:mean_absolute_error]
end
rescue
LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
end
else
if @validation_report_uri.nil? and validation_report_status == "Completed"
begin
update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
rescue
LOGGER.warn "Cannot create Validation Report for Task URI #{@validation_report_task_uri} "
end
end
if @validation_qmrf_uri.nil? and validation_qmrf_status == "Completed"
begin
update :validation_qmrf_uri => RestClient.get(File.join(@validation_qmrf_task_uri, 'resultURI')).body
rescue
LOGGER.warn "Cannot create QMRF Report for Task URI #{@validation_qmrf_task_uri} "
end
end
end
end
=end
private
def check_policy
OpenTox::Authorization.check_policy(web_uri, subjectid)
end
end
#DataMapper.auto_upgrade!
|