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
|
class ToxCreateModel
include DataMapper::Resource
property :id, Serial
property :name, String, :length => 255
property :warnings, Text, :length => 2**32-1
property :type, String
property :created_at, DateTime
property :task_uri, String, :length => 255
property :uri, String, :length => 255
property :validation_task_uri, String, :length => 255
property :validation_uri, String, :length => 255
property :validation_report_task_uri, String, :length => 255
property :validation_report_uri, String, :length => 255
property :validation_qmrf_task_uri, String, :length => 255
property :validation_qmrf_uri, String, :length => 255
property :nr_compounds, Integer
property :nr_predictions, Integer
property :true_positives, Integer
property :false_positives, Integer
property :true_negatives, Integer
property :false_negatives, Integer
property :correct_predictions, Integer
property :weighted_area_under_roc, Float
property :sensitivity, Float
property :specificity, Float
property :r_square, Float
property :root_mean_squared_error, Float
property :mean_absolute_error, Float
def status
#begin
RestClient.get(File.join(@task_uri, 'hasStatus')).body
#rescue
# "Service offline"
#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
def process
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)
case lazar.dependentVariables
when /classification/
update :type => "classification"
when /regression/
update :type => "regression"
else
update :type => "unknown"
end
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
DataMapper.auto_upgrade!
|
