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
|
class ToxCreateModel
include DataMapper::Resource
property :id, Serial
property :name, String, :length => 255
property :uri, String, :length => 255
property :task_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 :warnings, Text, :length => 2**32-1
property :nr_compounds, Integer
property :type, String
property :created_at, DateTime
def status
RestClient.get(File.join(@task_uri, 'hasStatus')).body
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 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 classification_validation
begin
uri = File.join(@validation_uri, 'statistics')
yaml = RestClient.get(uri).body
v = YAML.load(yaml)
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
{
:n => n,
:tp => tp,
:fp => fp,
:tn => tn,
:fn => fn,
:correct_predictions => sprintf("%.2f", 100*(tp+tn).to_f/n),
:weighted_area_under_roc => sprintf("%.3f", v[:classification_statistics][:weighted_area_under_roc].to_f),
:sensitivity => sprintf("%.3f", tp.to_f/(tp+fn)),
:specificity => sprintf("%.3f", tn.to_f/(tn+fp))
}
rescue
"Service offline"
end
end
def regression_validation
begin
uri = File.join(@validation_uri, 'statistics')
yaml = RestClient.get(uri).body
v = YAML.load(yaml)
rescue
"Service offline"
end
end
def process
if !@uri and status == "Completed"
@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/
@type = "classification"
when /regression/
@type = "regression"
else
@type = "unknown"
end
save
end
if !@validation_uri and validation_status == "Completed"
begin
@validation_uri = RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
LOGGER.debug "Validation URI: #{@validation_uri}"
@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}"
save
rescue
end
end
if @validation_report_task_uri and !@validation_report_uri and validation_report_status == 'Completed'
@validation_report_uri = RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
end
end
end
DataMapper.auto_upgrade!
|
