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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 :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
property :type, String
property :created_at, DateTime
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 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 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
@nr_predictions = n
@true_positives = tp
@false_positives = fp
@true_negatives = tn
@false_negatives = fn
@correct_predictions = 100*(tp+tn).to_f/n
@weighted_area_under_roc = v[:classification_statistics][:weighted_area_under_roc].to_f
@sensitivity = tp.to_f/(tp+fn)
@specificity = tn.to_f/(tn+fp)
save
#: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)
@nr_predictions = v[:num_instances] - v[:num_unpredicted]
@r_square = v[:regression_statistics][:r_square]
@root_mean_squared_error = v[:regression_statistics][:root_mean_squared_error]
@mean_absolute_error = v[:regression_statistics][:mean_absolute_error]
save
rescue
"Service offline"
end
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}"
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
elsif @validation_report_uri.nil? and validation_report_status == "Completed"
begin
LOGGER.debug File.join(@validation_report_task_uri, 'resultURI')
LOGGER.debug "Report URI: "+RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
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
end
end
DataMapper.auto_upgrade!
|