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|
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!
|
