diff options
Diffstat (limited to 'model.rb')
| -rw-r--r-- | model.rb | 154 |
1 files changed, 0 insertions, 154 deletions
@@ -1,12 +1,7 @@ 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 @@ -49,45 +44,6 @@ class ToxCreateModel < Ohm::Model #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 @@ -112,115 +68,6 @@ def status 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) @@ -228,4 +75,3 @@ def status end -#DataMapper.auto_upgrade! |