class Array def to_html return "" unless size>0 s = "\n\n\n\n" s += join("
\n") s += "\n\n" return s end end module ReachReports def self.list_reports(type, model_uri=nil) case type when /(?i)QMRF/ params = {} params[:model_uri]=model_uri if model_uri ReachReports::QmrfReport.all(params).collect{ |r| r.report_uri }.join("\n")+"\n" when /(?i)QPRF/ ReachReports::QprfReport.all.collect{ |r| r.report_uri }.join("\n")+"\n" end end def self.create_report( type, params, subjectid, xml_data=nil ) case type when /(?i)QMRF/ if params[:model_uri] task = OpenTox::Task.create( "Create "+type+" report", $url_provider.url_for("/reach_report/"+type, :full) ) do |task| #, params report = ReachReports::QmrfReport.new :model_uri => params[:model_uri] report.subjectid = subjectid build_qmrf_report(report, task) report.report_uri end result_uri = task.uri elsif xml_data and (input = xml_data.read).to_s.size>0 report = ReachReports::QmrfReport.new report.subjectid = subjectid ReachReports::QmrfReport.from_xml(report,input) result_uri = report.report_uri else raise OpenTox::BadRequestError.new "illegal parameters for qmrf-report creation, either\n"+ "* give 'model_uri' as param\n"+ "* provide xml file\n"+ "params given: "+params.inspect end when /(?i)QPRF/ raise OpenTox::BadRequestError.new "qprf report creation not yet implemented" if params[:compound_uri] #report = ReachReports::QprfReport.new :compound_uri => params[:compound_uri] else raise OpenTox::BadRequestError.new "illegal parameters for qprf-report, use either\n"+ "* compound-uri\n"+ "params given: "+params.inspect end end result_uri end def self.build_qmrf_report(r, task=nil) #puts r.model_uri model = OpenTox::Model::Generic.find(r.model_uri, r.subjectid) feature_type = model.feature_type(r.subjectid) # chapter 1 r.qsar_identifier = QsarIdentifier.new r.qsar_identifier.qsar_title = model.metadata[DC.title] # TODO QSAR_models -> sparql same endpoint r.qsar_identifier.qsar_software << QsarSoftware.new( :url => model.uri, :name => model.metadata[DC.title], :contact => model.metadata[DC.creator] ) algorithm = OpenTox::Algorithm::Generic.find(model.metadata[OT.algorithm], r.subjectid) if model.metadata[OT.algorithm] r.qsar_identifier.qsar_software << QsarSoftware.new( :url => algorithm.uri, :name => algorithm.metadata[DC.title] ) task.progress(10) if task #chpater 2 r.qsar_general_information = QsarGeneralInformation.new r.qsar_general_information.qmrf_date = DateTime.now.to_s # EMPTY: qmrf_authors, qmrf_date_revision, qmrf_revision # TODO: model_authors ? r.qsar_general_information.model_date = model.metadata[DC.date].to_s # TODO: references? # EMPTY: info_availablity # TODO: related_models = find qmrf reports for QSAR_models task.progress(20) if task # chapter 3 # TODO "model_species" ? r.qsar_endpoint = QsarEndpoint.new model.metadata[OT.predictedVariables].each do |p| r.qsar_endpoint.model_endpoint << ModelEndpoint.new( :name => p ) end if model.metadata[OT.predictedVariables] # TODO "endpoint_comments" => "3.3", "endpoint_units" => "3.4", r.qsar_endpoint.endpoint_variable = model.metadata[OT.dependentVariables] if model.metadata[OT.dependentVariables] # TODO "endpoint_protocol" => "3.6", "endpoint_data_quality" => "3.7", task.progress(30) if task # chapter 4 # TODO algorithm_type (='type of model') # TODO algorithm_explicit.equation # TODO algorithm_explicit.algorithms_catalog # TODO algorithms_descriptors, descriptors_selection, descriptors_generation, descriptors_generation_software, descriptors_chemicals_ratio task.progress(40) if task # chapter 5 # TODO app_domain_description, app_domain_method, app_domain_software, applicability_limits #training_dataset = model.trainingDataset ? OpenTox::Dataset.find(model.trainingDataset+"/metadata") : nil if ( OpenTox::Dataset.exist?(model.metadata[OT.trainingDataset], r.subjectid) ) training_dataset = OpenTox::Dataset.new( model.metadata[OT.trainingDataset], r.subjectid ) training_dataset.load_metadata( r.subjectid ) else training_dataset = nil LOGGER.warn "build qmrf: training_dataset not found "+model.metadata[OT.trainingDataset].to_s end task.progress(50) if task # chapter 6 r.qsar_robustness = QsarRobustness.new if training_dataset r.qsar_robustness.training_set_availability = "Yes" r.qsar_robustness.training_set_data = TrainingSetData.new(:chemname => "Yes", :cas => "Yes", :smiles => "Yes", :inchi => "Yes", :mol => "Yes", :formula => "Yes") end #TODO "training_set_data" => "6.2", # "training_set_descriptors" => "6.3", # "dependent_var_availability" => "6.4", "other_info" => "6.5", "preprocessing" => "6.6", "goodness_of_fit" => "6.7", # "loo" => "6.8", val_datasets = [] if algorithm cvs = Validation::Crossvalidation.find_all_uniq({:algorithm_uri => algorithm.uri, :finished => true},r.subjectid) # PENDING: cv classification/regression hack cvs = cvs.delete_if do |cv| #val = Validation::Validation.first( :all, :conditions => { :crossvalidation_id => cv.id } ) val = Validation::Validation.find( :crossvalidation_id => cv.id ).first raise "should not happen: no validations found for crossvalidation "+cv.id.to_s unless val (val.classification_statistics!=nil) != (feature_type=="classification") end lmo = [ "found "+cvs.size.to_s+" crossvalidation/s for algorithm '"+algorithm.uri.to_s+"'" ] if cvs.size>0 cvs_same_data = [] cvs_other_data = [] cvs.each do |cv| if cv.dataset_uri == model.metadata[OT.trainingDataset] cvs_same_data << cv else cvs_other_data << cv end end lmo << cvs_same_data.size.to_s+" crossvalidations/s where performed on the training dataset of the model ("+ model.metadata[OT.trainingDataset].to_s+")" lmo << cvs_other_data.size.to_s+" crossvalidations/s where performed on the other datasets" lmo << "" {cvs_same_data => "training dataset", cvs_other_data => "other datasets"}.each do |cvs,desc| next if cvs.size==0 lmo << "crossvalidation/s on "+desc cvs.each do |cv| begin lmo << "crossvalidation: "+cv.crossvalidation_uri lmo << "dataset (see 9.3 Validation data): "+cv.dataset_uri val_datasets << cv.dataset_uri lmo << "settings: num-folds="+cv.num_folds.to_s+", random-seed="+cv.random_seed.to_s+", stratified:"+cv.stratified.to_s val = YAML.load( OpenTox::RestClientWrapper.get(File.join(cv.crossvalidation_uri,"statistics"),{:subjectid => r.subjectid}) ) case feature_type when "classification" lmo << "percent_correct: "+val[OT.classificationStatistics][OT.percentCorrect].to_s lmo << "weighted AUC: "+val[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_s when "regression" lmo << "root_mean_squared_error: "+val[OT.regressionStatistics][OT.rootMeanSquaredError].to_s lmo << "r_square "+val[OT.regressionStatistics][OT.rSquare].to_s end reports = OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], "report/crossvalidation?crossvalidation_uris="+cv.crossvalidation_uri),{:subjectid => r.subjectid}) if reports and reports.chomp.size>0 lmo << "for more info see report: "+reports.split("\n")[0] else lmo << "for more info see report: not yet created for '"+cv.crossvalidation_uri+"'" end rescue => ex LOGGER.warn "could not add cv "+cv.crossvalidation_uri+" : "+ex.message end end lmo << "" end end else lmo = [ "no prediction algortihm for model found, crossvalidation not possible" ] end r.qsar_robustness.lmo = lmo.to_html # "lmo" => "6.9", "yscrambling" => "6.10", "bootstrap" => "6.11", "other_statistics" => "6.12", LOGGER.debug "looking for validations with "+{:model_uri => model.uri}.inspect #vals = Lib::Validation.find(:all, :conditions => {:model_uri => model.uri}) vals = Validation::Validation.find({:model_uri => model.uri}) uniq_vals = [] vals.each do |val| match = false uniq_vals.each do |val2| if val.test_dataset_uri == val2.test_dataset_uri match = true break end end uniq_vals << val unless match end r.qsar_predictivity = QsarPredictivity.new if uniq_vals.size > 0 r.qsar_predictivity.validation_set_availability = "Yes" r.qsar_predictivity.validation_set_data = ValidationSetData.new(:chemname => "Yes", :cas => "Yes", :smiles => "Yes", :inchi => "Yes", :mol => "Yes", :formula => "Yes") v = [ "found '"+uniq_vals.size.to_s+"' test-set validations of model '"+model.uri+"'" ] v << "" uniq_vals.each do |validation| v << "validation: "+validation.validation_uri v << "dataset (see 9.3 Validation data): "+validation.test_dataset_uri val_datasets << validation.test_dataset_uri case feature_type when "classification" v << "percent_correct: "+validation.classification_statistics[:percent_correct].to_s v << "average AUC: "+validation.classification_statistics[:average_area_under_roc].to_s when "regression" v << "root_mean_squared_error: "+validation.regression_statistics[:root_mean_squared_error].to_s v << "r_square "+validation.regression_statistics[:r_square].to_s end report = OpenTox::ValidationReport.find_for_validation(validation.validation_uri,r.subjectid) #reports = OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], # "report/validation?validation_uris="+validation.validation_uri),{:subjectid => r.subjectid}) if report v << "for more info see report: "+report.uri else v << "for more info see report: not yet created for '"+validation.validation_uri+"'" end v << "" end else v = [ "no validation for model '"+model.uri+"' found" ] end r.qsar_predictivity.validation_predictivity = v.to_html task.progress(60) if task # chapter 7 # "validation_set_availability" => "7.1", "validation_set_data" => "7.2", "validation_set_descriptors" => "7.3", # "validation_dependent_var_availability" => "7.4", "validation_other_info" => "7.5", "experimental_design" => "7.6", # "validation_predictivity" => "7.7", "validation_assessment" => "7.8", "validation_comments" => "7.9", task.progress(70) if task # chapter 8 # "mechanistic_basis" => "8.1", "mechanistic_basis_comments" => "8.2", "mechanistic_basis_info" => "8.3", task.progress(80) if task # chapter 9 # "comments" => "9.1", "bibliography" => "9.2", "attachments" => "9.3", r.qsar_miscellaneous = QsarMiscellaneous.new r.qsar_miscellaneous.attachment_training_data << AttachmentTrainingData.new( { :description => training_dataset.title, :filetype => "owl-dl", :url => training_dataset.uri} ) if training_dataset val_datasets.each do |data_uri| if OpenTox::Dataset.exist?(data_uri, r.subjectid) d = OpenTox::Dataset.new(data_uri, r.subjectid) d.load_metadata( r.subjectid) r.qsar_miscellaneous.attachment_validation_data << AttachmentValidationData.new( { :description => d.title, :filetype => "owl-dl", :url => data_uri} ) end end task.progress(90) if task mysql_lite_retry do r.save end task.progress(100) if task end # def self.get_report_content(type, id, *keys) # # report_content = get_report(type, id).get_content # keys.each do |k| # $sinatra.raise OpenTox::BadRequestError.new type+" unknown report property '#{key}'" unless report_content.is_a?(Hash) and report_content.has_key?(k) # report_content = report_content[k] # end # report_content # end def self.get_report(type, id) report = nil mysql_lite_retry(3) do case type when /(?i)QMRF/ report = ReachReports::QmrfReport.get(id) when /(?i)QPRF/ report = ReachReports::QprfReport.get(id) end raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report end return report end def self.delete_report(type, id, subjectid=nil) case type when /(?i)QMRF/ report = ReachReports::QmrfReport.get(id) when /(?i)QPRF/ report = ReachReports::QprfReport.get(id) end raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report OpenTox::Authorization.delete_policies_from_uri(report.report_uri, subjectid) if subjectid return report.destroy end end