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Diffstat (limited to 'reach_reports/reach_service.rb')
| -rwxr-xr-x | reach_reports/reach_service.rb | 319 |
1 files changed, 319 insertions, 0 deletions
diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb new file mode 100755 index 0000000..53acb62 --- /dev/null +++ b/reach_reports/reach_service.rb @@ -0,0 +1,319 @@ + +class Array + + def to_html + return "" unless size>0 + s = "<html>\n<head>\n</head>\n<body>\n" + s += join(" <br>\n") + s += "</body>\n</html>\n" + return s + end +end + +module ReachReports + + def self.list_reports(type) + case type + when /(?i)QMRF/ + ReachReports::QmrfReport.all.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]) ) + training_dataset = OpenTox::Dataset.new( model.metadata[OT.trainingDataset] ) + 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 = Lib::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.first( :crossvalidation_id => cv.id ) + 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| + 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 + 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 = Lib::Validation.all({: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 << "weighted AUC: "+validation.classification_statistics[:weighted_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) + 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 + + r.save + 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.halt 400, 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) + + 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 + 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 |