diff options
Diffstat (limited to 'lib/report.rb')
| -rw-r--r-- | lib/report.rb | 193 |
1 files changed, 7 insertions, 186 deletions
diff --git a/lib/report.rb b/lib/report.rb index f576106..7c06d60 100644 --- a/lib/report.rb +++ b/lib/report.rb @@ -1,208 +1,29 @@ # Get a list of all possible reports to prediction models # @param [Header] Accept one of text/uri-list, # @return [text/uri-list] list of all prediction models -get "/report/?" do +get "/api/report/?" do models = Model::Validation.all case @accept when "text/uri-list" - uri_list = models.collect{|model| uri("/report/#{model.model_id}")} + uri_list = models.collect{|model| uri("/api/report/#{model.model_id}")} return uri_list.join("\n") + "\n" when "application/json" models = JSON.parse models.to_json list = [] - models.each{|m| list << uri("/report/#{m["model_id"]["$oid"]}")} + models.each{|m| list << uri("/api/report/#{m["_id"]["$oid"]}")} return list.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end -get "/report/:id/?" do +get "/api/report/:id/?" do case @accept when "application/xml" - model = Model::Lazar.find params[:id] - not_found_error "Model with id: #{params[:id]} not found." unless model - prediction_model = Model::Validation.find_by :model_id => params[:id] - validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") - - if File.directory?("#{File.dirname(__FILE__)}/../../lazar") - lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip - lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}" - else - lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}" - end - - report = OpenTox::QMRFReport.new - - # QSAR Identifier Title 1.1 - report.value "QSAR_title", "Lazar model for #{prediction_model.species} #{prediction_model.endpoint}" - - # Software coding the model 1.3 - report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :description => "lazar Lazy Structure- Activity Relationships", :number => "1", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware - - # Date of QMRF 2.1 - report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}" - - # QMRF author(s) and contact details 2.1 - report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} - report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor - - # Model developer(s) and contact details 2.5 - report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} - report.ref_catalog :model_authors, :authors_catalog, :modelauthor - - # Date of model development and/or publication 2.6 - report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}" - - # Reference(s) to main scientific papers and/or software package 2.7 - report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz, Guetlein, Rautenberg, Vorgrimmler, Gebele and Helma (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} - report.ref_catalog :references, :publications_catalog, :publications_catalog_1 - - # Reference(s) to main scientific papers and/or software package 2.7 - report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Maunz A and Helma C (2008) Prediction of chemical toxicity with local support vector regression and activity-specific kernels. SAR & QSAR in Environmental Research 19 (5-6), 413-431", :url => "http://dx.doi.org/10.1080/10629360802358430"} - report.ref_catalog :references, :publications_catalog, :publications_catalog_2 - - # Species 3.1 - report.value "model_species", prediction_model.species - - # Endpoint 3.2 - report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""} - report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1 - - # Endpoint Units 3.4 - report.value "endpoint_units", "#{prediction_model.unit}" - - model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','') - - # Type of model 4.1 - report.value "algorithm_type", "#{model_type}" - - # Explicit algorithm 4.2 - report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.algorithms["similarity"]["method"].gsub('_',' ').titleize}#{(model.algorithms["similarity"][:min] ? ' with similarity > ' + model.algorithms["similarity"][:min].to_s : '')}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1 - report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3 - if model.algorithms["prediction"] - pred_algorithm_params = (model.algorithms["prediction"][:method] == "rf" ? "random forest" : model.algorithms["prediction"][:method]) - end - report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.algorithms["prediction"].to_s.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2 - - # Descriptors in the model 4.3 - if model.algorithms["descriptors"][:type] - report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.algorithms["descriptors"][:type]}", :publication_ref => "", :units => ""} - report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1 - end - - # Descriptor selection 4.4 - report.value "descriptors_selection", "#{model.algorithms["feature_selection"].gsub('_',' ')} #{model.algorithms["feature_selection"].collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.algorithms["feature_selection"] - - # Algorithm and descriptor generation 4.5 - report.value "descriptors_generation", "exhaustive breadth first search for paths in chemical graphs (simplified MolFea algorithm)" - - # Software name and version for descriptor generation 4.6 - report.change_catalog :software_catalog, :software_catalog_2, {:name => "lazar, submitted version: #{lazar_commit}", :description => "simplified MolFea algorithm", :number => "2", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :descriptors_generation_software, :software_catalog, :software_catalog_2 - - # Chemicals/Descriptors ratio 4.7 - report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)" - - # Description of the applicability domain of the model 5.1 - report.value "app_domain_description", "<html><head></head><body> - <p> - The applicability domain (AD) of the training set is characterized by - the confidence index of a prediction (high confidence index: close to - the applicability domain of the training set/reliable prediction, low - confidence: far from the applicability domain of the - trainingset/unreliable prediction). The confidence index considers (i) - the similarity and number of neighbors and (ii) contradictory examples - within the neighbors. A formal definition can be found in Helma 2006. - </p> - <p> - The reliability of predictions decreases gradually with increasing - distance from the applicability domain (i.e. decreasing confidence index) - </p> - </body> - </html>" - - # Method used to assess the applicability domain 5.2 - report.value "app_domain_method", "see Helma 2006 and Maunz 2008" - - # Software name and version for applicability domain assessment 5.3 - report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3 - - # Limits of applicability 5.4 - report.value "applicability_limits", "Predictions with low confidence index, unknown substructures and neighbors that might act by different mechanisms" - - # Availability of the training set 6.1 - report.change_attributes "training_set_availability", {:answer => "Yes"} - - # Available information for the training set 6.2 - report.change_attributes "training_set_data", {:cas => "Yes", :chemname => "Yes", :formula => "Yes", :inchi => "Yes", :mol => "Yes", :smiles => "Yes"} - - # Data for each descriptor variable for the training set 6.3 - report.change_attributes "training_set_descriptors", {:answer => "No"} - - # Data for the dependent variable for the training set 6.4 - report.change_attributes "dependent_var_availability", {:answer => "All"} - - # Other information about the training set 6.5 - report.value "other_info", "#{prediction_model.source}" - - # Pre-processing of data before modelling 6.6 - report.value "preprocessing", (model.class == OpenTox::Model::LazarRegression ? "-log10 transformation" : "none") - - # Robustness - Statistics obtained by leave-many-out cross-validation 6.9 - if prediction_model.repeated_crossvalidation - crossvalidations = prediction_model.crossvalidations - out = haml File.read(validation_template), :layout=> false, :locals => {:model => prediction_model} - report.value "lmo", out - end - - # Mechanistic basis of the model 8.1 - report.value "mechanistic_basis","<html><head></head><body> - <p> - Compounds with similar structures (neighbors) are assumed to have - similar activities as the query compound. For the determination of - activity specific similarities only statistically relevant subtructures - (paths) are used. For this reason there is a priori no bias towards - specific mechanistic hypothesis. - </p> - </body> - </html>" - - # A priori or a posteriori mechanistic interpretation 8.2 - report.value "mechanistic_basis_comments","a posteriori for individual predictions" - - # Other information about the mechanistic interpretation 8.3 - report.value "mechanistic_basis_info","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual - predictions by inspecting neighbors and relevant fragments.</p> - <p>Neighbors are compounds that are similar in respect to a certain - endpoint and it is likely that compounds with high similarity act by - similar mechanisms as the query compound. Links at the webinterface - prove an easy access to additional experimental data and literature - citations for the neighbors and the query structure.</p> - <p>Activating and deactivating parts of the query compound are highlighted - in red and green on the webinterface. Fragments that are unknown (or too - infrequent for statistical evaluation are marked in yellow and - additional statistical information about the individual fragments can be - retrieved. Please note that lazar predictions are based on neighbors and - not on fragments. Fragments and their statistical significance are used - for the calculation of activity specific similarities.</p>" - - # Bibliography 9.2 - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 - report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Helma (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 - - # output - response['Content-Type'] = "application/xml" + report = qmrf_report params[:id] return report.to_xml else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end |