lazar-rest 1.0.0

data/config.ru

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+SERVICE = "lazar-rest"
+require 'bundler'
+Bundler.require
+require File.expand_path './lib/lazar-rest.rb'
+run Sinatra::Application

data/lazar-rest.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name        = "lazar-rest"
+  s.version     = File.read("./VERSION")
+  s.authors     = ["Christoph Helma","Micha Rautenberg","Denis Gebele"]
+  s.email       = ["supprot@in-silico.ch"]
+  s.homepage    = "http://github.com/opentox/lazar-rest"
+  s.summary     = %q{lazar-rest}
+  s.description = %q{REST Interface for Lazar Toxicology Predictions}
+  s.license     = 'GPL-3'
+
+  s.rubyforge_project = "lazar-rest"
+
+  s.files         = `git ls-files`.split("\n")
+  s.require_paths = ["lib"]
+  s.required_ruby_version = '>= 2.0.0'
+
+  s.add_runtime_dependency "lazar"
+  s.add_runtime_dependency "qsar-report"
+  s.add_runtime_dependency "sinatra"
+  s.add_runtime_dependency "haml"
+  s.add_runtime_dependency "sass"
+  s.add_runtime_dependency "unicorn"
+  s.add_runtime_dependency 'rack-cors'
+end

data/lib/aa.rb

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+post "/aa/authenticate/?" do
+  mime_types = ["text/plain"]
+  bad_request_error "Mime type #{@accept} not supported here. Please request data as  #{mime_types.join(', ')}." unless mime_types.include? @accept
+  bad_request_error "Please send formdata username." unless params[:username]
+  bad_request_error "Please send formdata password." unless params[:password]
+  case @accept
+  when "text/plain"
+    if OpenTox::Authorization.authenticate(params[:username], params[:password])
+      return OpenTox::RestClientWrapper.subjectid
+    else
+      return nil
+    end
+  else
+    bad_request_error "'#{@accept}' is not a supported content type."
+   end
+end
+
+post "/aa/logout/?" do
+  mime_types = ["text/plain"]
+  bad_request_error "Mime type #{@accept} not supported here. Please request data as  #{mime_types.join(', ')}." unless mime_types.include? @accept
+  bad_request_error "Please send formdata subjectid." unless params[:subjectid]
+  case @accept
+  when "text/plain"
+    if OpenTox::Authorization.logout(params[:subjectid])
+      return "Successfully logged out. \n"
+    else
+      return "Logout failed.\n"
+    end
+  else
+    bad_request_error "'#{@accept}' is not a supported content type."
+   end
+end
+
+module OpenTox
+
+  AA = "https://opensso.in-silico.ch"
+  
+  module Authorization
+    #Authentication against OpenSSO. Returns token. Requires Username and Password.
+    # @param user [String] Username
+    # @param pw [String] Password
+    # @return [Boolean] true if successful
+    def self.authenticate(user, pw)
+      begin
+        res = RestClientWrapper.post("#{AA}/auth/authenticate",{:username=>user, :password => pw},{:subjectid => ""}).sub("token.id=","").sub("\n","")
+        if is_token_valid(res)
+          RestClientWrapper.subjectid = res
+          return true
+        else
+          bad_request_error "Authentication failed #{res.inspect}"
+        end
+      rescue
+        bad_request_error "Authentication failed #{res.inspect}"
+      end
+    end
+
+    #Logout on opensso. Make token invalid. Requires token
+    # @param [String] subjectid the subjectid
+    # @return [Boolean] true if logout is OK
+    def self.logout(subjectid=RestClientWrapper.subjectid)
+      begin
+        out = RestClientWrapper.post("#{AA}/auth/logout", :subjectid => subjectid)
+        return true unless is_token_valid(subjectid)
+      rescue
+        return false
+      end
+      return false
+    end
+
+    #Checks if a token is a valid token
+    # @param [String]subjectid subjectid from openSSO session
+    # @return [Boolean] subjectid is valid or not.
+    def self.is_token_valid(subjectid=RestClientWrapper.subjectid)
+      begin
+        return true if RestClientWrapper.post("#{AA}/auth/isTokenValid",:tokenid => subjectid) == "boolean=true\n"
+      rescue #do rescue because openSSO throws 401
+        return false
+      end
+      return false
+    end
+  end
+end

data/lib/api.rb

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+# route to swagger API file
+get "/api/api.json" do
+  response['Content-Type'] = "application/json"
+  api_file = File.join("api", "api.json")
+  bad_request_error "API Documentation in Swagger JSON is not implemented.", uri("/#{SERVICE}/api") unless File.exists?(api_file)
+  api_hash = JSON.parse(File.read(api_file))
+  api_hash["host"] = request.env['HTTP_HOST']
+  return api_hash.to_json
+end

data/lib/compound.rb

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+# Get a list of a single or all descriptors
+# @param [Header] Accept one of text/plain, application/json
+# @param [Path] Descriptor name or descriptor ID (e.G.: Openbabel.HBA1, 5755f8eb3cf99a00d8fedf2f)
+# @return [text/plain, application/json] list of all prediction models
+get "/compound/descriptor/?:descriptor?" do
+  case @accept
+  when "application/json"
+    return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} "  unless params[:descriptor]
+    return PhysChem.find_by(:name => params[:descriptor]).to_json if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return PhysChem.find(params[:descriptor]).to_json if PhysChem.find(params[:descriptor])
+  else
+    return PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
+    return PhysChem::DESCRIPTORS[params[:descriptor]] if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return "#{PhysChem.find(params[:descriptor]).name}: #{PhysChem.find(params[:descriptor]).description}" if PhysChem.find(params[:descriptor])
+  end
+end
+
+post "/compound/descriptor/?" do
+  bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor]
+  descriptors = params['descriptor'].split(',')
+  compound = Compound.from_smiles params[:identifier]
+  physchem_descriptors = []
+  descriptors.each do |descriptor|
+    physchem_descriptors << PhysChem.find_by(:name => descriptor)
+  end
+  result = compound.physchem physchem_descriptors
+  csv = result.collect{|k,v| "\"#{PhysChem.find(k).name}\",#{v}" }.join("\n")
+  csv = "SMILES,#{params[:identifier]}\n#{csv}" if params[:identifier]
+  case @accept
+  when "text/csv","application/csv"
+    return csv
+  when "application/json"
+    result_hash = result.collect{|k,v|  {"#{PhysChem.find(k).name}" => "#{v}"}}  # result.collect{|k,v| "\"#{PhysChem.find(k).name}\"" => "#{v}"}.join(",")
+    data = {"compound" => {"SMILES" => "#{params[:identifier]}"}}
+    data["compound"]["InChI"] = "#{compound.inchi}" if compound.inchi
+    data["compound"]["results"] = result_hash
+    return JSON.pretty_generate(data)
+  end
+end
+
+get %r{/compound/(.+)} do |inchi|
+  bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/)
+  compound = Compound.from_inchi URI.unescape(inchi)
+  response['Content-Type'] = @accept
+  case @accept
+  when "application/json"
+    return JSON.pretty_generate JSON.parse(compound.to_json)
+  when "chemical/x-daylight-smiles"
+    return compound.smiles
+  when "chemical/x-inchi"
+    return compound.inchi
+  when "chemical/x-mdl-sdfile"
+    return compound.sdf
+  when "chemical/x-mdl-molfile"
+  when "image/png"
+    return compound.png
+  when "image/svg+xml"
+    return compound.svg
+  when "text/plain"
+    return "#{compound.names}\n"
+  else
+    return compound.inspect
+  end
+end

data/lib/dataset.rb

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+# Get all datasets
+get "/dataset/?" do
+  datasets = Dataset.all
+  case @accept
+  when "text/uri-list"
+    uri_list = datasets.collect{|dataset| uri("/dataset/#{dataset.id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    datasets = JSON.parse datasets.to_json
+    datasets.each_index do |idx|
+      datasets[idx][:URI] = uri("/dataset/#{datasets[idx]["_id"]["$oid"]}")
+    end
+    return datasets.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+# Get a dataset
+get "/dataset/:id/?" do
+  dataset = Dataset.find :id => params[:id]
+  resource_not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
+  case @accept
+  when "application/json"
+    dataset.data_entries.each do |k, v|
+      dataset.data_entries[k][:URI] = uri("/substance/#{k}")
+    end
+    dataset[:URI] = uri("/dataset/#{dataset.id}")
+    dataset[:substances] = uri("/dataset/#{dataset.id}/substances")
+    dataset[:features] = uri("/dataset/#{dataset.id}/features")
+    return dataset.to_json
+  when "text/csv", "application/csv"
+    return dataset.to_csv
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+# Get a dataset attribute. One of compounds, nanoparticles, substances, features 
+get "/dataset/:id/:attribute/?" do
+  dataset = Dataset.find :id => params[:id]
+  resource_not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
+  attribs = ["compounds", "nanoparticles", "substances", "features"]
+  return "Attribute '#{params[:attribute]}' is not available. Choose one of #{attribs.join(', ')}." unless attribs.include? params[:attribute]
+  out = dataset.send(params[:attribute])
+  return out.to_json
+end

data/lib/feature.rb

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+# Get all Features
+get "/feature/?" do
+  features = Feature.all
+  case @accept
+  when "text/uri-list"
+    uri_list = features.collect{|feature| uri("/feature/#{feature.id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    features = JSON.parse features.to_json
+    features.each_index do |idx|
+      features[idx][:URI] = uri("/feature/#{features[idx]["_id"]["$oid"]}")
+    end
+    return features.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+# Get a feature
+get "/feature/:id/?" do
+  feature = Feature.find :id => params[:id]
+  resource_not_found_error "Feature with id: #{params[:id]} not found." unless feature
+  feature[:URI] = uri("/feature/#{feature.id}")
+  return feature.to_json
+end

data/lib/lazar-rest.rb

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+require "sinatra"
+require "../lazar/lib/lazar.rb"
+require "../qsar-report/lib/qsar-report.rb"
+include OpenTox
+
+require 'rack/cors'
+
+
+set :show_exceptions => false
+
+# add CORS support for swagger
+use Rack::Cors do |config|
+  config.allow do |allow|
+    allow.origins '*'
+    allow.resource "/#{SERVICE}/*",
+      :methods => [:head, :get, :post, :put, :delete, :options],
+      :headers => :any,
+      :max_age => 0
+  end
+end
+before do
+  @accept = request.env['HTTP_ACCEPT']
+  response['Content-Type'] = @accept
+end
+
+[
+  "aa.rb",
+  "api.rb",
+  "compound.rb",
+  "dataset.rb",
+  "feature.rb",
+  "model.rb",
+  "nanoparticle.rb",
+  "report.rb",
+  "substance.rb",
+  "validation.rb"
+].each{ |f| require_relative f }

data/lib/model.rb

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+
+# Get a list of all prediction models
+# @param [Header] Accept one of text/uri-list,
+# @return [text/uri-list] list of all prediction models
+get "/model/?" do
+  models = Model::Prediction.all
+  case @accept
+  when "text/uri-list"
+    uri_list = models.collect{|model| uri("/model/#{model.model_id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    models = JSON.parse models.to_json
+    models.each_index do |idx|
+      models[idx][:URI] = uri("/model/#{models[idx]["model_id"]["$oid"]}")
+      models[idx][:crossvalidation_uri] = uri("/crossvalidation/#{models[idx]["crossvalidation_id"]["$oid"]}") if models[idx]["crossvalidation_id"]
+    end
+    return models.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+get "/model/:id/?" do
+  model = Model::Lazar.find params[:id]
+  resource_not_found_error "Model with id: #{params[:id]} not found." unless model
+  model[:URI] = uri("/model/#{model.id}")
+  model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id]
+  model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id
+  model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id
+  return model.to_json
+end
+
+
+post "/model/:id/?" do
+  identifier = params[:identifier].split(",")
+  begin
+    # get compound from SMILES
+    compounds = identifier.collect{ |i| Compound.from_smiles i.strip }
+  rescue
+    @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
+    return @error_report
+  end
+  model = Model::Lazar.find params[:id]
+  batch = {}
+  compounds.each do |compound|
+    prediction = model.predict(compound)
+    batch[compound] = {:id => compound.id, :inchi => compound.inchi, :smiles => compound.smiles, :model => model, :prediction => prediction}
+  end
+  return batch.to_json
+end

data/lib/nanoparticle.rb

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+# Get all Nanoparticles
+get "/nanoparticle/?" do
+  nanoparticles = Nanoparticle.all
+  case @accept
+  when "text/uri-list"
+    uri_list = nanoparticles.collect{|nanoparticle| uri("/nanoparticle/#{nanoparticle.id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    nanoparticles = JSON.parse nanoparticles.to_json
+    nanoparticles.each_index do |idx|
+      nanoparticles[idx][:URI] = uri("/nanoparticle/#{nanoparticles[idx]["_id"]["$oid"]}")
+    end
+    return nanoparticles.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+# Get a nanoparticle
+get "/nanoparticle/:id/?" do
+  nanoparticle = Nanoparticle.find :id => params[:id]
+  resource_not_found_error "Nanoparticle with id: #{params[:id]} not found." unless nanoparticle
+  nanoparticle[:URI] = uri("/nanoparticle/#{nanoparticle.id}")
+  return nanoparticle.to_json
+end

data/lib/report.rb

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+# 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
+  models = Model::Prediction.all
+  case @accept
+  when "text/uri-list"
+    uri_list = models.collect{|model| uri("/report/#{model.model_id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    reports = [{}]
+    #models = JSON.parse models.to_json
+    models.each_index do |idx|
+      reports[idx] = {}
+      reports[idx][:URI] = uri("/report/#{models[idx]["model_id"]}")
+      reports[idx][:repeated_crossvalidation_uri] = uri("/validation/repeatedcrossvalidation/#{models[idx]["repeated_crossvalidation_id"]}") if models[idx]["repeated_crossvalidation_id"]
+      reports[idx][:leave_one_out_validation_uri] = uri("/validation/leaveoneoutvalidation/#{models[idx]["leave_one_out_validation_id"]}") if models[idx]["leave_one_out_validation_id"]
+      reports[idx][:training_dataset_URI] = uri("/dataset/#{models[idx].training_dataset.id}") if models[idx].training_dataset.id 
+    end
+    return reports.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+get "/report/:id/?" do
+  model = Model::Lazar.find params[:id]
+  resource_not_found_error "Model with id: #{params[:id]} not found." unless model
+  prediction_model = Model::Prediction.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.neighbor_algorithm.gsub('_',' ').titleize}#{(model.neighbor_algorithm_parameters[:min_sim] ? ' with similarity > ' + model.neighbor_algorithm_parameters[:min_sim].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.prediction_algorithm_parameters
+    pred_algorithm_params = (model.prediction_algorithm_parameters[:method] == "rf" ? "random forest" : model.prediction_algorithm_parameters[: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.prediction_algorithm.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.neighbor_algorithm_parameters[:type]
+    report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.neighbor_algorithm_parameters[:type]}", :publication_ref => "", :units => ""}
+    report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1
+  end
+
+  # Descriptor selection 4.4
+  report.value "descriptors_selection", "#{model.feature_selection_algorithm.gsub('_',' ')} #{model.feature_selection_algorithm_parameters.collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.feature_selection_algorithm
+  
+  # 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"
+  return report.to_xml
+
+end