# require the qsar-report gem
require "qsar-report"

# generate a new report
report = OpenTox::QMRFReport.new

# lazar specific data resources for model information
model = Model::Lazar.find params[:id]
prediction_model = Model::Prediction.find_by :model_id => params[:id]
validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") #detailed validation results from lazar-rest


# Start filling the QMRF report 

# QSAR identifier (title) 1.1
report.value "QSAR_title", "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 => "Contact Email"}
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 => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
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 => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
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}"

# Type of model 4.1
report.value "algorithm_type", "#{model.class.to_s.gsub('OpenTox::Model::Lazar','')}"

# 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 => "modified k-nearest neighbor classification with activity specific similarities, weighted voting and exhaustive enumeration of fragments and neighbors"}
report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1

# Descriptors in the model 4.3
report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "all statistically relevant paths are used for similarity calculation", :name => "linear fragmens (paths)", :publication_ref => "", :units => "true/false (i.e. present/absent)"}
report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1

# Descriptor selection 4.4
report.value "descriptors_selection", "statistical filter (chi-square with Yates correction)"

# 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 => "Contact Email"}
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)"

# Some QMRF fields (tag contents) can have formatted HTML contents. 
# These contents have to have a complete HTML document structure with basic surrounding tags like <html><body>. 
# see Example below   

# 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 => "Contact Email"}
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.crossvalidations
  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>"

# Reference all publications to the bibliography 
# 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