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module ReachReports
def self.list_reports(type)
case type
when /(?i)QMRF/
ReachReports::QmrfReport.all.collect{ |r| r.report_uri }.join("\n")
when /(?i)QPRF/
ReachReports::QprfReport.all.collect{ |r| r.report_uri }.join("\n")
end
end
def self.create_report( type, params, xml_data=nil )
#content_type "text/uri-list"
#task_uri = OpenTox::Task.as_task do |task|
case type
when /(?i)QMRF/
if params[:model_uri]
report = ReachReports::QmrfReport.new :model_uri => params[:model_uri]
build_qmrf_report(report)
elsif xml_data and (input = xml_data.read).to_s.size>0
report = ReachReports::QmrfReport.new
ReachReports::QmrfReport.from_xml(report,input)
else
$sinatra.halt 400, "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/
$sinatra.halt 400,"qprf report creation not yet implemented"
if params[:compound_uri]
report = ReachReports::QprfReport.new :compound_uri => params[:compound_uri]
else
$sinatra.halt 400, "illegal parameters for qprf-report, use either\n"+
"* compound-uri\n"+
"params given: "+params.inspect
end
end
report.report_uri
#end
#halt 202,task_uri
end
def self.build_qmrf_report(r)
model = OpenTox::Model::Generic.find(r.model_uri)
# chapter 1
#r.QSAR_title = model.title
r.qsar_identifier = QsarIdentifier.new
r.qsar_identifier.qsar_title = model.title
# TODO
# QSAR_models -> sparql same endpoint
r.qsar_identifier.qsar_software << QsarSoftware.new( :url => model.uri, :name => model.title, :contact => model.creator )
algorithm = OpenTox::Algorithm::Generic.find(model.algorithm) if model.algorithm
r.qsar_identifier.qsar_software << QsarSoftware.new( :url => algorithm.uri, :name => algorithm.title )
#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.date.to_s
# TODO: references?
# EMPTY: info_availablity
# TODO: related_models = find qmrf reports for QSAR_models
# chapter 3
# TODO "model_species" ?
r.qsar_endpoint = QsarEndpoint.new
model.predictedVariables.each do |p|
r.qsar_endpoint.model_endpoint << ModelEndpoint.new( :name => p )
end
# TODO "endpoint_comments" => "3.3", "endpoint_units" => "3.4",
r.qsar_endpoint.endpoint_variable = model.dependentVariables if model.dependentVariables
# TODO "endpoint_protocol" => "3.6", "endpoint_data_quality" => "3.7",
# 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
# chapter 5
# TODO app_domain_description, app_domain_method, app_domain_software, applicability_limits
dataset = model.trainingDataset ? OpenTox::Dataset.find(model.trainingDataset) : nil
# chapter 6
r.qsar_robustness = QsarRobustness.new
r.qsar_robustness.training_set_availability = dataset ? "Yes" : "No"
#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",
puts Lib::Crossvalidation.find(:all, :conditions => {:algorithm_uri => model.algorithm}).inspect if model.algorithm
#exit
# "lmo" => "6.9", "yscrambling" => "6.10", "bootstrap" => "6.11", "other_statistics" => "6.12",
# 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",
# chapter 8
# "mechanistic_basis" => "8.1", "mechanistic_basis_comments" => "8.2", "mechanistic_basis_info" => "8.3",
# 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 => dataset.title,
:filetype => "owl-dl",
:url => dataset.uri} ) if dataset
r.save
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
$sinatra.halt 404, type+" report with id '#{id}' not found." unless report
return report
end
end
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