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|
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, model_uri=nil)
case type
when /(?i)QMRF/
params = {}
params[:model_uri]=model_uri if model_uri
ReachReports::QmrfReport.all(params).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], r.subjectid) )
training_dataset = OpenTox::Dataset.new( model.metadata[OT.trainingDataset], r.subjectid )
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 = Validation::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.find( :crossvalidation_id => cv.id ).first
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|
begin
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
rescue => ex
LOGGER.warn "could not add cv "+cv.crossvalidation_uri+" : "+ex.message
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 = Validation::Validation.find({: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 << "average AUC: "+validation.classification_statistics[:average_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, r.subjectid)
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
mysql_lite_retry do
r.save
end
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.raise OpenTox::BadRequestError.new 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)
report = nil
mysql_lite_retry(3) do
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
end
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
|
