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module OpenTox
class Validation
include OpenTox
# find validation, raises error if not found
# @param [String] uri
# @param [String,optional] subjectid
# @return [OpenTox::Validation]
def self.find( uri, subjectid=nil )
val = Validation.new(uri)
val.load_metadata( subjectid )
val
end
# creates a validation object from crossvaldiation statistics, raise error if not found
# (as crossvaldiation statistics are returned as an average valdidation over all folds)
# @param [String] crossvalidation uri
# @param [String,optional] subjectid
# @return [OpenTox::Validation]
def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
find( File.join(crossvalidation_uri, 'statistics'),subjectid )
end
# loads metadata via yaml from validation object
# fields (like for example the validated model) can be acces via validation.metadata[OT.model]
def load_metadata( subjectid=nil )
@metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
end
# PENDING: creates summary as used for ToxCreate
def summary
if @metadata[OT.classificationStatistics]
res = {
:nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
:correct_predictions => @metadata[OT.classificationStatistics][OT.percentCorrect],
:weighted_area_under_roc => @metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc],
}
@metadata[OT.classificationStatistics][OT.classValueStatistics].each do |s|
if s[OT.classValue].to_s=="true"
res[:true_positives] = s[OT.numTruePositives]
res[:false_positives] = s[OT.numFalsePositives]
res[:true_negatives] = s[OT.numTrueNegatives]
res[:false_negatives] = s[OT.numFalseNegatives]
res[:sensitivity] = s[OT.truePositiveRate]
res[:specificity] = s[OT.falsePositiveRate]
break
end
end
res
elsif @metadata[OT.regressionStatistics]
{
:nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
:r_square => @metadata[OT.regressionStatistics][OT.rSquare],
:root_mean_squared_error => @metadata[OT.regressionStatistics][OT.rootMeanSquaredError],
:mean_absolute_error => @metadata[OT.regressionStatistics][OT.meanAbsoluteError],
}
end
end
end
class Crossvalidation
include OpenTox
attr_reader :report
# find crossvalidation, raises error if not found
# @param [String] uri
# @param [String,optional] subjectid
# @return [OpenTox::Crossvalidation]
def self.find( uri, subjectid=nil )
cv = Crossvalidation.new(uri)
cv.load_metadata( subjectid )
cv
end
# creates a crossvalidations, waits until it finishes, may take some time
# @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
# @param [String,optional] subjectid
# @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
# @return [OpenTox::Crossvalidation]
def self.create( params, subjectid=nil, waiting_task=nil )
params[:subjectid] = subjectid if subjectid
uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation"),
params,{:content_type => "text/uri-list"},waiting_task )
Crossvalidation.new(uri)
end
# looks for report for this crossvalidation, creates a report if no report is found
# @param [String,optional] subjectid
# @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
# @return [String] report uri
def find_or_create_report( subjectid=nil, waiting_task=nil )
@report = CrossvalidationReport.find_for_crossvalidation(@uri, subjectid) unless @report
@report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report
@report.uri
end
# loads metadata via yaml from crossvalidation object
# fields (like for example the validations) can be acces via validation.metadata[OT.validation]
def load_metadata( subjectid=nil )
@metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
end
# PENDING: creates summary as used for ToxCreate
def summary( subjectid=nil )
Validation.from_cv_statistics( @uri, subjectid ).summary
end
end
class ValidationReport
include OpenTox
# finds ValidationReport for a particular validation
# @param [String] crossvalidation uri
# @param [String,optional] subjectid
# @return [OpenTox::ValidationReport] nil if no report found
def self.find_for_validation( validation_uri, subjectid=nil )
uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
"/report/validation?validation="+validation_uri), {:subjectid => subjectid}).chomp.split("\n")
uris.size==0 ? nil : ValidationReport.new(uris[-1])
end
end
class CrossvalidationReport
include OpenTox
# finds CrossvalidationReport via uri, raises error if not found
# @param [String] uri
# @param [String,optional] subjectid
# @return [OpenTox::CrossvalidationReport]
def self.find( uri, subjectid=nil )
# PENDING load report data?
OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
CrossvalidationReport.new(uri)
end
# finds CrossvalidationReport for a particular crossvalidation
# @param [String] crossvalidation uri
# @param [String,optional] subjectid
# @return [OpenTox::CrossvalidationReport] nil if no report found
def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
"/report/crossvalidation?crossvalidation="+crossvalidation_uri), {:subjectid => subjectid}).chomp.split("\n")
uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
end
# creates a crossvalidation report via crossvalidation
# @param [String] crossvalidation uri
# @param [String,optional] subjectid
# @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
# @return [OpenTox::CrossvalidationReport]
def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"),
{ :validation_uris => crossvalidation_uri, :subjectid => subjectid }, {}, waiting_task )
CrossvalidationReport.new(uri)
end
end
class QMRFReport
include OpenTox
# finds QMRFReport, raises Error if not found
# @param [String] uri
# @param [String,optional] subjectid
# @return [OpenTox::QMRFReport]
def self.find( uri, subjectid=nil )
# PENDING load crossvalidation data?
OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
QMRFReport.new(uri)
end
# finds QMRF report for a particular model
# @param [String] model_uri
# @param [String,optional] subjectid
# @return [OpenTox::QMRFReport] nil if no report found
def self.find_for_model( model_uri, subjectid=nil )
uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
"/reach_report/qmrf?model="+model_uri), {:subjectid => subjectid}).chomp.split("\n")
uris.size==0 ? nil : QMRFReport.new(uris[-1])
end
# creates a qmrf report via model
# @param [String] model_uri
# @param [String,optional] subjectid
# @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
# @return [OpenTox::QMRFReport]
def self.create( model_uri, subjectid=nil, waiting_task=nil )
uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"),
{ :model_uri => model_uri, :subjectid => subjectid }, {}, waiting_task )
QMRFReport.new(uri)
end
end
end
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