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|
=begin
* Name: dataset.rb
* Description: Dataset RDF tools
* Author: Andreas Maunz <andreas@maunz.de>
* Date: 10/2012
=end
module OpenTox
class Dataset
# Load features via RDF (slow)
# @param [String] uri Dataset URI
# @return [Array] features Features in order
def find_features_rdf
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.Feature]
pattern [:uri, RDF::OLO.index, :idx]
end
query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
end
# Load compounds via RDF (slow)
# @param [String] uri Dataset URI
# @return [Array] compounds Compounds in order
def find_compounds_rdf
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.Compound]
pattern [:uri, RDF::OLO.index, :idx]
end
query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new(s.uri.to_s)}
end
# Load data entries via RDF (slow)
# @param [String] uri Dataset uri
# @return [Array] entries Data entries, ordered primarily over cols and secondarily over rows
def find_data_entries_rdf
query = RDF::Query.new do
pattern [:data_entry, RDF::OLO.index, :cidx] # compound index: now a free variable
pattern [:data_entry, RDF::OT.values, :vals]
pattern [:vals, RDF::OT.feature, :f]
pattern [:f, RDF::OLO.index, :fidx]
pattern [:vals, RDF::OT.value, :val]
end
query.execute(@rdf).order_by(:fidx, :cidx).collect { |s| s.val.to_s }
end
# Query a dataset URI for ordered status
# by loading its metadata (OpenTox compliant)
# @param [String] uri Dataset uri
# @return [TrueClass, FalseClass] status Whether the dataset is ordered
def self.ordered?(uri)
ds = OpenTox::Dataset.new # dummy
ds.parse_rdfxml(RestClient.get([uri,"metadata"].join("/"),{:accept => "application/rdf+xml"}))
query = RDF::Query.new do
pattern [:dataset, RDF.type, RDF::OT.OrderedDataset]
end
query.execute(ds.rdf).size>0
end
# Load dataset URI from given RDF (slow)
# @param [String] rdf RDF
# @return [String] uri URI
def self.uri_from_rdf(rdf)
ds = OpenTox::Dataset.new # dummy
ds.parse_rdfxml(rdf)
query = RDF::Query.new do
pattern [:dataset, RDF.type, RDF::OT.Dataset]
end
query.execute(ds.rdf).collect { |s| s.dataset.to_s }[0]
end
end
end
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