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module OpenTox
# Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
class Dataset
attr_accessor :features, :compounds, :data_entries
def initialize uri=nil, subjectid=nil
super uri, subjectid
@features = []
@compounds = []
@data_entries = []
append RDF.type, RDF::OT.OrderedDataset
end
def upload filename
file = File.new filename
RestClientWrapper.put(@uri, {:file => file}, {:subjectid => @subjectid})
end
def get
super
@features = []
@compounds = []
@data_entries = []
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.OrderedDataset]
end
if query.execute(@rdf).first # ordered dataset
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.Compound]
pattern [:uri, RDF::OLO.index, :idx]
end
@compounds = query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Compound.new s.uri.to_s}
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.Feature]
pattern [:uri, RDF::OLO.index, :idx]
end
@features = query.execute(@rdf).sort_by{|s| s.idx}.collect{|s| OpenTox::Feature.new(s.uri.to_s)}
numeric_features = @features.collect{|f| f.get; f[RDF.type].include? RDF::OT.NumericFeature}
@compounds.each_with_index do |compound,i|
query = RDF::Query.new do
pattern [:data_entry, RDF::OLO.index, i]
pattern [:data_entry, RDF::OT.values, :values]
pattern [:values, RDF::OT.feature, :feature]
pattern [:feature, RDF::OLO.index, :feature_idx]
pattern [:values, RDF::OT.value, :value]
end
values = query.execute(@rdf).sort_by{|s| s.feature_idx}.collect do |s|
numeric_features[s.feature_idx] ? s.value.to_s.to_f : s.value.to_s
end
@data_entries << values
end
else
query = RDF::Query.new do
pattern [:uri, RDF.type, RDF::OT.Feature]
end
@features = query.execute(@rdf).collect{|s| OpenTox::Feature.new(s.uri.to_s)}
query = RDF::Query.new do
pattern [:data_entry, RDF::OT.compound, :compound]
end
@compounds = query.execute(@rdf).sort_by{|s| s.data_entry}.collect{|s| OpenTox::Compound.new s.compound.to_s}
numeric_features = @features.collect{|f| f.get; f[RDF.type].include? RDF::OT.NumericFeature}
@compounds.each do |compound|
values = []
@features.each_with_index do |feature,i|
query = RDF::Query.new do
pattern [:data_entry, RDF::OT.compound, RDF::URI.new(compound.uri)]
pattern [:data_entry, RDF::OT.values, :values]
pattern [:values, RDF::OT.feature, RDF::URI.new(feature.uri)]
pattern [:values, RDF::OT.value, :value]
end
value = query.execute(@rdf).first.value.to_s
value = value.to_f if numeric_features[i]
values << value
end
@data_entries << values
end
end
end
def get_metadata
uri = File.join(@uri,"metadata")
begin
parse_ntriples RestClientWrapper.get(uri,{},{:accept => "text/plain", :subjectid => @subjectid})
rescue # fall back to rdfxml
parse_rdfxml RestClientWrapper.get(uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
end
metadata
end
def << data_entry
compound = data_entry.shift
bad_request_error "Dataset features are empty." unless features
bad_request_error "data_entry size does not match features size." unless data_entry.size == features.size
bad_request_error "First data_entry is not a OpenTox::Compound" unless compound.class == OpenTox::Compound
@compounds << compound
@data_entries << data_entry
end
RDF_FORMATS.each do |format|
# redefine rdf serialization methods
send :define_method, "to_#{format}".to_sym do
# TODO: check, might affect appending to unordered datasets
features.each_with_index do |feature,i|
@rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)]
@rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
end
compounds.each_with_index do |compound,i|
@rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Compound)]
@rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
data_entry_node = RDF::Node.new
@rdf << [RDF::URI.new(@uri), RDF::URI.new(RDF::OT.dataEntry), data_entry_node]
@rdf << [data_entry_node, RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.DataEntry)]
@rdf << [data_entry_node, RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
@rdf << [data_entry_node, RDF::URI.new(RDF::OT.compound), RDF::URI.new(compound.uri)]
data_entries[i].each_with_index do |value,j|
value_node = RDF::Node.new
@rdf << [data_entry_node, RDF::URI.new(RDF::OT.values), value_node]
@rdf << [value_node, RDF::URI.new(RDF::OT.feature), RDF::URI.new(@features[j].uri)]
@rdf << [value_node, RDF::URI.new(RDF::OT.value), RDF::Literal.new(value)]
end
end
super()
end
end
end
end
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