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module OpenTox
class Dataset
include Owl
def initialize
super
end
# create/add to entry from uris or Redland::Resources
def add(compound,feature,value)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
values = @model.create_resource
@model.add data_entry, OT['values'], values
@model.add values, RDF['type'], OT['FeatureValue']
@model.add values, OT['feature'], feature
@model.add values, OT['value'], value.to_s
end
def add_tuple(compound,tuple)
compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
data_entry = @model.subject OT['compound'], compound
if data_entry.nil?
data_entry = @model.create_resource
@model.add data_entry, RDF['type'], OT["DataEntry"]
@model.add data_entry, OT['compound'], compound
end
@model.add data_entry, OT['values'], tuple
end
def create_tuple(feature,t)
feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
tuple = @model.create_resource
@model.add tuple, RDF['type'], OT["Tuple"]
@model.add tuple, OT['feature'], feature
t.each do |name,value|
f = self.find_or_create_feature name unless name.class == Redland::Resource
complex_value = @model.create_resource
feature = self.find_or_create_feature(name)
@model.add tuple, OT['complexValue'], complex_value
@model.add complex_value, RDF['type'], OT["FeatureValue"]
@model.add complex_value, OT['feature'], f
@model.add complex_value, OT['value'], value.to_s
end
tuple
end
# find or create a new compound and return the resource
def find_or_create_compound(uri)
compound = @model.subject(DC["identifier"], uri)
if compound.nil?
compound = @model.create_resource
@model.add compound, RDF['type'], OT["Compound"]
@model.add compound, DC["identifier"], uri
end
compound
end
# find or create a new feature and return the resource
def find_or_create_feature(uri)
feature = @model.subject(DC["identifier"], uri)
if feature.nil?
feature = @model.create_resource
@model.add feature, RDF['type'], OT["Feature"]
@model.add feature, DC["identifier"], uri
@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
@model.add feature, DC['source'], uri
end
feature
end
def self.create(data, content_type = 'application/rdf+xml')
uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
dataset = Dataset.new
dataset.read uri.to_s
dataset
end
def self.find(uri)
begin
dataset = Dataset.new
data = RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available
dataset.rdf = data
dataset
rescue
nil
end
end
def features
features = []
@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
features << @model.object(feature_node, DC["identifier"])#
end
features
end
def data
data = {}
@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
compound_node = @model.object(data_entry, OT['compound'])
@model.find(compound_node, OT['identifier'],nil) {|s,p,o| puts o.to_s}
compound_uri = @model.object(compound_node, DC['identifier']).to_s
data[compound_uri] = [] unless data[compound_uri]
@model.find(data_entry, OT['values'], nil) do |s,p,values|
entry = {}
feature_node = @model.object values, OT['feature']
feature_uri = @model.object(feature_node, DC['identifier']).to_s
# TODO simple features
type = @model.object(values, RDF['type'])
if type == OT['FeatureValue']
#entry[feature_uri] = [] unless entry[feature_uri]
entry[feature_uri] = @model.object(values, OT['value']).to_s
elsif type == OT['Tuple']
entry[feature_uri] = {} unless entry[feature_uri]
@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
name_node = @model.object complex_value, OT['feature']
name = @model.object(name_node, DC['title']).to_s
value = @model.object(complex_value, OT['value']).to_s
entry[feature_uri][name] = value
end
end
data[compound_uri] << entry
end
end
data
end
def feature_values(feature_uri)
features = {}
feature = @model.subject(DC["identifier"],feature_uri)
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compound = @model.object(compound_node, DC["identifier"]).to_s.sub(/^\[(.*)\]$/,'\1')
features[compound] = [] unless features[compound]
data_entry = @model.subject(OT['compound'], compound_node)
@model.find( data_entry, OT['values'], nil ) do |s,p,values|
if feature == @model.object(values, OT['feature'])
value = @model.object(values, OT['value'])
case value.to_s
when "true"
features[compound] << true
when "false"
features[compound] << false
else
features[compound] << value.to_s
end
end
end
end
features
end
=begin
def tuples
tuples = []
@model.subjects(RDF['type'], OT["Tuple"]).each do |t|
tuple = {}
compounds = []
@model.subjects(OT['values'], t).each do |data_entry|
compound_node = @model.object(data_entry,OT['compound'])
compounds << @model.object(compound_node, DC["identifier"]).to_s
end
@model.find(t, OT['tuple'],nil) do |s,p,pair|
feature_node = @model.object(pair, OT['feature'])
feature_name = @model.object(feature_node, DC['title']).to_s
value_node = @model.object(pair, OT['value'])
value = @model.object(value_node, OT['value']).to_s
value = value.to_f if value.match(/^[\d\.]+$/)
tuple[feature_name.to_sym] = value
end
tuple[:compounds] = compounds
tuples << tuple
end
tuples
end
def tuple(compound_uri)
compound_node = @model.subject(DC["identifier"],compound_uri)
#puts compound_uri
@model.subjects(OT['compound'], compound_node).each do |data_entry|
values_node = @model.object(data_entry, OT['values'])
@model.find(values_node, OT['tuple'], nil) do |s,p,tuple|
@model.find(tuple, OT['feature'], nil) do |s,p,feature|
name = @model.object(feature,DC['title']).to_s
#puts name
end
end
#puts values_node
end
end
=end
def compounds
compounds = []
@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
compounds << @model.object(compound_node, DC["identifier"]).to_s
end
compounds
end
# Delete a dataset
def delete
RestClient.delete @uri
end
def save
RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s
end
def to_yaml
{
:uri => self.uri,
:opentox_class => self.owl_class,
:title => self.title,
:source => self.source,
:identifier => self.identifier,
:compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')},
:features => self.features.collect{|f| f.to_s }
}.to_yaml
end
end
end
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