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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)
dataset = Dataset.new
data = `curl "#{uri}"`
#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
dataset.rdf = data
dataset
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'])
compound_uri = @model.object(compound_node, DC['identifier']).to_s
@model.find(data_entry, OT['values'], nil) do |s,p,values|
feature_node = @model.object values, OT['feature']
feature_uri = @model.object(feature_node, DC['identifier']).to_s.sub(/\^\^.*$/,'') # remove XML datatype
type = @model.object(values, RDF['type'])
if type == OT['FeatureValue']
value = @model.object(values, OT['value']).to_s
case value.to_s
when TRUE_REGEXP # defined in environment.rb
value = true
when FALSE_REGEXP # defined in environment.rb
value = false
else
LOGGER.warn compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
value = nil
end
data[compound_uri] = {} unless data[compound_uri]
data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
data[compound_uri][feature_uri] << value unless value.nil?
elsif type == OT['Tuple']
entry = {}
data[compound_uri] = {} unless data[compound_uri]
data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
name_node = @model.object complex_value, OT['feature']
name = @model.object(name_node, DC['title']).to_s
value = @model.object(complex_value, OT['value']).to_s
v = value.sub(/\^\^.*$/,'') # remove XML datatype
v = v.to_f if v.match(/^[\.|\d]+$/) # guess numeric datatype
entry[name] = v
end
data[compound_uri][feature_uri] << entry
end
end
end
data
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 },
:data => self.data
}.to_yaml
end
end
end
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