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LOGGER.progname = File.expand_path(__FILE__)
module OpenTox
class Dataset
attr_accessor :uri, :title, :creator, :data, :features, :compounds
def initialize
@data = {}
@features = []
@compounds = []
end
def self.find(uri, accept_header=nil)
unless accept_header
#if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /informatik/
if !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
accept_header = 'application/x-yaml'
else
accept_header = "application/rdf+xml"
end
end
case accept_header
when "application/x-yaml"
d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s
d.uri = uri unless d.uri
when "application/rdf+xml"
owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
d = Dataset.new
d.title = owl.get("title")
d.creator = owl.get("creator")
d.uri = owl.uri
# when loading a dataset from owl, only compound- and feature-uris are loaded
owl.load_dataset(d.compounds, d.features)
# all features are marked as dirty, loaded dynamically later
d.init_dirty_features(owl)
d.compounds.uniq!
d.features.uniq!
else
raise "cannot get datset with accept header: "+accept_header.to_s
end
return d
end
# creates a new dataset, using only those compounsd specified in new_compounds
# returns uri of new dataset
def create_new_dataset( new_compounds, new_features, new_title, new_creator )
raise "no new compounds selected" unless new_compounds and new_compounds.size>0
# load require features
if ((defined? @dirty_features) && (@dirty_features - new_features).size > 0)
(@dirty_features - new_features).each{|f| load_feature_values(f)}
end
dataset = OpenTox::Dataset.new
dataset.title = new_title
dataset.creator = new_creator
dataset.features = new_features
dataset.compounds = new_compounds
# Copy dataset data for compounds and features
# PENDING: why storing feature values in an array?
new_compounds.each do |c|
data_c = []
@data[c].each do |d|
m = {}
new_features.each do |f|
m[f] = d[f]
end
data_c << m
end
dataset.data[c] = data_c
end
return dataset.save
end
# returns classification value
def get_predicted_class(compound, feature)
v = get_value(compound, feature)
if v.is_a?(Hash)
if v.has_key?(:classification)
return v[:classification]
else
return "no classification key"
end
else
raise "predicted class value is not a hash\n"+
"value "+v.to_s+"\n"+
"value-class "+v.class.to_s+"\n"+
"dataset "+@uri.to_s+"\n"+
"compound "+compound.to_s+"\n"+
"feature "+feature.to_s+"\n"
end
end
# returns prediction confidence if available
def get_prediction_confidence(compound, feature)
v = get_value(compound, feature)
if v.is_a?(Hash)
if v.has_key?(:confidence)
return v[:confidence].abs
else
# PENDING: return nil isntead of raising an exception
raise "no confidence key"
end
else
raise "prediction confidence value is not a hash value\n"+
"value "+v.to_s+"\n"+
"value-class "+v.class.to_s+"\n"+
"dataset "+@uri.to_s+"\n"+
"compound "+compound.to_s+"\n"+
"feature "+feature.to_s+"\n"
end
end
# return compound-feature value
def get_value(compound, feature)
if (defined? @dirty_features) && @dirty_features.include?(feature)
load_feature_values(feature)
end
v = @data[compound]
raise "no values for compound "+compound.to_s if v==nil
if v.is_a?(Array)
# PENDING: why using an array here?
v.each do |e|
if e.is_a?(Hash)
if e.has_key?(feature)
return e[feature]
end
else
raise "invalid internal value type"
end
end
raise "feature value no found: "+feature.to_s
else
raise "value is not an array\n"+
"value "+v.to_s+"\n"+
"value-class "+v.class.to_s+"\n"+
"dataset "+@uri.to_s+"\n"+
"compound "+compound.to_s+"\n"+
"feature "+feature.to_s+"\n"
end
end
# loads specified feature and removes dirty-flag, loads all features if feature is nil
def load_feature_values(feature=nil)
if feature
raise "feature already loaded" unless @dirty_features.include?(feature)
@owl.load_dataset_feature_values(@compounds, @data, feature)
@dirty_features.delete(feature)
else
@data = {}
@owl.load_dataset_feature_values(@compounds, @data)
@dirty_features.clear
end
end
def save
# loads all features before loading
if ((defined? @dirty_features) && @dirty_features.size > 0)
load_feature_values()
end
@features.uniq!
@compounds.uniq!
OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type => "application/x-yaml"},self.to_yaml).strip
end
def init_dirty_features(owl)
@dirty_features = @features
@owl = owl
end
end
end
|
