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module OpenTox
class Dataset
attr_accessor :uri, :title, :creator, :data, :features, :compounds
def initialize( owl=nil )
@data = {}
@features = []
@compounds = []
# creates dataset object from Opentox::Owl object
# use Dataset.find( <uri> ) to load dataset from rdf-supporting datasetservice
# note: does not load all feature values, as this is time consuming
if owl
raise "invalid param" unless owl.is_a?(OpenTox::Owl)
@title = owl.get("title")
@creator = owl.get("creator")
@uri = owl.uri
# when loading a dataset from owl, only compound- and feature-uris are loaded
owl.load_dataset(@compounds, @features)
# all features are marked as dirty
# as soon as a feature-value is requested all values for this feature are loaded from the rdf
@dirty_features = @features.dclone
@owl = owl
end
end
# Find and a dataset and load all data from the dataset service
# @param [String] uri Dataset URI
# @return [OpenTox::Dataset] Dataset object
def self.find(uri, accept_header=nil)
unless accept_header
if (@@config[:yaml_hosts].include?(URI.parse(uri).host))
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(owl)
else
raise "cannot get datset with accept header: "+accept_header.to_s
end
d
end
# converts a dataset represented in owl to yaml
# (uses a temporary dataset)
# note: to_yaml is overwritten, loads complete owl dataset values
def self.owl_to_yaml( owl_data, uri)
owl = OpenTox::Owl.from_data(owl_data, uri, "Dataset")
d = Dataset.new(owl)
d.to_yaml
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 )
LOGGER.debug "create new dataset with "+new_compounds.size.to_s+"/"+compounds.size.to_s+" compounds"
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 = []
raise "no data for compound '"+c.to_s+"'" if @data[c]==nil
@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)
k = v.keys.grep(/classification/).first
unless k.empty?
#if v.has_key?(:classification)
return v[k]
else
return "no classification key"
end
elsif v.is_a?(Array)
raise "predicted class value is 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"
else
return v
end
end
# returns regression value
def get_predicted_regression(compound, feature)
v = get_value(compound, feature)
if v.is_a?(Hash)
k = v.keys.grep(/regression/).first
unless k.empty?
return v[k]
else
return "no regression key"
end
elsif v.is_a?(Array)
raise "predicted regression value is 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"
else
return v
end
end
# returns prediction confidence if available
def get_prediction_confidence(compound, feature)
v = get_value(compound, feature)
if v.is_a?(Hash)
k = v.keys.grep(/confidence/).first
unless k.empty?
#if v.has_key?(:confidence)
return v[k].abs
#return v["http://ot-dev.in-silico.ch/model/lazar#confidence"].abs
else
# PENDING: return nil isntead of raising an exception
raise "no confidence key"
end
else
LOGGER.warn "no confidence for compound: "+compound.to_s+", feature: "+feature.to_s
return 1
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]
return nil if v == nil # missing values for all features
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
return nil #missing value
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 = {} unless @data
@owl.load_dataset_feature_values(@compounds, @data, @dirty_features)
@dirty_features.clear
end
end
# overwrite to yaml:
# in case dataset is loaded from owl:
# * load all values
def to_yaml
# loads all features
if ((defined? @dirty_features) && @dirty_features.size > 0)
load_feature_values
end
super
end
# * remove @owl from yaml, not necessary
def to_yaml_properties
super - ["@owl"]
end
# saves (changes) as new dataset in dataset service
# returns uri
# uses to yaml method (which is overwritten)
def save
OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type => "application/x-yaml"},self.to_yaml).strip
end
end
end
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