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module OpenTox
# Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
# TODO: fix API Doc
class Dataset
#include OpenTox
#attr_reader :features, :compounds, :data_entries, :metadata
# Create dataset with optional URI. Does not load data into the dataset - you will need to execute one of the load_* methods to pull data from a service or to insert it from other representations.
# @example Create an empty dataset
# dataset = OpenTox::Dataset.new
# @example Create an empty dataset with URI
# dataset = OpenTox::Dataset.new("http:://webservices.in-silico/ch/dataset/1")
# @param [optional, String] uri Dataset URI
# @return [OpenTox::Dataset] Dataset object
def initialize(uri=nil,subjectid=nil)
super uri, subjectid
@features = {}
@compounds = []
@data_entries = {}
end
=begin
# Load YAML representation into the dataset
# @param [String] yaml YAML representation of the dataset
# @return [OpenTox::Dataset] Dataset object with YAML data
def self.from_yaml service_uri, yaml, subjectid=nil
Dataset.create(service_uri, subjectid).post yaml, :content_type => "application/x-yaml"
end
# Load RDF/XML representation from a file
# @param [String] file File with RDF/XML representation of the dataset
# @return [OpenTox::Dataset] Dataset object with RDF/XML data
def self.from_rdfxml service_uri, rdfxml, subjectid=nil
Dataset.create(service_uri, subjectid).post rdfxml, :content_type => "application/rdf+xml"
end
# Load CSV string (format specification: http://toxcreate.org/help)
# - loads data_entries, compounds, features
# - sets metadata (warnings) for parser errors
# - you will have to set remaining metadata manually
# @param [String] csv CSV representation of the dataset
# @return [OpenTox::Dataset] Dataset object with CSV data
def self.from_csv service_uri, csv, subjectid=nil
Dataset.from_file(service_uri, csv, subjectid)
end
# Load Spreadsheet book (created with roo gem http://roo.rubyforge.org/, excel format specification: http://toxcreate.org/help)
# - loads data_entries, compounds, features
# - sets metadata (warnings) for parser errors
# - you will have to set remaining metadata manually
# @param [Excel] book Excel workbook object (created with roo gem)
# @return [OpenTox::Dataset] Dataset object with Excel data
def self.from_xls service_uri, xls, subjectid=nil
Dataset.create(service_uri, subjectid).post xls, :content_type => "application/vnd.ms-excel"
end
def self.from_sdf service_uri, sdf, subjectid=nil
Dataset.create(service_uri, subjectid).post sdf, :content_type => 'chemical/x-mdl-sdfile'
end
=end
# Load all data (metadata, data_entries, compounds and features) from URI
# TODO: move to opentox-server
def data_entries reload=true
if reload
file = Tempfile.new("ot-rdfxml")
file.puts get :accept => "application/rdf+xml"
file.close
to_delete = file.path
data = {}
feature_values = {}
feature = {}
feature_accept_values = {}
other_statements = {}
`rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line|
triple = line.chomp.split(' ',3)
triple = triple[0..2].collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')}
case triple[1]
when /#{RDF::OT.values}|#{RDF::OT1.values}/i
data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
data[triple[0]][:values] << triple[2]
when /#{RDF::OT.value}|#{RDF::OT1.value}/i
feature_values[triple[0]] = triple[2]
when /#{RDF::OT.compound}|#{RDF::OT1.compound}/i
data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
data[triple[0]][:compound] = triple[2]
when /#{RDF::OT.feature}|#{RDF::OT1.feature}/i
feature[triple[0]] = triple[2]
when /#{RDF.type}/i
if triple[2]=~/#{RDF::OT.Compound}|#{RDF::OT1.Compound}/i and !data[triple[0]]
data[triple[0]] = {:compound => triple[0], :values => []}
end
when /#{RDF::OT.acceptValue}|#{RDF::OT1.acceptValue}/i # acceptValue in ambit datasets is only provided in dataset/<id> no in dataset/<id>/features
feature_accept_values[triple[0]] = [] unless feature_accept_values[triple[0]]
feature_accept_values[triple[0]] << triple[2]
else
end
end
File.delete(to_delete) if to_delete
data.each do |id,entry|
if entry[:values].size==0
# no feature values add plain compounds
@compounds << entry[:compound] unless @compounds.include? entry[:compound]
else
entry[:values].each do |value_id|
if feature_values[value_id]
split = feature_values[value_id].split(/\^\^/)
case split[-1]
when RDF::XSD.double, RDF::XSD.float
value = split.first.to_f
when RDF::XSD.boolean
value = split.first=~/(?i)true/ ? true : false
else
value = split.first
end
end
@compounds << entry[:compound] unless @compounds.include? entry[:compound]
@features[feature[value_id][value_id]] = {} unless @features[feature[value_id]]
@data_entries[entry[:compound].to_s] = {} unless @data_entries[entry[:compound].to_s]
@data_entries[entry[:compound].to_s][feature[value_id]] = [] unless @data_entries[entry[:compound]][feature[value_id]]
@data_entries[entry[:compound].to_s][feature[value_id]] << value if value!=nil
end
end
end
features subjectid
#feature_accept_values.each do |feature, values|
#self.features[feature][OT.acceptValue] = values
#end
self.metadata = metadata(subjectid)
end
@data_entries
end
# Load and return only compound URIs from the dataset service
# @return [Array] Compound URIs in the dataset
def compounds reload=true
reload ? @compounds = Compound.all(File.join(@uri,"compounds")) : @compounds
end
# Load and return only features from the dataset service
# @return [Hash] Features of the dataset
def features reload=true
reload ? @features = Feature.all(File.join(@uri,"features")) : @features
end
=begin
# returns the accept_values of a feature, i.e. the classification domain / all possible feature values
# @param [String] feature the URI of the feature
# @return [Array] return array with strings, nil if value is not set (e.g. when feature is numeric)
def accept_values(feature)
load_features
accept_values = features[feature][OT.acceptValue]
accept_values.sort if accept_values
accept_values
end
# Detect feature type(s) in the dataset
# @return [String] `classification", "regression", "mixed" or unknown`
def feature_type
load_features
feature_types = @features.collect{|f,metadata| metadata[RDF.type]}.flatten.uniq
if feature_types.include?(OT.NominalFeature)
"classification"
elsif feature_types.include?(OT.NumericFeature)
"regression"
else
"unknown"
end
end
=end
# Get Excel representation (alias for to_spreadsheet)
# @return [Spreadsheet::Workbook] Workbook which can be written with the spreadsheet gem (data_entries only, metadata will will be discarded))
def to_xls
get :accept => "application/vnd.ms-excel"
end
# Get CSV string representation (data_entries only, metadata will be discarded)
# @return [String] CSV representation
def to_csv
get :accept => "text/csv"
end
def to_sdf
get :accept => 'chemical/x-mdl-sdfile'
end
# Get OWL-DL in ntriples format
# @return [String] N-Triples representation
def to_ntriples
get :accept => "application/rdf+xml"
end
# Get OWL-DL in RDF/XML format
# @return [String] RDF/XML representation
def to_rdfxml
get :accept => "application/rdf+xml"
end
# Get name (DC.title) of a feature
# @param [String] feature Feature URI
# @return [String] Feture title
def feature_name(feature)
features[feature][DC.title]
end
def title
metadata[DC.title]
end
# Insert a statement (compound_uri,feature_uri,value)
# @example Insert a statement (compound_uri,feature_uri,value)
# dataset.add "http://webservices.in-silico.ch/compound/InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9", "http://webservices.in-silico.ch/dataset/1/feature/hamster_carcinogenicity", true
# @param [String] compound Compound URI
# @param [String] feature Compound URI
# @param [Boolean,Float] value Feature value
def add (compound,feature,value)
@compounds << compound unless @compounds.include? compound
@features[feature] = {} unless @features[feature]
@data_entries[compound] = {} unless @data_entries[compound]
@data_entries[compound][feature] = [] unless @data_entries[compound][feature]
@data_entries[compound][feature] << value if value!=nil
end
# Add a feature
# @param [String] feature Feature URI
# @param [Hash] metadata Hash with feature metadata
def add_feature(feature,metadata={})
@features[feature] = metadata
end
# Add/modify metadata for a feature
# @param [String] feature Feature URI
# @param [Hash] metadata Hash with feature metadata
def add_feature_metadata(feature,metadata)
metadata.each { |k,v| @features[feature][k] = v }
end
# Add a new compound
# @param [String] compound Compound URI
def add_compound (compound)
@compounds << compound unless @compounds.include? compound
end
# Creates a new dataset, by splitting the current dataset, i.e. using only a subset of compounds and features
# @param [Array] compounds List of compound URIs
# @param [Array] features List of feature URIs
# @param [Hash] metadata Hash containing the metadata for the new dataset
# @param [String] subjectid
# @return [OpenTox::Dataset] newly created dataset, already saved
def split( compounds, features, metadata)
LOGGER.debug "split dataset using "+compounds.size.to_s+"/"+@compounds.size.to_s+" compounds"
raise "no new compounds selected" unless compounds and compounds.size>0
dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"],@subjectid)
if features.size==0
compounds.each{ |c| dataset.add_compound(c) }
else
compounds.each do |c|
features.each do |f|
if @data_entries[c]==nil or @data_entries[c][f]==nil
dataset.add(c,f,nil)
else
@data_entries[c][f].each do |v|
dataset.add(c,f,v)
end
end
end
end
end
# set feature metadata in new dataset accordingly (including accept values)
features.each do |f|
self.features[f].each do |k,v|
dataset.features[f][k] = v
end
end
dataset.add_metadata(metadata)
dataset.save
dataset
end
# Save dataset at the dataset service
# - creates a new dataset if uri is not set
# - overwrites dataset if uri exists
# @return [String] Dataset URI
def save
@compounds.uniq!
# create dataset if uri is empty
self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => @subjectid}).to_s.chomp unless @uri
if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
RestClientWrapper.post(@uri,self.to_yaml,{:content_type => "application/x-yaml", :subjectid => @subjectid})
else
s = Serializer::Owl.new
s.add_dataset(self)
RestClientWrapper.post(@uri, s.to_rdfxml,{:content_type => "application/rdf+xml" , :subjectid => @subjectid})
end
@uri
end
private
# Copy a dataset (rewrites URI)
def copy(dataset)
@metadata = dataset.metadata
@data_entries = dataset.data_entries
@compounds = dataset.compounds
@features = dataset.features
if @uri
self.uri = @uri
else
@uri = dataset.metadata[XSD.anyURI]
end
end
end
end
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