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module OpenTox
# Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
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
@features = {}
@compounds = []
@data_entries = {}
end
# Create an empty dataset and save it at the dataset service (assigns URI to dataset)
# @example Create new dataset and save it to obtain a URI
# dataset = OpenTox::Dataset.create
# @param [optional, String] uri Dataset URI
# @return [OpenTox::Dataset] Dataset object
def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
dataset = Dataset.new(nil,subjectid)
dataset.save(subjectid)
dataset
end
# Create dataset from CSV file (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] file CSV file path
# @return [OpenTox::Dataset] Dataset object with CSV data
def self.create_from_csv_file(file, subjectid=nil)
dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
parser = Parser::Spreadsheets.new
parser.dataset = dataset
parser.load_csv(File.open(file).read)
dataset.save(subjectid)
dataset
end
# Find a dataset and load all data. This can be time consuming, use Dataset.new together with one of the load_* methods for a fine grained control over data loading.
# @param [String] uri Dataset URI
# @return [OpenTox::Dataset] Dataset object with all data
def self.find(uri, subjectid=nil)
return nil unless uri
dataset = Dataset.new(uri, subjectid)
dataset.load_all(subjectid)
dataset
end
# replaces find as exist check, takes not as long, does NOT raise an un-authorized exception
# @param [String] uri Dataset URI
# @return [Boolean] true if dataset exists and user has get rights, false else
def self.exist?(uri, subjectid=nil)
return false unless uri
dataset = Dataset.new(uri, subjectid)
begin
dataset.load_metadata( subjectid ).size > 0
rescue
false
end
end
# Get all datasets from a service
# @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration
# @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server)
def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil)
RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u, subjectid)}
end
# Load YAML representation into the dataset
# @param [String] yaml YAML representation of the dataset
# @return [OpenTox::Dataset] Dataset object with YAML data
def load_yaml(yaml)
copy YAML.load(yaml)
end
def load_rdfxml(rdfxml)
raise "rdfxml data is empty" if rdfxml.to_s.size==0
file = Tempfile.new("ot-rdfxml")
file.puts rdfxml
file.close
load_rdfxml_file file
file.delete
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 load_rdfxml_file(file, subjectid=nil)
parser = Parser::Owl::Dataset.new @uri, subjectid
parser.uri = file.path
copy parser.load_uri(subjectid)
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 load_csv(csv, subjectid=nil)
save(subjectid) unless @uri # get a uri for creating features
parser = Parser::Spreadsheets.new
parser.dataset = self
parser.load_csv(csv)
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 load_spreadsheet(book, subjectid=nil)
save(subjectid) unless @uri # get a uri for creating features
parser = Parser::Spreadsheets.new
parser.dataset = self
parser.load_spreadsheet(book)
end
# Load and return only metadata of a Dataset object
# @return [Hash] Metadata of the dataset
def load_metadata(subjectid=nil)
add_metadata Parser::Owl::Dataset.new(@uri, subjectid).load_metadata(subjectid)
self.uri = @uri if @uri # keep uri
@metadata
end
# Load all data (metadata, data_entries, compounds and features) from URI
def load_all(subjectid=nil)
if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid}))
else
parser = Parser::Owl::Dataset.new(@uri, subjectid)
copy parser.load_uri(subjectid)
end
end
# Load and return only compound URIs from the dataset service
# @return [Array] Compound URIs in the dataset
def load_compounds(subjectid=nil)
RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri|
@compounds << compound_uri.chomp
end
@compounds.uniq!
end
# Load and return only features from the dataset service
# @return [Hash] Features of the dataset
def load_features(subjectid=nil)
parser = Parser::Owl::Dataset.new(@uri, subjectid)
@features = parser.load_features(subjectid)
@features
end
# Detect feature type(s) in the dataset
# @return [String] `classification", "regression", "mixed" or unknown`
def feature_type
feature_types = @features.collect{|f,metadata| metadata[OT.isA]}.uniq
if feature_types.size > 1
"mixed"
else
case feature_types.first
when /NominalFeature/
"classification"
when /NumericFeature/
"regression"
else
"unknown"
end
end
end
# Get Spreadsheet representation
# @return [Spreadsheet::Workbook] Workbook which can be written with the spreadsheet gem (data_entries only, metadata will will be discarded))
def to_spreadsheet
Serializer::Spreadsheets.new(self).to_spreadsheet
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
to_spreadsheet
end
# Get CSV string representation (data_entries only, metadata will be discarded)
# @return [String] CSV representation
def to_csv
Serializer::Spreadsheets.new(self).to_csv
end
# Get OWL-DL in ntriples format
# @return [String] N-Triples representation
def to_ntriples
s = Serializer::Owl.new
s.add_dataset(self)
s.to_ntriples
end
# Get OWL-DL in RDF/XML format
# @return [String] RDF/XML representation
def to_rdfxml
s = Serializer::Owl.new
s.add_dataset(self)
s.to_rdfxml
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/modify metadata, existing entries will be overwritten
# @example
# dataset.add_metadata({DC.title => "any_title", DC.creator => "my_email"})
# @param [Hash] metadata Hash mapping predicate_uris to values
def add_metadata(metadata)
metadata.each { |k,v| @metadata[k] = v }
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, subjectid=nil)
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|
unless @data_entries[c][f]
dataset.add(c,f,nil)
else
@data_entries[c][f].each do |v|
dataset.add(c,f,v)
end
end
end
end
end
dataset.add_metadata(metadata)
dataset.save(subjectid)
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(subjectid=nil)
# TODO: rewrite feature URI's ??
@compounds.uniq!
if @uri
if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
RestClientWrapper.post(@uri,self.to_yaml,{:content_type => "application/x-yaml", :subjectid => subjectid})
else
File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp
#task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset`
Task.find(task_uri).wait_for_completion
self.uri = RestClientWrapper.get(task_uri,{:accept => 'text/uri-list', :subjectid => subjectid})
end
else
# create dataset if uri is empty
self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => subjectid}).to_s.chomp
end
@uri
end
# Delete dataset at the dataset service
def delete(subjectid=nil)
RestClientWrapper.delete(@uri, :subjectid => subjectid)
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
# Class with special methods for lazar prediction datasets
class LazarPrediction < Dataset
# Find a prediction dataset and load all data.
# @param [String] uri Prediction dataset URI
# @return [OpenTox::Dataset] Prediction dataset object with all data
def self.find(uri, subjectid=nil)
prediction = LazarPrediction.new(uri, subjectid)
prediction.load_all(subjectid)
prediction
end
def value(compound)
@data_entries[compound.uri].collect{|f,v| v.first if f.match(/prediction/)}.compact.first
end
def confidence(compound)
feature_uri = @data_entries[compound.uri].collect{|f,v| f if f.match(/prediction/)}.compact.first
@features[feature_uri][OT.confidence]
end
def descriptors(compound)
@data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/descriptor/)}.compact if @data_entries[compound.uri]
end
def measured_activities(compound)
source = @metadata[OT.hasSource]
@data_entries[compound.uri].collect{|f,v| v if f.match(/#{source}/)}.compact.flatten
end
def neighbors(compound)
@data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/neighbor/)}.compact
end
# def errors(compound)
# features = @data_entries[compound.uri].keys
# features.collect{|f| @features[f][OT.error]}.join(" ") if features
# end
end
end
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