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|
=begin
* Name: dataset.rb
* Description: Dataset shims
* Author: Andreas Maunz <andreas@maunz.de>
* Date: 10/2012
=end
module OpenTox
# Shims for the Dataset Class
class Dataset
attr_accessor :feature_positions, :compound_positions
# Load a dataset from URI
# @param [String] Dataset URI
# @return [OpenTox::Dataset] Dataset object
def self.find(uri, subjectid=nil)
return nil unless uri
ds = OpenTox::Dataset.new uri, subjectid
ds.get
ds
end
def self.exist?(uri, subjectid=nil)
ds = OpenTox::Dataset.new uri, subjectid
begin
ds.get_metadata
true
rescue
false
end
end
def split( compound_indices, feats, metadata, subjectid=nil)
raise "Dataset.split : pls give compounds as indices" if compound_indices.size==0 or !compound_indices[0].is_a?(Fixnum)
raise "Dataset.split : pls give features as feature objects (given: #{feats})" if feats!=nil and feats.size>0 and !feats[0].is_a?(OpenTox::Feature)
$logger.debug "split dataset using "+compound_indices.size.to_s+"/"+@compounds.size.to_s+" compounds"
dataset = OpenTox::Dataset.new(nil, subjectid)
dataset.metadata = metadata
dataset.features = (feats ? feats : self.features)
compound_indices.each do |c_idx|
dataset << [ self.compounds[c_idx] ] + dataset.features.each_with_index.collect{|f,f_idx| self.data_entries[c_idx][f_idx]}
end
#compound_indices.each do |c_idx|
# c = @compounds[c_idx]
# dataset.add_compound(c)
# if @data_entries[c]
# features.each do |f|
# if @data_entries[c][f]
# dataset.add_data_entry c,f,@data_entries[c][f][entry_index(c_idx)]
# else
# dataset.add_data_entry c,f,nil
# end
# end
# end
# end
dataset.put subjectid
dataset
end
# maps a compound-index from another dataset to a compound-index from this dataset
# mapping works as follows:
# (compound c is the compound identified by the compound-index of the other dataset)
# * c occurs only once in this dataset? map compound-index of other dataset to index in this dataset
# * c occurs >1 in this dataset?
# ** number of occurences is equal in both datasets? assume order is preserved(!) and map accordingly
# ** number of occurences is not equal in both datasets? cannot map, raise error
# @param [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded)
# @param [Fixnum] compound_index, corresponding to dataset
def compound_index( dataset, compound_index )
unless defined?(@index_map) and @index_map[dataset.uri]
map = {}
dataset.compounds.collect{|c| c.uri}.uniq.each do |compound|
self_indices = compound_indices(compound)
next unless self_indices
dataset_indices = dataset.compound_indices(compound)
if self_indices.size==1
dataset_indices.size.times do |i|
map[dataset_indices[i]] = self_indices[0]
end
elsif self_indices.size==dataset_indices.size
# we do assume that the order is preseverd!
dataset_indices.size.times do |i|
map[dataset_indices[i]] = self_indices[i]
end
else
raise "cannot map compound #{compound} from dataset #{dataset.uri} to dataset #{uri}, "+
"compound occurs #{dataset_indices.size} times and #{self_indices.size} times"
end
end
@index_map = {} unless defined?(@index_map)
@index_map[dataset.uri] = map
end
@index_map[dataset.uri][compound_index]
end
def compound_indices( compound )
unless defined?(@cmp_indices) and @cmp_indices.has_key?(compound)
@cmp_indices = {}
@compounds.size.times do |i|
c = @compounds[i].uri
if @cmp_indices[c]==nil
@cmp_indices[c] = [i]
else
@cmp_indices[c] = @cmp_indices[c]+[i]
end
end
end
@cmp_indices[compound]
end
def data_entry_value(compound_index, feature_uri)
build_feature_positions unless @feature_positions
@data_entries[compound_index][@feature_positions[feature_uri]]
end
### Index Structures
# Create value map
# @param [OpenTox::Feature] A feature
# @return [Hash] A hash with keys 1...feature.training_classes.size and values training classes
def value_map(feature)
training_classes = feature.accept_values
raise "no accept values for feature #{feature.uri} in dataset #{uri}" unless training_classes
training_classes.each_index.inject({}) { |h,idx| h[idx+1]=training_classes[idx]; h }
end
# Create feature positions map
# @return [Hash] A hash with keys feature uris and values feature positions
def build_feature_positions
unless @feature_positions
@feature_positions = @features.each_index.inject({}) { |h,idx|
internal_server_error "Duplicate Feature '#{@features[idx].uri}' in dataset '#{@uri}'" if h[@features[idx].uri]
h[@features[idx].uri] = idx
h
}
end
end
# Create compounds positions map
# @return [Hash] A hash with keys compound uris and values compound position arrays
def build_compound_positions
unless @compound_positions
@compound_positions = @compounds.each_index.inject({}) { |h,idx|
inchi=OpenTox::Compound.new(@compounds[idx].uri).inchi
h[inchi] = [] unless h[inchi]
h[inchi] << idx if inchi =~ /InChI/
h
}
end
end
### Associative Search Operations
# Search a dataset for a feature given its URI
# @param [String] Feature URI
# @return [OpenTox::Feature] Feature object, or nil if not present
def find_feature(uri)
build_feature_positions
res = @features[@feature_positions[uri]] if @feature_positions[uri]
res
end
# Search a dataset for a compound given its URI
# @param [String] Compound URI
# @return [OpenTox::Compound] Array of compound objects, or nil if not present
def find_compound(uri)
build_compound_positions
inchi = OpenTox::Compound.new(uri).inchi
res = @compounds[@compound_positions[inchi]] if inchi =~ /InChI/ and @compound_positions[inchi]
res
end
# Search a dataset for a data entry given compound URI and feature URI
# @param [String] Compound URI
# @param [String] Feature URI
# @return [Object] Data entry, or nil if not present
def find_data_entry(compound_uri, feature_uri)
build_compound_positions
build_feature_positions
inchi = OpenTox::Compound.new(compound_uri).inchi
if @compound_positions[inchi] && @feature_positions[feature_uri]
res = []
@compound_positions[inchi].each { |idx|
res << data_entries[idx][@feature_positions[feature_uri]]
}
end
res
end
end
end
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