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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
# Load features via SPARQL (fast)
# @param [String] Dataset URI
# @return [Array] Features in order
def self.find_features(uri)
sparql = "SELECT DISTINCT ?s FROM <#{uri}> WHERE {
?s <#{RDF.type}> <#{RDF::OT.Feature}> ;
<#{RDF::OLO.index}> ?fidx
} ORDER BY ?fidx"
OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Feature.new uri.strip }
end
# Load compounds via SPARQL (fast)
# @param [String] Dataset URI
# @return [Array] Compounds in order
def self.find_compounds(uri)
sparql = "SELECT DISTINCT ?compound FROM <#{uri}> WHERE {
?s <#{RDF.type}> <#{RDF::OT.DataEntry}> ;
<#{RDF::OLO.index}> ?cidx;
<#{RDF::OT.compound}> ?compound
} ORDER BY ?cidx"
OpenTox::Backend::FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Compound.new uri.strip }
end
# Load data entries via SPARQL (fast)
# @param [String] Dataset uri
# @return [Array] Data entries, ordered primarily over rows and secondarily over cols
def self.find_data_entries(uri)
sparql = "SELECT ?value FROM <#{uri}> WHERE {
?data_entry <#{RDF::OLO.index}> ?cidx ;
<#{RDF::OT.values}> ?v .
?v <#{RDF::OT.feature}> ?f;
<#{RDF::OT.value}> ?value .
?f <#{RDF::OLO.index}> ?fidx.
} ORDER BY ?cidx ?fidx"
OpenTox::Backend::FourStore.query(sparql,"text/uri-list").split("\n").collect { |val| val.strip }
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
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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