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=begin
* Name: dataset.rb
* Description: Dataset SPARQL tools
* Author: Andreas Maunz <andreas@maunz.de>
* Date: 10/2012
=end
module OpenTox
class Dataset
# Load features via SPARQL (fast)
# @param [String] uri Dataset URI
# @return [Array] features OpenTox::Features in order
def self.find_features_sparql(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 properties via SPARQL (fast)
# @param [Array] uris URIs (assumed ordered)
# @param [Hash] properties Properties (keys: user-defined identifier, values: rdf identifier as strings)
# @return [Array] types Properties in order of URIs
def self.find_props_sparql(uris, props)
selects = props.keys
conditions = selects.collect{ |k|
"<#{props[k]}> ?#{k.to_s}"
}
h={}
uris.each{ |uri|
sparql = "SELECT ?id #{selects.collect{|k| "?#{k.to_s}"}.join(" ")} FROM <#{uri}> WHERE { ?id #{conditions.join(";")} }"
res = OpenTox::Backend::FourStore.query(sparql, "text/uri-list")
res.split("\n").inject(h){ |h,row|
values = row.split("\t")
id=values.shift
h[id] = {}
values.each_with_index { |val,idx|
h[id][selects[idx]] = [] unless h[id][selects[idx]]
h[id][selects[idx]] << val.to_s
}
h
}
}
h
end
# Load compounds via SPARQL (fast)
# @param [String] uri Dataset URI
# @return [Array] compounds Compounds in order
def self.find_compounds_sparql(uri)
sparql = "SELECT DISTINCT ?compound FROM <#{uri}> WHERE {
?compound <#{RDF.type}> <#{RDF::OT.Compound}> ;
<#{RDF::OLO.index}> ?cidx;
} 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] uri Dataset uri
# @return [Array] entries Data entries, ordered primarily over cols and secondarily over rows
def self.find_data_entries_sparql(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 ?fidx ?cidx"
OpenTox::Backend::FourStore.query(sparql,"text/uri-list").split("\n").collect { |val| val.strip }
end
end
end
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