Class: QTL2RDF

Inherits:
Object
  • Object
show all
Defined in:
lib/r2rdf.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dir = '.') ⇒ QTL2RDF

Returns a new instance of QTL2RDF.



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# File 'lib/r2rdf.rb', line 9

def initialize(dir='.')
  @dir = File.absolute_path(dir)
  @R = Rserve::Connection.new()
  if File.exist?(dir + "/.RData")
    # puts "loading workspace #{dir}/.RData"
    @R.eval("load('#{dir}/.RData')")
  end

  if File.exist?(dir + "/.Rhistory")
    # puts "loading history #{dir}/.Rhistory"
    @R.eval("loadhistory('#{dir}/.Rhistory')")
  end

  @port_4s = 8080
end

Instance Attribute Details

#port_4s ⇒ Object

Returns the value of attribute port_4s.



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# File 'lib/r2rdf.rb', line 7

def port_4s
  @port_4s
end

Instance Method Details

#dump(var) ⇒ Object 



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# File 'lib/r2rdf.rb', line 68

def dump(var)
  x = @R.eval(var)
  if x.attr
    # if x.attr.payload["class"].to_a.include? 'data.frame'
      dump_dataframe var
    # end
  else
    if x.list?
      type = x.payload.class.to_s.split("::").last # seems hacky, but probably only temporary
      value = x.payload.map(&:payload).flatten
    elsif x.payload.size == 1
      type = x.class.to_s.split("::").last 
      value = x.payload.first
    else
      type = x.class.to_s.split("::").last 
      value = x.payload
    end
    {var => {"attr"=>{"class" => type}, :value => value}}
  end
end

#dump_dataframe(var) ⇒ Object 



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# File 'lib/r2rdf.rb', line 45

def dump_dataframe(var)
  h = {}
  h[var] = {"attr" => {}, "rows"=>{}}

  x = @R.eval(var)

  x.attr.payload.keys.map{ |a|
    h[var]["attr"][a] = x.attr.payload[a].to_ruby
  }

  rownames = x.attr.payload["row.names"].to_ruby
  colnames = x.payload.keys
  rownames.each_with_index.map{ |row,i|
    rh = {}
    colnames.map{ |col|
      rh[col] = x.payload[col].to_a[i].to_f
    }
    h[var]["rows"][row] = rh
  }

  h
end

#load_history(dir = @dir, file = '.Rhistory') ⇒ Object 



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# File 'lib/r2rdf.rb', line 35

def load_history(dir=@dir,file='.Rhistory')
  path = File.join(File.absolute_path(dir),file)
  if File.exist?(path)
    # puts "loading history #{dir}/.Rhistory"
    @R.eval("loadhistory('#{path}')")
  else
    puts "Couldn't find #{path}"
  end
end

#load_statements(statements) ⇒ Object 



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# File 'lib/r2rdf.rb', line 208

def load_statements(statements)
  #maybe a better way than inserting statements one at a time?
  repo = RDF::FourStore::Repository.new("http://localhost:#{@port_4s}")
  statements.each{|s| repo.insert(s)}
end

#load_workspace(dir = @dir, file = '.RData') ⇒ Object 



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# File 'lib/r2rdf.rb', line 25

def load_workspace(dir=@dir,file='.RData')
  path = File.join(File.absolute_path(dir),file)
    if File.exist?(path)
      # puts "loading workspace #{dir}/.RData"
      @R.eval("load('#{path}')")
    else
      puts "Couldn't find #{path}"
    end
end

#n3_for(h) ⇒ Object

get n3 for a dataframe using datacube vocabulary still needs range for measures and dimensions, sdmx-dimension equivalent for rows



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# File 'lib/r2rdf.rb', line 133

def n3_for(h)
  str = <<-EOF
@prefix : <http://www.rqtl.org/ns/#> .
@prefix qb: <http://purl.org/linked-data/cube#> .
@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix prop: <http://www.rqtl.org/dc/properties/> .
@prefix cs: <http://www.rqtl.org/dc/cs/> .

  EOF
  #@prefix sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#>
  var = h.keys.first
  names = h[var]["attr"]["names"]

  #generate data structure definition
  str << ":dsd-#{var} a qb:DataStructureDefinition ;\n"
  str << "\tqb:component cs:refRow ,\n"
  names.map{ |n|
    str << "\t\tcs:#{n} ,\n\n"
  }
  str[-3]="."

  #generate component specifications
  str << "cs:refRow a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for Row\" ;\n\tqb:dimension prop:refRow .\n\n"
  names.map{ |n|
    str << "cs:#{n} a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for #{n}\" ;\n\tqb:measure prop:#{n} .\n\n"
  }

  #generate dataset definition
  str << ":dataset-#{var} a qb:DataSet ;\n\trdfs:label \"#{var}\"@en ;\n\tqb:structure :dsd-#{var} .\n\n"

  #add DimensionProperty for row
  str << <<-EOF
:refRow a rdf:Property, qb:DimensionProperty ;
\trdfs:label "Row"@en .

  EOF

  #generate MeasureProperties
  names.map{ |n|
    str << ":#{n} a rdf:Property, qb:MeasureProperty ;\n\trdfs:label \"#{n}\"@en .\n\n"
  }

  #add observations
  h[var]["rows"].map{|k,v|
    str << ":obs#{k} a qb:Observation ;\n\tqb:dataSet :dataset-#{var} ;\n\tprop:refRow :#{k} ;\n"
    v.map{|l,w|
      str << "\tprop:#{l} #{w} ;\n"
    }
    str << "\t.\n\n"
  }

  #add row property definitions
  h[var]["rows"].map{|k,v|
    str << ":#{k} a prop:refRow ;\n\trdfs:label \"#{k}\" .\n\n"
  }

  str
end

#statements_for(string, type = :turtle) ⇒ Object 



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# File 'lib/r2rdf.rb', line 193

def statements_for(string,type=:turtle)
  statements = []
  RDF::Reader.for(:turtle).new(string) do |reader|
    reader.each_statement do |statement|
      # puts statement.inspect
      statements << statement
    end
  end
  statements
end

#to_store(var, parse_type = :turtle) ⇒ Object 



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# File 'lib/r2rdf.rb', line 214

def to_store(var, parse_type=:turtle)
  load_statements(triples_for(dump(var))) if parse_type==:ntriples
  
  #TODO: this doesn't work (needs to be converted to statments or 
  # a way of inserting raw strings needs to be figured out.
  load_statements(n3_for(dump(var))) if parse_type==:turtle
end

#triples_for(h) ⇒ Object 



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# File 'lib/r2rdf.rb', line 89

def triples_for(h)
  statements = []
  base_n = RDF::Node.new
  attr_n = RDF::Node.new
  vocab = RDF::Vocabulary.new('http://www.placeholder.com/rqtl#')
  base_uri = RDF::URI.new('http://www.placeholder.com/')
  var = h.keys.first

  statements << RDF::Statement.new(base_n, RDF::DC.title, RDF::Literal.new(var))

  if h[var].is_a? Hash
    if(h[var]["attr"])
      statements << RDF::Statement.new(base_n, vocab.attributes, attr_n)
      h[var]["attr"].map{ |k,v| statements << RDF::Statement.new(attr_n, vocab[k], RDF::Literal.new(v)) }
    end

    if h[var]["rows"]
      h[var]["rows"].map{ |k,v|
        row_uri = base_uri.join("row#{k}")
        statements << RDF::Statement.new(row_uri, vocab.row_of, base_n)
        statements << RDF::Statement.new(row_uri, RDF::DC.title, k)
        num = 1 # maybe container support exists in RDF.rb?
        v.map { |j,u|
          n = RDF::Node.new
          statements << RDF::Statement.new(n, vocab.entry_of, row_uri)
          statements << RDF::Statement.new(n, RDF::DC.title, j)
          statements << RDF::Statement.new(n, RDF::DC.title, j)
          statements << RDF::Statement.new(n, vocab["_#{num}"], RDF::Literal.new(u))
          num += 1
        }
      }
    end

    if h[var].has_key? :value        
      statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var][:value]))
    end
  else
    statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var]))
  end
  statements
end

#turtletype_for(value) ⇒ Object 



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# File 'lib/r2rdf.rb', line 204

def turtletype_for(value)
  #use for providing ranges to better define data (later)
end

#vars ⇒ Object 



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# File 'lib/r2rdf.rb', line 222

def vars
  @R.eval("ls()").payload
end