Class: PubliSci::Dataset

Inherits:
Object
  • Object
show all
Extended by:
Interactive, Registry
Defined in:
lib/bio-publisci/dataset/dataset.rb,
lib/bio-publisci/dsl/dataset_dsl.rb,
lib/bio-publisci/dataset/data_cube.rb,
lib/bio-publisci/dataset/dataset_for.rb,
lib/bio-publisci/dataset/configuration.rb

Defined Under Namespace

Modules: DSL, DataCube Classes: Configuration

Class Method Summary collapse

Methods included from Interactive

interact

Methods included from Registry

register, registry, symbol_for

Class Method Details

.configuration ⇒ Object 



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# File 'lib/bio-publisci/dataset/dataset.rb', line 6

def self.configuration
  @config ||= Dataset::Configuration.new
end

.download(uri) ⇒ Object 



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# File 'lib/bio-publisci/dataset/dataset_for.rb', line 41

def self.download(uri)
  out = Tempfile.new(uri.split('/').last)
  out.write open(uri).read
  out.close
  out
end

.for(object, options = {}, ask_on_ambiguous = true) ⇒ Object 



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# File 'lib/bio-publisci/dataset/dataset_for.rb', line 6

def self.for(object, options={}, ask_on_ambiguous=true)

  if options == false || options == true
    ask_on_ambiguous = options
    options = {}
  end

  if object.is_a? String
    if File.exist? object
      if File.extname(object).size > 0
        extension = File.extname(object)
      elsif File.basename(object)[0] == '.' && File.basename(object).count('.') == 1
        extension = File.basename(object)
      else
        raise "Can't load file #{object}; type inference not yet implemented"
      end

      case extension
      when ".RData"
        r_object(object, options, ask_on_ambiguous)
      when /.csv/i
        PubliSci::Reader::CSV.new.automatic(object,nil,options,ask_on_ambiguous)
      end
    elsif object =~ %r{http[s]://.+}
      self.for(download(object).path, options, ask_on_ambiguous)
    else
      raise "Unable to find reader for File or String #{object}"
    end
  elsif object.is_a? Rserve::REXP
    r_object(object, options, ask_on_ambiguous)
  else
    raise "not recognize Ruby objects of this type yet (#{object})"
  end
end

.r_object(object, options = {}, ask_on_ambiguous = true) ⇒ Object 



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# File 'lib/bio-publisci/dataset/dataset_for.rb', line 48

def self.r_object(object, options={}, ask_on_ambiguous=true)
  if object.is_a? String
    con = Rserve::Connection.new
    vars = con.eval("load('#{File.absolute_path object}')")
    if vars.to_ruby.size > 1 && ask_on_ambiguous
      puts "Which variable? #{vars.to_ruby}"
      var = vars.to_ruby[gets.to_i]
    else
      var = vars.to_ruby[0]
    end

    r_classes = con.eval("class(#{var})").to_ruby

    if r_classes.include? "data.frame"
      df = PubliSci::Reader::Dataframe.new
      unless options[:dimensions] || !ask_on_ambiguous
        dims = con.eval("names(#{var})").to_ruby
        puts "Which dimensions? #{dims}"
        selection = gets.chomp
        if selection.size > 0
          options[:dimensions] = selection.split(',').map(&:to_i).map{|i| dims[i]}
        end
      end
      unless options[:measures] || !ask_on_ambiguous
        meas = con.eval("names(#{var})").to_ruby
        puts "Which measures? #{meas} "
        selection = gets.chomp
        if selection.size > 0
          options[:measures] = selection.split(',').map(&:to_i).map{|i| meas[i]}
        end
      end

      df.generate_n3(con.eval(var),var,options)

    elsif r_classes.include? "cross"
      bc = PubliSci::Reader::RCross.new

      unless options[:measures] || !ask_on_ambiguous
        pheno_names = con.eval("names(#{var}$pheno)").to_ruby
        puts "Which phenotype traits? #{pheno_names}"
        selection = gets.chomp
        if selection.size > 0
          options[:measures] = selection.split(',').map(&:to_i).map{|i| pheno_names[i]}
        end
      end

      base = var
      if ask_on_ambiguous
        puts "Output file base?"
        base = gets.chomp
        base = var unless base.size > 0
      end

      bc.generate_n3(con, var, base, options)

    elsif r_classes.include? "matrix"
      mat = PubliSci::Reader::RMatrix.new

      unless options[:measures] || !ask_on_ambiguous
        puts "Row label"
        rows = gets.chomp
        rows = "row" unless rows.size > 0

        puts "Column label"
        cols = gets.chomp
        cols = "column" unless cols.size > 0

        puts "Entry label"
        vals = gets.chomp
        vals = "value" unless vals.size > 0

        options[:measures] = [cols,rows,vals]
      end

      base = var
      if ask_on_ambiguous
        puts "Output file base?"
        base = gets.chomp
        base = var unless base.size > 0
      end

      mat.generate_n3(con, var, base, options)
    else
      raise "no PubliSci::Reader found for #{r_classes}"
    end

  elsif object.is_a? Rserve::REXP
    if object.attr.payload["class"].payload.first

      df = PubliSci::Reader::Dataframe.new

      var = nil

      if ask_on_ambiguous
        var = interact("Dataset name?",nil)
      end

      unless options[:dimensions] || !ask_on_ambiguous
        dims = object.payload.names
        selection = interact("Which dimensions?","row",dims){|s| puts s; nil}
        options[:dimensions] = selection if selection
      end

      unless options[:measures] || !ask_on_ambiguous
        meas = object.payload.names
        options[:measures] = interact("Which measures?",meas,meas)
      end

      df.generate_n3(object,var,options)
    else
      raise "support for other Rserve objects coming shortly"
    end

  else
    raise "#{object} is not an R object"
  end
end