Class: PubliSci::Readers::RMatrix

Inherits:
Object
  • Object
show all
Includes:
Dataset::DataCube
Defined in:
lib/bio-publisci/readers/r_matrix.rb

Instance Method Summary collapse

Methods included from Dataset::DataCube

#abbreviate_known, #code_lists, #component_gen, #component_specifications, #concept_codes, #data_structure_definition, #dataset, #defaults, #dimension_properties, #encode_data, #generate, #generate_resources, #measure_properties, #observations, #prefixes, #vocabulary

Methods included from Parser

#add_node, #bnode_value, #encode_value, #get_ary, #get_hashes, #is_complex?, #is_uri?, #load_string, #observation_hash, #sanitize, #sanitize_hash, #strip_prefixes, #strip_uri, #to_literal, #to_resource, #turtle_indent

Instance Method Details

#codes(client, var, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 100

def codes(client, var, options={})
	[]
end

#dimensions(client, var, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 95

def dimensions(client, var, options={})
	# dimension_properties([""],var)
	[]
end

#generate_n3(client, var, outfile_base, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 12

def generate_n3(client, var, outfile_base, options={})
	meas = measures(client,var,options)
	dim = dimensions(client,var,options)
	codes = codes(client,var,options)

	outvar = sanitize([var]).first

	probes_per_file = options[:probes_per_file] || 100
	col_select = "colnames"
	col_select = "names" if options[:type] == :dataframe

	#write structure
	open(outfile_base+'_structure.ttl','w'){|f| f.write structure(client,var,outvar,options)}

	probes=client.eval("#{col_select}(#{var})").to_ruby
	if probes == nil
		client.eval("colnames(#{var})=1:ncol(#{var})")
		probes=client.eval("#{col_select}(#{var})").to_ruby
	end
	markers = rows(client,var,options)

     if options[:print]
         puts prefixes(var,options)
     end

     if options[:output] == :string
         str = prefixes(var,options)
     end

	probes.each_with_index{|probe,i|
		#write prefixes and erase old file on first run
       unless options[:print] || options[:output] == :string
				open(outfile_base+"_#{i/probes_per_file}.ttl",'w'){|f| f.write prefixes(var,options)} if i % probes_per_file == 0
       end
		i+=1
		obs_data = observation_data(client,var,i,markers,options)
		labels = labels_for(client,var,probe)

		# labels = sanitize(labels)
		# return obs_data
       if options[:print]
         observations(meas,dim,codes,obs_data,labels,outvar,options).each{|obs| puts obs}
       end

       if options[:output] == :string
         observations(meas,dim,codes,obs_data,labels,outvar,options).each{|obs| str << obs}
       end

       unless options[:print] || options[:output] == :string
				open(outfile_base+"_#{i/probes_per_file}.ttl",'a'){|f| observations(meas,dim,codes,obs_data,labels,outvar,options).map{|obs| f.write obs}}
				puts "#{i}/#{probes.size}" unless options[:quiet]
       end
	}

     if options[:output] == :string
       str
     end
end

#labels_for(connection, var, probe_id, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 104

def labels_for(connection,var,probe_id,options={})
	row_names = connection.eval("row.names(#{var})")
	# row_names = ([email protected]_ruby.size).to_a unless row_names.first
	if row_names == connection.eval('NULL')
		row_names = (1..connection.eval("nrow(#{var})").payload.first).to_a
	else
		row_names = row_names.payload
	end

    labels = (1..(row_names.size)).to_a.map(&:to_s)
    labels = labels.map{|l|
    	l.insert(0,probe_id.to_s + "_")
    }

    labels
end

#measures(client, var, options = {}) ⇒ Object

for now just make everything a measure



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 86

def measures(client, var, options={})
	if options[:measures]
			options[:measures]
	else
		["probe","marker","value"]
	end
	# measure_properties(measures,var,options)
end

#observation_data(client, var, probe_number, row_names, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 132

def observation_data(client, var, probe_number, row_names, options={})

	data = {}
	# geno_chr = client.eval("#{var}$geno$'#{chr}'")
	# n_individuals = client.eval("#{var}$pheno[[1]]").to_ruby.size
	# entries_per_individual = @rexp.payload["geno"].payload[row_individ].payload["map"].payload.size * @rexp.payload["geno"].payload.names.size
	col_label = "probe"
	row_label = "marker"
	val_label = "value"

	if options[:measures]
		col_label = options[:measures][0] || "probe"
		row_label = options[:measures][1] || "marker"
		val_label = options[:measures][2] || "value"
	end

	data["#{col_label}"] = []
	data["#{row_label}"] = []
	data["#{val_label}"] = []

	# n_individuals.times{|row_individ|
		# puts "#{row_individ}/#{n_individuals}"

	col_select = "colnames"
	col_select = "names" if options[:type] == :dataframe

	if options[:type] == :dataframe
		probe_obj = client.eval("#{var}[[#{probe_number}]]").to_ruby
	else
		probe_obj = client.eval("#{var}[,#{probe_number}]").to_ruby
	end
	# puts probe_obj
	probe_id = client.eval("#{col_select}(#{var})[[#{probe_number}]]").to_ruby
	data["#{col_label}"] = (1..(probe_obj.size)).to_a.fill(probe_id)
	probe_obj.each_with_index{|lod,i|
		data["#{row_label}"] << row_names[i]
		data["#{val_label}"] << lod
	}

	data.map{|k,v| v.flatten!}
	data
end

#rows(connection, var, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 121

def rows(connection,var,options={})
	row_names = connection.eval("row.names(#{var})")
	#hacky solution because rserve client's .to_ruby method doesn't fully work
	if row_names == connection.eval('NULL')
		row_names = (1..connection.eval("nrow(#{var})").payload.first).to_a
	else
		row_names = row_names.payload
	end
    row_names
end

#structure(client, var, outvar, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/r_matrix.rb', line 71

def structure(client,var,outvar,options={})
	meas = measures(client,var,options)
	dim = dimensions(client,var,options)
	codes = codes(client,var,options)

	str = prefixes(var, options)
	str << data_structure_definition(meas,[],codes,outvar,options)
	str << dataset(outvar,options)
 		component_specifications(meas, dim, codes, var, options).map{ |c| str << c }
	measure_properties(meas,var,options).map{|m| str << m}

	str
end