Class: PubliSci::Reader::CSV

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

Instance Method Summary collapse

Methods included from Interactive

#interact

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

#get_ary, #get_hashes, #is_uri?, #load_string, #observation_hash, #sanitize, #sanitize_hash, #strip_prefixes, #strip_uri, #to_literal, #to_resource

Instance Method Details

#automatic(file = nil, dataset_name = nil, options = {}, interactive = true) ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 7

def automatic(file=nil,dataset_name=nil,options={},interactive=true)
  #to do
  # puts "f #{file} \n ds #{dataset_name} opts #{options}"

  unless file || !interactive
    puts "Input file?"
    file = gets.chomp
  end

  raise "CSV reader needs an input file" unless file && file.size > 0


  unless dataset_name
    if interactive
      dataset_name = interact("Dataset name?","#{File.basename(file).split('.').first}"){|sel| File.basename(file).split('.').first }
    else
      dataset_name = File.basename(file).split('.').first
    end
  end


  categories = ::CSV.read(file)[0]


  unless options[:dimensions] || !interactive
    options[:dimensions] = Array(interact("Dimensions?",categories[0],categories))
  end

  unless options[:measures] || !interactive
    meas = categories - (options[:dimensions] || [categories[0]])
    selection = interact("Measures?",meas,meas){|s| nil}
    options[:measures] = Array(selection) unless selection == nil
  end

  generate_n3(file,dataset_name,options)
end

#codes ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 54

def codes
	@options[:codes] || dimensions()
end

#dimensions ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 50

def dimensions
	@options[:dimensions] || [@data[0][0]]
end

#generate_n3(file, dataset_name, options = {}) ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 44

def generate_n3(file, dataset_name, options={})
	@data = ::CSV.read(file)
	@options = options
	generate(measures, dimensions, codes, observation_data, observation_labels, dataset_name, options)
end

#measures ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 58

def measures
	@options[:measures] || @data[0] - dimensions()
end

#observation_data ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 74

def observation_data
	obs = {}
	@data[0].map{|label|
		obs[label] = []
	}
	tmp = @data.dup
	tmp.shift

	tmp.map{|row|
		row.each_with_index{|entry,i|
			obs[@data[0][i]] << entry
		}
	}
	obs
end

#observation_labels ⇒ Object 



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# File 'lib/bio-publisci/readers/csv.rb', line 62

def observation_labels
	if @options[:label_column]
		tmp = @data.dup
		tmp.shift
		tmp.map{|row|
			row[@options[:label_column]]
		}
	else
		(1..@data.size - 1).to_a
	end
end