Class: PubliSci::Readers::CSV
- Inherits:
-
Base
- Object
- Base
- PubliSci::Readers::CSV
show all
- Defined in:
- lib/bio-publisci/readers/csv.rb
Instance Method Summary
collapse
Methods inherited from Base
#next_label, #sio_attribute, #sio_value
#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
#interact
Methods included from Analyzer
#check_integrity, #dirty?, #recommend_range, #recommend_range_strings
Methods included from Query
#execute, #execute_from_file, #property_names, #property_values, #row_names, #vocabulary
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 4
def automatic(file=nil,dataset_name=nil,options={},interactive=true)
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
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#codes ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 51
def codes
@options[:codes] || dimensions()
end
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#dimensions ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 47
def dimensions
@options[:dimensions] || [@data[0][0]]
end
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#generate_n3(file, dataset_name, options = {}) ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 41
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
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#measures ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 55
def measures
@options[:measures] || @data[0] - dimensions()
end
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#observation_data ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 71
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
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#observation_labels ⇒ Object
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# File 'lib/bio-publisci/readers/csv.rb', line 59
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
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