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require 'spreadsheet'
require 'roo'
module OpenTox
module Parser
module Owl
def initialize(uri)
@uri = uri
@metadata = {}
end
def metadata
# TODO: load parameters
if @dataset
uri = File.join(@uri,"metadata")
else
uri = @uri
end
statements = []
`rapper -i rdfxml -o ntriples #{uri}`.each_line do |line|
triple = line.chomp.split('> ')
statements << triple.collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')}
end
statements.each do |triple|
@metadata[triple[1]] = triple[2].split('^^').first if triple[0] == @uri and triple[1] != RDF['type']
end
@metadata
end
class Generic
include Owl
end
class Dataset
include Owl
def initialize(uri)
super uri
@dataset = ::OpenTox::Dataset.new(@uri)
end
def load_uri
data = {}
feature_values = {}
feature = {}
other_statements = {}
ntriples = `rapper -i rdfxml -o ntriples #{@uri}`
ntriples.each_line do |line|
triple = line.chomp.split(' ',3)
triple = triple[0..2].collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')}
case triple[1] # Ambit namespaces are case insensitive
when /#{OT.values}/i
data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
data[triple[0]][:values] << triple[2]
when /#{OT.value}/i
feature_values[triple[0]] = triple[2]
when /#{OT.compound}/i
data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]]
data[triple[0]][:compound] = triple[2]
when /#{OT.feature}/i
feature[triple[0]] = triple[2]
else
end
end
data.each do |id,entry|
entry[:values].each do |value_id|
value = feature_values[value_id].split(/\^\^/).first # remove XSD.type
@dataset.add entry[:compound],feature[value_id],value
end
end
load_features
@dataset.metadata = metadata
@dataset
end
def load_features
@dataset.features.keys.each do |feature|
@dataset.features[feature] = Parser::Owl::Generic.new(feature).metadata
end
end
end
end
class Spreadsheet
def initialize(dataset)
@dataset = dataset
@format_errors = ""
@smiles_errors = []
@activity_errors = []
@duplicates = {}
@nr_compounds = 0
@data = []
@activities = []
@type = "classification"
end
def load_excel(book)
book.default_sheet = 0
1.upto(book.last_row) do |row|
if row == 1
@feature = File.join(@dataset.uri,"feature",book.cell(row,2))
else
add( book.cell(row,1), book.cell(row,2), row ) # smiles, activity
end
end
parse
end
def load_csv(csv)
row = 0
csv.each_line do |line|
row += 1
raise "Invalid CSV format at line #{row}: #{line.chomp}" unless line.chomp.match(/^.+[,;].*$/) # check CSV format
items = line.chomp.gsub(/["']/,'').split(/\s*[,;]\s*/) # remove quotes
if row == 1
@feature = File.join(@dataset.uri,"feature",items[1])
else
add(items[0], items[1], row)
end
end
parse
end
def parse
# create dataset
@data.each do |items|
case @type
when "classification"
case items[1].to_s
when TRUE_REGEXP
@dataset.add(items[0], @feature, true )
when FALSE_REGEXP
@dataset.add(items[0], @feature, false)
end
when "regression"
if items[1].to_f == 0
@activity_errors << "Row #{items[2]}: Zero values not allowed for regression datasets - entry ignored."
else
@dataset.add items[0], @feature, items[1].to_f
end
end
end
warnings = ''
warnings += "<p>Incorrect Smiles structures (ignored):</p>" + @smiles_errors.join("<br/>") unless @smiles_errors.empty?
warnings += "<p>Irregular activities (ignored):</p>" + @activity_errors.join("<br/>") unless @activity_errors.empty?
duplicate_warnings = ''
@duplicates.each {|inchi,lines| duplicate_warnings << "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
warnings += "<p>Duplicated structures (all structures/activities used for model building, please make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
@dataset.metadata[OT.Warnings] = warnings
@dataset
end
def add(smiles, act, row)
compound = Compound.from_smiles(smiles)
if compound.nil? or compound.inchi.nil? or compound.inchi == ""
@smiles_errors << "Row #{row}: " + [smiles,act].join(", ")
return false
end
unless numeric?(act) or classification?(act)
@activity_errors << "Row #{row}: " + [smiles,act].join(", ")
return false
end
@duplicates[compound.inchi] = [] unless @duplicates[compound.inchi]
@duplicates[compound.inchi] << "Row #{row}: " + [smiles, act].join(", ")
@type = "regression" unless classification?(act)
# TODO: set OT.NumericalFeature, ...
@nr_compounds += 1
@data << [ compound.uri, act , row ]
end
def numeric?(object)
true if Float(object) rescue false
end
def classification?(object)
!object.to_s.strip.match(TRUE_REGEXP).nil? or !object.to_s.strip.match(FALSE_REGEXP).nil?
end
end
end
end
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