1 files changed, 0 insertions, 119 deletions
diff --git a/parser.rb b/parser.rb
deleted file mode 100644
index 8468cea..0000000
--- a/parser.rb
+++ /dev/null
@@ -1,119 +0,0 @@
-require 'spreadsheet'
-require 'roo'
-class Parser
-
-  attr_accessor :dataset, :format_errors, :smiles_errors, :activity_errors, :duplicates, :nr_compounds, :dataset_uri
-
-  def initialize(file, endpoint_uri)
-
-		@file = file
-    @dataset = OpenTox::Dataset.new
-    @feature_uri = endpoint_uri
-		@dataset.features << endpoint_uri
-		@dataset.title = URI.decode(endpoint_uri.split(/#/).last)
-    @format_errors = ""
-    @smiles_errors = []
-    @activity_errors = []
-    @duplicates = {}
-    @nr_compounds = 0
-		@data = []
-		@activities = []
-		@type = "classification"
-
-		# check format by extension - not all browsers provide correct content-type]) 
-		case File.extname(@file[:filename])
-		when ".csv"
-			self.csv
-		when ".xls", ".xlsx"
-			self.excel
-		else
-			@format_errors = "#{@file[:filename]} is a unsupported file type."
-			return false
-		end
-
-		# create dataset
-		@data.each do |items|
-			@dataset.compounds << items[0]
-        @dataset.data[items[0]] = [] unless @dataset.data[items[0]]
-				case @type
-				when "classification"
-					case items[1].to_s
-					when TRUE_REGEXP
-						@dataset.data[items[0]] << {@feature_uri => true }
-					when FALSE_REGEXP
-						@dataset.data[items[0]] << {@feature_uri => 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.data[items[0]] << {@feature_uri => items[1].to_f}
-					end
-				end
-		end
-		@dataset_uri = @dataset.save
-
-  end
-
-  def csv
-		row = 0
-    @file[:tempfile].each_line do |line|
-			row += 1
-      unless line.chomp.match(/^.+[,;].*$/) # check CSV format 
-				@format_errors = "#{@file[:filename]} is not a valid CSV file."
-        return false
-      end
-      items = line.chomp.gsub(/["']/,'').split(/\s*[,;]\s*/) # remove quotes
-			LOGGER.debug items.join(",")
-			input = validate(items[0], items[1], row) # smiles, activity
-			@data << input if input
-		end
-  end
-
-  def excel
-		excel = 'tmp/' + @file[:filename]
-		File.mv(@file[:tempfile].path,excel)
-		begin
-			if File.extname(@file[:filename]) == ".xlsx"    
-			 book = Excelx.new(excel)
-			else
-			 book = Excel.new(excel)
-			end
-			book.default_sheet = 0
-			1.upto(book.last_row) do |row|
-				input = validate( book.cell(row,1), book.cell(row,2), row ) # smiles, activity
-				@data << input if input
-			end
-			File.safe_unlink(@file[:tempfile])
-		rescue
-			@format_errors = "#{@file[:filename]} is not a valid Excel input file."
-			return false
-		end
-  end
-
-	def validate(smiles, act, row)
-		compound = OpenTox::Compound.new(: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)
-		@nr_compounds += 1
-		[ 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