GCAT5.0 released

Rails/app/helpers/application_helper.rb

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+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+module ApplicationHelper
+
+  def relative_path(fullpath)
+    fullpath.to_s.gsub(Rails.root.to_s + "/public","")
+  end
+
+  #find all directories in generatedFiles/ and remove
+  #any that are more than a day old
+  def remove_old_files(path)
+  	cur_date = extract_date(path)
+  	dirs = Dir.glob(Rails.root + "public/generatedFiles/*") + Dir.glob(Rails.root + "public/uploadedFiles/*")
+  	dirs.compact.each do |dir|
+  		date = extract_date(dir)
+  		if(date != cur_date)
+        puts "Removing: " + dir #log deletions
+  			%x[ rm -rf #{dir} ]
+	    end
+	  end
+  end
+
+  private
+
+    def extract_date(path)
+  	  part = "Files/"
+  	  segment = path.partition(part).last
+  	  date = segment.split(/-[0-9]+/).first
+  	  date.to_i
+    end
+
+
+end

Rails/app/helpers/assays_helper.rb

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+#
+# Copyright 2012 The Board of Regents of the University of Wisconsin System.
+# Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,
+# Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman
+#
+# This file is part of GCAT.
+#
+# GCAT is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GCAT is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with GCAT.  If not, see <http://www.gnu.org/licenses/>.
+#
+module AssaysHelper
+  
+  def date_time_options
+    
+    [['Y-m-d H:M:S', '%Y-%m-%d %H:%M:%S'],['Y-m-d H:M:S p', '%Y-%m-%d %I:%M:%S %p'],['m/d/y H:M:S','%m/%d/%y %H:%M:%S'],['m/d/y H:M:S p','%m/%d/%y %I:%M:%S %p'],['d/m/y H:M:S','%d/%m/%y %H:%M:%S'],['d/m/y H:M:S p','%d/%m/%y %I:%M:%S %p'],['m/d/Y H:M', '%m/%d/%Y %H:%M']]
+    
+  end
+  
+end

Rails/app/helpers/table_builder.rb

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+module TableBuilder
+
+	# I decided to parse the output file produced by the R library
+	# and build an html table rather than using the YUI JS library
+	# previously implemented.
+	#
+	# This method takes the result hash returned by the R bridge routine and
+	# builds an array of row arrays
+	def output_table result, has_layout
+		# if the user submits a layout file, there will be more columns in the output file
+		offsets = {:pdf => -2, :page => -1}
+		if(has_layout)
+			offsets[:pdf] = -7
+			offsets[:page] = -6
+		end
+		rel_path = result[:txtFile]
+		pdf_path = File.dirname @result[:txtFile] #Rails.root.join("public/"+result[:pdfFile])
+		path = Rails.root.join("public/"+rel_path)
+		raise "File not found" unless File.exists? path
+		file = File.open path
+		output = []
+		file.each_line do |line|
+			if(output.empty?)
+				# the headers seem to be enclosed in quotations
+				# will need to parse a bit differently
+				l_ar = line.split "\"\t\""
+				l_ar.first.delete! "\""
+      	l_ar.last.delete! "\"\n"
+      	l_ar.collect! {|l| l.gsub ".", " "}
+      	output << l_ar
+    	else
+    		l_ar = line.split "\t"
+      	l_ar.last.delete! "\"\n"
+      	break unless l_ar.size > 1
+      	output << format_row(l_ar, pdf_path, offsets)
+    	end
+		end
+		return output
+	end
+
+	# this method: removes quotations from strings, truncates floats to 2 sig. digits,
+	# and creates html links to PDF files
+	# params: 
+	# 	l_ar--An array of the one row of data
+	#   path--directory path where the pdf file is located
+	#   offsets-- a hash containing the negative array offsets for cells needed to build pdf link
+	#
+	# returns: A formatted array of one row from the output.txt data
+	def format_row l_ar, path, offsets
+		result = l_ar.collect! do |entry|
+			if(entry.to_f.zero?)
+				entry.gsub "\"", ""
+			elsif(view_context.number_with_precision(entry.to_f, precision: 2, significant: true).size > 15)
+				"%E" % view_context.number_with_precision(entry.to_f, precision: 2, significant: true)
+			else
+				view_context.number_with_precision(entry.to_f, precision: 2, significant: true)
+			end
+		end
+		result[offsets[:page]] = result[offsets[:page]].to_i  # page number
+		# result[-7] == pdf.name
+		result[0] = "<a href=\"#{path}/#{result[offsets[:pdf]]}?#page=#{result[offsets[:page]]}\" target='_blank'>#{result[0].to_i}</a>".html_safe  # add pdf link to first row
+		return result
+	end
+end