GCAT5.0 released

Rails/app/controllers/application_controller.rb

@@ -0,0 +1,23 @@
+#
+# 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/>.
+#
+class ApplicationController < ActionController::Base
+  protect_from_forgery
+end

Rails/app/controllers/assays_controller.rb

@@ -0,0 +1,73 @@
+include ApplicationHelper
+include TableBuilder
+
+#
+# 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/>.
+#
+class AssaysController < ApplicationController
+
+  def new
+    @assay= Assay.new
+  end
+
+  def create 
+    #Lazy mass assign from form params
+    @assay = Assay.new(params[:assay])
+
+    if @assay.valid?
+    
+      # Add the calls to methods to parse the form input in @assay and execute R script.
+      # return the results from R into a new instance variable and display results via show template
+      
+      #reassign some parameters. Validate on form input params or after manipulations?
+      @assay = @assay.parse_form_params
+      #debugger
+      
+      #execute R calculation and assign instance variable to display     
+      @result = @assay.r_calculation
+
+      # no need to keep storing old data
+      
+      #temp fix for pdfFiles see ticket #424. string of pdfFiles returned rather than array
+      unless @result[:pdfFiles].nil?
+       @result[:pdfFiles] = @result[:pdfFile].split('pdf')
+       @result[:pdfFiles].collect{|element| element + 'pdf'}
+       end
+      
+      if  ( @result.has_key? :error_message )  #h.has_key?("a") # @result.has_key? :error_message
+        flash.now[:error] = @result[:error_message] #.join("\n")
+        #do not allow bad guys to fill disc space with invalid files
+        FileUtils.rm @result[:path]
+        render :action => 'inputfile_error_message' 
+      else
+        # parse the output text file into a hash in order to create a table in Assays#show
+        @table = output_table(@result, !@result[:layout_file].nil?)
+        remove_old_files(relative_path(@result[:zipfile]))
+        flash.now[:notice] = "Your assay processed!\nPlease click on any of plate diagrams to save your results to a zip archive."  
+        render :action => 'show'
+      end    
+    else
+
+      render :action => 'new'
+    end  
+  end  
+
+
+end