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Updated master to SVN trunk revision 572

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This commit is contained in:
Yury V Bukhman
2015-06-26 15:04:35 -05:00
parent 67544a10e6
commit 2d658405a1
184 changed files with 8236 additions and 6182 deletions
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Rails/app/models/assay.rb
+71 -12
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@@ -32,8 +32,10 @@ class Assay
include ActiveModel::Validations
include ActiveModel::Conversion
extend ActiveModel::Naming
attr_accessor :input_file, :transformation, :transformation_input, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
:plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input
attr_accessor :input_file, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type,
:plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input, :console_out, :specg_min,
:specg_max, :totg_min, :totg_max, :lagT_min, :lagT_max,:transformation, :transformation_input
# (1) Validation of input data file
validates_presence_of :input_file, :message => '- No input file was specified.'
@@ -117,7 +119,7 @@ class Assay
if self.transformation == '-1'
self.transformation = Float(self.transformation_input)
else
self.transformation = self.transformation.to_i
self.transformation = self.transformation.to_f
end
# Soothing parameter for growth curve model. Applied for Loess model only.
@@ -128,6 +130,8 @@ class Assay
# (3) blank value (A Real Number)
if self.blank_value == 'default'
self.blank_value = nil
elsif self.blank_value == 'zero'
self.blank_value = 0
else
self.blank_value = Float(self.blank_value_input)
end
@@ -156,6 +160,20 @@ class Assay
self.remove_jumps = false
end
## (7) Heatmap values
if (self.specg_min != '' && self.specg_max != '')
self.specg_max = Float(self.specg_max)
self.specg_min = Float(self.specg_min)
end
if (self.totg_min != '' && self.totg_max != '')
self.totg_min = Float(self.totg_min)
self.totg_max = Float(self.totg_max)
end
if (self.lagT_min != '' && self.lagT_max != '')
self.lagT_max = Float(self.lagT_max)
self.lagT_min = Float(self.lagT_min)
end
############################################################################################
@@ -201,7 +219,11 @@ class Assay
if(File.size(inputfile) > MAX_FILE_SIZE)
return {:error_message => "Error: File too big. Maximum file size allowed is #{MAX_FILE_SIZE/(10**6)} MB.", :path => inputfile}
end
# Try to override stdout to redirect the console output.
$stdout = File.new(out_dir_path + '/console.out', 'w')
$stdout.sync = true
# use web interface parsed parameters to call R function/library via Rinruby
R.eval ('library(GCAT)')
R.assign "out.dir", out_dir_path
@@ -253,9 +275,12 @@ class Assay
# (2) transformation. N value (A Real Number)
R.assign "add.constant", self.transformation
# R.assign "add.constant", 0
# (3) blank value (A Real Number)
if (self.blank_value == nil)
R.eval "blank.value <- NULL"
elsif (self.blank_value == 0)
R.eval "blank.value <- 0"
else
R.assign "blank.value", self.blank_value
end
@@ -303,16 +328,40 @@ class Assay
R.assign 'use.linear.param', 'F'
R.assign 'smooth.param', 0.1 # default value
end
## Heatmap values
if (self.specg_max != '' && self.specg_min != '')
R.assign 'specMin', self.specg_min
R.assign 'specMax', self.specg_max
R.eval "specRange <- c(specMin, specMax)"
else
R.eval 'specRange <- NA'
end
if (self.totg_min != '' && self.totg_max != '')
R.assign 'totMin', self.totg_min
R.assign 'totMax', self.totg_max
R.eval "totalRange <- c(totMin, totMax)"
else
R.eval 'totalRange <- NA'
end
if (self.lagT_min != '' && self.lagT_max != '')
R.assign 'lagT_min', self.lagT_min
R.assign 'lagT_max', self.lagT_max
R.eval "lagRange <- c(lagT_min, lagT_max)"
else
R.eval 'lagRange <- NA'
end
# This block evaluates the files (csv or xlsx, single.plate or multiple.plate)
R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value,
start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,
points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, lagRange = lagRange,
totalRange = totalRange, specRange = specRange, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8,
plate.ncol = 12, input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"),
layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T)')
# good file returns a list of file path(length is more than 1), bad file returns error message string(array length = 1)
print R.R_file_return_value
R.eval ('R_array_return_length <- length(R_file_return_value)')
unless R.R_array_return_length == 1
puts R.R_file_return_value, "\n"
@@ -323,16 +372,23 @@ class Assay
if(error_message.include? "Error in <remove.points>")
num_data_points = error_message.split("data has ").last.gsub("\n\n", "")
error_message = "Invalid 'Points to ignore'. Please select a value in the range (1-#{num_data_points})."
else
# debugger
console_message = error_message
split_s = error_message.split(":")
print split_s
split_s.each {|x| error_message = x}
end
return {:error_message => error_message, :path => inputfile}
return {:error_message => error_message, :path => inputfile, :console_msg => console_message}
end
# process generated files
raise "no files generated" if files.empty?
#search for "_overview.jpg files" from Array of files
overviewFiles = ""
pdfFile = ""
txtFile = ""
consoleOut = ""
files_Array_Size = files.size - 1
for i in 0..files_Array_Size
@@ -368,6 +424,7 @@ class Assay
# build array named overviewFiles that contains "_overview.jpg files"
overviewFiles = overviewFiles.split("\n")
raise "no overview files generated" if overviewFiles.empty?
if self.plate_type == 'm'
@@ -375,18 +432,20 @@ class Assay
else
zipfile = out_dir_path + "/singlePlateAnalysis.zip"
end
consoleOut = out_dir_path + "/console.out"
self.console_out = consoleOut
# create Zip files at current directory
Zip::File.open(zipfile, Zip::File::CREATE) { |zf|
files.each{|file| zf.add(File.basename(file), file)}
#files.each{|file| zf.add(file.sub(out_dir_path + "/", ""), file))}
#zf.add(File.basename(consoleOut), consoleOut)
}
#return results unless error
#zip files, jpg of overviews, txt file for datagrid, pdf file
{:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model}
{:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model,
:consoleout => consoleOut}
end # end of r_calculation method