diff options
Diffstat (limited to 'lib/lazar.rb')
| -rw-r--r-- | lib/lazar.rb | 45 |
1 files changed, 22 insertions, 23 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index cc66841..a28ba3a 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -8,6 +8,7 @@ require 'mongoid' require 'rserve' require "nokogiri" require "base64" +require 'openbabel' # Environment setup ENV["LAZAR_ENV"] ||= "production" @@ -24,7 +25,6 @@ Mongoid.load_configuration({ } }) Mongoid.raise_not_found_error = false # return nil if no document is found -#$mongo = Mongoid.default_client $mongo = Mongo::Client.new("mongodb://127.0.0.1:27017/#{ENV['LAZAR_ENV']}") $gridfs = $mongo.database.fs @@ -41,26 +41,27 @@ when "development" end # R setup +rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R")) +# should work on POSIX including os x +# http://stackoverflow.com/questions/19619582/number-of-processors-cores-in-command-line +NR_CORES = `getconf _NPROCESSORS_ONLN`.to_i R = Rserve::Connection.new -R.eval "library(ggplot2)" -R.eval "library(grid)" -R.eval "library(gridExtra)" - -# Require sub-Repositories -require_relative '../libfminer/libbbrc/bbrc' # include before openbabel -require_relative '../libfminer/liblast/last' # -require_relative '../last-utils/lu.rb' -require_relative '../openbabel/lib/openbabel' - -# Fminer environment variables -ENV['FMINER_SMARTS'] = 'true' -ENV['FMINER_NO_AROMATIC'] = 'true' -ENV['FMINER_PVALUES'] = 'true' -ENV['FMINER_SILENT'] = 'true' -ENV['FMINER_NR_HITS'] = 'true' +R.eval " +suppressPackageStartupMessages({ + library(iterators,lib=\"#{rlib}\") + library(foreach,lib=\"#{rlib}\") + library(ggplot2,lib=\"#{rlib}\") + library(grid,lib=\"#{rlib}\") + library(gridExtra,lib=\"#{rlib}\") + library(pls,lib=\"#{rlib}\") + library(caret,lib=\"#{rlib}\") + library(doMC,lib=\"#{rlib}\") + registerDoMC(#{NR_CORES}) +}) +" # OpenTox classes and includes -CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules [ # be aware of the require sequence as it affects class/method overwrites "overwrite.rb", @@ -68,18 +69,16 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","Repeat "error.rb", "opentox.rb", "feature.rb", + "physchem.rb", "compound.rb", "dataset.rb", - "descriptor.rb", "algorithm.rb", - "descriptor.rb", - "bbrc.rb", "model.rb", - "similarity.rb", "classification.rb", "regression.rb", "validation.rb", "crossvalidation.rb", + "leave-one-out-validation.rb", "experiment.rb", ].each{ |f| require_relative f } - +OpenTox::PhysChem.descriptors # load descriptor features |