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authorChristoph Helma <helma@in-silico.ch>2015-08-10 13:26:06 +0200
committerChristoph Helma <helma@in-silico.ch>2015-08-10 13:26:06 +0200
commitb7cd3ebbb858a8891c35c45896f1bdd525f3534e (patch)
treea9df6b1f4fc15f2f953e9a23c6dd00b74a967754 /lib/lazar.rb
parent23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c (diff)
algorithm libraries added, fminer tests pass
Diffstat (limited to 'lib/lazar.rb')
-rw-r--r--lib/lazar.rb31
1 files changed, 27 insertions, 4 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 8831ba2..2e7e7c2 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -6,6 +6,9 @@ require 'json'
require 'logger'
require 'mongoid'
require 'rserve'
+require "nokogiri"
+require "base64"
+
# Mongo setup
# TODO retrieve correct environment from Rack/Sinatra
@@ -27,8 +30,21 @@ Mongo::Logger.logger = $logger
Mongo::Logger.level = Logger::WARN
#Mongoid.logger = $logger
+# Require sub-Repositories
+require_relative '../libfminer/libbbrc/bbrc' # include before openbabel
+require_relative '../libfminer/liblast/last' #
+require_relative '../last-utils/lu.rb'
+require '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'
+
# OpenTox classes and includes
-CLASSES = ["Feature","Compound", "Dataset", "Validation", "CrossValidation"]# Algorithm and Models are modules
+CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation"]# Algorithm and Models are modules
[ # be aware of the require sequence as it affects class/method overwrites
"overwrite.rb",
@@ -39,8 +55,15 @@ CLASSES = ["Feature","Compound", "Dataset", "Validation", "CrossValidation"]# A
"compound.rb",
"dataset.rb",
"descriptor.rb",
- #"algorithm.rb",
- #"model.rb",
- #"validation.rb"
+ "algorithm.rb",
+ "descriptor.rb",
+ "bbrc.rb",
+ "lazar.rb",
+ "similarity.rb",
+ "neighbor.rb",
+ "classification.rb",
+ "regression.rb",
+ "validation.rb",
+ "crossvalidation.rb",
].each{ |f| require_relative f }