initial installation fixes, installs on Debian 3.16.7

6 files changed, 35 insertions, 24 deletions

diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index 0c86985..d274c4d 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -28,11 +28,12 @@ Dir.chdir main_dir do
   puts "Downloading OpenBabel sources"
   system "git clone https://github.com/openbabel/openbabel.git"
 end
+
 FileUtils.mkdir_p build_dir
 FileUtils.mkdir_p install_dir
 Dir.chdir build_dir do
   puts "Configuring OpenBabel"
-  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUBY_BINDINGS=ON"
+  cmake = "cmake #{src_dir} -DCMAKE_INSTALL_PREFIX=#{install_dir} -DBUILD_GUI=OFF -DENABLE_TESTS=OFF -DRUN_SWIG=ON -DRUBY_BINDINGS=ON"
   # set rpath for local installations
   # http://www.cmake.org/Wiki/CMake_RPATH_handling
   # http://vtk.1045678.n5.nabble.com/How-to-force-cmake-not-to-remove-install-rpath-td5721193.html
@@ -55,19 +56,12 @@ ob_lib= File.expand_path "../../openbabel/lib"
 # compile ruby bindings
 puts "Compiling and installing OpenBabel Ruby bindings."
 Dir.chdir ruby_src_dir do
-  #p `pwd`
   # fix rpath
   system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}"
   system "#{RbConfig.ruby} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
   system "make -j#{nr_processors}"
 end
 
-#p(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
-#FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
-FileUtils.mkdir_p lib_dir
-FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}", lib_dir
-#FileUtils.remove_entry_secure src_dir, build_dir
-
 # install fminer
 fminer_dir = File.join main_dir, "libfminer"
 system "git clone git://github.com/amaunz/fminer2.git #{fminer_dir}"
@@ -86,5 +80,7 @@ end
 # install last-utils
 FileUtils.cd main_dir
 system "git clone git://github.com/amaunz/last-utils.git"
+FileUtils.cd File.join(main_dir,"last-utils")
+`sed -i '8s/"openbabel", //' lu.rb`
 
 # install R packagemain_dir
diff --git a/lazar.gemspec b/lazar.gemspec
index 8da29b7..6fe3f5b 100644
--- a/lazar.gemspec
+++ b/lazar.gemspec
@@ -22,7 +22,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "bundler"
   s.add_runtime_dependency "rest-client"
   s.add_runtime_dependency 'nokogiri'
-  s.add_runtime_dependency "openbabel"
+  #s.add_runtime_dependency "openbabel"
   s.add_runtime_dependency 'rserve-client'
   s.add_runtime_dependency "mongoid", '~> 5.0beta'  
 
diff --git a/lib/compound.rb b/lib/compound.rb
index 10deabc..e51e9ad 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -62,7 +62,7 @@ module OpenTox
       # Temporary workaround for OpenBabels Inchi bug
       # http://sourceforge.net/p/openbabel/bugs/957/
       # bug has not been fixed in latest git/development version
-      smiles = `echo "#{inchi}" | babel -iinchi - -ocan`.chomp.strip
+      smiles = `echo "#{inchi}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -iinchi - -ocan`.chomp.strip
       if smiles.empty?
         Compound.find_or_create_by(:warning => "InChi parsing failed for #{inchi}, this may be caused by an incorrect InChi string or a bug in OpenBabel libraries.")
       else
@@ -91,7 +91,8 @@ module OpenTox
     # @return [String] InChI string
     def inchi
       unless self["inchi"]
-        result = `echo "#{self.smiles}" | babel -ismi - -oinchi`.chomp
+
+        result = `echo "#{self.smiles}" | "#{File.join(File.dirname(__FILE__),"..","openbabel","bin","babel")}" -ismi - -oinchi`.chomp
         update(:inchi => result.chomp) unless result.empty?
       end
       self["inchi"]
@@ -182,21 +183,23 @@ module OpenTox
       #reqbits = [count['_id'] for count in db.mfp_counts.find({'_id': {'$in': qfp}}).sort('count', 1).limit(qn - qmin + 1)]
       aggregate = [
         #{'$match': {'mfp.count': {'$gte': qmin, '$lte': qmax}, 'mfp.bits': {'$in': reqbits}}},
-        {'$match':  {'_id': {'$ne': self.id}}}, # remove self
-        {'$project': {
-          'tanimoto': {'$let': {
-            'vars': {'common': {'$size': {'$setIntersection': ['$fp4', fp4]}}},
-            'in': {'$divide': ['$$common', {'$subtract': [{'$add': [qn, '$fp4_size']}, '$$common']}]}
+        {'$match' =>  {'_id' => {'$ne' => self.id}}}, # remove self
+        {'$project' => {
+          'tanimoto' => {'$let' => {
+            'vars' => {'common' => {'$size' => {'$setIntersection' => ['$fp4', fp4]}}},
+            'in' => {'$divide' => ['$$common', {'$subtract' => [{'$add' => [qn, '$fp4_size']}, '$$common']}]}
           }},
-          '_id': 1
+          '_id' => 1
         }},
-        {'$match':  {'tanimoto': {'$gte': threshold}}},
-        {'$sort': {'tanimoto': -1}}
+        {'$match' =>  {'tanimoto' => {'$gte' => threshold}}},
+        {'$sort' => {'tanimoto' => -1}}
       ]
       
       $mongo["compounds"].aggregate(aggregate).collect{ |r| [r["_id"], r["tanimoto"]] }
         
     end
+=begin
+=end
 
     private
 
@@ -210,11 +213,12 @@ module OpenTox
       when /smi|can|inchi/
         obconversion.write_string(obmol).gsub(/\s/,'').chomp
       when /sdf/
-        OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
+# TODO set 3D
+        #OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
         sdf = obconversion.write_string(obmol)
         if sdf.match(/.nan/)
           $logger.warn "3D generation failed for compound #{identifier}, trying to calculate 2D structure"
-          OpenBabel::OBOp.find_type("Gen2D").do(obmol) 
+          #OpenBabel::OBOp.find_type("Gen2D").do(obmol) 
           sdf = obconversion.write_string(obmol)
           if sdf.match(/.nan/)
             $logger.warn "2D generation failed for compound #{identifier}"
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 0c5e18b..9e2363c 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -14,7 +14,7 @@ require "base64"
 # TODO retrieve correct environment from Rack/Sinatra
 ENV["MONGOID_ENV"] ||= "development"
 # TODO remove config files, change default via ENV or directly in Mongoid class
-Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml")
+Mongoid.load!("#{File.expand_path(File.join(File.dirname(__FILE__),'..','mongoid.yml'))}")
 # TODO get Mongo::Client from Mongoid
 $mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
 # TODO same for GridFS
@@ -31,10 +31,13 @@ Mongo::Logger.level = Logger::WARN
 #Mongoid.logger = $logger
 
 # Require sub-Repositories
+# TODO: set 
+ENV["LD_LIBRARY_PATH"] = "#{File.join File.dirname(__FILE__),'..','openbabel','lib'}"
+p ENV["LD_LIBRARY_PATH"] 
 require_relative '../libfminer/libbbrc/bbrc' # include before openbabel
 require_relative '../libfminer/liblast/last' # 
 require_relative '../last-utils/lu.rb'
-require 'openbabel'
+require_relative '../openbabel/lib/openbabel'
 
 # Fminer environment variables
 ENV['FMINER_SMARTS'] = 'true'
diff --git a/mongoid.yml b/mongoid.yml
new file mode 100644
index 0000000..20b644b
--- /dev/null
+++ b/mongoid.yml
@@ -0,0 +1,8 @@
+development:
+  clients:
+    default:
+      database: opentox
+      hosts:
+        - localhost:27017
+      options:
+        raise_not_found_error: false
diff --git a/test/compound.rb b/test/compound.rb
index b45e3d0..40b9f9e 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -83,7 +83,7 @@ class CompoundTest < MiniTest::Test
   end
 
   def test_neighbors
-    d = Dataset.from_csv_file "data/EPAFHM.csv"
+    d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
     d.compounds.each do |c|
       refute_nil c.fp4
     end