Passenger (re)start fixed

4 files changed, 129 insertions, 17 deletions

diff --git a/Rakefile b/Rakefile
index 2c4322f..9d042a5 100644
--- a/Rakefile
+++ b/Rakefile
@@ -15,10 +15,13 @@ begin
 		gem.add_dependency "rack"
 		gem.add_dependency "rack-contrib"
 		gem.add_dependency "thin"
-		gem.add_dependency "cucumber"
 		gem.add_dependency "ezmobius-redis-rb"
 		gem.add_dependency "emk-sinatra-url-for"
 		gem.add_dependency "cehoffman-sinatra-respond_to"
+		gem.add_dependency "dm-core"
+		gem.add_dependency "datamapper"
+		gem.add_dependency "do_sqlite3"
+		gem.add_development_dependency "cucumber"
 		gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
 		gem.files.include %w(lib/tasks/opentox.rb, lib/tasks/redis.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/feature.rb, lib/model.rb, lib/utils.rb, lib/templates/*)
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
diff --git a/bin/opentox-install-debian.sh b/bin/opentox-install-debian.sh
new file mode 100644
index 0000000..cf173da
--- /dev/null
+++ b/bin/opentox-install-debian.sh
@@ -0,0 +1,105 @@
+#!/bin/bash
+#Installation is tested on Debian Lenny Ubuntu 9.04
+#Update the system
+
+ERRLOG='install_err.log'
+INSTALLLOG='install_log.log'
+DATE=$(date +%Y/%m/%d\ %H:%M:%S)
+
+echo "================================================="
+echo "Please enshure that the sudo package is installed"
+echo "on your system. "
+echo "On Ubuntu Linux sudo is installed by default."
+echo "If you are unshure check with it 'sudo ls'"
+echo "and installed it with 'apt-get install sudo'"
+echo "and add your username with visudo."
+echo "================================================="
+echo -n "To continue installation press y: "
+read answer
+if [ "$answer" != "y" ]
+then
+  echo "exiting the script..."
+  exit 1
+fi
+
+echo "opentox webservice install log - " $DATE > $INSTALLLOG
+echo "Installing: build-essential"
+sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing: ruby 1.8 with its dev files"
+sudo apt-get install ruby ruby1.8-dev >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing: gems rdoc rubygems and rake"
+sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG
+
+echo "Installing rubygems from source. This may take some time"
+wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG
+tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG
+cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG
+sudo ruby setup.rb 2>>$ERRLOG
+cd ..
+
+echo "Adding http://gems.github.com to ruby gem sources"
+sudo gem sources -a http://gems.github.com >> $INSTALLLOG 2>>$ERRLOG
+
+#for debian lenny:
+echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5"
+sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5  >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing git from source"
+wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG
+tar xzfv git-1.6.5.2.tar.gz  2>>$ERRLOG
+cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG
+./configure 2>>$ERRLOG
+make 2>>$ERRLOG
+make install 2>>$ERRLOG
+
+echo "Installing the opentox webservices"
+mkdir webservices >> $INSTALLLOG 2>>$ERRLOG
+cd webservices >> $INSTALLLOG 2>>$ERRLOG
+
+git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-feature.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-dataset.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-algorithm.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-model.git >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-test.git  >> $INSTALLLOG 2>>$ERRLOG
+
+cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+cd .. >> $INSTALLLOG 2>>$ERRLOG
+git clone git://github.com/helma/opentox-ruby-api-wrapper.git >> $INSTALLLOG 2>>$ERRLOG
+cd opentox-ruby-api-wrapper >> $INSTALLLOG 2>>$ERRLOG
+git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG
+rake install >> $INSTALLLOG 2>>$ERRLOG
+
+
+cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing libopenssl-ruby"
+sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing dtach"
+rake dtach:install >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing openbabel"
+rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG
+
+#debian lenny missed liblink:
+ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG
+
+rake redis:download >> $INSTALLLOG 2>>$ERRLOG
+rake redis:install >> $INSTALLLOG 2>>$ERRLOG
+#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices
+sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG
+cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG
+echo "Installing fminer"
+rake fminer:install >> $INSTALLLOG 2>>$ERRLOG
+sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG
+
+
+mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
index 8018fff..38202dd 100644
--- a/lib/tasks/opentox.rb
+++ b/lib/tasks/opentox.rb
@@ -22,16 +22,6 @@ end
 
 namespace :opentox do
 
-	desc "Install required gems"
-	task :install do
-		puts `sudo gem install #{@gems}`
-	end
-
-	desc "Update gems"
-	task :update do
-		puts `sudo gem update #{@gems}`
-	end
-
 	namespace :services do
 
 		desc "Run opentox services"
@@ -51,7 +41,8 @@ namespace :opentox do
 						puts "Cannot start #{service} on port #{port}."
 					end
 				when 'passenger'
-					`touch #{File.join(dir, 'tmp/restart.txt')}`
+					FileUtils.mkdir_p File.join(dir, 'tmp')
+					FileUtils.touch File.join(dir, 'tmp/restart.txt')
 					puts "#{service} restarted."
 				else
 					puts "not yet implemented"
@@ -108,7 +99,8 @@ task :start do
 				puts "Cannot start #{service} on port #{port}."
 			end
 		when 'passenger'
-			`touch tmp/restart.txt`
+			FileUtils.mkdir_p File.join(dir, 'tmp')
+			FileUtils.touch File.join(dir, 'tmp/restart.txt')
 			puts "#{service} restarted."
 		else
 			puts "not yet implemented"
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 17be199..c5b293d 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,13 +5,15 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.1.1"
+  s.version = "1.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
   s.date = %q{2009-11-17}
+  s.default_executable = %q{opentox-install-debian.sh}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
+  s.executables = ["opentox-install-debian.sh"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -21,6 +23,7 @@ Gem::Specification.new do |s|
      "README.rdoc",
      "Rakefile",
      "VERSION",
+     "bin/opentox-install-debian.sh",
      "lib/algorithm.rb",
      "lib/compound.rb",
      "lib/dataset.rb",
@@ -56,20 +59,26 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<rack>, [">= 0"])
       s.add_runtime_dependency(%q<rack-contrib>, [">= 0"])
       s.add_runtime_dependency(%q<thin>, [">= 0"])
-      s.add_runtime_dependency(%q<cucumber>, [">= 0"])
       s.add_runtime_dependency(%q<ezmobius-redis-rb>, [">= 0"])
       s.add_runtime_dependency(%q<emk-sinatra-url-for>, [">= 0"])
       s.add_runtime_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
+      s.add_runtime_dependency(%q<dm-core>, [">= 0"])
+      s.add_runtime_dependency(%q<datamapper>, [">= 0"])
+      s.add_runtime_dependency(%q<do_sqlite3>, [">= 0"])
+      s.add_development_dependency(%q<cucumber>, [">= 0"])
     else
       s.add_dependency(%q<rest-client>, [">= 0"])
       s.add_dependency(%q<sinatra>, [">= 0"])
       s.add_dependency(%q<rack>, [">= 0"])
       s.add_dependency(%q<rack-contrib>, [">= 0"])
       s.add_dependency(%q<thin>, [">= 0"])
-      s.add_dependency(%q<cucumber>, [">= 0"])
       s.add_dependency(%q<ezmobius-redis-rb>, [">= 0"])
       s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"])
       s.add_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
+      s.add_dependency(%q<dm-core>, [">= 0"])
+      s.add_dependency(%q<datamapper>, [">= 0"])
+      s.add_dependency(%q<do_sqlite3>, [">= 0"])
+      s.add_dependency(%q<cucumber>, [">= 0"])
     end
   else
     s.add_dependency(%q<rest-client>, [">= 0"])
@@ -77,9 +86,12 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<rack>, [">= 0"])
     s.add_dependency(%q<rack-contrib>, [">= 0"])
     s.add_dependency(%q<thin>, [">= 0"])
-    s.add_dependency(%q<cucumber>, [">= 0"])
     s.add_dependency(%q<ezmobius-redis-rb>, [">= 0"])
     s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"])
     s.add_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
+    s.add_dependency(%q<dm-core>, [">= 0"])
+    s.add_dependency(%q<datamapper>, [">= 0"])
+    s.add_dependency(%q<do_sqlite3>, [">= 0"])
+    s.add_dependency(%q<cucumber>, [">= 0"])
   end
 end