Updated installer

7 files changed, 45 insertions, 29 deletions

diff --git a/Gemfile b/Gemfile
index 4c1098b..77a45db 100644
--- a/Gemfile
+++ b/Gemfile
@@ -2,4 +2,4 @@ source :gemcutter
 
 gem 'opentox-server', :path => "~/opentox-ruby/opentox-server"
 gem "opentox-client", :path => "~/opentox-ruby/opentox-client"
-gem "openbabel", "2.3.1"
+gem "openbabel", "2.3.1.2"
diff --git a/Gemfile.lock b/Gemfile.lock
index 4a69514..fa2d686 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,7 +1,7 @@
 PATH
   remote: ~/opentox-ruby/opentox-client
   specs:
-    opentox-client (0.0.1pre)
+    opentox-client (1.0.0)
       bundler
       open4
       rdf
@@ -11,46 +11,52 @@ PATH
 PATH
   remote: ~/opentox-ruby/opentox-server
   specs:
-    opentox-server (0.0.1pre)
-      emk-sinatra-url-for
+    opentox-server (1.0.0)
       opentox-client
       rack
       rack-contrib
+      rdf-n3
       roo
       sinatra
       sinatra-contrib
+      spreadsheet (= 0.6.8)
       unicorn
 
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.2.7)
-    backports (2.5.0)
+    addressable (2.2.8)
+    backports (2.6.1)
     choice (0.1.6)
-    emk-sinatra-url-for (0.2.1)
-      sinatra (>= 0.9.1.1)
     eventmachine (0.12.10)
-    faraday (0.7.6)
-      addressable (~> 2.2)
+    faraday (0.8.1)
       multipart-post (~> 1.1)
-      rack (~> 1.1)
     ffi (1.0.11)
-    google-spreadsheet-ruby (0.1.8)
-      nokogiri (>= 1.4.3.1)
+    google-spreadsheet-ruby (0.3.0)
+      google_drive (>= 0.3.0)
+    google_drive (0.3.1)
+      nokogiri (>= 1.4.4, != 1.5.2, != 1.5.1)
       oauth (>= 0.3.6)
       oauth2 (>= 0.5.0)
+    httpauth (0.1)
+    json (1.7.3)
+    jwt (0.1.4)
+      json (>= 1.2.4)
     kgio (2.7.4)
     log4r (1.1.10)
-    mime-types (1.18)
-    multi_json (1.2.0)
+    mime-types (1.19)
+    multi_json (1.3.6)
     multipart-post (1.1.5)
-    nokogiri (1.5.2)
-    oauth (0.4.5)
-    oauth2 (0.5.2)
-      faraday (~> 0.7)
+    nokogiri (1.5.5)
+    oauth (0.4.6)
+    oauth2 (0.8.0)
+      faraday (~> 0.8)
+      httpauth (~> 0.1)
+      jwt (~> 0.1.4)
       multi_json (~> 1.0)
+      rack (~> 1.2)
     open4 (1.3.0)
-    openbabel (2.3.1)
+    openbabel (2.3.1.2)
     rack (1.4.1)
     rack-contrib (1.1.0)
       rack (>= 0.9.1)
@@ -58,9 +64,11 @@ GEM
       rack
     rack-test (0.6.1)
       rack (>= 1.0)
-    raindrops (0.8.0)
-    rdf (0.3.5.1)
+    raindrops (0.10.0)
+    rdf (0.3.7)
       addressable (>= 2.2.6)
+    rdf-n3 (0.3.7)
+      rdf (>= 0.3.4)
     rdf-raptor (0.4.1)
       ffi (>= 1.0)
       rdf (~> 0.3.0)
@@ -73,8 +81,8 @@ GEM
       rubyzip (>= 0.9.4)
       spreadsheet (> 0.6.4)
       todonotes (>= 0.1.0)
-    ruby-ole (1.2.11.3)
-    rubyzip (0.9.6.1)
+    ruby-ole (1.2.11.4)
+    rubyzip (0.9.9)
     sinatra (1.3.2)
       rack (~> 1.3, >= 1.3.6)
       rack-protection (~> 1.2)
@@ -91,7 +99,7 @@ GEM
     tilt (1.3.3)
     todonotes (0.1.0)
       log4r
-    unicorn (4.2.1)
+    unicorn (4.3.1)
       kgio (~> 2.6)
       rack
       raindrops (~> 0.7)
@@ -100,6 +108,6 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  openbabel (= 2.3.1)
+  openbabel (= 2.3.1.2)
   opentox-client!
   opentox-server!
diff --git a/application.rb b/application.rb
index 53c8e51..dcbb465 100644
--- a/application.rb
+++ b/application.rb
@@ -17,7 +17,7 @@ module OpenTox
         response['Content-Type'] = 'text/uri-list'
         uri_list
       else
-        response['Content-Type'] = 'application/rdf+xml'
+        response['Content-Type'] = 'text/plain'
         uri_list
       end
     end
diff --git a/bin/algorithm-install b/bin/algorithm-install
index af65d97..07ef24a 100755
--- a/bin/algorithm-install
+++ b/bin/algorithm-install
@@ -7,7 +7,7 @@ SELF=$(basename $0 -install)
 [ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
 
 # Adjust ruby version here!
-RUBY_NUM_VER="1.9.3-p125"
+RUBY_NUM_VER="1.9.3-p194"
 
 echo
 echo "Welcome to service installation (<Return> to continue)."
@@ -45,12 +45,19 @@ fi
 # log directory for this service
 [ -d $OT_CONFIG_DIR/config/$SELF ] || cmd="mkdir -p $OT_CONFIG_DIR/config/$SELF" && run_cmd "$cmd" "Config directory"
 
+# ruby
 [ "`$RBENV local 2>/dev/null`" = "$RUBY_NUM_VER" ] || install_ruby
+
+# fminer
 ( [ -n "`$FIND libfminer/ -name bbrc.so 2>/dev/null`" ] && [ -n "`$FIND libfminer/ -name last.so 2>/dev/null`" ] ) || . ./bin/fminer-install
 
+# self
 echo
 install_with_bundler
 
+# config
+echo '$aa = { :uri => nil }' > $OT_CONFIG_DIR/config/$SELF.rb
+
 echo
 echo "Installation finished."
 echo
diff --git a/bin/fminer-install b/bin/fminer-install
index 5f43624..12d180d 100755
--- a/bin/fminer-install
+++ b/bin/fminer-install
@@ -24,7 +24,7 @@ fi
 
 check_utils "git make sed"
 printf "\n%50s\n" "FMINER"
-local DIR=`pwd`
+DIR=`pwd`
 eval RUBY_INC="-I`dirname $RUBY_DIR/include/ruby*/*linux/ruby`\ -I`dirname $RUBY_DIR/include/ruby*/ruby`"
 eval OPBB_INC="-I/usr/include/openbabel-2.0"
 cmd="$GIT submodule init" && run_cmd "$cmd" "Fminer Init"
diff --git a/config.ru b/config.ru
index 2e5285d..56d5041 100644
--- a/config.ru
+++ b/config.ru
@@ -1,3 +1,4 @@
+SERVICE="algorithm"
 require 'bundler'
 Bundler.require
 require './application.rb'
diff --git a/last-utils b/last-utils
-Subproject cf0238477127e54509b6ab8b5c38f50dd6ffce0
+Subproject 6562a3d581a6141f946098e68fc2a3f80f0446b