solve merge conflicts

4 files changed, 63 insertions, 10 deletions

diff --git a/VERSION b/VERSION
index 3eefcb9..274edc4 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.0.0
+1.0.0pre1
diff --git a/bin/opentox-server-install b/bin/opentox-server-install
new file mode 100755
index 0000000..e832cd4
--- /dev/null
+++ b/bin/opentox-server-install
@@ -0,0 +1,50 @@
+#!/bin/sh
+
+# Installs Opentox Webservice.
+# Author: Christoph Helma, Andreas Maunz.
+
+SELF=$(basename $0 -install)
+[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
+
+echo
+echo "Welcome to service installation (<Return> to continue)."
+read delete_me
+
+
+# check wd is root of service
+DIR=`pwd`
+if echo $DIR | grep "$SELF/bin" >/dev/null 2>&1 ; then cd ..; fi
+
+# # # Boot the script
+
+# load base config, helper funs, environment
+OT_CONFIG_DIR="$HOME/.opentox"
+! [ -f "$OT_CONFIG_DIR/config/install/config.sh" ] && echo "config.sh not found." 1>&2 && exit 1 || . $OT_CONFIG_DIR/config/install/config.sh
+! [ -f "$OT_PREFIX/install/utils.sh" ] && echo "utils.sh not found." 1>&2 && exit 1 || . $OT_PREFIX/install/utils.sh
+[ -f $OT_CONFIG_DIR/opentox-ui.sh ] && . $OT_CONFIG_DIR/opentox-ui.sh # should have been done by user already
+RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
+
+
+# # # Install
+
+check_utils "rbenv find"
+check_log $SELF
+
+if [ "$OT_BRANCH" = "development" ]; then
+  cmd="test -d $OT_PREFIX/opentox-client" && run_cmd "$cmd" "Opentox-client"
+fi
+
+# Adjust ruby version here!
+RUBY_NUM_VER="1.9.3-p194"
+
+# ruby
+install_ruby
+
+# self
+echo
+install_with_bundler
+
+notify
+
+# return to wd
+cd "$DIR"
diff --git a/lib/4store.rb b/lib/4store.rb
index f6879b0..8715ea7 100644
--- a/lib/4store.rb
+++ b/lib/4store.rb
@@ -29,11 +29,11 @@ module OpenTox
         bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.join(", ")}." unless @@content_type_formats.include? mime_type or mime_type == "multipart/form-data"
         bad_request_error "Reqest body empty." unless rdf 
         mime_type = "application/x-turtle" if mime_type == "text/plain" # ntriples is turtle in 4store
-        #begin
+        begin
           RestClient.post File.join(four_store_uri,"data")+"/", :data => rdf, :graph => uri, "mime-type" => mime_type 
-        #rescue
-          #rest_call_error $!.message, File.join(four_store_uri,"data")+"/"
-        #end
+        rescue
+          bad_request_error $!.message, File.join(four_store_uri,"data")+"/"
+        end
       end
 
       def self.put uri, rdf, mime_type
@@ -41,9 +41,9 @@ module OpenTox
         bad_request_error "Reqest body empty." unless rdf 
         mime_type = "application/x-turtle" if mime_type == "text/plain"
         #begin
-          RestClient.put File.join(four_store_uri,"data",uri), rdf, :content_type => mime_type 
+          RestClientWrapper.put File.join(four_store_uri,"data",uri), rdf, :content_type => mime_type 
         #rescue
-          #rest_call_error $!.message, File.join(four_store_uri,"data",uri)
+          #bad_request_error $!.message, File.join(four_store_uri,"data",uri)
         #end
       end
 
@@ -91,8 +91,8 @@ module OpenTox
           # TODO: check if this prevents SPARQL injections
           bad_request_error "Only SELECT and CONSTRUCT are accepted SPARQL statements."
         end
-      #rescue
-        #rest_call_error $!.message, sparql_uri
+      rescue
+        bad_request_error $!.message, sparql_uri
       end
 
       def self.klass
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 551e318..3fb0088 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,6 +1,6 @@
 require 'sinatra/base'
+require "sinatra/reloader" 
 ENV["RACK_ENV"] ||= "production"
-require "sinatra/reloader" if ENV["RACK_ENV"] == "development"
 require File.join(ENV["HOME"],".opentox","config","default.rb") if File.exist? File.join(ENV["HOME"],".opentox","config","default.rb")
 require File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
 
@@ -21,6 +21,9 @@ module OpenTox
 
     configure :development do
       register Sinatra::Reloader
+      also_reload "./*.rb"
+      also_reload "../opentox-client/lib/*.rb"
+      also_reload File.join(ENV["HOME"],".opentox","config","#{SERVICE}.rb")
     end
 
     before do