From 5e8461b65787ac2f4dbb321dd258cee90b4a91ab Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 14 Jun 2012 11:28:01 +0000
Subject: Initial version of 4store based dataset service

---
 Gemfile           |  4 ++++
 Rakefile          |  1 +
 VERSION           |  1 +
 application.rb    | 29 +++++++++++++++++++++++++++++
 config.ru         | 10 ++++------
 data/.gitignore   |  3 ---
 dataset.gemspec   | 25 +++++++++++++++++++++++++
 public/.gitignore |  2 --
 public/robots.txt |  2 --
 9 files changed, 64 insertions(+), 13 deletions(-)
 create mode 100644 Gemfile
 create mode 100644 Rakefile
 create mode 100644 VERSION
 delete mode 100644 data/.gitignore
 create mode 100644 dataset.gemspec
 delete mode 100644 public/.gitignore
 delete mode 100644 public/robots.txt

diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..36f1a90
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source :gemcutter
+gemspec
+gem "opentox-server", :path => "~/opentox-server"
+gem "opentox-client", :path => "~/opentox-client"
diff --git a/Rakefile b/Rakefile
new file mode 100644
index 0000000..2995527
--- /dev/null
+++ b/Rakefile
@@ -0,0 +1 @@
+require "bundler/gem_tasks"
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..3eefcb9
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+1.0.0
diff --git a/application.rb b/application.rb
index bda0ff9..b3e3843 100644
--- a/application.rb
+++ b/application.rb
@@ -1,3 +1,31 @@
+module OpenTox
+  class Application < Service
+
+    # Get metadata of the dataset
+    # @return [application/rdf+xml] Metadata OWL-DL
+    get '/:id/metadata' do
+    end
+
+    # Get a dataset feature
+    # @param [Header] Accept one of `application/rdf+xml or application-x-yaml` (default application/rdf+xml)
+    # @return [application/rdf+xml,application/x-yaml] Feature metadata 
+    get %r{/(\d+)/feature/(.*)$} do |id,feature|
+    end
+
+    # Get a list of all features
+    # @param [Header] Accept one of `application/rdf+xml, application-x-yaml, text/uri-list` (default application/rdf+xml)
+    # @return [application/rdf+xml, application-x-yaml, text/uri-list] Feature list 
+    get '/:id/features' do
+    end
+
+    # Get a list of all compounds
+    # @return [text/uri-list] Feature list 
+    get '/:id/compounds' do
+    end
+  end
+end
+
+=begin
 require 'rubygems'
 gem "opentox-ruby", "~> 3"
 require 'opentox-ruby'
@@ -410,3 +438,4 @@ delete '/?' do
   response['Content-Type'] = 'text/plain'
   "All datasets deleted."
 end
+=end
diff --git a/config.ru b/config.ru
index a1aab0d..39d9385 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,4 @@
-require 'rubygems'
-require 'opentox-ruby'
-require 'config/config_ru'
-run Sinatra::Application
-set :raise_errors, false
-set :show_exceptions, false
\ No newline at end of file
+SERVICE = "dataset"
+require 'bundler'
+Bundler.require
+run OpenTox::Service
diff --git a/data/.gitignore b/data/.gitignore
deleted file mode 100644
index 59e3edd..0000000
--- a/data/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*.rdfxml
-*.xls
-*.yaml
diff --git a/dataset.gemspec b/dataset.gemspec
new file mode 100644
index 0000000..37d2d62
--- /dev/null
+++ b/dataset.gemspec
@@ -0,0 +1,25 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+
+Gem::Specification.new do |s|
+  s.name        = "feature"
+  s.version     = File.read("./VERSION")
+  s.authors     = ["Christoph Helma"]
+  s.email       = ["helma@in-silico.ch"]
+  s.homepage    = ""
+  s.summary     = %q{Simple OpenTox Dataset Service}
+  s.description = %q{TODO: Write a gem description}
+  s.license     = 'GPL-3'
+
+  s.rubyforge_project = "feature"
+
+  s.files         = `git ls-files`.split("\n")
+  #s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  #s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  #s.require_paths = ["lib"]
+  s.required_ruby_version = '>= 1.9.2'
+
+  # specify any dependencies here; for example:
+  s.add_runtime_dependency "opentox-server"
+  s.post_install_message = "Please configure your service in ~/.opentox/config/dataset.rb"
+end
diff --git a/public/.gitignore b/public/.gitignore
deleted file mode 100644
index debc7d4..0000000
--- a/public/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*.rdfxml
-*.xls
diff --git a/public/robots.txt b/public/robots.txt
deleted file mode 100644
index 1f53798..0000000
--- a/public/robots.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-User-agent: *
-Disallow: /
-- 
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