From cfa65920c08dec306afbce85ba376d348b45b8f3 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 20 Feb 2012 15:15:17 +0000
Subject: initial skeleton

---
 .gitignore                    |  4 +++
 Gemfile                       |  4 +++
 Rakefile                      |  1 +
 lib/environment.rb            | 74 +++++++++++++++++++++++++++++++++++++++++++
 lib/opentox-server.rb         |  7 ++++
 lib/opentox-server/version.rb |  5 +++
 opentox-server.gemspec        | 29 +++++++++++++++++
 7 files changed, 124 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 Gemfile
 create mode 100644 Rakefile
 create mode 100644 lib/environment.rb
 create mode 100644 lib/opentox-server.rb
 create mode 100644 lib/opentox-server/version.rb
 create mode 100644 opentox-server.gemspec

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..4040c6c
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+*.gem
+.bundle
+Gemfile.lock
+pkg/*
diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..2bdc706
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+# Specify your gem's dependencies in opentox-server.gemspec
+gemspec
+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/lib/environment.rb b/lib/environment.rb
new file mode 100644
index 0000000..300c431
--- /dev/null
+++ b/lib/environment.rb
@@ -0,0 +1,74 @@
+# set default environment
+
+ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV']
+
+# load/setup configuration
+basedir = File.join(ENV['HOME'], ".toxbank")
+config_dir = File.join(basedir, "config")
+config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
+
+TMP_DIR = File.join(basedir, "tmp")
+LOG_DIR = File.join(basedir, "log")
+
+if File.exist?(config_file)
+	CONFIG = YAML.load_file(config_file)
+  raise "could not load config, config file: "+config_file.to_s unless CONFIG
+else
+	FileUtils.mkdir_p TMP_DIR
+	FileUtils.mkdir_p LOG_DIR
+	FileUtils.mkdir_p config_dir
+	puts "Please edit #{config_file} and restart your application."
+	#exit
+end
+
+logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
+#LOGGER = OTLogger.new(logfile,'daily') # daily rotation
+LOGGER = OTLogger.new(logfile) # no rotation
+LOGGER.formatter = Logger::Formatter.new #this is neccessary to restore the formating in case active-record is loaded
+if CONFIG[:logger] and CONFIG[:logger] == "debug"
+	LOGGER.level = Logger::DEBUG
+else
+	LOGGER.level = Logger::WARN 
+end
+
+# Regular expressions for parsing classification data
+TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
+
+# OWL Namespaces
+=begin
+class OwlNamespace
+
+  attr_accessor :uri
+  def initialize(uri)
+    @uri = uri
+  end
+
+  def [](property)
+    @uri+property.to_s
+  end
+
+  def type # for RDF.type
+    "#{@uri}type"
+  end
+
+  def method_missing(property)
+    @uri+property.to_s
+  end
+
+end
+=end
+
+AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil
+CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request]
+CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
+CONFIG[:authorization][:free_request] =  [""] unless CONFIG[:authorization][:free_request]
+
+#RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+#OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#'
+#DC =  OwlNamespace.new 'http://purl.org/dc/elements/1.1/'
+#OT =  OwlNamespace.new 'http://www.opentox.org/api/1.1#'
+#OTA =  OwlNamespace.new 'http://www.opentox.org/algorithmTypes.owl#'
+#XSD = OwlNamespace.new 'http://www.w3.org/2001/XMLSchema#'
+
+
diff --git a/lib/opentox-server.rb b/lib/opentox-server.rb
new file mode 100644
index 0000000..fa8a37f
--- /dev/null
+++ b/lib/opentox-server.rb
@@ -0,0 +1,7 @@
+require "opentox-client"
+require 'rack'
+require 'rack/contrib'
+require 'sinatra'
+require 'sinatra/url_for'
+require File.join(File.dirname(__FILE__),"environment.rb")
+
diff --git a/lib/opentox-server/version.rb b/lib/opentox-server/version.rb
new file mode 100644
index 0000000..a637142
--- /dev/null
+++ b/lib/opentox-server/version.rb
@@ -0,0 +1,5 @@
+module Opentox
+  module Server
+    VERSION = "0.0.1"
+  end
+end
diff --git a/opentox-server.gemspec b/opentox-server.gemspec
new file mode 100644
index 0000000..66d4852
--- /dev/null
+++ b/opentox-server.gemspec
@@ -0,0 +1,29 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "opentox-server/version"
+
+Gem::Specification.new do |s|
+  s.name        = "opentox-server"
+  s.version     = Opentox::Server::VERSION
+  s.authors     = ["Christoph Helma"]
+  s.email       = ["helma@in-silico.ch"]
+  s.homepage    = ""
+  s.summary     = %q{Ruby library for opentox services}
+  s.description = %q{Ruby library for opentox services}
+
+  s.rubyforge_project = "opentox-server"
+
+  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"]
+
+  # specify any dependencies here; for example:
+  s.add_runtime_dependency "opentox-client"
+  s.add_runtime_dependency 'rack'
+  s.add_runtime_dependency 'rack-contrib'
+  s.add_runtime_dependency 'sinatra'
+  s.add_runtime_dependency 'emk-sinatra-url-for'
+  s.add_runtime_dependency 'spreadsheet'
+  s.add_runtime_dependency 'roo'
+end
-- 
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