diff options
author | Christoph Helma <helma@in-silico.ch> | 2012-02-20 15:15:17 +0000 |
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committer | Christoph Helma <helma@in-silico.ch> | 2012-02-20 15:15:17 +0000 |
commit | cfa65920c08dec306afbce85ba376d348b45b8f3 (patch) | |
tree | adfdf23135efb7a040812e6a25ec54338002c83f /lib |
initial skeleton
Diffstat (limited to 'lib')
-rw-r--r-- | lib/environment.rb | 74 | ||||
-rw-r--r-- | lib/opentox-server.rb | 7 | ||||
-rw-r--r-- | lib/opentox-server/version.rb | 5 |
3 files changed, 86 insertions, 0 deletions
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 |