diff options
| -rw-r--r-- | Rakefile | 2 | ||||
| -rw-r--r-- | VERSION | 2 | ||||
| -rw-r--r-- | lib/algorithm.rb | 1 | ||||
| -rw-r--r-- | lib/compound.rb | 10 | ||||
| -rw-r--r-- | lib/config/config_ru.rb (renamed from lib/tasks/config.rb) | 0 | ||||
| -rw-r--r-- | lib/dataset.rb | 2 | ||||
| -rw-r--r-- | lib/environment.rb | 22 | ||||
| -rw-r--r-- | lib/model.rb | 8 | ||||
| -rw-r--r-- | lib/task.rb | 41 | ||||
| -rw-r--r-- | opentox-ruby-api-wrapper.gemspec | 1 |
10 files changed, 65 insertions, 24 deletions
@@ -10,7 +10,7 @@ begin gem.email = "helma@in-silico.ch" gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper" gem.authors = ["Christoph Helma"] - ["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep| + ["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets", "do_sqlite3", "do_postgres"].each do |dep| gem.add_dependency dep end gem.add_development_dependency "cucumber" @@ -1 +1 @@ -1.2.6 +1.2.7 diff --git a/lib/algorithm.rb b/lib/algorithm.rb index c5d162a..25ae4cb 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -39,6 +39,7 @@ module OpenTox end def self.create_model(params) + LOGGER.debug params @uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer") end diff --git a/lib/compound.rb b/lib/compound.rb index 562baaa..56646c0 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -21,20 +21,20 @@ module OpenTox @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) elsif params[:uri] @uri = params[:uri] - if params[:uri].match(/InChI/) # shortcut for IST services + case params[:uri] + when /ambit/ # Ambit does not deliver InChIs reliably + smiles = RestClient.get @uri, :accept => 'chemical/x-daylight-smiles' + @inchi = obconversion(smiles,'smi','inchi') + when /InChI/ # shortcut for IST services @inchi = params[:uri].sub(/^.*InChI/, 'InChI') else @inchi = RestClient.get @uri, :accept => 'chemical/x-inchi' - # AMBIT does not provide InChIs - #smiles = RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output - #@inchi = obconversion(smiles,'smi','inchi') end end end # Get the (canonical) smiles def smiles - #RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output obconversion(@inchi,'inchi','can') end diff --git a/lib/tasks/config.rb b/lib/config/config_ru.rb index 3720ef3..3720ef3 100644 --- a/lib/tasks/config.rb +++ b/lib/config/config_ru.rb diff --git a/lib/dataset.rb b/lib/dataset.rb index 0a49e87..bd523a3 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -87,7 +87,7 @@ module OpenTox def self.find(uri) dataset = Dataset.new data = `curl "#{uri}"` - #data = RestClient.get uri, :accept => 'application/rdf+xml' # unclear why this does not work for complex uris, Dataset.find works from irb + #data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb dataset.rdf = data dataset end diff --git a/lib/environment.rb b/lib/environment.rb index a9d0797..fedc3cf 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -2,7 +2,7 @@ require 'logger' # set default environment ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV'] -# load configuration +# load/setup configuration basedir = File.join(ENV['HOME'], ".opentox") config_dir = File.join(basedir, "config") config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml") @@ -19,6 +19,26 @@ else puts "Please edit #{config_file} and restart your application." exit end + +# database +if @@config[:database] + ['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types'].each{|lib| require lib } + case @@config[:database][:adapter] + when /sqlite/i + db_dir = File.join(basedir, "db") + FileUtils.mkdir_p db_dir + DataMapper::setup(:default, "sqlite3://#{db_dir}/opentox.sqlite3") + else + DataMapper.setup(:default, { + :adapter => @@config[:database][:adapter], + :database => @@config[:database][:database], + :username => @@config[:database][:username], + :password => @@config[:database][:password], + :host => @@config[:database][:host]}) + end +end + +# logging logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log" LOGGER = Logger.new(logfile,'daily') # daily rotation LOGGER.level = Logger::DEBUG diff --git a/lib/model.rb b/lib/model.rb index bd9d546..a585b59 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -50,6 +50,14 @@ module OpenTox RestClient.post(@@config[:services]["opentox-model"], data, :content_type => "application/x-yaml").to_s end +# def self.create(task) +# @uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri) +# end + +# def yaml=(data) +# RestClient.put(@@uri, data, :content_type => "application/x-yaml").to_s +# end + def endpoint YAML.load(RestClient.get(uri))[:endpoint] end diff --git a/lib/task.rb b/lib/task.rb index 24bd944..70d22bf 100644 --- a/lib/task.rb +++ b/lib/task.rb @@ -10,7 +10,7 @@ module OpenTox end def self.create - uri = RestClient.post @@config[:services]["opentox-task"], nil + uri = RestClient.post @@config[:services]["opentox-task"], {} Task.new(uri) end @@ -26,19 +26,6 @@ module OpenTox task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/) task_uris.collect{|uri| Task.new(uri)} end - - def started - #LOGGER.info File.join(@uri,'started') - RestClient.put File.join(@uri,'started'), {} - end - - def cancel - RestClient.put File.join(@uri,'cancelled'), {} - end - - def completed(uri) - RestClient.put File.join(@uri,'completed'), :resource => uri - end def created_at RestClient.get File.join(@uri, 'created_at') @@ -55,6 +42,26 @@ module OpenTox def resource RestClient.get File.join(@uri, 'resource') end + + def started + RestClient.put File.join(@uri,'started'), {} + end + + def cancel + RestClient.put File.join(@uri,'cancelled'), {} + end + + def failed + RestClient.put File.join(@uri,'failed'), {} + end + + def parent=(task) + RestClient.put File.join(@uri,'parent'), {:uri => task.uri} + end + + def completed(uri) + RestClient.put File.join(@uri,'completed'), :resource => uri + end def pid=(pid) RestClient.put File.join(@uri, 'pid'), :pid => pid @@ -64,8 +71,12 @@ module OpenTox self.status.to_s == 'completed' end + def failed? + self.status.to_s == 'failed' + end + def wait_for_completion - until self.completed? + until self.completed? or self.failed? sleep 1 end end diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec index c8a0c1a..75f5d6b 100644 --- a/opentox-ruby-api-wrapper.gemspec +++ b/opentox-ruby-api-wrapper.gemspec @@ -26,6 +26,7 @@ Gem::Specification.new do |s| "bin/yaml2owl.rb", "lib/algorithm.rb", "lib/compound.rb", + "lib/config/config_ru.rb", "lib/config/database.rb", "lib/dataset.rb", "lib/environment.rb", |