diff options
author | Christoph Helma <helma@in-silico.de> | 2010-02-02 17:00:48 +0100 |
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committer | Christoph Helma <helma@in-silico.de> | 2010-02-02 17:00:48 +0100 |
commit | 3d65a42cf68bd5128666d810ec3c29673624ee5d (patch) | |
tree | 741c204dfe70cbe11d20a6f840025fe30699563c /lib | |
parent | e42bf74be6c6cd7001307d5df661665218001d2e (diff) |
centralized database configuration
Diffstat (limited to 'lib')
-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/environment.rb | 22 | ||||
-rw-r--r-- | lib/task.rb | 2 |
5 files changed, 28 insertions, 7 deletions
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/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/task.rb b/lib/task.rb index 24bd944..9e60c2e 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 |