diff options
Diffstat (limited to 'lib')
| -rw-r--r-- | lib/compound.rb | 6 | ||||
| -rw-r--r-- | lib/dataset.rb | 35 | ||||
| -rw-r--r-- | lib/environment.rb | 17 | ||||
| -rw-r--r-- | lib/features.rb | 6 |
4 files changed, 50 insertions, 14 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 6ab78e0..7c7c3d8 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -69,6 +69,12 @@ module OpenTox smarts_array.collect{|s| s if match?(s)}.compact end + # AM + # Match an array of smarts features, returns (0)1 for (non)matching features at each pos + def match_all(smarts_array) + smarts_array.collect{|s| match?(s) ? 1 : 0 } + end + def sdf2inchi(sdf) obconversion(sdf,'sdf','inchi') end diff --git a/lib/dataset.rb b/lib/dataset.rb index 1254992..af72403 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -86,8 +86,10 @@ module OpenTox def get_predicted_class(compound, feature) v = get_value(compound, feature) if v.is_a?(Hash) - if v.has_key?(:classification) - return v[:classification] + k = v.keys.grep(/classification/).first + unless k.empty? + #if v.has_key?(:classification) + return v[k] else return "no classification key" end @@ -103,12 +105,37 @@ module OpenTox end end + # returns regression value + def get_predicted_regression(compound, feature) + v = get_value(compound, feature) + if v.is_a?(Hash) + k = v.keys.grep(/regression/).first + unless k.empty? + return v[k] + else + return "no regression key" + end + elsif v.is_a?(Array) + raise "predicted regression value is an array\n"+ + "value "+v.to_s+"\n"+ + "value-class "+v.class.to_s+"\n"+ + "dataset "+@uri.to_s+"\n"+ + "compound "+compound.to_s+"\n"+ + "feature "+feature.to_s+"\n" + else + return v + end + end + # returns prediction confidence if available def get_prediction_confidence(compound, feature) v = get_value(compound, feature) if v.is_a?(Hash) - if v.has_key?(:confidence) - return v[:confidence].abs + k = v.keys.grep(/confidence/).first + unless k.empty? + #if v.has_key?(:confidence) + return v[k].abs + #return v["http://ot-dev.in-silico.ch/model/lazar#confidence"].abs else # PENDING: return nil isntead of raising an exception raise "no confidence key" diff --git a/lib/environment.rb b/lib/environment.rb index b53167b..abc7287 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -41,7 +41,7 @@ if @@config[:database] end end -# mail for error messages +# load mail settings for error messages load File.join config_dir,"mail.rb" if File.exists?(File.join config_dir,"mail.rb") # hack: store sinatra in global var to make url_for and halt methods accessible @@ -107,12 +107,11 @@ end logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log" LOGGER = MyLogger.new(logfile,'daily') # daily rotation -LOGGER.level = Logger::WARN if ENV["RACK_ENV"] == 'production' - -#LOGGER = MyLogger.new(STDOUT) -#LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " - -#LOGGER.level = Logger::DEBUG +if @@config[:logger] and @@config[:logger] == "debug" + LOGGER.level = Logger::DEBUG +else + LOGGER.level = Logger::WARN +end if File.exist?(user_file) @@users = YAML.load_file(user_file) @@ -137,8 +136,8 @@ OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#' XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#' # Regular expressions for parsing classification data -TRUE_REGEXP = /^(true|active|$1^)/ -FALSE_REGEXP = /^(false|inactive|$0^)/ +TRUE_REGEXP = /^(true|active|1|1.0)$/i +FALSE_REGEXP = /^(false|inactive|0|0.0)$/i # Task durations DEFAULT_TASK_MAX_DURATION = @@config[:default_task_max_duration] diff --git a/lib/features.rb b/lib/features.rb index c56f3e4..0fa1cf0 100644 --- a/lib/features.rb +++ b/lib/features.rb @@ -1,3 +1,7 @@ +# CH: should go into validation service +# - not a complete OT object +# - only used twice +# - what about ./validation/validation/validation_service.rb:241: value = OpenTox::Feature.new(:uri => a.uri).value(prediction_feature).to_s module OpenTox module Feature @@ -12,4 +16,4 @@ module OpenTox end end -end
\ No newline at end of file +end |