diff options
Diffstat (limited to 'dataset.rb')
| -rw-r--r-- | dataset.rb | 159 |
1 files changed, 6 insertions, 153 deletions
@@ -39,6 +39,10 @@ class Dataset @@redis.set_members "datasets" end + def member?(uri) + @@redis.set_member? @uri, uri + end + def add(member_uri) @@redis.set_add @uri , member_uri @members << member_uri @@ -65,8 +69,8 @@ class Dataset p_sum_union = 0.0 p_sum_intersect = 0.0 - union.each{ |f| p_sum_union += OpenTox::Utils::gauss(Feature.value(f,'p_value').to_f) } - intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(Feature.value(f,'p_value').to_f) } + union.each{ |f| p_sum_union += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) } + intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) } "#{p_sum_intersect/p_sum_union}" end @@ -77,154 +81,3 @@ class Dataset end -=begin -class Dataset - - include OpenTox::Utils - attr_reader :uri, :name - - def initialize(uri) - @name = File.basename(uri) - @uri = uri - @members = [] - end - - def self.create(uri) - dataset = Dataset.new(uri) - dataset.save - dataset - end - - def self.find(uri) - if @@redis.set_member? "datasets", uri - Dataset.new(uri) - else - nil - end - end - - def self.exists?(uri) - @@redis.set_member? "datasets", uri - end - - def self.find_all - @@redis.set_members("datasets") - end - - def save - @@redis.set_add "datasets", @uri - end - - def destroy - @@redis.set_members(@uri + '::compounds').each do |compound_uri| - @@redis.delete @uri + '::' + compound_uri - end - @@redis.delete @uri + '::compounds' - @@redis.set_members(@uri + '::features').each do |feature_uri| - @@redis.delete @uri + '::' + feature_uri - end - @@redis.delete @uri + '::features' - @@redis.set_delete "datasets", @uri - end - - def add(compound_uri,feature_uri) - @@redis.set_add @uri + '::compounds', compound_uri - @@redis.set_add @uri + '::features', feature_uri - @@redis.set_add @uri + '::' + compound_uri + '::features', feature_uri - @@redis.set_add @uri + '::' + feature_uri + '::compounds', compound_uri - end - - def compound_uris - @@redis.set_members(@uri + "::compounds") - end - - def feature_uris - @@redis.set_members(@uri + "::features") - end - - def feature_uris_for_compound(compound_uri) - @@redis.set_members(@uri + '::' + compound_uri + '::features') - end - - def compound_uris_for_feature(feature_uri) - @@redis.set_members(@uri + '::' + feature_uri + '::compounds') - end - - def self.tanimoto(features) - raise "Exactly 2 compounds are needed for similarity calculations" unless features.size == 2 - compound_keys = features.collect{ |f| f[:dataset_uri] + '::' + f[:compound_uri] + "::features" } - union_size = @@redis.set_union(compound_keys[0], compound_keys[1]).size - intersect_size = @@redis.set_intersect(compound_keys[0], compound_keys[1]).size - intersect_size.to_f/union_size.to_f - end - - def self.weighted_tanimoto(features) - raise "Exactly 2 compounds are needed for similarity calculations" unless features.size == 2 - compound_keys = features.collect{ |f| f[:dataset_uri] + '::' + f[:compound_uri] + "::features" } - union = @@redis.set_union(compound_keys[0], compound_keys[1]) - intersect = @@redis.set_intersect(compound_keys[0], compound_keys[1]) - - p_sum_union = 0.0 - p_sum_intersect = 0.0 - - union.each{ |f| p_sum_union += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) } - intersect.each{ |f| p_sum_intersect += OpenTox::Utils::gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) } - "#{p_sum_intersect/p_sum_union}" - end - -end - -class Dataset - - attr_accessor :uri, :set_uris - - def initialize(uri, set_uris) - @uri = uri - @set_uris = set_uris - end - - def self.create(uri, set_uris) - collection = DatasetCollection.new(uri, set_uris) - collection.save - collection - end - - def self.find(uri) - if @@redis.set_member? "collections", uri - set_uris = @@redis.set_members uri - DatasetCollection.new(uri, set_uris) - else - nil - end - end - - def self.exists?(uri) - @@redis.set_member? "collections", uri - end - - def self.find_all - @@redis.set_members("collections").collect{ |uri| self.find(uri) } - end - - def save - @@redis.set_add "collections", @uri - @set_uris.each do |uri| - @@redis.set_add @uri + '::sets', uri - end - end - - def destroy - @set_uris.each do |uri| - Dataset.new(uri).destroy - end - @@redis.delete @uri + '::sets' - @@redis.set_delete "collections", @uri - end - - def add(set_uri) - @set_uris << set_uri - @@redis.set_add @uri, set_uri - end - -end -=end |