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class Dataset
include OpenTox::Utils
attr_reader :uri, :name, :members
def initialize(uri)
@uri = uri
begin
@name = URI.split(uri)[5]
rescue
puts "Bad URI #{uri}"
end
@members = @@redis.set_members(uri)
end
def self.create(uri)
@@redis.set_add "datasets", uri
Dataset.new(uri)
end
def self.find(uri)
if @@redis.set_member? "datasets", uri
Dataset.new(uri)
else
nil
end
end
def self.find_or_create(uri)
dataset = Dataset.create(uri) unless dataset = Dataset.find(uri)
dataset
end
def self.find_all_keys
@@redis.keys "*"
end
def self.find_all
@@redis.set_members "datasets"
end
def add(member_uri)
@@redis.set_add @uri , member_uri
@members << member_uri
end
def union(set_uri)
@@redis.set_union(@uri,set_uri)
end
def intersection(set_uri)
@@redis.set_intersect(@uri,set_uri)
end
def tanimoto(set_uri)
union_size = @@redis.set_union(@uri,set_uri).size
intersect_size = @@redis.set_intersect(@uri,set_uri).size
"#{intersect_size.to_f/union_size.to_f}"
end
def weighted_tanimoto(set_uri)
union = @@redis.set_union(@uri,set_uri)
intersect = @@redis.set_intersect(@uri,set_uri)
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) }
"#{p_sum_intersect/p_sum_union}"
end
def delete
@@redis.delete @uri
@@redis.set_delete "datasets", @uri
end
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
|
