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authormguetlein <martin.guetlein@gmail.com>2011-04-08 15:39:55 +0200
committermguetlein <martin.guetlein@gmail.com>2011-05-03 11:46:30 +0200
commit78751b778a5dabfac142a017fc1e0d8d1c045acd (patch)
tree6257c90d38d1082637a65e3846944bd313464edd /validation/validation_service.rb
parentd5fe870fa184ef44390a0311664b7813360a44f5 (diff)
switch from datamapper/mysql to redis (sqlite for qmrf)
Diffstat (limited to 'validation/validation_service.rb')
-rwxr-xr-xvalidation/validation_service.rb53
1 files changed, 25 insertions, 28 deletions
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index a1efba5..93c167f 100755
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -30,7 +30,7 @@ end
module Validation
- class Validation < Lib::Validation
+ class Validation
# constructs a validation object, Rsets id und uri
#def initialize( params={} )
@@ -43,7 +43,7 @@ module Validation
# deletes a validation
# PENDING: model and referenced datasets are deleted as well, keep it that way?
- def delete( delete_all=true )
+ def delete_validation( delete_all=true )
if (delete_all)
to_delete = [:model_uri, :training_dataset_uri, :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri ]
case self.validation_type
@@ -72,7 +72,7 @@ module Validation
end
end
end
- self.destroy
+ self.delete
if (subjectid)
begin
res = OpenTox::Authorization.delete_policies_from_uri(validation_uri, subjectid)
@@ -222,17 +222,13 @@ module Validation
# :percent_unpredicted => prediction.percent_unpredicted,
# :finished => true}
# self.save!
- self.attributes= {:num_instances => prediction.num_instances,
+ self.update :num_instances => prediction.num_instances,
:num_without_class => prediction.num_without_class,
:percent_without_class => prediction.percent_without_class,
:num_unpredicted => prediction.num_unpredicted,
:percent_unpredicted => prediction.percent_unpredicted,
- :finished => true}
- begin
- self.save
- rescue DataMapper::SaveFailureError => e
- raise "could not save validation: "+e.resource.errors.inspect
- end
+ :finished => true
+ raise unless self.valid?
end
task.progress(100) if task
@@ -240,7 +236,7 @@ module Validation
end
end
- class Crossvalidation < Lib::Crossvalidation
+ class Crossvalidation
# constructs a crossvalidation, id and uri are set
#def initialize( params={} )
@@ -262,12 +258,12 @@ module Validation
end
# deletes a crossvalidation, all validations are deleted as well
- def delete
- Validation.all(:crossvalidation_id => self.id).each do |v|
+ def delete_crossvalidation
+ Validation.find(:crossvalidation_id => self.id).each do |v|
v.subjectid = self.subjectid
- v.delete
+ v.delete_validation
end
- self.destroy
+ self.delete
if (subjectid)
begin
res = OpenTox::Authorization.delete_policies_from_uri(crossvalidation_uri, subjectid)
@@ -281,6 +277,9 @@ module Validation
# creates the cv folds
def create_cv_datasets( prediction_feature, task=nil )
+ self.random_seed = 1 unless self.random_seed
+ self.num_folds = 10 unless self.num_folds
+ self.stratified = false unless self.stratified
if copy_cv_datasets( prediction_feature )
# dataset folds of a previous crossvalidaiton could be used
task.progress(100) if task
@@ -296,7 +295,7 @@ module Validation
i = 0
task_step = 100 / self.num_folds.to_f;
@tmp_validations.each do | val |
- validation = Validation.new val
+ validation = Validation.create val
validation.subjectid = self.subjectid
validation.validate_algorithm( algorithm_params,
OpenTox::SubTask.create(task, i * task_step, ( i + 1 ) * task_step) )
@@ -316,8 +315,7 @@ module Validation
# copies datasets from an older crossvalidation on the same dataset and the same folds
# returns true if successfull, false otherwise
def copy_cv_datasets( prediction_feature )
-
- cvs = Crossvalidation.all( {
+ cvs = Crossvalidation.find( {
:dataset_uri => self.dataset_uri,
:num_folds => self.num_folds,
:stratified => self.stratified,
@@ -332,7 +330,7 @@ module Validation
OpenTox::Dataset.exist?(v.training_dataset_uri,self.subjectid) and
OpenTox::Dataset.exist?(v.test_dataset_uri,self.subjectid)
#make sure self.id is set
- self.save if self.new?
+ #self.save if self.new?
tmp_val << { :validation_type => "crossvalidation",
:training_dataset_uri => v.training_dataset_uri,
:test_dataset_uri => v.test_dataset_uri,
@@ -354,16 +352,14 @@ module Validation
# creates cv folds (training and testdatasets)
# stores uris in validation objects
def create_new_cv_datasets( prediction_feature, task = nil )
-
- raise "random seed not set "+self.inspect unless self.random_seed
LOGGER.debug "creating datasets for crossvalidation"
orig_dataset = OpenTox::Dataset.find(self.dataset_uri,self.subjectid)
raise OpenTox::NotFoundError.new "Dataset not found: "+self.dataset_uri.to_s unless orig_dataset
shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed )
- unless self.stratified
- split_compounds = shuffled_compounds.chunk( self.num_folds )
+ unless self.stratified
+ split_compounds = shuffled_compounds.chunk( self.num_folds.to_i )
else
class_compounds = {} # "inactive" => compounds[], "active" => compounds[] ..
shuffled_compounds.each do |c|
@@ -406,7 +402,7 @@ module Validation
@tmp_validations = []
- (1..self.num_folds).each do |n|
+ (1..self.num_folds.to_i).each do |n|
datasetname = 'cv'+self.id.to_s +
#'_d'+orig_dataset.name.to_s +
@@ -418,7 +414,7 @@ module Validation
test_compounds = []
train_compounds = []
- (1..self.num_folds).each do |nn|
+ (1..self.num_folds.to_i).each do |nn|
compounds = split_compounds.at(nn-1)
if n == nn
@@ -428,7 +424,7 @@ module Validation
end
end
- raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds - test_compounds.size).abs <= 1
+ raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds.to_i - test_compounds.size).abs <= 1
raise "internal error, num train compounds not correct" unless shuffled_compounds.size - test_compounds.size == train_compounds.size
LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compounds.size.to_s
@@ -442,7 +438,7 @@ module Validation
{ DC.title => datasetname + '_test', DC.creator => source }, self.subjectid ).uri
#make sure self.id is set
- self.save if self.new?
+ #self.save if self.new?
tmp_validation = { :validation_type => "crossvalidation",
:training_dataset_uri => train_dataset_uri,
:test_dataset_uri => test_dataset_uri,
@@ -551,9 +547,10 @@ module Validation
# splits a dataset into test and training dataset
# returns map with training_dataset_uri and test_dataset_uri
def self.train_test_dataset_split( orig_dataset_uri, prediction_feature, subjectid, split_ratio=nil, random_seed=nil, task=nil )
-
split_ratio=0.67 unless split_ratio
+ split_ratio = split_ratio.to_f
random_seed=1 unless random_seed
+ random_seed = random_seed.to_i
orig_dataset = OpenTox::Dataset.find orig_dataset_uri, subjectid
orig_dataset.load_all subjectid