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module ValidationExamples
class Util
@@dataset_uris = {}
@@prediction_features = {}
def self.upload_dataset(file, subjectid=nil, dataset_service=CONFIG[:services]["opentox-dataset"]) #, file_type="application/x-yaml")
raise "File not found: "+file.path.to_s unless File.exist?(file.path)
if @@dataset_uris[file.path.to_s]==nil
LOGGER.debug "uploading file: "+file.path.to_s
if (file.path =~ /yaml$/)
data = File.read(file.path)
#data_uri = OpenTox::RestClientWrapper.post(dataset_service,{:content_type => file_type},data).to_s.chomp
#@@dataset_uris[file.path.to_s] = data_uri
#LOGGER.debug "uploaded dataset: "+data_uri
d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
d.load_yaml(data)
d.save( subjectid )
@@dataset_uris[file.path.to_s] = d.uri
elsif (file.path =~ /csv$/)
d = OpenTox::Dataset.create_from_csv_file(file.path, subjectid)
raise "num features not 1 (="+d.features.keys.size.to_s+"), what to predict??" if d.features.keys.size != 1
@@prediction_features[file.path.to_s] = d.features.keys[0]
@@dataset_uris[file.path.to_s] = d.uri
elsif (file.path =~ /rdf$/)
d = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
d.load_rdfxml_file(file, subjectid)
d.save(subjectid)
@@dataset_uris[file.path.to_s] = d.uri
else
raise "unknown file type: "+file.path.to_s
end
LOGGER.debug "uploaded dataset: "+d.uri
else
LOGGER.debug "file already uploaded: "+@@dataset_uris[file.path.to_s]
end
return @@dataset_uris[file.path.to_s]
end
def self.prediction_feature_for_file(file)
@@prediction_features[file.path.to_s]
end
def self.build_compare_report(validation_examples, subjectid)
@comp = validation_examples[0].algorithm_uri==nil ? :model_uri : :algorithm_uri
return nil if @comp == :model_uri
to_compare = []
validation_examples.each do |v|
to_compare << v.validation_uri if v.validation_uri and v.validation_error==nil
end
return nil if to_compare.size < 2
#begin
return validation_post "report/algorithm_comparison",{ :validation_uris => to_compare.join("\n") }, subjectid
#rescue => ex
#return "error creating comparison report "+ex.message
#end
end
def self.validation_post(uri, params, subjectid, waiting_task=nil )
params[:subjectid] = subjectid if subjectid
if $test_case
$test_case.post uri,params
return wait($test_case.last_response.body)
else
return OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],uri),params,nil,waiting_task).to_s
end
end
def self.validation_get(uri, subjectid, accept_header='application/rdf+xml')
params = {}
params[:subjectid] = subjectid if subjectid
if $test_case
#puts "getting "+uri+","+accept_header
$test_case.get uri,params,'HTTP_ACCEPT' => accept_header
return wait($test_case.last_response.body)
else
params[:accept] = accept_header
return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),params)
end
end
def self.validation_delete(uri, accept_header='application/rdf+xml')
if $test_case
$test_case.delete uri,{:subjectid => SUBJECTID},'HTTP_ACCEPT' => accept_header
return wait($test_case.last_response.body)
else
return OpenTox::RestClientWrapper.delete(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header,:subjectid => SUBJECTID})
end
end
def self.wait(uri)
if uri.task_uri?
task = OpenTox::Task.find(uri.to_s.chomp)
task.wait_for_completion
#raise "task failed: "+uri.to_s+", description: '"+task.description.to_s+"'" if task.error?
LOGGER.error "task failed :\n"+task.to_yaml if task.error?
uri = task.result_uri
end
uri
end
def self.verify_crossvalidation(val_yaml)
val = YAML.load(val_yaml)
#puts val.inspect
assert_integer val["random_seed".to_sym],nil,nil,"random_seed"
assert_boolean val["stratified".to_sym],"stratified"
assert_integer val["num_folds".to_sym],0,1000,"num_folds"
num_folds = val["num_folds".to_sym].to_i
validations = val["validation_uris".to_sym]
assert_int_equal(num_folds, validations.size, "num_folds != validations.size")
end
def self.verify_validation(val_yaml)
val = YAML.load(val_yaml)
#puts val.inspect
assert_integer val["num_instances".to_sym],0,1000,"num_instances"
num_instances = val["num_instances".to_sym].to_i
assert_integer val["num_unpredicted".to_sym],0,num_instances,"num_unpredicted"
num_unpredicted = val["num_unpredicted".to_sym].to_i
assert_float val["percent_unpredicted".to_sym],0,100
assert_float_equal(val["percent_unpredicted".to_sym].to_f,100*num_unpredicted/num_instances.to_f,"percent_unpredicted")
assert_integer val["num_without_class".to_sym],0,num_instances,"num_without_class"
num_without_class = val["num_without_class".to_sym].to_i
assert_float val["percent_without_class".to_sym],0,100
assert_float_equal(val["percent_without_class".to_sym].to_f,100*num_without_class/num_instances.to_f,"percent_without_class")
class_stats = val["classification_statistics".to_sym]
if class_stats
class_value_stats = class_stats["class_value_statistics".to_sym]
class_values = []
class_value_stats.each do |cvs|
class_values << cvs["class_value".to_sym]
end
#puts class_values.inspect
confusion_matrix = class_stats["confusion_matrix".to_sym]
confusion_matrix_cells = confusion_matrix["confusion_matrix_cell".to_sym]
predictions = 0
confusion_matrix_cells.each do |confusion_matrix_cell|
predictions += confusion_matrix_cell["confusion_matrix_value".to_sym].to_i
end
assert_int_equal(predictions, num_instances-num_unpredicted)
else
regr_stats = val["regression_statistics".to_sym]
assert_not_nil regr_stats
end
end
def self.compare_yaml_and_owl(hash, owl, nested_params=[] )
hash.each do |k,v|
p = nested_params + [ k.to_s.to_rdf_format ]
if (v.is_a?(Hash))
compare_yaml_and_owl( v, owl, p )
elsif (v.is_a?(Array))
v.each do |vv|
compare_yaml_and_owl( vv, owl, p )
end
else
owl_value = owl.get_nested( p )
if owl_value.size == 0
raise "owl_value is nil, yaml value is '"+v.to_s+"'" unless v==nil or v.to_s.size==0
elsif owl_value.size == 1
assert_equal(v, owl_value[0], p.join(".")+" (yaml != rdf)")
else
raise p.join(".")+" yaml value '"+v.to_s+"' not included in rdf values '"+
owl_value.inspect+"'" unless owl_value.include?(v)
end
end
end
end
private
def self.assert_not_nil(val,msg_suffix=nil)
raise msg_suffix.to_s+" is nil" if val==nil
end
def self.assert_int_equal(val1,val2,msg_suffix=nil)
assert_equal(val1, val2, msg_suffix)
end
def self.assert_equal(val1,val2,msg_suffix=nil)
raise msg_suffix.to_s+" not equal: "+val1.to_s+" != "+val2.to_s unless val1==val2
end
def self.assert_float_equal(val1,val2,msg_suffix=nil,epsilon=0.0001)
raise msg_suffix.to_s+" not equal: "+val1.to_s+" != "+val2.to_s+", diff:"+(val1-val2).abs.to_s unless (val1-val2).abs<epsilon
end
def self.assert_boolean(bool_val,prop=nil)
raise "'"+bool_val.to_s+"' not an boolean "+prop.to_s unless bool_val.to_s=="true" or bool_val.to_s=="false"
end
def self.assert_integer(string_val, min=nil, max=nil, prop=nil)
raise "'"+string_val.to_s+"' not an integer "+prop.to_s unless string_val.to_i.to_s==string_val.to_s
raise unless string_val.to_i>=min if min!=nil
raise unless string_val.to_i<=max if max!=nil
end
def self.assert_float(string_val, min=nil, max=nil)
raise string_val.to_s+" not a float (!="+string_val.to_f.to_s+")" unless (string_val.to_f.to_s==string_val.to_s || (string_val.to_f.to_s==(string_val.to_s+".0")))
raise unless string_val.to_f>=min if min!=nil
raise unless string_val.to_f<=max if max!=nil
end
end
class ValidationExample
#params
attr_accessor :name,
:prediction_feature,
:algorithm_uri,
:model_uri,
:test_dataset_uri,
:test_dataset_file,
:test_target_dataset_uri,
:test_target_dataset_file,
:training_dataset_uri,
:training_dataset_file,
:dataset_uri,
:dataset_file,
:algorithm_params,
:split_ratio,
:random_seed,
:num_folds,
:stratified,
:subjectid
#results
attr_accessor :validation_uri,
:report_uri,
:validation_error,
:report_error
def upload_files
[[:test_dataset_uri, :test_dataset_file],
[:test_target_dataset_uri, :test_target_dataset_file],
[:training_dataset_uri, :training_dataset_file],
[:dataset_uri, :dataset_file]].each do |a|
uri = a[0]
file = a[1]
if send(uri)==nil and send(file)!=nil
dataset_uri = Util.upload_dataset(send(file), @subjectid)
send("#{uri.to_s}=".to_sym, dataset_uri)
@uploaded_datasets = [] unless @uploaded_datasets
@uploaded_datasets << dataset_uri
end
end
if (params.include?(:prediction_feature) and @prediction_feature==nil and @dataset_uri and @dataset_file)
@prediction_feature = Util.prediction_feature_for_file(@dataset_file)
end
end
def check_requirements
params.each do |r|
raise "values not set: "+r.to_s if send(r)==nil
end
end
def delete
#begin
if @validation_uri =~ /crossvalidation/
cv = "crossvalidation/"
else
cv = ""
end
Util.validation_delete '/'+cv+@validation_uri.split('/')[-1] if @validation_uri
#rescue => ex
#puts "Could not delete validation: "+ex.message
#end
#begin
Util.validation_delete '/report/'+report_type+'/'+@report_uri.split('/')[-1] if @report_uri
#rescue => ex
#puts "Could not delete report:' "+@report_uri+" "+ex.message
#end
@uploaded_datasets.each do |d|
# begin
puts "deleting dataset "+d
OpenTox::RestClientWrapper.delete(d,{:subjectid => SUBJECTID})
# rescue => ex
#puts "Could not delete dataset:' "+d+" "+ex.message
#end
end
end
def report( waiting_task=nil )
#begin
@report_uri = Util.validation_post '/report/'+report_type,{:validation_uris => @validation_uri},@subjectid,waiting_task if @validation_uri
Util.validation_get "/report/"+report_uri.split("/")[-2]+"/"+report_uri.split("/")[-1], @subjectid if @report_uri
#rescue => ex
#puts "could not create report: "+ex.message
#raise ex
#@report_error = ex.message
#end
end
def validate( waiting_task=nil )
#begin
@validation_uri = Util.validation_post '/'+validation_type, get_params, @subjectid, waiting_task
#rescue => ex
#puts "could not validate: "+ex.message
#@validation_error = ex.message
#LOGGER.error ex.message
#end
end
def compare_yaml_vs_rdf
if @validation_uri
yaml = YAML.load(Util.validation_get(@validation_uri.split("/")[-1],@subjectid,'application/x-yaml'))
owl = OpenTox::Owl.from_data(Util.validation_get(@validation_uri.split("/")[-1],@subjectid),@validation_uri,"Validation")
Util.compare_yaml_and_owl(yaml,owl)
end
if @report_uri
yaml = YAML.load(Util.validation_get(@report_uri.split("/")[-3..-1].join("/"),@subjectid,'application/x-yaml'))
owl = OpenTox::Owl.from_data(Util.validation_get(@report_uri.split("/")[-3..-1].join("/"),@subjectid),@report_uri,"ValidationReport")
Util.compare_yaml_and_owl(yaml,owl)
Util.validation_get(@report_uri.split("/")[-3..-1].join("/"),@subjectid,'text/html')
else
puts "no report"
end
end
def verify_yaml
raise "cannot very validation, validation_uri is null" unless @validation_uri
if @validation_uri =~ /crossvalidation/
Util.verify_crossvalidation(Util.validation_get("crossvalidation/"+@validation_uri.split("/")[-1],'application/x-yaml'))
Util.validation_get("crossvalidation/"+@validation_uri.split("/")[-1]+"/statistics",'application/x-yaml')
Util.verify_validation(Util.validation_get("crossvalidation/"+@validation_uri.split("/")[-1]+"/statistics",'application/x-yaml'))
else
Util.verify_validation(Util.validation_get(@validation_uri.split("/")[-1],@subjectid,'application/x-yaml'))
end
end
def title
self.class.humanize
end
protected
def report_type
"validation"
end
def validation_type
""
end
def get_params
p = {}
( params + opt_params ).each do |pp|
p[pp] = send(pp) if send(pp)!=nil
end
return p
end
end
class ModelValidation < ValidationExample
def params
[:model_uri, :test_dataset_uri]
end
def opt_params
[ :prediction_feature, :test_target_dataset_uri ]
end
def validation_type
"test_set_validation"
end
end
class TrainingTestValidation < ValidationExample
def params
[:algorithm_uri, :training_dataset_uri, :test_dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :test_target_dataset_uri ]
end
def validation_type
"training_test_validation"
end
end
class SplitTestValidation < ValidationExample
def params
[:algorithm_uri, :dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :split_ratio, :random_seed ]
end
def validation_type
"training_test_split"
end
end
class BootstrappingValidation < ValidationExample
def params
[:algorithm_uri, :dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :random_seed ]
end
def validation_type
"bootstrapping"
end
end
class CrossValidation < ValidationExample
def params
[:algorithm_uri, :dataset_uri, :prediction_feature]
end
def opt_params
[ :algorithm_params, :num_folds, :stratified, :random_seed ]
end
def report_type
"crossvalidation"
end
def validation_type
"crossvalidation"
end
end
end
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