From 5a743cbe5fb69dcb86bf16f7a9437a188fc975d3 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 7 May 2010 15:36:40 +0200 Subject: Initial changes from Martin merged --- lazar.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'lazar.rb') diff --git a/lazar.rb b/lazar.rb index fd0067c..5d3eea6 100644 --- a/lazar.rb +++ b/lazar.rb @@ -136,9 +136,9 @@ get '/:id/algorithm/?' do YAML.load(Lazar.get(params[:id]).yaml).algorithm end -get '/:id/training_dataset/?' do +get '/:id/trainingDataset/?' do response['Content-Type'] = 'text/plain' - YAML.load(Lazar.get(params[:id]).yaml).activity_dataset_uri + YAML.load(Lazar.get(params[:id]).yaml).trainingDataset end get '/:id/feature_dataset/?' do -- cgit v1.2.3 From b45adee3aaf134dd240d19cf5b19cf3348030107 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 12 May 2010 12:31:40 +0200 Subject: Modification for new RestClient: body instead of to_s --- lazar.rb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) (limited to 'lazar.rb') diff --git a/lazar.rb b/lazar.rb index 5d3eea6..ef786f0 100644 --- a/lazar.rb +++ b/lazar.rb @@ -57,16 +57,17 @@ class Lazar < Model lazar = YAML.load self.yaml db_activities = lazar.activities[compound_uri] if db_activities - prediction.source = lazar.trainingDataset + prediction.creator = lazar.trainingDataset feature_uri = lazar.dependentVariables prediction.compounds << compound_uri prediction.features << feature_uri prediction.data[compound_uri] = [] unless prediction.data[compound_uri] db_activities.each do |act| - tuple = { - :classification => act, - :confidence => 1} - prediction.data[compound_uri] << {feature_uri => tuple} + prediction.data[compound_uri] << {feature_uri => act} + #tuple = { + # :classification => act} + #:confidence => "experimental"} + #prediction.data[compound_uri] << {feature_uri => tuple} end true else @@ -76,8 +77,8 @@ class Lazar < Model def to_owl data = YAML.load(yaml) - activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) - feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) + activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').body) + feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').body) owl = OpenTox::Owl.create 'Model', uri owl.set("creator","http://github.com/helma/opentox-model") owl.set("title","#{URI.decode(activity_dataset.title)} lazar classification") -- cgit v1.2.3 From 246b58b92fe28c2c7d001d0fd2f1d2f66dd7ecea Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 25 May 2010 19:06:31 +0200 Subject: fix for rdf/xml serialisation (commented, to be tested) --- lazar.rb | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'lazar.rb') diff --git a/lazar.rb b/lazar.rb index ef786f0..5ab9402 100644 --- a/lazar.rb +++ b/lazar.rb @@ -46,6 +46,11 @@ class Lazar < Model :confidence => conf, :similarities => similarities, :features => compound_matches + # uncomment to enable owl-dl serialisation of predictions + # url_for("/lazar#classification") => classification, + # url_for("/lazar#confidence") => conf, + # url_for("/lazar#similarities") => similarities, + # url_for("/lazar#features") => compound_matches } prediction.data[compound_uri] << {feature_uri => tuple} end -- cgit v1.2.3 From 013dd9ea96501a12f28c7d52d8f47ad9febfbf9b Mon Sep 17 00:00:00 2001 From: ch Date: Fri, 28 May 2010 12:24:12 +0200 Subject: catching error during saving prediction dataset --- lazar.rb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'lazar.rb') diff --git a/lazar.rb b/lazar.rb index 5ab9402..9dad1c4 100644 --- a/lazar.rb +++ b/lazar.rb @@ -3,8 +3,6 @@ class Lazar < Model attr_accessor :prediction_dataset def classify(compound_uri,prediction) - - prediction.title += " lazar classification" lazar = YAML.load self.yaml compound = OpenTox::Compound.new(:uri => compound_uri) @@ -171,6 +169,7 @@ post '/:id/?' do # create prediction prediction = OpenTox::Dataset.new prediction.creator = lazar.uri prediction.title = URI.decode YAML.load(lazar.yaml).dependentVariables.split(/#/).last + prediction.title += " lazar classification" if compound_uri lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction) @@ -191,7 +190,11 @@ elsif dataset_uri input_dataset.compounds.each do |compound_uri| lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction) end - uri = prediction.save.chomp + begin + uri = prediction.save.chomp + rescue + halt 500, "Could not save prediction dataset" + end end halt 202,task_uri end -- cgit v1.2.3