diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 34 |
1 files changed, 28 insertions, 6 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index bd523a3..b5b2e06 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -1,3 +1,5 @@ +LOGGER.progname = File.expand_path(__FILE__) + module OpenTox class Dataset @@ -14,6 +16,8 @@ module OpenTox data_entry = @model.subject OT['compound'], compound if data_entry.nil? data_entry = @model.create_resource + dataset = @model.subject(RDF['type'],OT[self.owl_class]) + @model.add dataset, OT['dataEntry'], data_entry @model.add data_entry, RDF['type'], OT["DataEntry"] @model.add data_entry, OT['compound'], compound end @@ -29,6 +33,8 @@ module OpenTox data_entry = @model.subject OT['compound'], compound if data_entry.nil? data_entry = @model.create_resource + dataset = @model.subject(RDF['type'],OT[self.owl_class]) + @model.add dataset, OT['dataEntry'], data_entry @model.add data_entry, RDF['type'], OT["DataEntry"] @model.add data_entry, OT['compound'], compound end @@ -57,7 +63,7 @@ module OpenTox def find_or_create_compound(uri) compound = @model.subject(DC["identifier"], uri) if compound.nil? - compound = @model.create_resource + compound = @model.create_resource(uri) @model.add compound, RDF['type'], OT["Compound"] @model.add compound, DC["identifier"], uri end @@ -68,7 +74,7 @@ module OpenTox def find_or_create_feature(uri) feature = @model.subject(DC["identifier"], uri) if feature.nil? - feature = @model.create_resource + feature = @model.create_resource(uri) @model.add feature, RDF['type'], OT["Feature"] @model.add feature, DC["identifier"], uri @model.add feature, DC["title"], File.basename(uri).split(/#/)[1] @@ -78,7 +84,8 @@ module OpenTox end def self.create(data, content_type = 'application/rdf+xml') - uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type + resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) + uri = resource.post data, :content_type => content_type dataset = Dataset.new dataset.read uri.to_s dataset @@ -86,7 +93,9 @@ module OpenTox def self.find(uri) dataset = Dataset.new + LOGGER.debug "Getting data from #{uri}" data = `curl "#{uri}"` + #LOGGER.debug data #data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb dataset.rdf = data dataset @@ -152,11 +161,24 @@ module OpenTox # Delete a dataset def delete - RestClient.delete @uri - end + resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) + resource.delete + end def save - RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s + LOGGER.debug "Saving dataset" + #task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type => "application/rdf+xml").to_s + task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.rdf, :content_type => "application/rdf+xml").to_s + task = OpenTox::Task.find(task_uri) + LOGGER.debug "Waiting for task #{task_uri}" + task.wait_for_completion + LOGGER.debug "Dataset task #{task_uri} completed" + if task.failed? + LOGGER.error "Saving dataset failed" + task.failed + exit + end + task.resource end def to_yaml |