diff options
| -rw-r--r-- | lib/authorization.rb | 4 | ||||
| -rw-r--r-- | lib/dataset.rb | 48 |
2 files changed, 27 insertions, 25 deletions
diff --git a/lib/authorization.rb b/lib/authorization.rb index f9499e6..dab228a 100644 --- a/lib/authorization.rb +++ b/lib/authorization.rb @@ -114,7 +114,9 @@ module OpenTox begin resource = RestClient::Resource.new("#{AA_SERVER}/pol") out = resource.get(:subjectid => subjectid) - return out.split("\n") + return out.split("\n") + rescue RestClient::InternalServerError => e + raise e.response rescue return nil end diff --git a/lib/dataset.rb b/lib/dataset.rb index 7c70c9d..52b41a7 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -14,7 +14,7 @@ module OpenTox # dataset = OpenTox::Dataset.new("http:://webservices.in-silico/ch/dataset/1") # @param [optional, String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object - def initialize(uri=nil) + def initialize(uri=nil,subjectid=nil) super uri @features = {} @compounds = [] @@ -27,7 +27,7 @@ module OpenTox # @param [optional, String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil) - dataset = Dataset.new + dataset = Dataset.new(nil,subjectid) dataset.save(subjectid) dataset end @@ -38,29 +38,29 @@ module OpenTox # - you will have to set remaining metadata manually # @param [String] file CSV file path # @return [OpenTox::Dataset] Dataset object with CSV data - def self.create_from_csv_file(file) - dataset = Dataset.create + def self.create_from_csv_file(file, subjectid=nil) + dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) parser = Parser::Spreadsheets.new parser.dataset = dataset parser.load_csv(File.open(file).read) - dataset.save + dataset.save(subjectid) dataset end # Find a dataset and load all data. This can be time consuming, use Dataset.new together with one of the load_* methods for a fine grained control over data loading. # @param [String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object with all data - def self.find(uri) - dataset = Dataset.new(uri) - dataset.load_all + def self.find(uri, subjectid=nil) + dataset = Dataset.new(uri, subjectid) + dataset.load_all(subjectid) dataset end # Get all datasets from a service # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration # @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server) - def self.all(uri=CONFIG[:services]["opentox-dataset"]) - RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.each_line.collect{|u| Dataset.new(u)} + def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil) + RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u)} end # Load YAML representation into the dataset @@ -89,8 +89,8 @@ module OpenTox # - you will have to set remaining metadata manually # @param [String] csv CSV representation of the dataset # @return [OpenTox::Dataset] Dataset object with CSV data - def load_csv(csv) - save unless @uri # get a uri for creating features + def load_csv(csv, subjectid=nil) + save(subjectid) unless @uri # get a uri for creating features parser = Parser::Spreadsheets.new parser.dataset = self parser.load_csv(csv) @@ -102,8 +102,8 @@ module OpenTox # - you will have to set remaining metadata manually # @param [Excel] book Excel workbook object (created with roo gem) # @return [OpenTox::Dataset] Dataset object with Excel data - def load_spreadsheet(book) - save unless @uri # get a uri for creating features + def load_spreadsheet(book, subjectid=nil) + save(subjectid) unless @uri # get a uri for creating features parser = Parser::Spreadsheets.new parser.dataset = self parser.load_spreadsheet(book) @@ -118,9 +118,9 @@ module OpenTox end # Load all data (metadata, data_entries, compounds and features) from URI - def load_all + def load_all(subjectid=nil) if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)) - copy YAML.load(RestClientWrapper.get(@uri, :accept => "application/x-yaml")) + copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid})) else parser = Parser::Owl::Dataset.new(@uri) copy parser.load_uri @@ -129,8 +129,8 @@ module OpenTox # Load and return only compound URIs from the dataset service # @return [Array] Compound URIs in the dataset - def load_compounds - RestClientWrapper.get(File.join(uri,"compounds"),:accept=> "text/uri-list").to_s.each_line do |compound_uri| + def load_compounds(subjectid=nil) + RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri| @compounds << compound_uri.chomp end @compounds.uniq! @@ -258,7 +258,7 @@ module OpenTox task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset` Task.find(task_uri).wait_for_completion - self.uri = RestClientWrapper.get(task_uri,:accept => 'text/uri-list') + self.uri = RestClientWrapper.get(task_uri,{:accept => 'text/uri-list', :subjectid => subjectid}) end else # create dataset if uri is empty @@ -268,8 +268,8 @@ module OpenTox end # Delete dataset at the dataset service - def delete - RestClientWrapper.delete @uri + def delete(subjectid=nil) + RestClientWrapper.delete(@uri, :subjectid => subjectid) end private @@ -293,9 +293,9 @@ module OpenTox # Find a prediction dataset and load all data. # @param [String] uri Prediction dataset URI # @return [OpenTox::Dataset] Prediction dataset object with all data - def self.find(uri) - prediction = LazarPrediction.new(uri) - prediction.load_all + def self.find(uri, subjectid=nil) + prediction = LazarPrediction.new(uri, subjectid) + prediction.load_all(subjectid) prediction end |