diff options
author | Christoph Helma <helma@in-silico.ch> | 2010-12-16 16:55:23 +0100 |
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committer | Christoph Helma <helma@in-silico.ch> | 2010-12-16 16:55:23 +0100 |
commit | c923250bccd4023447feb46935f3b59ce5cfb843 (patch) | |
tree | 0a692283d175f0a3f1d4024bc102ce9133ccb2b0 /lib/dataset.rb | |
parent | 2d692f13d3bd0b894f1ec67c4b860a09de3e746c (diff) | |
parent | b22110ae0d8e902d700e0a3dc629ebfde1edfe10 (diff) |
Merge branch 'development' of https://github.com/rautenberg/opentox-ruby into development
Diffstat (limited to 'lib/dataset.rb')
-rw-r--r-- | lib/dataset.rb | 36 |
1 files changed, 16 insertions, 20 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index bbd8b8b..aba7754 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -6,7 +6,6 @@ module OpenTox include OpenTox attr_reader :features, :compounds, :data_entries, :metadata - attr_accessor :token_id # Create dataset with optional URI. Does not load data into the dataset - you will need to execute one of the load_* methods to pull data from a service or to insert it from other representations. # @example Create an empty dataset @@ -15,9 +14,8 @@ 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,token_id=nil) + def initialize(uri=nil) super uri - @token_id = token_id @features = {} @compounds = [] @data_entries = {} @@ -28,10 +26,9 @@ module OpenTox # dataset = OpenTox::Dataset.create # @param [optional, String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object - def self.create(uri=CONFIG[:services]["opentox-dataset"], token_id=nil) + def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil) dataset = Dataset.new - dataset.token_id = token_id if token_id - dataset.save + dataset.save(subjectid) dataset end @@ -41,12 +38,12 @@ 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 @@ -92,8 +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) @@ -105,8 +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) @@ -250,29 +247,29 @@ module OpenTox # - creates a new dataset if uri is not set # - overwrites dataset if uri exists # @return [String] Dataset URI - def save + def save(subjectid=nil) # TODO: rewrite feature URI's ?? @compounds.uniq! if @uri if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)) - RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :token_id => @token_id},self.to_yaml) + RestClientWrapper.post(@uri,{:content_type => "application/x-yaml", :subjectid => subjectid},self.to_yaml) else File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path } - task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list"}).to_s.chomp + 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') end else # create dataset if uri is empty - self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:token_id => @token_id}).to_s.chomp + self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:subjectid => subjectid}).to_s.chomp end @uri end # Delete dataset at the dataset service - def delete - RestClientWrapper.delete @uri + def delete(subjectid=nil) + RestClientWrapper.delete(@uri, :subjectid => subjectid) end private @@ -282,7 +279,6 @@ module OpenTox @data_entries = dataset.data_entries @compounds = dataset.compounds @features = dataset.features - @token_id = dataset.token_id if @uri self.uri = @uri else |