diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 75 |
1 files changed, 57 insertions, 18 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index 4005c1c..5ebad0f 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -102,6 +102,13 @@ module OpenTox copy parser.load_uri(subjectid) end + def load_sdf(sdf,subjectid=nil) + save(subjectid) unless @uri # get a uri for creating features + parser = Parser::Sdf.new + parser.dataset = self + parser.load_sdf(sdf) + end + # Load CSV string (format specification: http://toxcreate.org/help) # - loads data_entries, compounds, features # - sets metadata (warnings) for parser errors @@ -149,7 +156,11 @@ module OpenTox # Load and return only compound URIs from the dataset service # @return [Array] Compound URIs in the dataset def load_compounds(subjectid=nil) - RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri| + # fix for datasets like http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50 + u = URI::parse(uri) + u.path = File.join(u.path,"compounds") + u = u.to_s + RestClientWrapper.get(u,{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri| @compounds << compound_uri.chomp end @compounds.uniq! @@ -167,19 +178,15 @@ module OpenTox @features end - def feature_classes(feature, subjectid=nil) - if Feature.find(feature, subjectid).feature_type == "classification" - classes = [] - @data_entries.each do |c,e| - e[feature].each { |v| classes << v.to_s } - end - classes.uniq.sort - else - nil - end + # returns the accept_values of a feature, i.e. the classification domain / all possible feature values + # @param [String] feature the URI of the feature + # @return [Array] return array with strings, nil if value is not set (e.g. when feature is numeric) + def accept_values(feature) + accept_values = features[feature][OT.acceptValue] + accept_values.sort if accept_values + accept_values end -=begin # Detect feature type(s) in the dataset # @return [String] `classification", "regression", "mixed" or unknown` def feature_type(subjectid=nil) @@ -193,6 +200,7 @@ module OpenTox "unknown" end end +=begin =end # Get Spreadsheet representation @@ -229,6 +237,30 @@ module OpenTox s.to_rdfxml end + # Get SDF representation of compounds + # @return [String] SDF representation + def to_sdf + sum="" + @compounds.each{ |c| + sum << OpenTox::Compound.new(c).to_inchi + sum << OpenTox::Compound.new(c).to_sdf.sub(/\n\$\$\$\$/,'') + @data_entries[c].each{ |f,v| + sum << "> <\"#{f}\">\n" + sum << v.join(", ") + sum << "\n\n" + } + sum << "$$$$\n" + } + sum + end + + def to_urilist + @compounds.inject { |sum, c| + sum << OpenTox::Compound.new(c).uri + sum + "\n" + } + end + # Get name (DC.title) of a feature # @param [String] feature Feature URI # @return [String] Feture title @@ -307,6 +339,12 @@ module OpenTox end end end + # set feature metadata in new dataset accordingly (including accept values) + features.each do |f| + self.features[f].each do |k,v| + dataset.features[f][k] = v + end + end dataset.add_metadata(metadata) dataset.save(subjectid) dataset @@ -369,12 +407,14 @@ module OpenTox end def value(compound) - @data_entries[compound.uri].collect{|f,v| v.first if f.match(/prediction/)}.compact.first + v = nil + v = @data_entries[compound.uri].collect{|f,v| v.first if f.match(/value/)}.compact.first if @data_entries[compound.uri] + v = nil if v.is_a? Array and v.empty? + v end def confidence(compound) - feature_uri = @data_entries[compound.uri].collect{|f,v| f if f.match(/prediction/)}.compact.first - @features[feature_uri][OT.confidence] + @data_entries[compound.uri].collect{|f,v| v.first if f.match(/confidence/)}.compact.first if @data_entries[compound.uri] end def descriptors(compound) @@ -382,12 +422,11 @@ module OpenTox end def measured_activities(compound) - source = @metadata[OT.hasSource] - @data_entries[compound.uri].collect{|f,v| v if f.match(/#{source}/)}.compact.flatten + @data_entries[compound.uri].collect{|f,v| v if f.match(/#{@metadata[OT.hasSource]}/)}.compact.flatten if @data_entries[compound.uri] end def neighbors(compound) - @data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/neighbor/)}.compact + @data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/neighbor/)}.compact if @data_entries[compound.uri] end # def errors(compound) |