From 0b936c71d8a1d5effa6c29d5ee9c227fff18a070 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Mon, 23 May 2011 14:03:02 +0000 Subject: owl-dl fixed for model and prediction datasets --- lib/dataset.rb | 7 ++- lib/model.rb | 136 ++++++++++++++++++++++++++++++------------------------ lib/serializer.rb | 27 +++++++---- 3 files changed, 95 insertions(+), 75 deletions(-) (limited to 'lib') diff --git a/lib/dataset.rb b/lib/dataset.rb index 4005c1c..4dc4296 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -179,7 +179,6 @@ module OpenTox end end -=begin # Detect feature type(s) in the dataset # @return [String] `classification", "regression", "mixed" or unknown` def feature_type(subjectid=nil) @@ -193,6 +192,7 @@ module OpenTox "unknown" end end +=begin =end # Get Spreadsheet representation @@ -369,12 +369,11 @@ module OpenTox end def value(compound) - @data_entries[compound.uri].collect{|f,v| v.first if f.match(/prediction/)}.compact.first + @data_entries[compound.uri].collect{|f,v| v.first if f.match(/value/)}.compact.first 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 end def descriptors(compound) diff --git a/lib/model.rb b/lib/model.rb index 998d2dc..d46152d 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -164,8 +164,6 @@ module OpenTox features = {} unless @prediction_dataset - #@prediction_dataset = cached_prediction - #return @prediction_dataset if cached_prediction @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) @prediction_dataset.add_metadata( { OT.hasSource => @uri, @@ -237,38 +235,90 @@ module OpenTox prediction = eval("#{@prediction_algorithm}(@neighbors,{:similarity_algorithm => @similarity_algorithm, :p_values => @p_values})") end - prediction_feature_uri = File.join( @prediction_dataset.uri, "feature", "prediction", File.basename(@metadata[OT.dependentVariables]),@prediction_dataset.compounds.size.to_s) - # TODO: fix dependentVariable - @prediction_dataset.metadata[OT.dependentVariables] = prediction_feature_uri + # TODO: reasonable feature name + #prediction_feature_uri = File.join( @prediction_dataset.uri, "feature", "prediction", File.basename(@metadata[OT.dependentVariables]),@prediction_dataset.compounds.size.to_s) + value_feature_uri = File.join( @prediction_dataset.uri, "feature", "prediction", File.basename(@metadata[OT.dependentVariables]),"value") + confidence_feature_uri = File.join( @prediction_dataset.uri, "feature", "prediction", File.basename(@metadata[OT.dependentVariables]),"confidence") + prediction_feature_uris = {value_feature_uri => prediction[:prediction], confidence_feature_uri => prediction[:confidence]} + prediction_feature_uris[value_feature_uri] = "No similar compounds in training dataset." if @neighbors.size == 0 or prediction[:prediction].nil? + + + #@prediction_dataset.metadata[OT.dependentVariables] = prediction_feature_uri + @prediction_dataset.metadata[OT.dependentVariables] = @metadata[OT.dependentVariables] + +=begin if @neighbors.size == 0 - @prediction_dataset.add_feature(prediction_feature_uri, { - RDF.type => [OT.MeasuredFeature], - OT.hasSource => @uri, - DC.creator => @uri, - DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), - OT.error => "No similar compounds in training dataset.", - OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}] - }) - @prediction_dataset.add @compound.uri, prediction_feature_uri, prediction[:prediction] + prediction_feature_uris.each do |prediction_feature_uri,value| + @prediction_dataset.add_feature(prediction_feature_uri, { + RDF.type => [OT.MeasuredFeature], + OT.hasSource => @uri, + DC.creator => @uri, + DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), + OT.error => "No similar compounds in training dataset.", + #OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}] + }) + @prediction_dataset.add @compound.uri, prediction_feature_uri, value + end else +=end + prediction_feature_uris.each do |prediction_feature_uri,value| + @prediction_dataset.metadata[OT.predictedVariables] = [] unless @prediction_dataset.metadata[OT.predictedVariables] + @prediction_dataset.metadata[OT.predictedVariables] << prediction_feature_uri @prediction_dataset.add_feature(prediction_feature_uri, { RDF.type => [OT.ModelPrediction], OT.hasSource => @uri, DC.creator => @uri, DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), - OT.prediction => prediction[:prediction], - OT.confidence => prediction[:confidence], - OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}] + # TODO: factor information to value }) - @prediction_dataset.add @compound.uri, prediction_feature_uri, prediction[:prediction] + #OT.prediction => prediction[:prediction], + #OT.confidence => prediction[:confidence], + #OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}] + @prediction_dataset.add @compound.uri, prediction_feature_uri, value + end - if verbose - if @feature_calculation_algorithm == "Substructure.match" - f = 0 - @compound_features.each do |feature| - feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s) + if verbose + if @feature_calculation_algorithm == "Substructure.match" + f = 0 + @compound_features.each do |feature| + feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s) + features[feature] = feature_uri + @prediction_dataset.add_feature(feature_uri, { + RDF.type => [OT.Substructure], + OT.smarts => feature, + OT.pValue => @p_values[feature], + OT.effect => @effects[feature] + }) + @prediction_dataset.add @compound.uri, feature_uri, true + f+=1 + end + else + @compound_features.each do |feature| + features[feature] = feature + @prediction_dataset.add @compound.uri, feature, true + end + end + n = 0 + @neighbors.each do |neighbor| + neighbor_uri = File.join( @prediction_dataset.uri, "feature", "neighbor", n.to_s ) + @prediction_dataset.add_feature(neighbor_uri, { + OT.compound => neighbor[:compound], + OT.similarity => neighbor[:similarity], + OT.measuredActivity => neighbor[:activity], + RDF.type => [OT.Neighbor] + }) + @prediction_dataset.add @compound.uri, neighbor_uri, true + f = 0 unless f + neighbor[:features].each do |feature| + if @feature_calculation_algorithm == "Substructure.match" + feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s) unless feature_uri = features[feature] + else + feature_uri = feature + end + @prediction_dataset.add neighbor[:compound], feature_uri, true + unless features.has_key? feature features[feature] = feature_uri @prediction_dataset.add_feature(feature_uri, { RDF.type => [OT.Substructure], @@ -276,49 +326,13 @@ module OpenTox OT.pValue => @p_values[feature], OT.effect => @effects[feature] }) - @prediction_dataset.add @compound.uri, feature_uri, true f+=1 end - else - @compound_features.each do |feature| - features[feature] = feature - @prediction_dataset.add @compound.uri, feature, true - end - end - n = 0 - @neighbors.each do |neighbor| - neighbor_uri = File.join( @prediction_dataset.uri, "feature", "neighbor", n.to_s ) - @prediction_dataset.add_feature(neighbor_uri, { - OT.compound => neighbor[:compound], - OT.similarity => neighbor[:similarity], - OT.measuredActivity => neighbor[:activity], - RDF.type => [OT.Neighbor] - }) - @prediction_dataset.add @compound.uri, neighbor_uri, true - f = 0 unless f - neighbor[:features].each do |feature| - if @feature_calculation_algorithm == "Substructure.match" - feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s) unless feature_uri = features[feature] - else - feature_uri = feature - end - @prediction_dataset.add neighbor[:compound], feature_uri, true - unless features.has_key? feature - features[feature] = feature_uri - @prediction_dataset.add_feature(feature_uri, { - RDF.type => [OT.Substructure], - OT.smarts => feature, - OT.pValue => @p_values[feature], - OT.effect => @effects[feature] - }) - f+=1 - end - end - n+=1 end - # what happens with dataset predictions? + n+=1 end end + #end @prediction_dataset.save(subjectid) @prediction_dataset diff --git a/lib/serializer.rb b/lib/serializer.rb index e4cb541..78e7709 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -17,6 +17,7 @@ module OpenTox # this should come from opentox.owl OT.Compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.Feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OT.Model => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.NominalFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.NumericFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.StringFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , @@ -27,6 +28,8 @@ module OpenTox OT.Parameter => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.Task => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OTA.PatternMiningSupervised => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OTA.ClassificationLazySingleTarget => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OTA.RegressionLazySingleTarget => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , #classes for validation OT.Validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , @@ -45,6 +48,9 @@ module OpenTox OT.values => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.parameters => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.featureDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.dependentVariables => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , #object props for validation# OT.model => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , @@ -126,7 +132,7 @@ module OpenTox OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.paramScope => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , - OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , + #OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , } @data_entries = {} @@ -157,23 +163,16 @@ module OpenTox # Add a dataset # @param [String] uri Dataset URI def add_dataset(dataset) - @dataset = dataset.uri - @object[dataset.uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } - add_metadata dataset.uri, dataset.metadata - dataset.compounds.each { |compound| add_compound compound } - dataset.features.each { |feature,metadata| add_feature feature,metadata } - dataset.data_entries.each do |compound,entry| entry.each do |feature,values| values.each { |value| add_data_entry compound,feature,value } end end - end # Add a algorithm @@ -188,6 +187,13 @@ module OpenTox def add_model(uri,metadata) @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Model }] } add_metadata uri, metadata + @object[metadata[OT.featureDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } + @object[metadata[OT.trainingDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } + @object[metadata[OT.dependentVariables]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] } + # TODO: add algorithms from parameters + @object["http://ot-dev.in-silico.ch/algorithm/fminer/bbrc"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + @object["http://ot-dev.in-silico.ch/algorithm/fminer/last"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + @object["http://ot-dev.in-silico.ch/algorithm/lazar"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } end # Add a task @@ -272,7 +278,7 @@ module OpenTox @object[genid][name] = [{"type" => type(entry), "value" => entry }] end end - elsif v.is_a? Array and u == RDF.type + elsif v.is_a? Array #and u == RDF.type @object[uri] = {} unless @object[uri] v.each do |value| @object[uri][u] = [] unless @object[uri][u] @@ -354,7 +360,8 @@ module OpenTox # @return [text/plain] Object OWL-DL in RDF/XML format def to_rdfxml Tempfile.open("owl-serializer"){|f| f.write(self.to_ntriples); @path = f.path} - `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:dc="#{DC.uri}"' -f 'xmlns:rdf="#{RDF.uri}"' -f 'xmlns:owl="#{OWL.uri}"' -o rdfxml #{@path} 2>/dev/null` + # TODO: add base uri for ist services + `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:ota="#{OTA.uri}"' -f 'xmlns:dc="#{DC.uri}"' -f 'xmlns:rdf="#{RDF.uri}"' -f 'xmlns:owl="#{OWL.uri}"' -o rdfxml #{@path} 2>/dev/null` end # Convert to JSON as specified in http://n2.talis.com/wiki/RDF_JSON_Specification -- cgit v1.2.3 From 87eb7cc1e079821c2f7c5e101e7e392e9bd10f00 Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 24 May 2011 09:35:11 +0200 Subject: Fixing regression detection --- lib/parser.rb | 66 +++++++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 51 insertions(+), 15 deletions(-) (limited to 'lib') diff --git a/lib/parser.rb b/lib/parser.rb index 7bdee95..8deaa91 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -277,7 +277,23 @@ module OpenTox def load_spreadsheet(book) book.default_sheet = 0 add_features book.row(1) - 2.upto(book.last_row) { |i| add_values book.row(i) } + + # AM: fix mixed read in + regression_features=false + 2.upto(book.last_row) { |i| + row = book.row(i) + smiles = row.shift + row.each_index do |i| + value = row[i] + type = feature_type(value) + if type == OT.NumericFeature + regression_features=true + break + end + end + } + + 2.upto(book.last_row) { |i| add_values book.row(i),regression_features } warnings @dataset end @@ -289,7 +305,23 @@ module OpenTox row = 0 input = csv.split("\n") add_features split_row(input.shift) - input.each { |row| add_values split_row(row) } + + + # AM: fix mixed read in + regression_features=false + input.each { |row| + row = split_row(row) + smiles = row.shift + row.each_index do |i| + value = row[i] + type = feature_type(value) + if type == OT.NumericFeature + regression_features=true + break + end + end + } + input.each { |row| add_values split_row(row),regression_features } warnings @dataset end @@ -335,7 +367,7 @@ module OpenTox end end - def add_values(row) + def add_values(row, regression_features=false) smiles = row.shift compound = Compound.from_smiles(smiles) @@ -353,19 +385,23 @@ module OpenTox @feature_types[feature] << type - case type - when OT.NominalFeature - case value.to_s - when TRUE_REGEXP - val = true - when FALSE_REGEXP - val = false - end - when OT.NumericFeature + if (regression_features) val = value.to_f - when OT.StringFeature - val = value.to_s - @activity_errors << smiles+", "+row.join(", ") + else + case type + when OT.NominalFeature + case value.to_s + when TRUE_REGEXP + val = true + when FALSE_REGEXP + val = false + end + when OT.NumericFeature + val = value.to_f + when OT.StringFeature + val = value.to_s + @activity_errors << smiles+", "+row.join(", ") + end end if val!=nil @dataset.add(compound.uri, feature, val) -- cgit v1.2.3 From 4a7ba2adb0743cd225ad5c2cf9f71c896d87b157 Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 24 May 2011 10:45:53 +0200 Subject: Created dedicated function for value sweeping --- lib/parser.rb | 35 +++++++++++++++++------------------ 1 file changed, 17 insertions(+), 18 deletions(-) (limited to 'lib') diff --git a/lib/parser.rb b/lib/parser.rb index 8deaa91..4984292 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -282,15 +282,8 @@ module OpenTox regression_features=false 2.upto(book.last_row) { |i| row = book.row(i) - smiles = row.shift - row.each_index do |i| - value = row[i] - type = feature_type(value) - if type == OT.NumericFeature - regression_features=true - break - end - end + regression_features = detect_regression_features row + break if regression_features=true } 2.upto(book.last_row) { |i| add_values book.row(i),regression_features } @@ -311,21 +304,15 @@ module OpenTox regression_features=false input.each { |row| row = split_row(row) - smiles = row.shift - row.each_index do |i| - value = row[i] - type = feature_type(value) - if type == OT.NumericFeature - regression_features=true - break - end - end + regression_features = detect_regression_features row + break if regression_features=true } input.each { |row| add_values split_row(row),regression_features } warnings @dataset end + private def warnings @@ -367,6 +354,18 @@ module OpenTox end end + def detect_regression_features row + regression_features=false + row.each_index do |i| + value = row[i] + type = feature_type(value) + if type == OT.NumericFeature + regression_features=true + end + end + regression_features + end + def add_values(row, regression_features=false) smiles = row.shift -- cgit v1.2.3 From 8a20cf940c346fd04649d3c3c8f7ad4c1fcb20cb Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Tue, 24 May 2011 14:00:16 +0200 Subject: Fix: break was too early --- lib/parser.rb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'lib') diff --git a/lib/parser.rb b/lib/parser.rb index 4984292..5f847c3 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -283,7 +283,7 @@ module OpenTox 2.upto(book.last_row) { |i| row = book.row(i) regression_features = detect_regression_features row - break if regression_features=true + break if regression_features==true } 2.upto(book.last_row) { |i| add_values book.row(i),regression_features } @@ -305,7 +305,7 @@ module OpenTox input.each { |row| row = split_row(row) regression_features = detect_regression_features row - break if regression_features=true + break if regression_features==true } input.each { |row| add_values split_row(row),regression_features } warnings @@ -355,6 +355,7 @@ module OpenTox end def detect_regression_features row + row.shift regression_features=false row.each_index do |i| value = row[i] -- cgit v1.2.3 From 0d87789eec37f7ae09d01937dbfc72af1ef17252 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Tue, 24 May 2011 16:06:05 +0200 Subject: fix small errors in to-html method --- lib/to-html.rb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'lib') diff --git a/lib/to-html.rb b/lib/to-html.rb index 66a3e74..51602d7 100644 --- a/lib/to-html.rb +++ b/lib/to-html.rb @@ -6,7 +6,7 @@ class String # encloses URI in text with with link tag # @return [String] new text with marked links def link_urls - self.gsub(/(?i)http(s?):\/\/[^\r\n\s']*/, '\0') + self.gsub(/(?i)http(s?):\/\/[^\r\n\s']*/, '\0') end end @@ -30,7 +30,7 @@ module OpenTox title = nil #$sinatra.url_for($sinatra.request.env['PATH_INFO'], :full) if $sinatra html = "" html += ""+title+"" if title - html += "" + html += "<\/img>" if AA_SERVER user = OpenTox::Authorization.get_user(subjectid) if subjectid @@ -63,7 +63,7 @@ module OpenTox html += "

Content

" if description || related_links html += "
"
     html += text.link_urls
-    html += "
" + html += "

" html end @@ -78,7 +78,7 @@ module OpenTox "password:"+ #""+ "" - html += "

" + html += "

" html end end -- cgit v1.2.3 From 524bda5ac60e07aa0805bfb215da718157849672 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Tue, 24 May 2011 16:08:22 +0200 Subject: fix lazar-non-predictions: replace "No similar compounds in training dataset." with nil --- lib/model.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'lib') diff --git a/lib/model.rb b/lib/model.rb index d46152d..139aed8 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -241,8 +241,8 @@ module OpenTox confidence_feature_uri = File.join( @prediction_dataset.uri, "feature", "prediction", File.basename(@metadata[OT.dependentVariables]),"confidence") prediction_feature_uris = {value_feature_uri => prediction[:prediction], confidence_feature_uri => prediction[:confidence]} - prediction_feature_uris[value_feature_uri] = "No similar compounds in training dataset." if @neighbors.size == 0 or prediction[:prediction].nil? - + #prediction_feature_uris[value_feature_uri] = "No similar compounds in training dataset." if @neighbors.size == 0 or prediction[:prediction].nil? + prediction_feature_uris[value_feature_uri] = nil if @neighbors.size == 0 or prediction[:prediction].nil? #@prediction_dataset.metadata[OT.dependentVariables] = prediction_feature_uri @prediction_dataset.metadata[OT.dependentVariables] = @metadata[OT.dependentVariables] -- cgit v1.2.3 From fe85fafc4b24cc8275ad67536d25d660249bb792 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Tue, 24 May 2011 16:10:10 +0200 Subject: adjust dataset-parser: predictedVariables may be array, do not request id/features from ambit services as not supported --- lib/parser.rb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'lib') diff --git a/lib/parser.rb b/lib/parser.rb index 5f847c3..a6878a2 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -56,7 +56,7 @@ module OpenTox `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line| triple = line.to_triple if triple[0] == @uri - if triple[1] == RDF.type # allow multiple types + if triple[1] == RDF.type || triple[1]==OT.predictedVariables # allow multiple types @metadata[triple[1]] = [] unless @metadata[triple[1]] @metadata[triple[1]] << triple[2].split('^^').first else @@ -228,7 +228,11 @@ module OpenTox file = Tempfile.new("ot-rdfxml") # do not concat /features to uri string, this would not work for dataset/R401577?max=3 uri = URI::parse(@uri) - uri.path = File.join(uri.path,"features") + # PENDING + # ambit models return http://host/dataset/id?feature_uris[]=sth but + # amibt dataset services does not support http://host/dataset/id/features?feature_uris[]=sth + # -> load features from complete dataset + uri.path = File.join(uri.path,"features") unless @uri=~/\?feature_uris\[\]/ uri = uri.to_s file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false file.close -- cgit v1.2.3 From aaff8d61a7b3bb96e79fbf575718764a071ced9a Mon Sep 17 00:00:00 2001 From: mguetlein Date: Tue, 24 May 2011 18:04:59 +0200 Subject: added missing prop to serializer --- lib/serializer.rb | 1 + 1 file changed, 1 insertion(+) (limited to 'lib') diff --git a/lib/serializer.rb b/lib/serializer.rb index 78e7709..62c1159 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -109,6 +109,7 @@ module OpenTox OT.precision => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.areaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.weightedAreaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , + OT.weightedAccuracy => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.fMeasure => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.percentIncorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , OT.validationType => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } , -- cgit v1.2.3 From 43572f94815a5ec4ca5b922dad3a1c1a140b7348 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Tue, 24 May 2011 19:44:53 +0200 Subject: remove empty space that produced a warning --- lib/algorithm.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 5b41cbf..96b9df1 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -202,7 +202,7 @@ module OpenTox acts_f = acts.collect {|v| v == true ? 1.0 : 0.0} sims = neighbors.collect{ |n| Algorithm.gauss(n[:similarity]) } # similarity values btwn q and nbors begin - prediction = local_svm (neighbors, acts_f, sims, "C-bsvc", params) + prediction = local_svm(neighbors, acts_f, sims, "C-bsvc", params) LOGGER.debug "Prediction is: '" + prediction.to_s + "'." rescue Exception => e LOGGER.debug "#{e.class}: #{e.message} #{e.backtrace}" -- cgit v1.2.3 From baca9424a84b6a21363cac891cdef72f44c116b1 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Wed, 25 May 2011 10:08:04 +0200 Subject: remove duplicate debug msg --- lib/rest_client_wrapper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb index 747a353..53887a2 100644 --- a/lib/rest_client_wrapper.rb +++ b/lib/rest_client_wrapper.rb @@ -131,7 +131,7 @@ module OpenTox raise "unknown content-type for task : '"+res.content_type.to_s+"'"+" base-uri: "+base_uri.to_s+" content: "+res[0..200].to_s end - LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion" + #LOGGER.debug "result is a task '"+task.uri.to_s+"', wait for completion" task.wait_for_completion waiting_task unless task.completed? # maybe task was cancelled / error if task.errorReport -- cgit v1.2.3 From 52e73a3da8e99da9a0a973b6ef9934297bc6511e Mon Sep 17 00:00:00 2001 From: mguetlein Date: Wed, 25 May 2011 11:55:41 +0200 Subject: remove check for task status when code is 201 (after discussion with nina and fabian) --- lib/task.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'lib') diff --git a/lib/task.rb b/lib/task.rb index 42d3d17..146a756 100644 --- a/lib/task.rb +++ b/lib/task.rb @@ -288,7 +288,8 @@ module OpenTox if @http_code == 202 raise "#{@uri}: illegal task state, code is 202, but hasStatus is not Running: '"+@metadata[OT.hasStatus]+"'" unless running? elsif @http_code == 201 - raise "#{@uri}: illegal task state, code is 201, but hasStatus is not Completed: '"+@metadata[OT.hasStatus]+"'" unless completed? + # ignore hasStatus + # raise "#{@uri}: illegal task state, code is 201, but hasStatus is not Completed: '"+@metadata[OT.hasStatus]+"'" unless completed? raise "#{@uri}: illegal task state, code is 201, resultURI is no task-URI: '"+@metadata[OT.resultURI].to_s+ "'" unless @metadata[OT.resultURI] and @metadata[OT.resultURI].to_s.uri? end -- cgit v1.2.3