diff options
Diffstat (limited to 'lib/parser.rb')
| -rw-r--r-- | lib/parser.rb | 43 |
1 files changed, 29 insertions, 14 deletions
diff --git a/lib/parser.rb b/lib/parser.rb index d2beeac..f1249ad 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -39,7 +39,14 @@ module OpenTox file = File.new(@uri) else file = Tempfile.new("ot-rdfxml") - uri = @dataset ? File.join(@uri,"metadata") : @uri + if @dataset + # do not concat /metadata to uri string, this would not work for dataset/R401577?max=3 + uri = URI::parse(@uri) + uri.path = File.join(uri.path,"metadata") + uri = uri.to_s + else + uri = @uri + end file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false file.close to_delete = file.path @@ -163,26 +170,31 @@ module OpenTox data[triple[0]] = {:compound => "", :values => []} unless data[triple[0]] data[triple[0]][:compound] = triple[2] when /#{OT.feature}/i - feature[triple[0]] = triple[2] + feature[triple[0]] = triple[2] else end end File.delete(to_delete) if to_delete data.each do |id,entry| - entry[:values].each do |value_id| - split = feature_values[value_id].split(/\^\^/) - case split[-1] - when XSD.double, XSD.float - value = split.first.to_f - when XSD.boolean - value = split.first=~/(?i)true/ ? true : false - else - value = split.first + if entry[:values].size==0 + # no feature values add plain compounds + @dataset.add_compound(entry[:compound]) + else + entry[:values].each do |value_id| + split = feature_values[value_id].split(/\^\^/) + case split[-1] + when XSD.double, XSD.float + value = split.first.to_f + when XSD.boolean + value = split.first=~/(?i)true/ ? true : false + else + value = split.first + end + @dataset.add entry[:compound],feature[value_id],value end - @dataset.add entry[:compound],feature[value_id],value end end - load_features + load_features subjectid @dataset.metadata = load_metadata(subjectid) @dataset end @@ -194,7 +206,10 @@ module OpenTox file = File.new(@uri) else file = Tempfile.new("ot-rdfxml") - uri = File.join(@uri,"features") + # 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") + uri = uri.to_s file.puts OpenTox::RestClientWrapper.get uri,{:subjectid => subjectid,:accept => "application/rdf+xml"},nil,false file.close to_delete = file.path |