diff options
Diffstat (limited to 'lib/parser.rb')
| -rw-r--r-- | lib/parser.rb | 40 |
1 files changed, 28 insertions, 12 deletions
diff --git a/lib/parser.rb b/lib/parser.rb index db746c1..7bdee95 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -163,6 +163,7 @@ module OpenTox data = {} feature_values = {} feature = {} + feature_accept_values = {} other_statements = {} `rapper -i rdfxml -o ntriples #{file.path} 2>/dev/null`.each_line do |line| triple = line.chomp.split(' ',3) @@ -182,6 +183,9 @@ module OpenTox if triple[2]=~/#{OT.Compound}/i and !data[triple[0]] data[triple[0]] = {:compound => triple[0], :values => []} end + when /#{OT.acceptValue}/i # acceptValue in ambit datasets is only provided in dataset/<id> no in dataset/<id>/features + feature_accept_values[triple[0]] = [] unless feature_accept_values[triple[0]] + feature_accept_values[triple[0]] << triple[2] else end end @@ -192,20 +196,25 @@ module OpenTox @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 + if feature_values[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 end @dataset.add entry[:compound],feature[value_id],value end end end load_features subjectid + feature_accept_values.each do |feature, values| + @dataset.features[feature][OT.acceptValue] = values + end @dataset.metadata = load_metadata(subjectid) @dataset end @@ -348,16 +357,23 @@ module OpenTox when OT.NominalFeature case value.to_s when TRUE_REGEXP - @dataset.add(compound.uri, feature, true ) + val = true when FALSE_REGEXP - @dataset.add(compound.uri, feature, false ) + val = false end when OT.NumericFeature - @dataset.add compound.uri, feature, value.to_f + val = value.to_f when OT.StringFeature - @dataset.add compound.uri, feature, value.to_s + val = value.to_s @activity_errors << smiles+", "+row.join(", ") end + if val!=nil + @dataset.add(compound.uri, feature, val) + if type!=OT.NumericFeature + @dataset.features[feature][OT.acceptValue] = [] unless @dataset.features[feature][OT.acceptValue] + @dataset.features[feature][OT.acceptValue] << val.to_s unless @dataset.features[feature][OT.acceptValue].include?(val.to_s) + end + end end end |