diff options
| -rw-r--r-- | lib/dataset.rb | 4 | ||||
| -rw-r--r-- | lib/owl.rb | 33 |
2 files changed, 23 insertions, 14 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index 3efff7d..257cc17 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -25,7 +25,7 @@ module OpenTox case accept_header when "application/x-yaml" - d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s + d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s d.uri = uri unless d.uri when "application/rdf+xml" owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset") @@ -172,7 +172,7 @@ module OpenTox raise "invalid internal value type" end end - raise "feature value no found: "+feature.to_s + return nil #missing value else raise "value is not an array\n"+ "value "+v.to_s+"\n"+ @@ -93,7 +93,7 @@ module OpenTox [ "crossvalidation" ].each{ |c| OBJECT_PROPERTY_CLASS[c] = "Crossvalidation"} # literals point to primitive values (not to other resources) - # the literal datatype is encoded is uri: + # the literal datatype is encoded via uri: LITERAL_DATATYPE_STRING = XML["string"].uri LITERAL_DATATYPE_URI = XML["anyURI"].uri LITERAL_DATATYPE_FLOAT = XML["float"].uri @@ -104,7 +104,7 @@ module OpenTox LITERAL_DATATYPE_INTEGER = XML["integer"].uri # list all literals (to distinguish from objectProperties) as keys, datatype as values - # (do not add dc-identifier, deprecated, object are identified over via name=uri) + # (do not add dc-identifier, deprecated, object are identified via name=uri) LITERAL_TYPES = {} [ "title", "creator", "format", "description", "hasStatus", "paramScope", "paramValue", "value", "classValue", "reportType", "confusionMatrixActual", @@ -150,6 +150,7 @@ module OpenTox # uri the uri of the object attr_accessor :ot_class, :root_node, :uri, :model + private def initialize @model = Redland::Model.new Redland::MemoryStore.new end @@ -157,6 +158,7 @@ module OpenTox # build new owl object # ot_class is the class of this object, should be a string like "Model", "Task", ... # uri is name and identifier of this object + public def self.create( ot_class, uri ) owl = OpenTox::Owl.new @@ -255,7 +257,15 @@ module OpenTox end public - # sets values of current_node, by default root_node + # sets values of current_node (by default root_node) + # + # note: this does not delete existing triples + # * there can be several triples for the same subject and predicate + # ( e.g. after set("description","bla1") and set("description","bla2") + # both descriptions are in the model, + # but the get("description") will give you only one object (by chance) + # * this does not matter in pratice (only dataset uses this -> load_dataset-methods) + # * identical values appear only once in rdf def set(predicate, object, current_node=@root_node) pred = predicate.to_s @@ -268,10 +278,10 @@ module OpenTox end if pred=="type" - # predicat is type, set class of current node + # predicate is type, set class of current node @model.add current_node, RDF_TYPE, node(object) @model.add node(object), RDF_TYPE, OWL_TYPE_CLASS - # example-triples: + # example-triples for setting rdf-type to model: # model_xy,rdf:type,ot:Model # ot:Model,rdf:type,owl:Class elsif LITERAL_TYPES.has_key?(pred) @@ -279,7 +289,7 @@ module OpenTox predicate_node = node(pred) @model.add current_node, predicate_node, Redland::Literal.create(object, LITERAL_TYPES[pred]) @model.add predicate_node, RDF_TYPE, OWL_TYPE_LITERAL - # example-triples: + # example-triples for setting description of a model: # model_xy,ot:description,bla..bla^^xml:string # ot:description,rdf:type,owl:Literal elsif OBJECT_PROPERTY_CLASS.has_key?(pred) @@ -291,7 +301,7 @@ module OpenTox object_class_node = node(OBJECT_PROPERTY_CLASS[pred]) @model.add object_node, RDF_TYPE, object_class_node @model.add object_class_node, RDF_TYPE, OWL_TYPE_CLASS - # example-triples: + # example-triples for setting algorithm property of a model: # model_xy,ot:algorithm,algorihtm_xy # ot:algorithm,rdf:type,owl:ObjectProperty # algorihtm_xy,rdf:type,ot:Algorithm @@ -301,7 +311,7 @@ module OpenTox end end - # this is (a recursiv method) to set not only simple properties but nested-data via hashes + # this is (a recursiv method) to set nested-data via hashes (not only simple properties) # example (for a dataset) # { :description => "bla", # :compound => { :uri => "compound_uri", @@ -406,7 +416,7 @@ module OpenTox @model.subjects(RDF_TYPE, node('Feature')).each do |feature| features << get_value(feature) end - LOGGER.debug "loaded "+compounds.size.to_s+" compounds and "+features.size.to_s+" features" + LOGGER.debug "loaded "+compounds.size.to_s+" compounds and "+features.size.to_s+" features from dataset "+uri.to_s end # loading feature values for the specified feature @@ -460,10 +470,9 @@ module OpenTox raise "feature value type not yet implemented "+value_node_type.to_s end count += 1 - LOGGER.debug "loaded "+count.to_s+" feature values" if (count%500 == 0) + LOGGER.debug "loading feature values ("+count.to_s+")" if (count%1000 == 0) end LOGGER.debug "loaded "+count.to_s+" feature values" end end -end - +end
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