opentox-ruby-api-wrapper 1.2.1 → 1.2.2

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Files changed (8) hide show
  1. data/VERSION +1 -1
  2. data/bin/yaml2owl.rb +18 -0
  3. data/lib/algorithm.rb +22 -0
  4. data/lib/dataset.rb +116 -133
  5. data/lib/model.rb +99 -48
  6. data/lib/opentox.owl +809 -0
  7. data/lib/owl.rb +69 -45
  8. metadata +6 -3
data/lib/owl.rb CHANGED
@@ -2,7 +2,7 @@ module OpenTox
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  module Owl
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- attr_reader :uri, :model
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+ attr_reader :uri
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  def initialize
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@@ -10,41 +10,74 @@ module OpenTox
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  @parser = Redland::Parser.new
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  @serializer = Redland::Serializer.ntriples
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- # explicit typing
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- # this should come from http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file (does not pass OWL-DL validation)
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- @parser.parse_into_model(@model,"http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file")
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- =begin
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- @model.add @uri, RDF['type'], OWL['Ontology']
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- # annotation properties
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- @model.add DC['source'], RDF['type'], OWL["AnnotationProperty"]
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- @model.add DC['identifier'], RDF['type'], OWL["AnnotationProperty"]
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- @model.add DC['title'], RDF['type'], OWL["AnnotationProperty"]
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- # object properties
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- @model.add OT['feature'], RDF['type'], OWL["ObjectProperty"]
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- @model.add OT['compound'], RDF['type'], OWL["ObjectProperty"]
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- @model.add OT['values'], RDF['type'], OWL["ObjectProperty"]
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- @model.add OT['tuple'], RDF['type'], OWL["ObjectProperty"] # added by ch
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- @model.add OT['parameters'], RDF['type'], OWL["ObjectProperty"]
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- # datatype properties
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- @model.add OT['value'], RDF['type'], OWL["DatatypeProperty"]
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- @model.add OT['paramValue'], RDF['type'], OWL["DatatypeProperty"]
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- @model.add OT['paramScope'], RDF['type'], OWL["DatatypeProperty"]
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- @model.add OT['hasSource'], RDF['type'], OWL["DatatypeProperty"]
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- # classes
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- @model.add OT['Dataset'], RDF['type'], OWL["Class"]
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- @model.add OT['FeatureValue'], RDF['type'], OWL["Class"]
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- @model.add OT['Tuple'], RDF['type'], OWL["Class"] # added by ch
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- @model.add OT['Feature'], RDF['type'], OWL["Class"]
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- @model.add OT['Compound'], RDF['type'], OWL["Class"]
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- @model.add OT['DataEntry'], RDF['type'], OWL["Class"]
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- @model.add OT['Parameter'], RDF['type'], OWL["Class"]
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- @model.add OT['Algorithm'], RDF['type'], OWL["Class"]
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- =end
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+ # read OT Ontology
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+ #@parser.parse_into_model(@model,"http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file")
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+ @parser.parse_string_into_model(@model,File.read(File.join(File.dirname(__FILE__),"opentox.owl")),'/')
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+ # reate an anonymous resource for metadata
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+ # this has to be rewritten with an URI as soon as the resource has been saved at an definitive location
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+ tmp = @model.create_resource
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+ @model.add tmp, RDF['type'], OWL['Ontology']
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+ @model.add tmp, RDF['type'], OT[self.owl_class]
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+ end
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+
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+ def uri=(uri)
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+ @uri = uri
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+ uri = Redland::Uri.new(uri)
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+ # rewrite uri
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+ @model.subjects(RDF['type'],OT[self.owl_class]).each do |me|
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+ @model.delete(me,RDF['type'],OT[self.owl_class])
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+ @model.add(uri,RDF['type'],OT[self.owl_class])
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+ id = @model.object(me, DC['identifier'])
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+ @model.delete me, DC['identifier'], id
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+ # find/replace metadata
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+ @model.find(me, nil, nil) do |s,p,o|
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+ @model.delete s,p,o
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+ @model.add uri,p,o
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+ end
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+ @model.add uri, DC['identifier'], @uri
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+ end
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+ end
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+
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+ def title
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+ # I have no idea, why 2 subjects are returned
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+ # iterating over all subjects leads to memory allocation problems
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+ # SPARQL queries also do not work
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+ me = @model.subjects(RDF['type'],OT[self.owl_class])[1]
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+ @model.object(me, DC['title']).to_s
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+ end
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+
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+ def title=(title)
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+ me = @model.subject(RDF['type'],OT[self.owl_class])
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+ begin
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+ t = @model.object(me, DC['title'])
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+ @model.delete me, DC['title'], t
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+ rescue
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+ end
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+ @model.add me, DC['title'], title
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+ end
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+
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+ def source
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+ me = @model.subject(RDF['type'],OT[self.owl_class])
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+ @model.object(me, DC['source']).to_s unless me.nil?
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+ end
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+
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+ def source=(source)
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+ me = @model.subject(RDF['type'],OT[self.owl_class])
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+ begin
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+ t = @model.object(me, DC['source'])
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+ @model.delete me, DC['source'], t
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+ rescue
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+ end
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+ @model.add me, DC['source'], source
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+ end
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+
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+ def identifier
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+ me = @model.subject(RDF['type'],OT[self.owl_class])
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+ @model.object(me, DC['identifier']).to_s unless me.nil?
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  end
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  def owl_class
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- self.class.to_s.sub(/^OpenTox::/,'')
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- #@model.subject RDF['type'], OT[self.class.to_s.sub(/^OpenTox::/,'')]
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+ self.class.to_s.sub(/^OpenTox::/,'').sub(/::.*$/,'')
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  end
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  def read(uri)
@@ -61,19 +94,10 @@ module OpenTox
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  @model.to_string
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  end
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- def uri=(uri)
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- identifier = uri
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- end
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-
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  def to_ntriples
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  @serializer.model_to_string(Redland::Uri.new(@uri), @model)
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  end
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- def title
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- #puts OT[self.owl_class]
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- @model.object(OT[self.owl_class], DC['title']).to_s
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- end
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-
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  def parameters=(params)
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  params.each do |name, settings|
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  parameter = @model.create_resource
@@ -84,15 +108,14 @@ module OpenTox
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  end
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  end
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+ =begin
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  def create_owl_statement(name,value)
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  r = @model.create_resource
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  dc_class = DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
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+ #puts "DC:" + name.gsub(/^[a-z]/) { |a| a.upcase }
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  @model.add dc_class, RDF['type'], OWL["Class"]
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  @model.add r, RDF['type'], dc_class
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  @model.add r, DC[name], value
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- #puts r
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- #puts DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
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- #puts DC[name] # capitalize only the first letter
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  end
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  def method_missing(name, *args)
@@ -103,6 +126,7 @@ module OpenTox
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  raise "No method #{name}"
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  end
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  end
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+ =end
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  end
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metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: opentox-ruby-api-wrapper
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  version: !ruby/object:Gem::Version
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- version: 1.2.1
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+ version: 1.2.2
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  platform: ruby
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  authors:
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  - Christoph Helma
@@ -9,8 +9,8 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2009-12-16 00:00:00 +01:00
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- default_executable: opentox-install-debian.sh
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+ date: 2009-12-20 00:00:00 +01:00
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+ default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rest-client
@@ -96,6 +96,7 @@ description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
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  email: helma@in-silico.ch
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  executables:
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  - opentox-install-debian.sh
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+ - yaml2owl.rb
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  extensions: []
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  extra_rdoc_files:
@@ -107,6 +108,7 @@ files:
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  - Rakefile
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  - VERSION
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  - bin/opentox-install-debian.sh
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+ - bin/yaml2owl.rb
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  - lib/algorithm.rb
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  - lib/compound.rb
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  - lib/dataset.rb
@@ -115,6 +117,7 @@ files:
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  - lib/helper.rb
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  - lib/model.rb
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  - lib/opentox-ruby-api-wrapper.rb
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+ - lib/opentox.owl
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  - lib/owl.rb
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  - lib/spork.rb
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  - lib/task.rb