Class: NCBO::ResourceIndex

Inherits:
Object
  • Object
show all
Defined in:
lib/ncbo_resource_index.rb,
lib/ncbo_resource_index/data.rb

Defined Under Namespace

Classes: Annotation, Annotations, RankedElements

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(args = {}) ⇒ ResourceIndex

Returns a new instance of ResourceIndex.

Raises:

  • (ArgumentError) 


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# File 'lib/ncbo_resource_index.rb', line 13

def initialize(args = {})
  @options = {}
  
  # Shared with Annotator
  @options[:resource_index_location] = "http://rest.bioontology.org/resource_index/"
  @options[:filterNumber] = true
  @options[:isStopWordsCaseSensitive] = false
  @options[:isVirtualOntologyId] = true
  @options[:levelMax] = 0
  @options[:longestOnly] = false
  @options[:ontologiesToExpand] = []
  @options[:ontologiesToKeepInResult] = []
  @options[:mappingTypes] = []
  @options[:minTermSize] = 3
  @options[:scored] = true
  @options[:semanticTypes] = []
  @options[:stopWords] = []
  @options[:wholeWordOnly] = true
  @options[:withDefaultStopWords] = true
  @options[:withSynonyms] = true
  
  # RI-specific
  @options[:conceptids] = []
  @options[:mode] = :union
  @options[:elementid] = []
  @options[:resourceids] = []
  @options[:elementDetails] = false
  @options[:withContext] = true
  @options[:offset] = 0
  @options[:limit] = 10
  @options[:format] = :xml
  @options[:counts] = false
  @options[:request_timeout] = 300
  
  @options.merge!(args)
  
  @ontologies = nil
  @options[:resourceids] ||= []
  
  # Check to make sure mappingTypes are capitalized
  fix_params

  raise ArgumentError, ":apikey is required, you can obtain one at http://bioportal.bioontology.org/accounts/new" if @options[:apikey].nil?
end

Class Method Details

.element_annotations(element, concepts, resource, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 87

def self.element_annotations(element, concepts, resource, options = {})
  new(options).element_annotations(element, concepts)
end

.find_by_concept(concepts, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 58

def self.find_by_concept(concepts, options = {})
  new(options).find_by_concept(concepts)
end

.find_by_element(element, resource, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 73

def self.find_by_element(element, resource, options = {})
  new(options).find_by_element(element, resource)
end

.ontologies(options) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 200

def self.ontologies(options)
  new(options).ontologies
end

.popular_concepts(resources = nil, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 178

def self.popular_concepts(resources = nil, options = {})
  new(options).popular_concepts(resources)
end

.ranked_elements(concepts, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 146

def self.ranked_elements(concepts, options = {})
  new(options).ranked_elements(concepts)
end

.resources(options) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 215

def self.resources(options)
  new(options).resources
end

.resources_hash(options) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 230

def self.resources_hash(options)
  new(options).resources_hash
end

Instance Method Details

#element_annotations(element, concepts, resource) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/ncbo_resource_index.rb', line 91

def element_annotations(element, concepts, resource)
  @options[:conceptids] = concepts unless concepts.nil? || concepts.empty?
  raise ArgumentError, ":conceptids must be included" if @options[:conceptids].nil? || @options[:conceptids].empty?
  raise ArgumentError, ":resourceids must be an array" unless @options[:resourceids].kind_of? Array
  resource = resource.upcase
  
  "http://rest.bioontology.org/resource_index/details/false/virtual/concept/1032/resource/AE/0/9999?conceptid=Melanoma&elementid=E-GEOD-18509"
  
  concept_annotations = []
  concepts.each do |concept|
    split_concept = concept.split("/")
    ontology_id = split_concept[0]
    concept_id = split_concept[1]
    virtual = @options[:isVirtualOntologyId] ? "/virtual" : ""
    puts ["#{@options[:resource_index_location]}",
                       "details/#{@options[:elementDetails]}",
                       virtual,
                       "/concept/#{ontology_id}",
                       "/resource/#{resource}",
                       "/#{@options[:offset]}",
                       "/#{@options[:limit]}",
                       "?conceptid=#{CGI.escape(concept_id)}",
                       "&elementid=#{CGI.escape(element)}",
                       "&apikey=#{@options[:apikey]}"].join("")
    result_xml = open(["#{@options[:resource_index_location]}",
                       "details/#{@options[:elementDetails]}",
                       virtual,
                       "/concept/#{ontology_id}",
                       "/resource/#{resource}",
                       "/#{@options[:offset]}",
                       "/#{@options[:limit]}",
                       "?conceptid=#{CGI.escape(concept_id)}",
                       "&elementid=#{CGI.escape(element)}",
                       "&apikey=#{@options[:apikey]}"].join("")).read

    annotations = Parser::ResourceIndex.parse_element_annotations(result_xml)
    concept_annotations << annotations
  end

  if concept_annotations.length > 1
    # Merge the two result sets
    primary_annotations = Annotations.new
    primary_annotations.annotations = []
    primary_annotations.resource = resource
    concept_annotations.each do |result|
      primary_annotations.annotations.concat result.annotations
    end
  elsif concept_annotations.length == 1
    primary_annotations = concept_annotations[0]
  else
    primary_annotations = nil
  end
  primary_annotations
end

#find_by_concept(concepts = [], options = {}) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/ncbo_resource_index.rb', line 62

def find_by_concept(concepts = [], options = {})
  @options[:conceptids] = concepts unless concepts.nil? || concepts.empty?
  @options.merge!(options) unless options.empty?
  fix_params
  
  raise ArgumentError, ":conceptids must be included" if @options[:conceptids].nil? || @options[:conceptids].empty?
  
  result_xml = resource_index_post
  Parser::ResourceIndex.parse_results(result_xml)
end

#find_by_element(element, resource, options = {}) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/ncbo_resource_index.rb', line 77

def find_by_element(element, resource, options = {})
  @options[:elementid] = element unless element.nil? || element.empty?
  @options[:resourceids] = [resource] unless resource.nil? || resource.empty?
  @options.merge!(options) unless options.empty?
  fix_params
  raise ArgumentError, ":elementid must be included" if @options[:elementid].nil? || @options[:elementid].empty?
  raise ArgumentError, ":resourceids must be included" if @options[:resourceids].nil? || @options[:resourceids].empty?
  Parser::ResourceIndex.parse_results(resource_index_post)
end

#ontologies(options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 204

def ontologies(options = {})
  @options.merge!(options) unless options.empty?

  if @ontologies.nil?
    ontologies_xml = open("#{@options[:resource_index_location]}ontologies?apikey=#{@options[:apikey]}").read
    @ontologies = Parser::ResourceIndex.parse_included_ontologies(ontologies_xml)
  else
    @ontologies
  end
end

#options ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 242

def options
  @options
end

#popular_concepts(resources = nil, options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 182

def popular_concepts(resources = nil, options = {})
  @options[:resourceids] = resources
  @options[:resourceids] = [resources] unless resources.nil? || resources.empty? || resources.kind_of?(Array)
  @options.merge!(options) unless options.empty?
  fix_params
  
  if @options[:resourceids].nil? || @options[:resourceids].empty?
    @options[:resourceids] = self.resources.collect {|resource| resource[:resourceId]}
  end
  
  popular_concepts = {}
  @options[:resourceids].each do |resource|
    popular_concepts_xml = open("#{@options[:resource_index_location]}most-used-concepts/#{resource}?apikey=#{@options[:apikey]}&offset=#{@options[:offset]}&limit=#{@options[:limit]}").read
    popular_concepts[resource] = Parser::ResourceIndex.parse_popular_concepts(popular_concepts_xml)
  end
  popular_concepts
end

#ranked_elements(concepts = [], options = {}) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/ncbo_resource_index.rb', line 150

def ranked_elements(concepts = [], options = {})
  @options[:conceptids] = concepts unless concepts.nil? || concepts.empty?
  @options[:resourceids] ||= []
  @options.merge!(options) unless options.empty?
  fix_params
  
  raise ArgumentError, ":conceptids must be included" if @options[:conceptids].nil? || @options[:conceptids].empty?
  raise ArgumentError, ":resourceids must be an array" unless @options[:resourceids].kind_of? Array
  
  puts ["#{@options[:resource_index_location]}",
                     "elements-ranked-by-concepts/#{@options[:resourceids].join(",")}",
                     "?offset=#{@options[:offset]}",
                     "&limit=#{@options[:limit]}",
                     "&conceptids=#{@options[:conceptids].join(",")}",
                     "&ontologiesToKeepInResult=#{@options[:ontologiesToKeepInResult]}",
                     "&isVirtualOntologyId=#{@options[:isVirtualOntologyId]}",
                     "&apikey=#{@options[:apikey]}"].join("")
  result_xml = open(["#{@options[:resource_index_location]}",
                     "elements-ranked-by-concepts/#{@options[:resourceids].join(",")}",
                     "?offset=#{@options[:offset]}",
                     "&limit=#{@options[:limit]}",
                     "&conceptids=#{@options[:conceptids].join(",")}",
                     "&ontologiesToKeepInResult=#{@options[:ontologiesToKeepInResult]}",
                     "&isVirtualOntologyId=#{@options[:isVirtualOntologyId]}",
                     "&apikey=#{@options[:apikey]}"].join("")).read
  Parser::ResourceIndex.parse_ranked_element_results(result_xml)
end

#resources(options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 219

def resources(options = {})
  @options.merge!(options) unless options.empty?

  if @resources.nil?
    resources_xml = open("#{@options[:resource_index_location]}resources?apikey=#{@options[:apikey]}").read
    @resources = Parser::ResourceIndex.parse_resources(resources_xml)
  else
    @resources
  end
end

#resources_hash(options = {}) ⇒ Object 



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# File 'lib/ncbo_resource_index.rb', line 234

def resources_hash(options = {})
  @options.merge!(options) unless options.empty?
  resources = resources()
  resources_hash = {}
  resources.each {|res| resources_hash[res[:resourceId].downcase.to_sym] = res}
  resources_hash
end