Class: SysMODB::SearchBiomodel

Inherits:
Object
  • Object
show all
Includes:
Singleton
Defined in:
lib/search_biomodel.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ SearchBiomodel

Returns a new instance of SearchBiomodel.



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# File 'lib/search_biomodel.rb', line 12

def initialize
  @connection = Savon.configure do |config|
    config.log = false
    HTTPI.log = false
    config.raise_errors = false
    Savon::Client.new do
      wsdl.document = "http://www.ebi.ac.uk/biomodels-main/services/BioModelsWebServices?wsdl"
      wsdl.namespace = "http://biomodels.ebi.ac.uk"
    end
  end

end

Instance Method Details

#get_all_models ⇒ Object 



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# File 'lib/search_biomodel.rb', line 144

def get_all_models
  client = connection
  response = client.request(:biom, "get_all_models") do
    soap.body = {:modelName => "?", :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
  end
  search_results = response.to_hash[:multi_ref][:item] unless response.nil?
  if search_results.nil?
    []
  else
    search_results
  end
end

#get_model_name_by_id(search_string) ⇒ Object

more used for testing



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# File 'lib/search_biomodel.rb', line 131

def get_model_name_by_id (search_string)
  client = connection
  response = client.request(:biom, "get_model_name_by_id") do
    soap.body = {:id => search_string, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
  end
  search_results = response.to_hash[:get_model_name_by_id_response][:get_model_name_by_id_return]
  if search_results.nil? || search_results.include?('is an invalid Model ID.')
    []
  else
    search_results
  end
end

#getModel(model_id) ⇒ Object 



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# File 'lib/search_biomodel.rb', line 51

def getModel(model_id)
  client = connection
  response = client.request(:biom, "get_model_by_id") do
    soap.body = {:id => model_id, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
  end

  search_results = response.to_hash[:get_model_by_id_response][:get_model_by_id_return] unless response.nil?
  if search_results.nil?
    []
  else
    search_results
  end
end

#getSimpleModel(model_id) ⇒ Object 



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# File 'lib/search_biomodel.rb', line 67

def getSimpleModel(model_id)
  client = connection
  response = client.request(:biom, "get_simple_model_by_id") do
    soap.body = {:id => model_id, :attributes! => {:id => {"xsi:type" => "xsd:string"}}}
  end

  if !response.nil?
     search_results = response.to_hash[:get_simple_model_by_id_response][:get_simple_model_by_id_return]
  end
  if search_results.nil?
    []
  else
    search_results
  end
end

#models(search_string) ⇒ Object 



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# File 'lib/search_biomodel.rb', line 26

def models(search_string)
  #collect results from sub-methods
  results = Array.new
  results << @connection.search_by_name(search_string)
  results << @connection.search_by_chebiid(search_string)
  results << @connection.search_by_person(search_string)

  #turn into one big array, remove duplicates and select first X
  results = results.flatten
  results = results.uniq
  results = results.first(10)

  sbml_results = Array.new

  results.each_with_index do |a, i| 
     if !a.nil?
      sbml_results[i] = Hash.new 
      sbml_results[i] = Nori.parse(@connection.getSimpleModel(a))[:simple_models][:simple_model] 
     end
  end
  sbml_results
end

#search_by_chebiid(search_string) ⇒ Object

search_by_chebiid search_by_name search_by_person



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

def search_by_chebiid(search_string)
  client = connection
  response = client.request(:biom, "get_models_id_by_ch_ebi_id") do
    soap.body = {:ChEBBId => search_string, :attributes! => {:ChEBBId => {"xsi:type" => "xsd:string"}}}
  end

  search_results = response.to_hash[:get_models_id_by_ch_ebi_id_response][:get_models_id_by_ch_ebi_id_return][:get_models_id_by_ch_ebi_id_return] unless response.nil?
  if search_results.nil?
    []
  else
    search_results
  end
end

#search_by_name(search_string) ⇒ Object 



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# File 'lib/search_biomodel.rb', line 102

def search_by_name (search_string)
  client = connection
  response = client.request(:biom, "get_models_id_by_name") do
    soap.body = {:modelName => search_string, :attributes! => {:modelName => {"xsi:type" => "xsd:string"}}}
  end
  search_results = response.to_hash[:get_models_id_by_name_response][:get_models_id_by_name_return][:get_models_id_by_name_return]
  if search_results.nil?
    []
  else
    search_results
  end
end

#search_by_person(search_string) ⇒ Object 



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# File 'lib/search_biomodel.rb', line 115

def search_by_person (search_string)
  client = connection
  response = client.request(:biom, "get_models_id_by_person") do
    soap.body = {:personName => search_string, :attributes! => {:personName => {"xsi:type" => "xsd:string"}}}
  end
  search_results = response.to_hash[:get_models_id_by_person_response][:get_models_id_by_person_return][:get_models_id_by_person_return]
  if search_results.nil?
    []
  else
    search_results
  end
end