Class: OpenBEL::Routes::Expressions::ParameterOrthologTransform

Inherits:
Object
  • Object
show all
Includes:
BEL::LibBEL
Defined in:
app/openbel/api/routes/expressions.rb

Constant Summary collapse

NAMESPACE_PREFERENCE = 
[
  "hgnc",
  "mgi",
  "rgd",
  "gocc",
  "scomp",
  "meshcs",
  "sfam",
  "gobp",
  "meshpp",
  "chebi",
  "schem",
  "do",
  "meshd",
  "sdis",
  "sp",
  "affx",
  "egid",
]

Instance Method Summary collapse

Constructor Details

#initialize(namespaces, annotations, species_tax_id) ⇒ ParameterOrthologTransform

Returns a new instance of ParameterOrthologTransform.



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# File 'app/openbel/api/routes/expressions.rb', line 367

def initialize(namespaces, annotations, species_tax_id)
  @namespaces = namespaces
  @orthology = OrthologAdapter.new(
    namespaces, species_tax_id
  )
  @species_tax_id = species_tax_id
  @parameter_errors = []
end

Instance Method Details

#call(ast_node) ⇒ Object 



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# File 'app/openbel/api/routes/expressions.rb', line 380

def call(ast_node)
  if ast_node.is_a?(BelAstNodeToken) &&
      ast_node.token_type == :BEL_TOKEN_NV

    ns_value = [
      ast_node.left.to_typed_node.value,
      ast_node.right.to_typed_node.value
    ]
    orthologs = @orthology[ns_value]
    if !orthologs.empty?
      orthologs.sort_by! { |ortholog| namespace_preference(ortholog) }
      ortholog = orthologs.first
      BEL::LibBEL::bel_free_ast_node(ast_node.left.pointer)
      ast_node.left  = BelAstNode.new(
        bel_new_ast_node_value(:BEL_VALUE_PFX, ortholog[0].upcase)
      )

      BEL::LibBEL::bel_free_ast_node(ast_node.right.pointer)
      ast_node.right = BelAstNode.new(
        bel_new_ast_node_value(:BEL_VALUE_VAL, ortholog[1])
      )
    else
      # flag as ortholog error if this parameter has a namespace and
      # the namespace value is either not known or its species differs
      # from our target
      if ns_value[0] != nil
        namespace, value = ns_value
        namespace        = @namespaces.find(namespace).first
        if namespace
          value = namespace.find(value).first
          if !value || value.fromSpecies != @species_tax_id
            @parameter_errors << value
          end
        end
      end
    end
  end
end

#parameter_errors ⇒ Object 



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# File 'app/openbel/api/routes/expressions.rb', line 376

def parameter_errors
  @parameter_errors.uniq
end