Class: Oncotator

Inherits:
Object
  • Object
show all
Defined in:
lib/oncotator.rb

Defined Under Namespace

Classes: Transcript

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(opts) ⇒ Oncotator

Returns a new instance of Oncotator.



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# File 'lib/oncotator.rb', line 86

def initialize(opts)
  if opts[:key]
    @mutation = opts[:key]
    @onco = get_json_object
  elsif opts[:text]
    @onco = get_json_object opts[:text]
  end
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(meth, *args, &block) ⇒ Object 



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# File 'lib/oncotator.rb', line 133

def method_missing(meth,*args,&block)
  meth = meth.to_s
  case 
  when @onco[meth]
    @onco[meth]
  when meth =~ /^txp_(.*)/
    txp ? txp.send($1) : nil
  else
    nil
  end
end

Instance Attribute Details

#mutation ⇒ Object

Returns the value of attribute mutation.



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# File 'lib/oncotator.rb', line 9

def mutation
  @mutation
end

Class Method Details

.db_cache ⇒ Object 



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# File 'lib/oncotator.rb', line 22

def self.db_cache
  @db ||= Sequel.connect(db_opts)
  @db[:onco_json_cache]
end

.db_connect(opts) ⇒ Object 



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# File 'lib/oncotator.rb', line 14

def self.db_connect opts
  @db_opts = opts
end

.db_obj ⇒ Object 



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# File 'lib/oncotator.rb', line 35

def self.db_obj
  if defined? Rails
    OncoJsonCache
  else
    Oncotator.db_cache
  end
end

.db_opts ⇒ Object 



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# File 'lib/oncotator.rb', line 18

def self.db_opts
  @db_opts ||= GermConfig.get_conf :oncotator
end

.delete_key(cache_key) ⇒ Object 



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# File 'lib/oncotator.rb', line 48

def self.delete_key cache_key
  db_obj.where(:CACHE_KEY => cache_key).delete
end

.find_key(cache_key) ⇒ Object 



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# File 'lib/oncotator.rb', line 43

def self.find_key cache_key
  # use the Rails environment if it is available
  db_obj.where(:CACHE_KEY => cache_key).first
end

.insert_onco(onco) ⇒ Object 



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# File 'lib/oncotator.rb', line 27

def self.insert_onco onco
  if defined? Rails
    OncoJsonCache.create onco
  else
    db_cache.insert_ignore.insert onco
  end
end

.persistent_connection ⇒ Object 



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# File 'lib/oncotator.rb', line 10

def self.persistent_connection
  @http ||= Net::HTTP::Persistent.new
end

Instance Method Details

#best_canonical_txp ⇒ Object 



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# File 'lib/oncotator.rb', line 113

def best_canonical_txp
  @best_canonical_txp ||= Transcript.new(transcripts[best_canonical_transcript]) if best_canonical_transcript
end

#best_effect_txp ⇒ Object 



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# File 'lib/oncotator.rb', line 109

def best_effect_txp
  @best_effect_txp ||= Transcript.new(transcripts[best_effect_transcript]) if best_effect_transcript
end

#empty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/oncotator.rb', line 95

def empty?
  !@onco || @onco.size == 0
end

#get_json_object(text = nil) ⇒ Object 



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# File 'lib/oncotator.rb', line 56

def get_json_object text=nil
  # first look it up in the sequel database.
  json = case text
  when nil
    result = Oncotator.find_key @mutation
    result ? result[:RAW_JSON] : nil
  else
    text
  end
  
  begin
    return JSON.parse(json) if json
  rescue JSON::ParserError => e
    # you have a bad data blob
    Oncotator.delete_key @mutation
  end

  # if that doesn't work, query Oncotator.
  response = Oncotator.persistent_connection.request(onco_uri)

  return {} if response.code != "200"
  
  json = response.body

  # save it
  Oncotator.insert_onco(:CACHE_KEY => @mutation, :RAW_JSON => json)

  return JSON.parse(json)
end

#is_cancerous ⇒ Object 



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# File 'lib/oncotator.rb', line 129

def is_cancerous
  self.Cosmic_overlapping_mutations || self.CGC_Tumor_Types_Somatic || self.CCLE_ONCOMAP_total_mutations_in_gene
end

#is_snp ⇒ Object 



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# File 'lib/oncotator.rb', line 117

def is_snp
  dbSNP_RS && dbSNP_Val_Status =~ /(byFrequency|by1000genomes)/
end

#onco_uri ⇒ Object 



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# File 'lib/oncotator.rb', line 52

def onco_uri
  URI "http://69.173.64.101/oncotator/mutation/#{@mutation}/"
end

#pph2_class ⇒ Object 



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# File 'lib/oncotator.rb', line 125

def pph2_class
  pph2 ? pph2["pph2_class"] : nil
end

#txp ⇒ Object 



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# File 'lib/oncotator.rb', line 121

def txp
  best_effect_txp
end