Class: ScbiDblastManager

Inherits:
ScbiMapreduce::WorkManager
  • Object
show all
Defined in:
lib/scbi_distributed_blast/scbi_dblast_manager.rb

Overview

MyWorkerManager class is used to implement the methods to send and receive the data to or from workers

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.end_work_manager ⇒ Object

end_work_manager is executed at the end, when all the process is done. You can use it to close files opened in init_work_manager



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# File 'lib/scbi_distributed_blast/scbi_dblast_manager.rb', line 32

def self.end_work_manager
  # close opened files
  @@fqr.close
  @@output_file.close if @@output_file!=STDOUT
end

.init_work_manager(input_file, blast_cmd, output_file) ⇒ Object

init_work_manager is executed at the start, prior to any processing. You can use init_work_manager to initialize global variables, open files, etc… Note that an instance of MyWorkerManager will be created for each worker connection, and thus, all global variables here should be class variables (starting with @@)



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# File 'lib/scbi_distributed_blast/scbi_dblast_manager.rb', line 14

def self.init_work_manager(input_file, blast_cmd, output_file)
  # save blast_cmd
  @@blast_cmd=blast_cmd
  
  # define output file
  if output_file.nil?
    @@output_file=STDOUT
  else
    @@output_file=File.open(output_file,'w')
  end

  # open input file in fasta
  @@fqr = FastaQualFile.new(input_file)
  
end

Instance Method Details

#next_work ⇒ Object

next_work method is called every time a worker needs a new work Here you can read data from disk This method must return the work data or nil if no more data is available



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# File 'lib/scbi_distributed_blast/scbi_dblast_manager.rb', line 48

def next_work
  
  # read next sequence from inputfile
  n,f = @@fqr.next_seq

  if n.nil?
    return nil
  else
    return [n,f]
  end

end

#work_received(results) ⇒ Object

work_received is executed each time a worker has finished a job. Here you can write results down to disk, perform some aggregated statistics, etc…



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# File 'lib/scbi_distributed_blast/scbi_dblast_manager.rb', line 64

def work_received(results)
  # write results to disk
  @@output_file.puts results
end

#worker_initial_config ⇒ Object

worker_initial_config is used to send initial parameters to workers. The method is executed once per each worker



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# File 'lib/scbi_distributed_blast/scbi_dblast_manager.rb', line 40

def worker_initial_config
  # send blast_cmd to workers
  {:blast_cmd=>@@blast_cmd}
end