Class: ScbiDblastWorker

Inherits:
ScbiMapreduce::Worker
  • Object
show all
Defined in:
lib/scbi_distributed_blast/scbi_dblast_worker.rb

Instance Method Summary collapse

Instance Method Details

#closing_worker ⇒ Object

called once, when the worker is about to be closed



61
62
63
 
# File 'lib/scbi_distributed_blast/scbi_dblast_worker.rb', line 61

def closing_worker

end

#process_object(objs) ⇒ Object

process_object method is called for each received object. Be aware that objs is always an array, and you must iterate over it if you need to process it independently

The value returned here will be received by the work_received method at your worker_manager subclass.



40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
 
# File 'lib/scbi_distributed_blast/scbi_dblast_worker.rb', line 40

def process_object(objs)
  chunk=[]
  # iterate over all objects received
  objs.each do |n,f|
    chunk<< ">"+n
    chunk<< f
    
    # convert to uppercase
    # f.downcase!
  end
  
  
  
  # puts "Doing blast to #{@params[:blast_cmd]}"
  blast=BatchBlast.do_blast_cmd(chunk.join("\n"),@params[:blast_cmd])
  
  # return objs back to manager
  return blast
end

#receive_initial_config(parameters) ⇒ Object

receive_initial_config is called only once just after the first connection, when initial parameters are received from manager



21
22
23
24
25
26
27
28
29
30
31
 
# File 'lib/scbi_distributed_blast/scbi_dblast_worker.rb', line 21

def receive_initial_config(parameters)

  # Reads the parameters

  # You can use worker logs at any time in this way:
  # $WORKER_LOG.info "Params received"

  # save received parameters, if any
  @params = parameters
  
end

#starting_worker ⇒ Object

starting_worker method is called one time at initialization and allows you to initialize your variables



10
11
12
13
14
15
 
# File 'lib/scbi_distributed_blast/scbi_dblast_worker.rb', line 10

def starting_worker

  # You can use worker logs at any time in this way:
  # $WORKER_LOG.info "Starting a worker"

end