Class: SequenceServer::BLAST::Job

Inherits:
Job
  • Object
show all
Defined in:
lib/sequenceserver/blast/job.rb

Overview

Extends SequenceServer::Job to describe a BLAST job.

Instance Attribute Summary collapse

Attributes inherited from Job

#completed_at, #exitstatus, #id, #submitted_at

Instance Method Summary collapse

Methods inherited from Job

all, create, delete, #dir, #done?, enqueue, fetch, #run, serializable_classes, #stderr, #stdout

Constructor Details

#initialize(params) ⇒ Job

Returns a new instance of Job.



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# File 'lib/sequenceserver/blast/job.rb', line 10

def initialize(params)
  if params.key?(:xml)
    super do
      @imported_xml_file = File.basename params[:xml]
      # Copy over the XML file to job directory so that a job dir in
      # itself is self-contained. This will help with tests among
      # other things.
      FileUtils.cp(params[:xml], dir)
      @databases = []
      done!
    end
  else
    validate params
    super do
      @method = params[:method]
      @query = params[:sequence]
      @qfile     = store('query.fa', params[:sequence])
      @databases = Database[params[:databases]]
      @advanced  = params[:advanced].to_s.strip
      @options   = @advanced + defaults
      # The following params are for analytics only
      @num_threads = config[:num_threads]
      @query_length = calculate_query_size
      @number_of_query_sequences = calculate_number_of_sequences
      @databases_ncharacters_total = calculate_databases_ncharacters_total
    end
  end
end

Instance Attribute Details

#advanced ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def advanced
  @advanced
end

#advanced_params ⇒ Object (readonly)

:nodoc: Deprecated; see Report#extract_params



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# File 'lib/sequenceserver/blast/job.rb', line 53

def advanced_params
  @advanced_params
end

#databases ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def databases
  @databases
end

#databases_ncharacters_total ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def databases_ncharacters_total
  @databases_ncharacters_total
end

#method ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def method
  @method
end

#num_threads ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def num_threads
  @num_threads
end

#number_of_query_sequences ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def number_of_query_sequences
  @number_of_query_sequences
end

#options ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def options
  @options
end

#qfile ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def qfile
  @qfile
end

#query_length ⇒ Object (readonly)

:nodoc: Attributes used by us - should be considered private.



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# File 'lib/sequenceserver/blast/job.rb', line 41

def query_length
  @query_length
end

Instance Method Details

#as_archived_file(&block) ⇒ Object

Use it with a block to get a self-cleaning temporary archive file of the contents of the job directory. job.as_archived_file do |tmp_file|

# do things with tmp_file

end



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# File 'lib/sequenceserver/blast/job.rb', line 78

def as_archived_file(&block)
  Dir.mktmpdir(id.to_s) do |tmp_dir|
    file_path = "#{tmp_dir}/#{id}.zip"
    ZipFileGenerator.new(dir, file_path).write
    File.open(file_path, 'r') do |file|
      block.call(file)
    end
  end
end

#command ⇒ Object

Returns the command that will be executed. Job super class takes care of actual execution.



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# File 'lib/sequenceserver/blast/job.rb', line 64

def command
  @command ||= "#{method} -db '#{databases.map(&:name).join(' ')}'" \
               " -query '#{qfile}' #{options}"
end

#imported_xml_file ⇒ Object

:nodoc: Returns path to the imported xml file if the job was created using the –import switch. Returns nil otherwise.



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# File 'lib/sequenceserver/blast/job.rb', line 58

def imported_xml_file
  File.join(dir, @imported_xml_file) if @imported_xml_file
end

#raise! ⇒ Object 



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# File 'lib/sequenceserver/blast/job.rb', line 69

def raise!
  SequenceServer::BLAST::Error.new(exitstatus: exitstatus, stdout: stdout, stderr: stderr).raise!
end