Class: SequenceServer::BLAST::Error

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(exitstatus:, stdout:, stderr:) ⇒ Error

Returns a new instance of Error.



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# File 'lib/sequenceserver/blast/error.rb', line 8

def initialize(exitstatus:, stdout:, stderr:)
  @exitstatus = exitstatus
  @stdout = stdout
  @stderr = stderr
end

Instance Attribute Details

#exitstatus ⇒ Object (readonly)

Returns the value of attribute exitstatus.



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# File 'lib/sequenceserver/blast/error.rb', line 6

def exitstatus
  @exitstatus
end

#stderr ⇒ Object (readonly)

Returns the value of attribute stderr.



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# File 'lib/sequenceserver/blast/error.rb', line 6

def stderr
  @stderr
end

#stdout ⇒ Object (readonly)

Returns the value of attribute stdout.



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# File 'lib/sequenceserver/blast/error.rb', line 6

def stdout
  @stdout
end

Instance Method Details

#raise! ⇒ Object 



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# File 'lib/sequenceserver/blast/error.rb', line 14

def raise!
  return true if exitstatus.zero? && !File.zero?(stdout)

  case exitstatus
  when 1..2
    # 1: Error in query sequences or options.
    # 2: Error in BLAST databases.
    error = IO.foreach(stderr).grep(ERROR_LINE).join
    error = File.read(stderr) if error.empty?
    fail InputError, "(#{exitstatus}) #{error}"
  when 4
    # Out of memory. User can retry with a shorter search, so raising
    # InputError here instead of SystemError.
    fail InputError, <<~MSG
      Ran out of memory. Please try a smaller query, fewer and smaller
      databases, or limiting the output by using advanced options.
    MSG
  when 6
    # Error creating output files. It can't be a permission issue as that
    # would have been caught while creating job directory. But we can run
    # out of storage after creating the job directory and while running
    # the job. This is a SystemError.
    fail SystemError, 'Ran out of disk space.'
  else
    # I am not sure what the exit codes 3 means and we should not
    # encounter exit code 5. The only other error that I know can happen
    # but is not yet handled is when BLAST+ binaries break such as after
    # macOS updates. So raise SystemError, include the exit status in the
    # message, and say that that the "most likely" reason is broken BLAST+
    # binaries.

    error = File.read(stderr)
    error = 'Most likely there is a problem with the BLAST+ binaries.' if error.empty?

    fail SystemError, "BLAST failed abruptly (exit status: #{exitstatus}). #{error}"
  end
end