The check statement

Synopsis


1.    check {
         < statements to validate results >
      } 

2.    check(<check name>) {
         < statements to validate results >
      } 


3.    check {
         < statements to validate results >
      } otherwise {
          <statements to execute on failure >
      }

4.    check(<check name>) {
         < statements to validate results >
      } otherwise {
          <statements to execute on failure >
      }


Availability

0.9.8.6_beta_2 + (without otherwise clause, 0.9.9.5+).

Behavior

The check statement gives a convenient way to implement validation of a pipeline's outputs or progress and implement an alternative action if the validation fails. The check clause is executed and any exec or other statements inside are processed. If one of these fails, then the otherwise clause executes.

The check statement is stateful. Bpipe remembers the result and does not re-execute a check unless the input files are updated. Thus it is possible to implement long-running, intensive tasks to perform checks as just like normal Bpipe commands, they will not be re-executed if the pipeline is re-executed. The state is remembered by files that are created in the .bpipe/checks directory in the pipeline directory. Effectively, the created check file is treated as an implicit output of the check clause.

A convenient use of check is in conjunction with succeed, fail and send commands.

Note: a check does not have to result in aborting of the pipeline. You may choose to do nothing in the otherwise clause of the check (it must still exist though), in which case the check is merely informational. Alternatively, the succeed command will cause the current branch to terminate and not produce any output files, but leave other branches running. To fail the whole pipeline, use the fail command.

Note 2: due to a quirk of Groovy syntax, the otherwise command must be placed on the same line as the preceding curly bracket of the check clause.

Examples

Check that there are 38 lines in the output file

check { exec """ [ wc -l $output -eq 38 ] """ }

Check that output file is non-zero length and fail the whole pipeline if it is not


  check {
        exec "[ -s $output ]"
  } otherwise {
        fail "The output file had zero length"
  }

Check that output file is non-zero length and terminate only this branch if it is not


  check {
        exec "[ -s $output ]"
  } otherwise {
        succeed "The output file had zero length"
  }

Check that output file is non-zero length and notify by email if it is not


  check {
        exec "[ -s $output ]"
  } otherwise {
        send "Output file $output had zero size" to gmail
  }