GitLab

* master:
  Numbers are returned as real numbers, not strings;
  Clearer flags in register_worker_death()
  support "accumulation" of a scalar by using an empty signature
  Failed tests are not expected to succeed at the next attempt
  bugfix: jobs could not trigger MEMLIMIT events
  bugfix: release the unfinished batch if the worker is contaminated

This is needed for pipeline_wide_parameters as each value is destringified
independently and the JSON writer would otherwise force writing numbers as
strings

"self-burial" had two meanings:
 - should we release the undone jobs ?
 - should we update the last_check_in field in the worker table ?
The former can simply be found by checking whether the worker already has a
role attached to it.
The latter is only set when a worker registers its own death, and is not set
by the GarbageCollector.

bugfix [to ee51e74e] : restore the password-hiding functionality between beekeeper.pl and runWorker.pl

* version/2.2:
  The main index is docs/index.html

* version/2.1:
  The main index is docs/index.html

Conflicts:
	docs/scripts/index.html

* version/2.0:
  The main index is docs/index.html

* version/1.9:
  The main index is docs/index.html

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"
- bugfix: jobs could not trigger MEMLIMIT events
- bugfix: release the unfinished batch if the worker is contaminated

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"

PR #5

  bugfix: jobs could not trigger MEMLIMIT events
  bugfix: release the unfinished batch if the worker is contaminated

(and probably RUNLIMIT as well)
The problem was in Queen::register_worker_death(). The code fetches the
current role, finalizes it, and then updates the worker table. The role
that is fetched from the database with fetch_last_unfinished_by_worker_id()
is not connected to any workers and later, when
AnalysisJobAdaptor::release_undone_jobs_from_role() needs to know the cause
of death and the number of work done by the worker, the role would load
another instance of the worker using the information currently stored in
the database, that is: before it has been updated.
Hence, the code was complaining that cause_of_death was not populated.
By associating the role to the worker, we allow the method to read the
existing information

This is done by setting "self_burial" to 0