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ensembl-gh-mirror
ensembl-hive
Commits
27633e4a
Commit
27633e4a
authored
Sep 09, 2010
by
Leo Gordon
Browse files
moved autoflow where it belongs - into the AnalysisJob
parent
61ef5b2e
Changes
3
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3 changed files
with
25 additions
and
21 deletions
+25
-21
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+22
-0
modules/Bio/EnsEMBL/Hive/Process.pm
modules/Bio/EnsEMBL/Hive/Process.pm
+1
-19
modules/Bio/EnsEMBL/Hive/Worker.pm
modules/Bio/EnsEMBL/Hive/Worker.pm
+2
-2
No files found.
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
View file @
27633e4a
...
...
@@ -139,6 +139,28 @@ sub stderr_file {
return
$self
->
{'
_stderr_file
'};
}
=head2 autoflow
Title : autoflow
Function: Gets/sets flag for whether the job should
be automatically dataflowed on branch 1 when the job completes.
If the subclass manually sends a job along branch 1 with dataflow_output_id,
the autoflow will turn itself off.
Returns : boolean (1=default|0)
=cut
sub
autoflow
{
my
$self
=
shift
;
$self
->
{'
_autoflow
'}
=
shift
if
(
@
_
);
$self
->
{'
_autoflow
'}
=
1
unless
(
defined
(
$self
->
{'
_autoflow
'}));
return
$self
->
{'
_autoflow
'};
}
##-----------------[indicators to the Worker]--------------------------------
...
...
modules/Bio/EnsEMBL/Hive/Process.pm
View file @
27633e4a
...
...
@@ -270,24 +270,6 @@ sub input_job {
return
$self
->
{'
_input_job
'};
}
=head2 autoflow_inputjob
Title : autoflow_inputjob
Function: Gets/sets flag for whether the input_job should
be automatically dataflowed on branch code 1 when the
job completes. If the subclass manually sends a job along
branch 1 with dataflow_output_id, the autoflow will be turned off.
Returns : boolean (1/0/undef)
=cut
sub
autoflow_inputjob
{
my
$self
=
shift
;
$self
->
{'
_autoflow_inputjob
'}
=
shift
if
(
@
_
);
$self
->
{'
_autoflow_inputjob
'}
=
1
unless
(
defined
(
$self
->
{'
_autoflow_inputjob
'}));
return
$self
->
{'
_autoflow_inputjob
'};
}
=head2 dataflow_output_id
Title : dataflow_output_id
...
...
@@ -323,7 +305,7 @@ sub dataflow_output_id {
my
$semaphored_job_id
=
$create_job_options
->
{'
-semaphored_job_id
'}
||=
$self
->
input_job
->
semaphored_job_id
();
# if branch_code is set to 1 (explicitly or impliticly), turn off automatic dataflow:
$self
->
autoflow_
inputjob
(
0
)
if
(
$branch_code
==
1
);
$self
->
input
_
job
->
autoflow
(
0
)
if
(
$branch_code
==
1
);
my
@output_job_ids
=
();
my
$job_adaptor
=
$self
->
db
->
get_AnalysisJobAdaptor
;
...
...
modules/Bio/EnsEMBL/Hive/Worker.pm
View file @
27633e4a
...
...
@@ -656,7 +656,7 @@ sub run_module_with_job {
$runObj
->
queen
(
$self
->
queen
);
$runObj
->
worker
(
$self
);
$runObj
->
debug
(
$self
->
debug
);
$
runObj
->
autoflow
_inputjob
(
1
);
$
job
->
autoflow
(
1
);
}
else
{
$runObj
->
input_id
(
$job
->
input_id
);
$runObj
->
db
(
$self
->
db
);
...
...
@@ -687,7 +687,7 @@ sub run_module_with_job {
$runObj
->
write_output
;
$self
->
{'
writing_stopwatch
'}
->
pause
();
if
(
$native_hive_process
and
$
runObj
->
autoflow
_inputjob
)
{
if
(
$native_hive_process
and
$
job
->
autoflow
)
{
printf
("
AUTOFLOW input->output
\n
")
if
(
$self
->
debug
);
$runObj
->
dataflow_output_id
();
}
...
...
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