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ensembl-gh-mirror
ensembl-hive
Commits
12ef1ec6
Commit
12ef1ec6
authored
Nov 27, 2019
by
Matthieu Muffato
Browse files
Defer the creation of the funnel job
parent
8071c155
Changes
3
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3 changed files
with
5 additions
and
11 deletions
+5
-11
modules/Bio/EnsEMBL/Hive/Analysis.pm
modules/Bio/EnsEMBL/Hive/Analysis.pm
+2
-7
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+2
-2
scripts/seed_pipeline.pl
scripts/seed_pipeline.pl
+1
-2
No files found.
modules/Bio/EnsEMBL/Hive/Analysis.pm
View file @
12ef1ec6
...
...
@@ -391,16 +391,11 @@ sub dataflow {
die
"
Asked to dataflow into
$funnel_job_count
funnel jobs instead of 1
";
}
else
{
my
$funnel_job
=
Bio::EnsEMBL::Hive::
AnalysisJob
->
new
(
@$common_params
,
'
input_id
'
=>
$output_ids_for_this_rule
->
[
0
],
'
status
'
=>
'
SEMAPHORED
',
);
# NB: $job_adaptor happens to belong to the $funnel_job, but not necesarily to $fan_jobs or $emitting_job
my
(
$semaphore_id
,
$funnel_job_id
,
@fan_job_ids
)
=
$job_adaptor
->
store_a_semaphored_group_of_jobs
(
$
funnel_job
,
$fan_jobs
,
$emitting_job
);
my
(
$semaphore_id
,
@fan_job_ids
)
=
$job_adaptor
->
store_a_semaphored_group_of_jobs
(
$
output_ids_for_this_rule
->
[
0
]
,
$fan_jobs
,
$emitting_job
);
push
@output_job_ids
,
$funnel_job_id
,
@fan_job_ids
;
push
@output_job_ids
,
@fan_job_ids
;
}
}
else
{
# non-semaphored dataflow (but potentially propagating any existing semaphores)
my
@non_semaphored_jobs
=
map
{
Bio::EnsEMBL::Hive::
AnalysisJob
->
new
(
...
...
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
View file @
12ef1ec6
...
...
@@ -238,7 +238,7 @@ sub store_jobs_and_adjust_counters {
=cut
sub
store_a_semaphored_group_of_jobs
{
my
(
$self
,
$funnel_
job
,
$fan_jobs
,
$emitting_job
,
$no_leeching
)
=
@_
;
my
(
$self
,
$funnel_
input_id
,
$fan_jobs
,
$emitting_job
,
$no_leeching
,
$dependent_dataflow_rule
)
=
@_
;
my
$emitting_job_id
;
...
...
@@ -317,7 +317,7 @@ sub store_a_semaphored_group_of_jobs {
my
(
@fan_job_ids
)
=
@
{
$self
->
store_jobs_and_adjust_counters
(
$fan_jobs
,
1
,
$emitting_job_id
)
};
return
(
$funnel_semaphore
->
dbID
,
$funnel_job_id
,
@fan_job_ids
);
return
(
$funnel_semaphore
->
dbID
,
@fan_job_ids
);
}
...
...
scripts/seed_pipeline.pl
View file @
12ef1ec6
...
...
@@ -135,8 +135,7 @@ sub main {
my
(
$semaphore_id
,
$job_id
);
if
(
$wrap_in_semaphore
)
{
my
$dummy
;
(
$semaphore_id
,
$dummy
,
$job_id
)
=
$job_adaptor
->
store_a_semaphored_group_of_jobs
(
undef
,
[
$job
],
undef
);
(
$semaphore_id
,
$job_id
)
=
$job_adaptor
->
store_a_semaphored_group_of_jobs
(
undef
,
[
$job
],
undef
);
}
else
{
(
$job_id
)
=
@
{
$job_adaptor
->
store_jobs_and_adjust_counters
(
[
$job
]
)
};
}
...
...
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