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ensembl-gh-mirror
ensembl-hive
Commits
60f1d5e5
Commit
60f1d5e5
authored
May 22, 2012
by
Leo Gordon
Browse files
untangling a bit. Queen does not need to re-sync and beekeeper does not need to fetch
parent
2af05379
Changes
2
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2 changed files
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18 additions
and
19 deletions
+18
-19
modules/Bio/EnsEMBL/Hive/Queen.pm
modules/Bio/EnsEMBL/Hive/Queen.pm
+17
-18
scripts/beekeeper.pl
scripts/beekeeper.pl
+1
-1
No files found.
modules/Bio/EnsEMBL/Hive/Queen.pm
View file @
60f1d5e5
...
@@ -141,8 +141,11 @@ sub create_new_worker {
...
@@ -141,8 +141,11 @@ sub create_new_worker {
if
(
$analysis_id
)
{
if
(
$analysis_id
)
{
die
"
When you specify -job_id, please omit both -logic_name and -analysis_id to avoid confusion
\n
";
die
"
When you specify -job_id, please omit both -logic_name and -analysis_id to avoid confusion
\n
";
}
else
{
}
else
{
print
"
fetching job for job_id '
$job_id
'
\n
";
print
"
resetting and fetching job for job_id '
$job_id
'
\n
";
if
(
$job
=
$self
->
reset_and_fetch_job_by_dbID
(
$job_id
))
{
my
$job_adaptor
=
$self
->
db
->
get_AnalysisJobAdaptor
;
$job_adaptor
->
reset_job_by_dbID
(
$job_id
);
if
(
$job
=
$job_adaptor
->
fetch_by_dbID
(
$job_id
))
{
$analysis_id
=
$job
->
analysis_id
;
$analysis_id
=
$job
->
analysis_id
;
}
else
{
}
else
{
die
"
job_id '
$job_id
' could not be fetched from the database
\n
";
die
"
job_id '
$job_id
' could not be fetched from the database
\n
";
...
@@ -350,36 +353,32 @@ sub check_in_worker {
...
@@ -350,36 +353,32 @@ sub check_in_worker {
}
}
=head2 reset_
and_fetch_
job_by_dbID
=head2 reset_job_by_dbID
_and_sync
Arg [1]: int $job_id
Arg [1]: int $job_id
Example:
Example:
my $job = $queen->reset_
and_fetch_
job_by_dbID($job_id);
my $job = $queen->reset_job_by_dbID
_and_sync
($job_id);
Description:
Description:
For the specified job_id it will fetch just that job,
For the specified job_id it will fetch just that job,
reset it completely as if it has never run, and return it.
reset it completely as if it has never run, and return it.
Specifying a specific job bypasses the safety checks,
Specifying a specific job bypasses the safety checks,
thus multiple workers could be running the
thus multiple workers could be running the
same job simultaneously (use only for debugging).
same job simultaneously (use only for debugging).
Returntype :
Returntype : none
Bio::EnsEMBL::Hive::AnalysisJob object
Exceptions :
Exceptions :
Caller : beekeeper
s, runWorker.pl scripts
Caller : beekeeper
.pl
=cut
=cut
sub
reset_and_fetch_job_by_dbID
{
sub
reset_job_by_dbID_and_sync
{
my
$self
=
shift
;
my
(
$self
,
$job_id
)
=
@_
;
my
$job_id
=
shift
;
my
$jobDBA
=
$self
->
db
->
get_AnalysisJobAdaptor
;
$jobDBA
->
reset_job_by_dbID
(
$job_id
);
my
$job
=
$jobDBA
->
fetch_by_dbID
(
$job_id
);
my
$job_adaptor
=
$self
->
db
->
get_AnalysisJobAdaptor
;
my
$stats
=
$self
->
db
->
get_AnalysisStatsAdaptor
->
fetch_by_analysis_id
(
$job
->
analysis_id
);
$job_adaptor
->
reset_job_by_dbID
(
$job_id
);
$self
->
synchronize_AnalysisStats
(
$stats
);
my
$job
=
$job_adaptor
->
fetch_by_dbID
(
$job_id
);
return
$job
;
my
$stats
=
$self
->
db
->
get_AnalysisStatsAdaptor
->
fetch_by_analysis_id
(
$job
->
analysis_id
);
$self
->
synchronize_AnalysisStats
(
$stats
);
}
}
...
...
scripts/beekeeper.pl
View file @
60f1d5e5
...
@@ -186,7 +186,7 @@ sub main {
...
@@ -186,7 +186,7 @@ sub main {
}
}
$current_meadow
->
submit_workers_max
(
$submit_workers_max
);
$current_meadow
->
submit_workers_max
(
$submit_workers_max
);
if
(
$reset_job_id
)
{
$queen
->
reset_
and_fetch_
job_by_dbID
(
$reset_job_id
);
}
if
(
$reset_job_id
)
{
$queen
->
reset_job_by_dbID
_and_sync
(
$reset_job_id
);
}
if
(
$job_id_for_output
)
{
if
(
$job_id_for_output
)
{
printf
("
===== job output
\n
");
printf
("
===== job output
\n
");
...
...
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