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ensembl-gh-mirror
ensembl
Commits
4e3fc21a
Commit
4e3fc21a
authored
12 years ago
by
Andreas Kusalananda Kähäri
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In initial_stable_id():
Do not try to use ${type}_stable_id tables that do not any longer exist. Reformat.
parent
d2743a85
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1 changed file
modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+29
-22
29 additions, 22 deletions
...Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
with
29 additions
and
22 deletions
modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+
29
−
22
View file @
4e3fc21a
...
...
@@ -117,54 +117,61 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
=cut
sub
initial_stable_id
{
my
$self
=
shift
;
my
$type
=
shift
;
my
(
$self
,
$type
)
=
@_
;
my
$init_stable_id
;
# use stable ID from configuration if set
if
(
$init_stable_id
=
$self
->
conf
->
param
("
starting_
${type}
_stable_id
"))
{
$self
->
logger
->
debug
("
Using pre-configured
$init_stable_id
as base for new
$type
stable IDs.
\n
");
# Use stable ID from configuration if set.
$init_stable_id
=
$self
->
conf
->
param
("
starting_
${type}
_stable_id
");
if
(
defined
(
$init_stable_id
)
)
{
$self
->
logger
->
debug
(
"
Using pre-configured
$init_stable_id
"
.
"
as base for new
$type
stable IDs.
\n
"
);
return
$init_stable_id
;
}
my
$s_dba
=
$self
->
cache
->
get_DBAdaptor
('
source
');
my
$s_dbh
=
$s_dba
->
dbc
->
db_handle
;
# look in the ${type}
_stable_id
table first
# look in the ${type} table first
my
$sql
=
qq(
SELECT MAX(stable_id)
FROM ${type}
_stable_id
FROM ${type}
WHERE stable_id LIKE "ENS%"
OR stable_id LIKE "ASMPATCH%"
)
;
$init_stable_id
=
$self
->
fetch_value_from_db
(
$s_dbh
,
$sql
);
$init_stable_id
=
$self
->
fetch_value_from_db
(
$s_dbh
,
$sql
);
# also look in gene_archive to make sure there are no larger Ids there
unless
(
$type
eq
'
exon
')
{
# Also look in gene_archive to make sure there are no larger IDs
# there.
if
(
$type
ne
'
exon
'
)
{
$sql
=
qq(SELECT MAX(${type}_stable_id) FROM gene_archive)
;
my
$archived_stable_id
=
$self
->
fetch_value_from_db
(
$s_dbh
,
$sql
);
if
(
$archived_stable_id
and
$self
->
is_valid
(
$archived_stable_id
)
and
(
$archived_stable_id
gt
$init_stable_id
))
{
my
$archived_stable_id
=
$self
->
fetch_value_from_db
(
$s_dbh
,
$sql
);
if
(
$archived_stable_id
&&
$self
->
is_valid
(
$archived_stable_id
)
&&
(
$archived_stable_id
gt
$init_stable_id
)
)
{
$init_stable_id
=
$archived_stable_id
;
}
}
if
(
$init_stable_id
)
{
#
s
ince $init_stable_id now is the highest existing stable I
d
for
this
# object type, we need to increment it to find the first one we
want to use
# for new assignments
if
(
defined
(
$init_stable_id
)
)
{
#
S
ince $init_stable_id now is the highest existing stable I
D
for
#
this
object type, we need to increment it to find the first one we
#
want to use
for new assignments
.
$init_stable_id
=
$self
->
increment_stable_id
(
$init_stable_id
);
$self
->
logger
->
debug
("
Using
$init_stable_id
as base for new
$type
stable IDs.
\n
");
}
else
{
$self
->
logger
->
warning
("
Can't find highest
${type}
_stable_id in source db.
\n
");
$self
->
logger
->
debug
(
"
Using
$init_stable_id
as base for new
$type
stable IDs.
\n
");
}
else
{
$self
->
logger
->
warning
(
"
Can't find highest
${type}
_stable_id in source db.
\n
"
);
}
return
$init_stable_id
;
}
}
## end sub initial_stable_id
=head2 increment_stable_id
...
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