From 623aa3495a44b7cecd16f33bce4e9a1d5e2de22a Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 5 Oct 2011 14:57:42 +0000
Subject: [PATCH] Backing out stable_id merging changes until databases are
patched
---
.../EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 5 +-
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm | 1 -
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm | 68 +++++++-----
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 92 +++++++++------
modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm | 84 +++++++++-----
.../EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm | 72 +++++++-----
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 105 ++++++++++--------
modules/Bio/EnsEMBL/UnmappedObject.pm | 2 +-
8 files changed, 259 insertions(+), 170 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index a424187a85..e056bf6064 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -1022,7 +1022,7 @@ sub add_all_current_to_history {
# get current stable IDs from db
my $sql = qq(
- SELECT stable_id, version FROM ${type}
+ SELECT stable_id, version FROM ${type}_stable_id
WHERE stable_id IN ('$id_string')
);
my $sth = $self->prepare($sql);
@@ -1442,7 +1442,7 @@ sub lookup_current {
}
my $sql = qq(
- SELECT version FROM ${type}
+ SELECT version FROM ${type}_stable_id
WHERE stable_id = ?
);
my $sth = $self->prepare($sql);
@@ -1510,4 +1510,3 @@ sub _resolve_type {
1;
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index 7675e5269d..fb833745a7 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -788,5 +788,4 @@ sub get_dumped_data {
return eval ($data);
}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index 5273c2c271..e0e3ed5f37 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -69,7 +69,7 @@ sub _tables {
return @{ $self->{'tables'} };
}
- return ( [ 'exon', 'e' ] );
+ return ( [ 'exon', 'e' ], [ 'exon_stable_id', 'esi' ] );
}
@@ -95,11 +95,14 @@ sub _columns {
'e.exon_id', 'e.seq_region_id', 'e.seq_region_start',
'e.seq_region_end', 'e.seq_region_strand', 'e.phase',
'e.end_phase', 'e.is_current', 'e.is_constitutive',
- 'e.stable_id', 'e.version', $created_date,
+ 'esi.stable_id', 'esi.version', $created_date,
$modified_date
);
}
+sub _left_join {
+ return ( [ 'exon_stable_id', "esi.exon_id = e.exon_id" ] );
+}
# _final_clause
@@ -142,7 +145,7 @@ sub fetch_all {
sub fetch_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "e.stable_id = ? AND e.is_current = 1";
+ my $constraint = "esi.stable_id = ? AND e.is_current = 1";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
my ($exon) = @{ $self->generic_fetch($constraint) };
@@ -169,7 +172,7 @@ sub fetch_by_stable_id {
sub fetch_all_versions_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "e.stable_id = ?";
+ my $constraint = "esi.stable_id = ?";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
@@ -297,19 +300,9 @@ sub store {
my $exon_sql = q{
INSERT into exon ( seq_region_id, seq_region_start,
seq_region_end, seq_region_strand, phase,
- end_phase, is_current, is_constitutive
+ end_phase, is_current, is_constitutive )
+ VALUES ( ?,?,?,?,?,?,?,? )
};
- if ( defined($exon->stable_id) ) {
- my $created = $self->db->dbc->from_seconds_to_date($exon->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($exon->modified_date());
- $exon_sql .= ", stable_id, version, created_date, modified_date) VALUES ( ?,?,?,?,?,?,?,?,?,?,". $created . ",". $modified ." )";
-
- } else {
- $exon_sql .= q{
- ) VALUES ( ?,?,?,?,?,?,?,?)
- };
- }
-
my $exonst = $self->prepare($exon_sql);
@@ -329,16 +322,32 @@ sub store {
$exonst->bind_param( 7, $is_current, SQL_TINYINT );
$exonst->bind_param( 8, $is_constitutive, SQL_TINYINT );
- if ( defined($exon->stable_id) ) {
-
- $exonst->bind_param( 9, $exon->stable_id, SQL_VARCHAR );
- my $version = ($exon->version()) ? $exon->version() : 1;
- $exonst->bind_param( 10, $version, SQL_INTEGER );
- }
-
$exonst->execute();
$exonId = $exonst->{'mysql_insertid'};
+ #store any stable_id information
+ if ($exon->stable_id && $exon->version()) {
+
+ my $statement =
+ "INSERT INTO exon_stable_id " .
+ "SET version = ?, " .
+ "stable_id = ?, " .
+ "exon_id = ?, ";
+
+ $statement .= "created_date = " .
+ $self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
+ $statement .= "modified_date = " .
+ $self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
+
+ my $sth = $self->prepare( $statement );
+
+ $sth->bind_param(1,( $exon->version || 1 ),SQL_INTEGER);
+ $sth->bind_param(2,$exon->stable_id,SQL_VARCHAR);
+ $sth->bind_param(3,$exonId,SQL_INTEGER);
+
+ $sth->execute();
+ }
+
# Now the supporting evidence
my $esf_adaptor = $db->get_SupportingFeatureAdaptor;
$esf_adaptor->store($exonId, $exon->get_all_supporting_features);
@@ -452,6 +461,12 @@ sub remove {
$sth->execute();
$sth->finish();
+ # delete the exon stable identifier
+
+ $sth = $self->prepare( "DELETE FROM exon_stable_id WHERE exon_id = ?" );
+ $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
+ $sth->execute();
+ $sth->finish();
# delete the exon
@@ -502,7 +517,7 @@ sub list_dbIDs {
sub list_stable_ids {
my ($self) = @_;
- return $self->_list_dbIDs("exon", "stable_id");
+ return $self->_list_dbIDs("exon_stable_id", "stable_id");
}
#_objs_from_sth
@@ -780,12 +795,11 @@ sub get_stable_entry_info {
#$self->throw("can't fetch stable info with no dbID");
return;
}
-
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
my $sth = $self->prepare("SELECT stable_id, " . $created_date . ",
" . $modified_date . ", version
- FROM exon
+ FROM exon_stable_id
WHERE exon_id = ");
$sth->bind_param(1, $exon->dbID, SQL_INTEGER);
@@ -868,5 +882,3 @@ sub fetch_all_by_gene_id {
1;
-
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 0af1f92ca4..6e8f8cc056 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -85,6 +85,7 @@ use vars '@ISA';
sub _tables {
return (
[ 'gene', 'g' ],
+ [ 'gene_stable_id', 'gsi' ],
[ 'xref', 'x' ],
[ 'external_db', 'exdb' ] );
}
@@ -104,9 +105,9 @@ sub _columns {
my ($self) = @_;
my $created_date =
- $self->db()->dbc()->from_date_to_seconds("g.created_date");
+ $self->db()->dbc()->from_date_to_seconds("gsi.created_date");
my $modified_date =
- $self->db()->dbc()->from_date_to_seconds("g.modified_date");
+ $self->db()->dbc()->from_date_to_seconds("gsi.modified_date");
return (
'g.gene_id', 'g.seq_region_id',
@@ -116,7 +117,7 @@ sub _columns {
'g.description', 'g.status',
'g.source', 'g.is_current',
'g.canonical_transcript_id', 'g.canonical_annotation',
- 'g.stable_id', 'g.version',
+ 'gsi.stable_id', 'gsi.version',
$created_date, $modified_date,
'x.display_label', 'x.dbprimary_acc',
'x.description', 'x.version',
@@ -129,6 +130,7 @@ sub _columns {
sub _left_join {
return (
+ [ 'gene_stable_id', "gsi.gene_id = g.gene_id" ],
[ 'xref', "x.xref_id = g.display_xref_id" ],
[ 'external_db', "exdb.external_db_id = x.external_db_id" ] );
}
@@ -167,7 +169,7 @@ sub list_dbIDs {
sub list_stable_ids {
my ($self) = @_;
- return $self->_list_dbIDs("gene", "stable_id");
+ return $self->_list_dbIDs("gene_stable_id", "stable_id");
}
@@ -225,7 +227,7 @@ sub fetch_by_display_label {
sub fetch_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "g.stable_id = ? AND g.is_current = 1";
+ my $constraint = "gsi.stable_id = ? AND g.is_current = 1";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
my ($gene) = @{ $self->generic_fetch($constraint) };
@@ -308,7 +310,7 @@ sub fetch_all {
sub fetch_all_versions_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "g.stable_id = ?";
+ my $constraint = "gsi.stable_id = ?";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
return $self->generic_fetch($constraint);
}
@@ -339,10 +341,12 @@ sub fetch_by_exon_stable_id {
SELECT t.gene_id
FROM transcript as t,
exon_transcript as et,
- exon as e
+ exon as e,
+ exon_stable_id as esi
WHERE t.transcript_id = et.transcript_id
+ AND et.exon_id = esi.exon_id
AND et.exon_id = e.exon_id
- AND e.stable_id = ?
+ AND esi.stable_id = ?
AND e.is_current = 1
);
@@ -696,10 +700,11 @@ sub fetch_by_transcript_stable_id {
my ($self, $trans_stable_id) = @_;
my $sth = $self->prepare(qq(
- SELECT gene_id
- FROM transcript
- WHERE stable_id = ?
- AND is_current = 1
+ SELECT tr.gene_id
+ FROM transcript tr, transcript_stable_id tcl
+ WHERE tcl.stable_id = ?
+ AND tr.transcript_id = tcl.transcript_id
+ AND tr.is_current = 1
));
$sth->bind_param(1, $trans_stable_id, SQL_VARCHAR);
@@ -735,8 +740,10 @@ sub fetch_by_translation_stable_id {
my $sth = $self->prepare(qq(
SELECT tr.gene_id
FROM transcript tr,
- translation tl
- WHERE tl.stable_id = ?
+ translation tl,
+ translation_stable_id as trs
+ WHERE trs.stable_id = ?
+ AND trs.translation_id = tl.translation_id
AND tr.transcript_id = tl.transcript_id
AND tr.is_current = 1
));
@@ -1149,14 +1156,6 @@ sub store {
canonical_transcript_id = ?,
canonical_annotation = ?
);
-
- if (defined($gene->stable_id)) {
- my $created = $self->db->dbc->from_seconds_to_date($gene->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($gene->modified_date());
- $store_gene_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;
-
- }
-
# column status is used from schema version 34 onwards (before it was
# confidence)
@@ -1178,18 +1177,32 @@ sub store {
$sth->bind_param( 12, $gene->canonical_annotation(), SQL_VARCHAR );
- if ( defined($gene->stable_id) ) {
-
- $sth->bind_param( 13, $gene->stable_id, SQL_VARCHAR );
- my $version = ($gene->version()) ? $gene->version() : 1;
- $sth->bind_param( 14, $version, SQL_INTEGER );
- }
-
$sth->execute();
$sth->finish();
my $gene_dbID = $sth->{'mysql_insertid'};
+ # store stable ids if they are available
+ if ( defined( $gene->stable_id() ) ) {
+ my $statement = sprintf(
+ "INSERT INTO gene_stable_id SET "
+ . "gene_id = ?, "
+ . "stable_id = ?, "
+ . "version = ?, "
+ . "created_date = %s, "
+ . "modified_date = %s",
+ $self->db()->dbc()->from_seconds_to_date( $gene->created_date() ),
+ $self->db()->dbc()->from_seconds_to_date( $gene->modified_date() )
+ );
+
+ $sth = $self->prepare($statement);
+ $sth->bind_param( 1, $gene_dbID, SQL_INTEGER );
+ $sth->bind_param( 2, $gene->stable_id(), SQL_VARCHAR );
+ $sth->bind_param( 3, ($gene->version() || 1), SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+ }
+
# store the dbentries associated with this gene
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
@@ -1256,7 +1269,6 @@ sub store {
$sth->bind_param( 2, $gene_dbID, SQL_INTEGER );
$sth->execute();
- $sth->finish();
}
# update gene to point to display xref if it is set
@@ -1269,7 +1281,7 @@ sub store {
}
if(defined($dxref_id)) {
- my $sth = $self->prepare
+ $sth = $self->prepare
("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
$sth->bind_param(1, $dxref_id, SQL_INTEGER);
$sth->bind_param(2, $gene_dbID, SQL_INTEGER);
@@ -1360,6 +1372,14 @@ sub remove {
$transcriptAdaptor->remove($trans);
}
+ # remove the gene stable identifier
+
+ $sth =
+ $self->prepare("DELETE FROM gene_stable_id WHERE gene_id = ? ");
+ $sth->bind_param( 1, $gene->dbID, SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+
# remove any unconventional transcript associations involving this gene
$sth =
@@ -1412,9 +1432,9 @@ sub get_Interpro_by_geneid {
protein_feature pf,
interpro i,
xref x,
- gene g
- WHERE g.stable_id = ?
- AND t.gene_id = g.gene_id
+ gene_stable_id gsi
+ WHERE gsi.stable_id = ?
+ AND t.gene_id = gsi.gene_id
AND t.is_current = 1
AND tl.transcript_id = t.transcript_id
AND tl.translation_id = pf.translation_id
@@ -2281,7 +2301,7 @@ sub get_stable_entry_info {
my $sth = $self->prepare("SELECT stable_id, " . $created_date . "," .
$modified_date . ", version
- FROM gene
+ FROM gene_stable_id
WHERE gene_id = ?");
$sth->bind_param(1, $gene->dbID, SQL_INTEGER);
@@ -2313,5 +2333,3 @@ sub fetch_all_by_DBEntry {
1;
-
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
index c2472e5087..1ab406b4d8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
@@ -1,4 +1,3 @@
-
=head1 LICENSE
Copyright (c) 1999-2011 The European Bioinformatics Institute and
@@ -63,7 +62,7 @@ use vars '@ISA';
# Status : Stable
sub _tables {
- return ( [ 'operon', 'o' ] );
+ return ( [ 'operon', 'o' ], [ 'operon_stable_id', 'osi' ] );
}
# _columns
@@ -80,16 +79,20 @@ sub _columns {
my ($self) = @_;
my $created_date =
- $self->db()->dbc()->from_date_to_seconds("o.created_date");
+ $self->db()->dbc()->from_date_to_seconds("osi.created_date");
my $modified_date =
- $self->db()->dbc()->from_date_to_seconds("o.modified_date");
+ $self->db()->dbc()->from_date_to_seconds("osi.modified_date");
return ( 'o.operon_id', 'o.seq_region_id', 'o.seq_region_start',
'o.seq_region_end', 'o.seq_region_strand', 'o.display_label',
- 'o.analysis_id', 'o.stable_id', 'o.version',
+ 'o.analysis_id', 'osi.stable_id', 'osi.version',
$created_date, $modified_date );
}
+sub _left_join {
+ return ( [ 'operon_stable_id', "osi.operon_id = o.operon_id" ] );
+}
+
=head2 list_dbIDs
Example : @operon_ids = @{$operon_adaptor->list_dbIDs()};
@@ -122,7 +125,7 @@ sub list_dbIDs {
sub list_stable_ids {
my ($self) = @_;
- return $self->_list_dbIDs( "operon", "stable_id" );
+ return $self->_list_dbIDs( "operon_stable_id", "stable_id" );
}
sub list_seq_region_ids {
@@ -177,7 +180,7 @@ sub fetch_by_name {
sub fetch_by_stable_id {
my ( $self, $stable_id ) = @_;
- my $constraint = "o.stable_id = ?";
+ my $constraint = "osi.stable_id = ? AND o.is_current = 1";
$self->bind_param_generic_fetch( $stable_id, SQL_VARCHAR );
my ($operon) = @{ $self->generic_fetch($constraint) };
@@ -221,7 +224,7 @@ sub fetch_all {
sub fetch_all_versions_by_stable_id {
my ( $self, $stable_id ) = @_;
- my $constraint = "o.stable_id = ?";
+ my $constraint = "osi.stable_id = ?";
$self->bind_param_generic_fetch( $stable_id, SQL_VARCHAR );
return $self->generic_fetch($constraint);
}
@@ -395,11 +398,11 @@ sub fetch_by_operon_transcript_id {
return $operon;
}
-=head2 fetch_by_operon_transcript_stable_id
+=head2 fetch_by_transcript_stable_id
Arg [1] : string $trans_stable_id
transcript stable ID whose operon should be retrieved
- Example : my $operon = $operon_adaptor->fetch_by_operon_transcript_stable_id
+ Example : my $operon = $operon_adaptor->fetch_by_transcript_stable_id
('ENST0000234');
Description: Retrieves a operon from the database via the stable ID of one of
its transcripts
@@ -415,9 +418,11 @@ sub fetch_by_operon_transcript_stable_id {
my $sth = $self->prepare(
qq(
- SELECT operon_id
- FROM operon_transcript
- WHERE stable_id = ?
+ SELECT tr.operon_id
+ FROM operon_transcript tr, operon_transcript_stable_id tcl
+ WHERE tcl.stable_id = ?
+ AND tr.operon_transcript_stable_id = tcl.operon_transcript_stable_id
+ AND tr.is_current = 1
) );
$sth->bind_param( 1, $trans_stable_id, SQL_VARCHAR );
@@ -490,14 +495,7 @@ sub store {
display_label = ?,
analysis_id = ?
);
-
- if ( defined($operon->stable_id()) ) {
- my $created = $self->db->dbc->from_seconds_to_date($operon->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($operon->modified_date());
- $store_operon_sql .= ", stable_id = ?, version = ?, created_date = " . $created . ",modified_date = " . $modified;
- }
-
- # column status is used from schema version 34 onwards (before it was
+ # column status is used from schema version 34 onwards (before it was
# confidence)
my $sth = $self->prepare($store_operon_sql);
@@ -508,12 +506,6 @@ sub store {
$sth->bind_param( 5, $operon->display_label(), SQL_VARCHAR );
$sth->bind_param( 6, $analysis_id, SQL_INTEGER );
- if ( defined($operon->stable_id()) ) {
- $sth->bind_param( 7, $operon->stable_id(), SQL_VARCHAR );
- my $version = ($operon->version()) ? $operon->version() : 1;
- $sth->bind_param( 8, $version, SQL_INTEGER );
- }
-
$sth->execute();
$sth->finish();
@@ -528,6 +520,29 @@ sub store {
}
}
+ # store stable ids if they are available
+ if ( defined( $operon->stable_id() ) ) {
+ my $statement = sprintf( "INSERT INTO operon_stable_id SET "
+ . "operon_id = ?, "
+ . "stable_id = ?, "
+ . "version = ?, "
+ . "created_date = %s, "
+ . "modified_date = %s",
+ $self->db()->dbc()->from_seconds_to_date(
+ $operon->created_date()
+ ),
+ $self->db()->dbc()->from_seconds_to_date(
+ $operon->modified_date()
+ ) );
+
+ $sth = $self->prepare($statement);
+ $sth->bind_param( 1, $operon_dbID, SQL_INTEGER );
+ $sth->bind_param( 2, $operon->stable_id(), SQL_VARCHAR );
+ $sth->bind_param( 3, $operon->version(), SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+ }
+
# store the dbentries associated with this operon
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
@@ -589,15 +604,27 @@ sub remove {
$dbe_adaptor->remove_from_object( $dbe, $operon, 'Operon' );
}
+ # # remove the attributes associated with this transcript
+ # my $attrib_adaptor = $self->db->get_AttributeAdaptor;
+ # $attrib_adaptor->remove_from_Operon($operon);
+
# remove all of the transcripts associated with this operon
my $transcriptAdaptor = $self->db->get_OperonTranscriptAdaptor();
foreach my $trans ( @{ $operon->get_all_OperonTranscripts() } ) {
$transcriptAdaptor->remove($trans);
}
+ # remove the operon stable identifier
+
+ my $sth =
+ $self->prepare("DELETE FROM operon_stable_id WHERE operon_id = ? ");
+ $sth->bind_param( 1, $operon->dbID, SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+
# remove this operon from the database
- my $sth = $self->prepare("DELETE FROM operon WHERE operon_id = ? ");
+ $sth = $self->prepare("DELETE FROM operon WHERE operon_id = ? ");
$sth->bind_param( 1, $operon->dbID, SQL_INTEGER );
$sth->execute();
$sth->finish();
@@ -779,4 +806,3 @@ sub _objs_from_sth {
} ## end sub _objs_from_sth
1;
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
index 34c2184a8a..e6c2091de8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
@@ -1,4 +1,3 @@
-
=head1 LICENSE
Copyright (c) 1999-2011 The European Bioinformatics Institute and
@@ -67,7 +66,8 @@ use vars '@ISA';
# Status : Stable
sub _tables {
- return ( [ 'operon_transcript', 'o' ] );
+ return ( [ 'operon_transcript', 'o' ],
+ [ 'operon_transcript_stable_id', 'osi' ] );
}
# _columns
@@ -84,18 +84,23 @@ sub _columns {
my ($self) = @_;
my $created_date =
- $self->db()->dbc()->from_date_to_seconds("o.created_date");
+ $self->db()->dbc()->from_date_to_seconds("osi.created_date");
my $modified_date =
- $self->db()->dbc()->from_date_to_seconds("o.modified_date");
+ $self->db()->dbc()->from_date_to_seconds("osi.modified_date");
return ( 'o.operon_transcript_id', 'o.seq_region_id',
'o.seq_region_start', 'o.seq_region_end',
'o.seq_region_strand', 'o.display_label',
- 'o.analysis_id', 'o.stable_id',
- 'o.version', $created_date,
+ 'o.analysis_id', 'osi.stable_id',
+ 'osi.version', $created_date,
$modified_date );
}
+sub _left_join {
+ return ( [ 'operon_transcript_stable_id',
+ "osi.operon_transcript_id = o.operon_transcript_id" ] );
+}
+
=head2 list_dbIDs
Example : @ot_ids = @{$ot_adaptor->list_dbIDs()};
@@ -111,7 +116,7 @@ sub _columns {
sub list_dbIDs {
my ( $self, $ordered ) = @_;
- return $self->_list_dbIDs( "operon_transcript", undef, $ordered );
+ return $self->_list_dbIDs( "operon", undef, $ordered );
}
=head2 list_stable_ids
@@ -128,7 +133,7 @@ sub list_dbIDs {
sub list_stable_ids {
my ($self) = @_;
- return $self->_list_dbIDs( "operon_transcript", "stable_id" );
+ return $self->_list_dbIDs( "operon_stable_id", "stable_id" );
}
sub list_seq_region_ids {
@@ -158,7 +163,7 @@ sub list_seq_region_ids {
sub fetch_by_stable_id {
my ( $self, $stable_id ) = @_;
- my $constraint = "o.stable_id = ?";
+ my $constraint = "osi.stable_id = ? AND o.is_current = 1";
$self->bind_param_generic_fetch( $stable_id, SQL_VARCHAR );
my ($operon_transcript) = @{ $self->generic_fetch($constraint) };
@@ -226,7 +231,7 @@ sub fetch_all {
sub fetch_all_versions_by_stable_id {
my ( $self, $stable_id ) = @_;
- my $constraint = "o.stable_id = ?";
+ my $constraint = "osi.stable_id = ?";
$self->bind_param_generic_fetch( $stable_id, SQL_VARCHAR );
return $self->generic_fetch($constraint);
}
@@ -545,14 +550,6 @@ sub store {
operon_id = ?,
analysis_id =?
);
-
- if ( defined($operon_transcript->stable_id()) ) {
- my $created = $self->db->dbc->from_seconds_to_date($operon_transcript->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($operon_transcript->modified_date());
- $store_operon_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . ",modified_date = " . $modified;
- }
-
-
# column status is used from schema version 34 onwards (before it was
# confidence)
@@ -565,17 +562,34 @@ sub store {
$sth->bind_param( 6, $operon_id, SQL_INTEGER );
$sth->bind_param( 7, $analysis_id, SQL_INTEGER );
- if ( defined($operon_transcript->stable_id()) ) {
- $sth->bind_param( 8, $operon_transcript->stable_id(), SQL_VARCHAR );
- my $version = ($operon_transcript->version()) ? $operon_transcript->version() : 1;
- $sth->bind_param( 9, $version, SQL_INTEGER );
- }
-
$sth->execute();
$sth->finish();
my $operon_transcript_dbID = $sth->{'mysql_insertid'};
+ # store stable ids if they are available
+ if ( defined( $operon_transcript->stable_id() ) ) {
+ my $statement = sprintf( "INSERT INTO operon_transcript_stable_id SET "
+ . "operon_transcript_id = ?, "
+ . "stable_id = ?, "
+ . "version = ?, "
+ . "created_date = %s, "
+ . "modified_date = %s",
+ $self->db()->dbc()->from_seconds_to_date(
+ $operon_transcript->created_date()
+ ),
+ $self->db()->dbc()->from_seconds_to_date(
+ $operon_transcript->modified_date()
+ ) );
+
+ $sth = $self->prepare($statement);
+ $sth->bind_param( 1, $operon_transcript_dbID, SQL_INTEGER );
+ $sth->bind_param( 2, $operon_transcript->stable_id(), SQL_VARCHAR );
+ $sth->bind_param( 3, $operon_transcript->version(), SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+ }
+
# store the dbentries associated with this gene
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
@@ -676,8 +690,15 @@ sub remove {
# my $attrib_adaptor = $self->db->get_AttributeAdaptor;
# $attrib_adaptor->remove_from_OperonTranscript($operon_transcript);
- # remove from the database
+ # remove the stable identifier
my $sth = $self->prepare(
+"DELETE FROM operon_transcript_stable_id WHERE operon_transcript_id = ? " );
+ $sth->bind_param( 1, $operon_transcript->dbID, SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+
+ # remove from the database
+ $sth = $self->prepare(
"DELETE FROM operon_transcript WHERE operon_transcript_id = ? ");
$sth->bind_param( 1, $operon_transcript->dbID, SQL_INTEGER );
$sth->execute();
@@ -861,4 +882,3 @@ sub _objs_from_sth {
} ## end sub _objs_from_sth
1;
-
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index bf2369ac02..0f6f9dcc02 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -85,6 +85,7 @@ use vars qw(@ISA);
sub _tables {
return (
[ 'transcript', 't' ],
+ [ 'transcript_stable_id', 'tsi' ],
[ 'xref', 'x' ],
[ 'external_db', 'exdb' ] );
}
@@ -112,7 +113,7 @@ sub _columns {
't.seq_region_start', 't.seq_region_end',
't.seq_region_strand', 't.analysis_id',
't.gene_id', 't.is_current',
- 't.stable_id', 't.version',
+ 'tsi.stable_id', 'tsi.version',
$created_date, $modified_date,
't.description', 't.biotype',
't.status', 'exdb.db_name',
@@ -126,6 +127,7 @@ sub _columns {
sub _left_join {
return (
+ [ 'transcript_stable_id', "tsi.transcript_id = t.transcript_id" ],
[ 'xref', "x.xref_id = t.display_xref_id" ],
[ 'external_db', "exdb.external_db_id = x.external_db_id" ]
);
@@ -148,7 +150,7 @@ sub _left_join {
sub fetch_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "t.stable_id = ? AND t.is_current = 1";
+ my $constraint = "tsi.stable_id = ? AND t.is_current = 1";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
@@ -184,7 +186,7 @@ sub fetch_all {
sub fetch_all_versions_by_stable_id {
my ($self, $stable_id) = @_;
- my $constraint = "t.stable_id = ?";
+ my $constraint = "tsi.stable_id = ?";
$self->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
@@ -213,9 +215,11 @@ sub fetch_by_translation_stable_id {
my $sth = $self->prepare(qq(
SELECT t.transcript_id
- FROM translation tl,
- transcript t
- WHERE tl.stable_id = ?
+ FROM translation_stable_id tsi,
+ transcript t,
+ translation tl
+ WHERE tsi.stable_id = ?
+ AND tl.translation_id = tsi.translation_id
AND tl.transcript_id = t.transcript_id
AND t.is_current = 1
));
@@ -662,10 +666,10 @@ sub fetch_all_by_exon_stable_id {
my $sth = $self->prepare(qq(
SELECT t.transcript_id
- FROM exon_transcript et, exon e, transcript t
- WHERE e.exon_id = et.exon_id
+ FROM exon_transcript et, exon_stable_id esi, transcript t
+ WHERE esi.exon_id = et.exon_id
AND et.transcript_id = t.transcript_id
- AND e.stable_id = ?
+ AND esi.stable_id = ?
AND t.is_current = 1
));
@@ -777,30 +781,16 @@ sub store {
#
# Store transcript
#
- my $store_transcript_sql = qq(
- INSERT INTO transcript
- SET gene_id = ?,
- analysis_id = ?,
- seq_region_id = ?,
- seq_region_start = ?,
- seq_region_end = ?,
- seq_region_strand = ?,
- biotype = ?,
- status = ?,
- description = ?,
- is_current = ?,
- canonical_translation_id = ?
- );
-
- if ( defined( $transcript->stable_id() ) ) {
-
- my $created = $self->db->dbc->from_seconds_to_date($transcript->created_date());
- my $modified = $self->db->dbc->from_seconds_to_date($transcript->modified_date());
- $store_transcript_sql .= ", stable_id = ?, version = ?, created_date = " . $created . " , modified_date = " . $modified;
+ my $tst = $self->prepare(
+ qq(
+ INSERT INTO transcript (
+ gene_id, analysis_id, seq_region_id, seq_region_start,
+ seq_region_end, seq_region_strand, biotype, status, description,
+ is_current, canonical_translation_id
+ )
+ VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+ ) );
- }
-
- my $tst = $self->prepare($store_transcript_sql);
$tst->bind_param( 1, $gene_dbID, SQL_INTEGER );
$tst->bind_param( 2, $new_analysis_id, SQL_INTEGER );
$tst->bind_param( 3, $seq_region_id, SQL_INTEGER );
@@ -815,14 +805,6 @@ sub store {
# If the transcript has a translation, this is updated later:
$tst->bind_param( 11, undef, SQL_INTEGER );
- if ( defined( $transcript->stable_id() ) ) {
-
- $tst->bind_param( 12, $transcript->stable_id(), SQL_VARCHAR );
- my $version = ($transcript->version()) ? $transcript->version() : 1;
- $tst->bind_param( 13, $version, SQL_INTEGER );
- }
-
-
$tst->execute();
$tst->finish();
@@ -1006,6 +988,33 @@ sub store {
$etst->finish();
+ #
+ # Store stable_id
+ #
+ if ( defined( $transcript->stable_id() ) ) {
+
+ my $statement = "INSERT INTO transcript_stable_id "
+ . "SET transcript_id = ?, stable_id = ?, version = ?, ";
+
+ $statement .=
+ "created_date = "
+ . $self->db()->dbc()
+ ->from_seconds_to_date( $transcript->created_date() ) . ",";
+
+ $statement .=
+ "modified_date = "
+ . $self->db()->dbc()
+ ->from_seconds_to_date( $transcript->modified_date() );
+
+ my $sth = $self->prepare($statement);
+ my $version = ($transcript->version()) ? $transcript->version() : 1;
+ $sth->bind_param( 1, $transc_dbID, SQL_INTEGER );
+ $sth->bind_param( 2, $transcript->stable_id(), SQL_VARCHAR );
+ $sth->bind_param( 3, $version, SQL_INTEGER );
+ $sth->execute();
+ $sth->finish();
+ } ## end if ( defined( $transcript...))
+
# Now the supporting evidence
my $tsf_adaptor = $db->get_TranscriptSupportingFeatureAdaptor();
$tsf_adaptor->store( $transc_dbID,
@@ -1046,16 +1055,18 @@ sub get_Interpro_by_transid {
my $sth = $self->prepare(qq(
SELECT STRAIGHT_JOIN i.interpro_ac, x.description
- FROM transcript t,
+ FROM transcript_stable_id tsi,
+ transcript t,
translation tl,
protein_feature pf,
interpro i,
xref x
- WHERE t.stable_id = ?
- AND tl.transcript_id = t.transcript_id
+ WHERE tsi.stable_id = ?
+ AND tl.transcript_id = tsi.transcript_id
AND tl.translation_id = pf.translation_id
AND i.id = pf.hit_name
AND i.interpro_ac = x.dbprimary_acc
+ AND tsi.transcript_id = t.transcript_id
AND t.is_current = 1
));
@@ -1220,6 +1231,10 @@ sub remove {
WHERE transcript_id = ?" );
$sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
$sth->execute();
+ $sth = $self->prepare( "DELETE FROM transcript_stable_id
+ WHERE transcript_id = ?" );
+ $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
+ $sth->execute();
$sth->finish();
@@ -1336,7 +1351,7 @@ sub list_dbIDs {
sub list_stable_ids {
my ($self) = @_;
- return $self->_list_dbIDs("transcript", "stable_id");
+ return $self->_list_dbIDs("transcript_stable_id", "stable_id");
}
@@ -1816,7 +1831,7 @@ sub get_stable_entry_info {
my $sth = $self->prepare(qq(
SELECT stable_id, version
- FROM transcript
+ FROM transcript_stable_id
WHERE transcript_id = ?
));
diff --git a/modules/Bio/EnsEMBL/UnmappedObject.pm b/modules/Bio/EnsEMBL/UnmappedObject.pm
index bc4ed1577a..827fac51dc 100644
--- a/modules/Bio/EnsEMBL/UnmappedObject.pm
+++ b/modules/Bio/EnsEMBL/UnmappedObject.pm
@@ -328,7 +328,7 @@ sub stable_id{
my $handle = $self->adaptor;
if(defined($handle)){
- my $sql = "select stable_id from ".lc($self->{'ensembl_object_type'})." where ".
+ my $sql = "select stable_id from ".lc($self->{'ensembl_object_type'})."_stable_id where ".
lc($self->{'ensembl_object_type'})."_id = ".
$self->{'ensembl_id'};
my $sth = $handle->prepare($sql);
--
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