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Commit c116305e authored by Alessandro Vullo's avatar Alessandro Vullo
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[ENSCORESW-752]. Updated _columns, store, update and _objs_from_sth methods to take into account 

the addition of column 'source' to transcript table.
parent 1e1e227b
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modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 113
− 103
View file @ c116305e
......@@ -116,21 +116,26 @@ sub _columns {
my $modified_date =
$self->db()->dbc()->from_date_to_seconds("modified_date");
return (
't.transcript_id', 't.seq_region_id',
'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',
$created_date, $modified_date,
't.description', 't.biotype',
't.status', 'exdb.db_name',
'exdb.status', 'exdb.db_display_name',
'x.xref_id', 'x.display_label',
'x.dbprimary_acc', 'x.version',
'x.description', 'x.info_type',
'x.info_text'
);
my @columns =
(
't.transcript_id', 't.seq_region_id',
'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',
$created_date, $modified_date,
't.description', 't.biotype',
't.status', 'exdb.db_name',
'exdb.status', 'exdb.db_display_name',
'x.xref_id', 'x.display_label',
'x.dbprimary_acc', 'x.version',
'x.description', 'x.info_type',
'x.info_text'
);
$self->schema_version > 74 and push @columns, 't.source';
return @columns;
}
sub _left_join {
......@@ -848,20 +853,9 @@ 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 = ?
);
my $store_transcript_sql =
sprintf "INSERT INTO transcript SET gene_id = ?, analysis_id = ?, seq_region_id = ?, seq_region_start = ?, seq_region_end = ?, seq_region_strand = ?,%s biotype = ?, status = ?, description = ?, is_current = ?, canonical_translation_id = ?", ($self->schema_version > 74)?" source = ?,":'';
if ( defined( $transcript->stable_id() ) ) {
......@@ -872,28 +866,32 @@ sub store {
}
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 );
$tst->bind_param( 4, $transcript->start(), SQL_INTEGER );
$tst->bind_param( 5, $transcript->end(), SQL_INTEGER );
$tst->bind_param( 6, $transcript->strand(), SQL_TINYINT );
$tst->bind_param( 7, $transcript->biotype(), SQL_VARCHAR );
$tst->bind_param( 8, $transcript->status(), SQL_VARCHAR );
$tst->bind_param( 9, $transcript->description(), SQL_LONGVARCHAR );
$tst->bind_param( 10, $is_current, SQL_TINYINT );
my $i = 0;
$tst->bind_param( ++$i, $gene_dbID, SQL_INTEGER );
$tst->bind_param( ++$i, $new_analysis_id, SQL_INTEGER );
$tst->bind_param( ++$i, $seq_region_id, SQL_INTEGER );
$tst->bind_param( ++$i, $transcript->start(), SQL_INTEGER );
$tst->bind_param( ++$i, $transcript->end(), SQL_INTEGER );
$tst->bind_param( ++$i, $transcript->strand(), SQL_TINYINT );
$self->schema_version > 74 and
$tst->bind_param( ++$i, $transcript->source(), SQL_VARCHAR );
$tst->bind_param( ++$i, $transcript->biotype(), SQL_VARCHAR );
$tst->bind_param( ++$i, $transcript->status(), SQL_VARCHAR );
$tst->bind_param( ++$i, $transcript->description(), SQL_LONGVARCHAR );
$tst->bind_param( ++$i, $is_current, SQL_TINYINT );
# If the transcript has a translation, this is updated later:
$tst->bind_param( 11, undef, SQL_INTEGER );
$tst->bind_param( ++$i, undef, SQL_INTEGER );
if ( defined( $transcript->stable_id() ) ) {
$tst->bind_param( 12, $transcript->stable_id(), SQL_VARCHAR );
$tst->bind_param( ++$i, $transcript->stable_id(), SQL_VARCHAR );
my $version = ($transcript->version()) ? $transcript->version() : 1;
$tst->bind_param( 13, $version, SQL_INTEGER );
$tst->bind_param( ++$i, $version, SQL_INTEGER );
}
$tst->execute();
$tst->finish();
......@@ -1376,17 +1374,8 @@ sub update {
throw("Must update a transcript object, not a $transcript");
}
my $update_transcript_sql = qq(
UPDATE transcript
SET analysis_id = ?,
display_xref_id = ?,
description = ?,
biotype = ?,
status = ?,
is_current = ?,
canonical_translation_id = ?
WHERE transcript_id = ?
);
my $update_transcript_sql =
sprintf "UPDATE transcript SET analysis_id = ?, display_xref_id = ?, description = ?,%s biotype = ?, status = ?, is_current = ?, canonical_translation_id = ? WHERE transcript_id = ?", ($self->schema_version > 74)?" source = ?,":'';
my $display_xref = $transcript->display_xref();
my $display_xref_id;
......@@ -1398,19 +1387,23 @@ sub update {
}
my $sth = $self->prepare($update_transcript_sql);
$sth->bind_param( 1, $transcript->analysis()->dbID(), SQL_INTEGER );
$sth->bind_param( 2, $display_xref_id, SQL_INTEGER );
$sth->bind_param( 3, $transcript->description(), SQL_LONGVARCHAR );
$sth->bind_param( 4, $transcript->biotype(), SQL_VARCHAR );
$sth->bind_param( 5, $transcript->status(), SQL_VARCHAR );
$sth->bind_param( 6, $transcript->is_current(), SQL_TINYINT );
$sth->bind_param( 7, (
my $i = 0;
$sth->bind_param( ++$i, $transcript->analysis()->dbID(), SQL_INTEGER );
$sth->bind_param( ++$i, $display_xref_id, SQL_INTEGER );
$sth->bind_param( ++$i, $transcript->description(), SQL_LONGVARCHAR );
$self->schema_version > 74 and
$sth->bind_param( ++$i, $transcript->source(), SQL_VARCHAR );
$sth->bind_param( ++$i, $transcript->biotype(), SQL_VARCHAR );
$sth->bind_param( ++$i, $transcript->status(), SQL_VARCHAR );
$sth->bind_param( ++$i, $transcript->is_current(), SQL_TINYINT );
$sth->bind_param( ++$i, (
defined( $transcript->translation() )
? $transcript->translation()->dbID()
: undef ),
SQL_INTEGER );
$sth->bind_param( 8, $transcript->dbID(), SQL_INTEGER );
$sth->bind_param( ++$i, $transcript->dbID(), SQL_INTEGER );
$sth->execute();
} ## end sub update
......@@ -1493,21 +1486,36 @@ sub _objs_from_sth {
$external_db, $external_status, $external_db_name,
$xref_id, $xref_display_label, $xref_primary_acc,
$xref_version, $xref_description, $xref_info_type,
$xref_info_text
$xref_info_text, $source
);
$sth->bind_columns(
\(
$transcript_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $analysis_id,
$gene_id, $is_current, $stable_id,
$version, $created_date, $modified_date,
$description, $biotype, $status,
$external_db, $external_status, $external_db_name,
$xref_id, $xref_display_label, $xref_primary_acc,
$xref_version, $xref_description, $xref_info_type,
$xref_info_text
) );
if ($self->schema_version() > 74) {
$sth->bind_columns(
\(
$transcript_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $analysis_id,
$gene_id, $is_current, $stable_id,
$version, $created_date, $modified_date,
$description, $biotype, $status,
$external_db, $external_status, $external_db_name,
$xref_id, $xref_display_label, $xref_primary_acc,
$xref_version, $xref_description, $xref_info_type,
$xref_info_text, $source
) );
} else {
$sth->bind_columns(
\(
$transcript_id, $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $analysis_id,
$gene_id, $is_current, $stable_id,
$version, $created_date, $modified_date,
$description, $biotype, $status,
$external_db, $external_status, $external_db_name,
$xref_id, $xref_display_label, $xref_primary_acc,
$xref_version, $xref_description, $xref_info_type,
$xref_info_text
) );
}
my $asm_cs;
my $cmp_cs;
......@@ -1733,33 +1741,35 @@ sub _objs_from_sth {
# Finally, create the new Transcript.
push(
@transcripts,
$self->_create_feature_fast(
'Bio::EnsEMBL::Transcript',
{
'analysis' => $analysis,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'adaptor' => $self,
'slice' => $slice,
'dbID' => $transcript_id,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date || undef,
'external_name' => $xref_display_label,
'external_db' => $external_db,
'external_status' => $external_status,
'external_display_name' => $external_db_name,
'display_xref' => $display_xref,
'description' => $description,
'biotype' => $biotype,
'status' => $status,
'is_current' => $is_current,
'edits_enabled' => 1
} ) );
my $params =
{
'analysis' => $analysis,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'adaptor' => $self,
'slice' => $slice,
'dbID' => $transcript_id,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date || undef,
'external_name' => $xref_display_label,
'external_db' => $external_db,
'external_status' => $external_status,
'external_display_name' => $external_db_name,
'display_xref' => $display_xref,
'description' => $description,
'biotype' => $biotype,
'status' => $status,
'is_current' => $is_current,
'edits_enabled' => 1
};
$self->schema_version > 74 and $params->{'source'} = $source;
push( @transcripts,
$self->_create_feature_fast('Bio::EnsEMBL::Transcript',
$params) );
}
......
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