From c116305e498eb1f6d716f88c8b03c76190f4fd10 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Thu, 28 Nov 2013 11:44:25 +0000
Subject: [PATCH] [ENSCORESW-752]. Updated _columns, store, update and
_objs_from_sth methods to take into account the addition of column 'source'
to transcript table.
---
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 216 +++++++++---------
1 file changed, 113 insertions(+), 103 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 4dc3f09389..19f260d4dd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -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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