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Commit fc198f11 authored by Daniel Rios's avatar Daniel Rios
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modified to use functions instead of the calls to UNIX methods from MySQL

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modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+ 25
− 17
View file @ fc198f11
......@@ -80,10 +80,15 @@ sub _tables {
sub _columns {
my $self = shift;
return qw( e.exon_id e.seq_region_id e.seq_region_start e.seq_region_end
e.seq_region_strand e.phase e.end_phase
esi.stable_id esi.version UNIX_TIMESTAMP(created_date)
UNIX_TIMESTAMP(modified_date) );
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
return ( 'e.exon_id', 'e.seq_region_id', 'e.seq_region_start' ,'e.seq_region_end',
'e.seq_region_strand', 'e.phase','e.end_phase',
'esi.stable_id', 'esi.version',$created_date,
$modified_date );
# esi.stable_id esi.version UNIX_TIMESTAMP(created_date)
# UNIX_TIMESTAMP(modified_date) );
}
......@@ -263,17 +268,18 @@ sub store {
"stable_id = ?, " .
"exon_id = ?, ";
if( $exon->created_date() ) {
$statement .= "created_date = from_unixtime( ".$exon->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
if( $exon->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$exon->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
$statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($exon->created_date()) . ",";
# if( $exon->created_date() ) {
# $statement .= "created_date = from_unixtime( ".$exon->created_date()."),";
# } else {
# $statement .= "created_date = \"0000-00-00 00:00:00\",";
# }
$statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($exon->modified_date()) ;
# if( $exon->modified_date() ) {
# $statement .= "modified_date = from_unixtime( ".$exon->modified_date().")";
# } else {
# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
# }
my $sth = $self->prepare( $statement );
......@@ -650,8 +656,10 @@ sub get_stable_entry_info {
#$self->throw("can't fetch stable info with no dbID");
return;
}
my $sth = $self->prepare("SELECT stable_id, UNIX_TIMESTAMP(created),
UNIX_TIMESTAMP(modified), version
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_stable_id
WHERE exon_id = ");
......
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+ 40
− 35
View file @ fc198f11
......@@ -91,13 +91,15 @@ sub _tables {
sub _columns {
my $self = shift;
return qw( g.gene_id g.seq_region_id g.seq_region_start g.seq_region_end
g.seq_region_strand g.analysis_id g.biotype g.display_xref_id
g.description g.status g.source
gsi.stable_id gsi.version UNIX_TIMESTAMP(gsi.created_date)
UNIX_TIMESTAMP(gsi.modified_date)
x.display_label x.dbprimary_acc x.description x.version
exdb.db_name exdb.status exdb.release exdb.db_display_name );
my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
return ( 'g.gene_id', 'g.seq_region_id', 'g.seq_region_start', 'g.seq_region_end',
'g.seq_region_strand', 'g.analysis_id' ,'g.biotype', 'g.display_xref_id',
'g.description', 'g.status', 'g.source',
'gsi.stable_id', 'gsi.version', $created_date,
$modified_date,
'x.display_label' ,'x.dbprimary_acc', 'x.description', 'x.version',
'exdb.db_name', 'exdb.status', 'exdb.release' ,'exdb.db_display_name' );
}
......@@ -829,17 +831,18 @@ sub store {
SET gene_id = ?,
stable_id = ?,
version = ?, ";
if( $gene->created_date() ) {
$statement .= "created_date = from_unixtime( ".$gene->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
if( $gene->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$gene->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
$statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($gene->created_date()) . ",";
# if( $gene->created_date() ) {
# $statement .= "created_date = from_unixtime( ".$gene->created_date()."),";
# } else {
# $statement .= "created_date = \"0000-00-00 00:00:00\",";
# }
$statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($gene->modified_date());
# if( $gene->modified_date() ) {
# $statement .= "modified_date = from_unixtime( ".$gene->modified_date().")";
# } else {
# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
# }
$sth = $self->prepare($statement);
$sth->bind_param(1,$gene_dbID,SQL_INTEGER);
......@@ -851,11 +854,11 @@ sub store {
# store the dbentries associated with this gene
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$gene->get_all_DBEntries} ) {
$dbEntryAdaptor->store( $dbe, $gene, "Gene" );
}
# we allow transcripts not to share equal exons and instead have copies
# For the database we still want sharing though, to have easier time with
# stable ids. So we need to have a step to merge exons together before store
......@@ -864,7 +867,6 @@ sub store {
foreach my $trans ( @{$gene->get_all_Transcripts} ) {
foreach my $e ( @{$trans->get_all_Exons} ) {
my $key = $e->hashkey();
if( exists $exons{ $key } ) {
$trans->swap_exons( $e, $exons{$key} );
} else {
......@@ -904,7 +906,6 @@ sub store {
}
if(defined($dxref_id)) {
$sth = $self->prepare
("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
$sth->bind_param(1,$dxref_id,SQL_INTEGER);
......@@ -1451,17 +1452,17 @@ sub fetch_all_by_transcript_supporting_evidence {
my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
my $sql = "SELECT DISTINCT(g.gene_id)
FROM gene g,
transcript t,
transcript_supporting_feature sf,
$feature_type f
$anal_from
WHERE g.gene_id = t.gene_id
AND t.transcript_id = sf.transcript_id
AND sf.feature_id = f.${feature_type}_id
AND sf.feature_type = ?
AND f.hit_name=?
$anal_where";
FROM gene g,
transcript t,
transcript_supporting_feature sf,
$feature_type f
$anal_from
WHERE g.gene_id = t.gene_id
AND t.transcript_id = sf.transcript_id
AND sf.feature_id = f.${feature_type}_id
AND sf.feature_type = ?
AND f.hit_name=?
$anal_where";
my $sth = $self->prepare($sql);
......@@ -1627,10 +1628,14 @@ sub get_stable_entry_info {
throw("Needs a gene object, not a $gene");
}
my $sth = $self->prepare("SELECT stable_id, UNIX_TIMESTAMP(created),
UNIX_TIMESTAMP(modified), version
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 gene_stable_id
WHERE gene_id = ?");
$sth->bind_param(1,$gene->dbID,SQL_INTEGER);
$sth->execute();
......
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 21
− 15
View file @ fc198f11
......@@ -98,11 +98,14 @@ sub _tables {
sub _columns {
my $self = shift;
return qw( t.transcript_id t.seq_region_id t.seq_region_start t.seq_region_end
t.seq_region_strand t.gene_id
t.display_xref_id tsi.stable_id tsi.version UNIX_TIMESTAMP(created_date)
UNIX_TIMESTAMP(modified_date) t.description t.biotype t.status
x.display_label exdb.db_name exdb.status exdb.db_display_name);
my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
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.gene_id',
't.display_xref_id', 'tsi.stable_id','tsi.version', $created_date,
$modified_date, 't.description', 't.biotype', 't.status',
'x.display_label', 'exdb.db_name' ,'exdb.status', 'exdb.db_display_name');
}
......@@ -698,17 +701,20 @@ sub store {
" stable_id = ?, ".
"version = ?, ";
if( $transcript->created_date() ) {
$statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
$statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($transcript->created_date()) . ",";
if( $transcript->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
# if( $transcript->created_date() ) {
# $statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
# } else {
# $statement .= "created_date = \"0000-00-00 00:00:00\",";
# }
$statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($transcript->modified_date()) ;
# if( $transcript->modified_date() ) {
# $statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
# } else {
# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
# }
my $sth = $self->prepare($statement);
$sth->bind_param(1,$transc_dbID,SQL_INTEGER);
......
modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+ 24
− 18
View file @ fc198f11
......@@ -77,12 +77,14 @@ sub fetch_by_Transcript {
throw("Bio::EnsEMBL::Transcript argument is required.");
}
my $lsi_created_date = $self->db->dbc->from_date_to_seconds("tlsi.created_date");
my $lsi_modified_date = $self->db->dbc->from_date_to_seconds("tlsi.modified_date");
my $sql = "
SELECT tl.translation_id, tl.start_exon_id,
tl.end_exon_id, tl.seq_start, tl.seq_end,
tlsi.stable_id, tlsi.version, UNIX_TIMESTAMP(tlsi.created_date),
UNIX_TIMESTAMP(tlsi.modified_date)
FROM translation tl
tlsi.stable_id, tlsi.version, " . $lsi_created_date . ", ". $lsi_modified_date .
" FROM translation tl
LEFT JOIN translation_stable_id tlsi
ON tlsi.translation_id = tl.translation_id
WHERE tl.transcript_id = ?";
......@@ -257,18 +259,19 @@ sub store {
"SET translation_id = ?, ".
" stable_id = ?, ".
"version = ?, ";
if( $translation->created_date() ) {
$statement .= "created_date = from_unixtime( ".$translation->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
if( $translation->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$translation->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
$statement .= "created_date = " . $self->db->dbc->from_seconds_to_date($translation->created_date()) . ",";
# if( $translation->created_date() ) {
# $statement .= "created_date = from_unixtime( ".$translation->created_date()."),";
# } else {
# $statement .= "created_date = \"0000-00-00 00:00:00\",";
# }
$statement .= "modified_date = " . $self->db->dbc->from_seconds_to_date($translation->modified_date()) ;
# if( $translation->modified_date() ) {
# $statement .= "modified_date = from_unixtime( ".$translation->modified_date().")";
# } else {
# $statement .= "modified_date = \"0000-00-00 00:00:00\"";
# }
my $sth = $self->prepare($statement);
......@@ -528,12 +531,15 @@ sub fetch_all_by_Transcript_list {
$id_str = " = " . $ids[0];
}
my $created_date = $self->db->dbc->from_date_to_seconds("tlsi.created_date");
my $modified_date = $self->db->dbc->from_date_to_seconds("tlsi.modified_date");
my $sth = $self->prepare
("SELECT tl.transcript_id, tl.translation_id, tl.start_exon_id,
tl.end_exon_id, tl.seq_start, tl.seq_end,
tlsi.stable_id, tlsi.version, UNIX_TIMESTAMP(tlsi.created_date),
UNIX_TIMESTAMP(tlsi.modified_date)
FROM translation tl
tlsi.stable_id, tlsi.version, " . $created_date . "," .
$modified_date .
" FROM translation tl
LEFT JOIN translation_stable_id tlsi
ON tlsi.translation_id = tl.translation_id
WHERE tl.transcript_id $id_str");
......
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