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Commit 22756a9e authored by Daniel Rios's avatar Daniel Rios
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changes introduced in release 52: new column description in external_db and... 

changes introduced in release 52: new column description in external_db and new column in dna_align_feature
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modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+ 38
− 37
View file @ 22756a9e
......@@ -71,7 +71,6 @@ sub fetch_by_dbID {
xref.dbprimary_acc,
xref.display_label,
xref.version,
xref.description,
exDB.dbprimary_acc_linkable,
exDB.display_label_linkable,
exDB.priority,
......@@ -83,7 +82,8 @@ sub fetch_by_dbID {
xref.info_text,
exDB.type,
exDB.secondary_db_name,
exDB.secondary_db_table
exDB.secondary_db_table,
exDB.description
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es ON
es.xref_id = xref.xref_id
......@@ -98,16 +98,17 @@ sub fetch_by_dbID {
my $max_rows = 1000;
while ( my $rowcache = $sth->fetchall_arrayref( undef, $max_rows ) ) {
#$description refers to the external_db description, while $desc was referring the xref description
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $refID, $dbprimaryId,
$displayid, $version,
$desc, $primary_id_linkable,
$primary_id_linkable,
$display_id_linkable, $priority,
$dbname, $db_display_name,
$release, $synonym,
$info_type, $info_text,
$type, $secondary_db_name,
$secondary_db_table
$secondary_db_table, $description
) = @$arrayref;
if ( !defined($exDB) ) {
......@@ -128,10 +129,10 @@ sub fetch_by_dbID {
-info_text => $info_text,
-type => $type,
-secondary_db_name => $secondary_db_name,
-secondary_db_table => $secondary_db_table
-secondary_db_table => $secondary_db_table,
-description => $description
);
if ( defined($desc) ) { $exDB->description($desc) }
}
......@@ -176,7 +177,6 @@ sub fetch_by_db_accession {
xref.dbprimary_acc,
xref.display_label,
xref.version,
xref.description,
exDB.dbprimary_acc_linkable,
exDB.display_label_linkable,
exDB.priority,
......@@ -188,7 +188,8 @@ sub fetch_by_db_accession {
xref.info_text,
exDB.type,
exDB.secondary_db_name,
exDB.secondary_db_table
exDB.secondary_db_table,
exDB.description
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es ON
es.xref_id = xref.xref_id
......@@ -231,13 +232,13 @@ sub fetch_by_db_accession {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$desc, $primary_id_linkable,
$primary_id_linkable,
$display_id_linkable, $priority,
$dbname, $db_display_name,
$release, $synonym,
$info_type, $info_text,
$type, $secondary_db_name,
$secondary_db_table
$secondary_db_table, $description
) = @$arrayref;
if ( !defined($exDB) ) {
......@@ -258,10 +259,10 @@ sub fetch_by_db_accession {
-info_text => $info_text,
-type => $type,
-secondary_db_name => $secondary_db_name,
-secondary_db_table => $secondary_db_table
-secondary_db_table => $secondary_db_table,
-description => $description
);
if ( defined($desc) ) { $exDB->description($desc) }
}
......@@ -834,7 +835,6 @@ sub _fetch_by_object_type {
# my $sth = $self->prepare("
my $sql = (<<SSQL);
SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
xref.description,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable,
exDB.priority,
exDB.db_name, exDB.db_release, exDB.status, exDB.db_display_name,
......@@ -846,7 +846,7 @@ sub _fetch_by_object_type {
idt.cigar_line, idt.score, idt.evalue, idt.analysis_id,
gx.linkage_type,
xref.info_type, xref.info_text, exDB.type, gx.source_xref_id,
oxr.linkage_annotation
oxr.linkage_annotation, exDB.description
FROM (xref xref, external_db exDB, object_xref oxr)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
......@@ -872,7 +872,7 @@ SSQL
while ( my $arrRef = shift( @{$rowcache} ) ) {
my ( $refID, $dbprimaryId,
$displayid, $version,
$desc, $primary_id_linkable,
$primary_id_linkable,
$display_id_linkable, $priority,
$dbname, $release,
$exDB_status, $exDB_db_display_name,
......@@ -885,7 +885,8 @@ SSQL
$evalue, $analysis_id,
$linkage_type, $info_type,
$info_text, $type,
$source_xref_id, $link_annotation
$source_xref_id, $link_annotation,
$description
) = @$arrRef;
my $linkage_key =
......@@ -903,15 +904,16 @@ SSQL
'secondary_db_name' => $exDB_secondary_db_name,
'secondary_db_table' => $exDB_secondary_db_table,
'dbname' => $dbname,
'description' => $description,
'linkage_annotation' => $link_annotation );
# Using an outer join on the synonyms as well as on identity_xref,
# we now have to filter out the duplicates (see v.1.18 for
# original). Since there is at most one identity_xref row per
# xref, this is easy enough; all the 'extra' bits are synonyms.
my $source_xref;
if ( !$seen{$refID} ) {
my $exDB;
if ( ( defined($queryid) ) ) { # an xref with similarity scores
$exDB = Bio::EnsEMBL::IdentityXref->new_fast( \%obj_hash );
$exDB->query_identity($queryid);
......@@ -934,7 +936,7 @@ SSQL
} elsif ( defined $linkage_type && $linkage_type ne "" ) {
$exDB = Bio::EnsEMBL::GoXref->new_fast( \%obj_hash );
my $source_xref = ( defined($source_xref_id)
$source_xref = ( defined($source_xref_id)
? $self->fetch_by_dbID($source_xref_id)
: undef );
$exDB->add_linkage_type( $linkage_type, $source_xref || () );
......@@ -944,7 +946,6 @@ SSQL
$exDB = Bio::EnsEMBL::DBEntry->new_fast( \%obj_hash );
}
if ( defined($desc) ) { $exDB->description($desc) }
if ( defined($exDB_status) ) { $exDB->status($exDB_status) }
$exDB->primary_id_linkable($primary_id_linkable);
......@@ -971,7 +972,7 @@ SSQL
&& $linkage_type ne ""
&& !$linkage_types{$refID}->{$linkage_key} )
{
my $source_xref = ( defined($source_xref_id)
$source_xref = ( defined($source_xref_id)
? $self->fetch_by_dbID($source_xref_id)
: undef );
$seen{$refID}
......@@ -1224,8 +1225,8 @@ sub _type_by_external_id {
$sth->bind_param( 2, "$name", SQL_VARCHAR );
$sth->bind_param( 3, $ensType, SQL_VARCHAR );
$sth->execute();
while ( my $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
my $r;
while ( $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
$sth = $self->prepare($query2);
......@@ -1233,7 +1234,7 @@ sub _type_by_external_id {
$sth->bind_param( 2, $ensType, SQL_VARCHAR );
$sth->execute();
while ( my $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
while ( $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
return keys(%result);
......@@ -1348,11 +1349,11 @@ sub fetch_all_by_description {
my $sql =
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version, xref.description,
xref.version,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
xref.info_type, xref.info_text, exDB.type, exDB.secondary_db_name,
exDB.secondary_db_table
exDB.secondary_db_table, exDB.description
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE xref.description like ?
......@@ -1376,13 +1377,13 @@ sub fetch_all_by_description {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$desc, $primary_id_linkable,
$primary_id_linkable,
$display_id_linkable, $priority,
$dbname, $db_display_name,
$ex_dbname, $db_display_name,
$release, $synonym,
$info_type, $info_text,
$type, $secondary_db_name,
$secondary_db_table
$secondary_db_table, $ex_description
) = @$arrayref;
my $exDB =
......@@ -1393,7 +1394,7 @@ sub fetch_all_by_description {
-display_id => $displayid,
-version => $version,
-release => $release,
-dbname => $dbname,
-dbname => $ex_dbname,
-primary_id_linkable => $primary_id_linkable,
-display_id_linkable => $display_id_linkable,
-priority => $priority,
......@@ -1402,10 +1403,10 @@ sub fetch_all_by_description {
-info_text => $info_text,
-type => $type,
-secondary_db_name => $secondary_db_name,
-secondary_db_table => $secondary_db_table
-secondary_db_table => $secondary_db_table,
-description => $ex_description
);
if ($desc) { $exDB->description($desc) }
if ($synonym) { $exDB->add_synonym($synonym) }
push @results, $exDB;
......@@ -1440,11 +1441,11 @@ sub fetch_all_by_source {
my $sql =
"SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label,
xref.version, xref.description,
xref.version,
exDB.dbprimary_acc_linkable, exDB.display_label_linkable, exDB.priority,
exDB.db_name, exDB.db_display_name, exDB.db_release, es.synonym,
xref.info_type, xref.info_text, exDB.type, exDB.secondary_db_name,
exDB.secondary_db_table
exDB.secondary_db_table, exDB.description
FROM (xref, external_db exDB)
LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
WHERE exDB.db_name like ?
......@@ -1463,13 +1464,13 @@ sub fetch_all_by_source {
while ( my $arrayref = shift( @{$rowcache} ) ) {
my ( $dbID, $dbprimaryId,
$displayid, $version,
$desc, $primary_id_linkable,
$primary_id_linkable,
$display_id_linkable, $priority,
$dbname, $db_display_name,
$release, $synonym,
$info_type, $info_text,
$type, $secondary_db_name,
$secondary_db_table
$secondary_db_table, $description
) = @$arrayref;
my $exDB =
......@@ -1489,10 +1490,10 @@ sub fetch_all_by_source {
-info_text => $info_text,
-type => $type,
-secondary_db_name => $secondary_db_name,
-secondary_db_table => $secondary_db_table
-secondary_db_table => $secondary_db_table,
-description => $description
);
if ($desc) { $exDB->description($desc) }
if ($synonym) { $exDB->add_synonym($synonym) }
push @results, $exDB;
......
modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
+ 15
− 8
View file @ 22756a9e
......@@ -100,6 +100,7 @@ sub _columns {
daf.external_db_id
daf.hcoverage
daf.external_data
daf.pair_dna_align_feature_id
exdb.db_name
exdb.db_display_name);
}
......@@ -140,8 +141,9 @@ sub store {
"INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
seq_region_strand, hit_start, hit_end,
hit_strand, hit_name, cigar_line,
analysis_id, score, evalue, perc_ident, external_db_id, hcoverage)
VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)");
analysis_id, score, evalue, perc_ident, external_db_id,
hcoverage, pair_dna_align_feature_id)
VALUES (?,?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?, ?)");
FEATURE: foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") ) {
......@@ -199,6 +201,7 @@ sub store {
$sth->bind_param(13,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(14,$feat->external_db_id,SQL_INTEGER);
$sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE);
$sth->bind_param(16,$feat->pair_dna_align_feature_id, SQL_INTEGER);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
......@@ -221,7 +224,7 @@ sub save {
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sql = qq{INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_start, hit_end, hit_strand, hit_name, cigar_line, analysis_id, score, evalue, perc_ident, external_db_id, hcoverage, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};
my $sql = qq{INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_start, hit_end, hit_strand, hit_name, cigar_line, analysis_id, score, evalue, perc_ident, external_db_id, hcoverage, pair_dna_align_feature_id, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};
my $sth = $self->prepare($sql);
......@@ -284,7 +287,9 @@ sub save {
$sth->bind_param(13,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(14,$feat->external_db_id,SQL_INTEGER);
$sth->bind_param(15,$feat->hcoverage,SQL_DOUBLE);
$sth->bind_param(16,$extra_data,SQL_LONGVARCHAR);
$sth->bind_param(16,$feat->pair_dna_align_feature_id,SQL_INTEGER);
$sth->bind_param(17,$extra_data,SQL_LONGVARCHAR);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
......@@ -332,14 +337,15 @@ sub _objs_from_sth {
my($dna_align_feature_id, $seq_region_id, $analysis_id, $seq_region_start,
$seq_region_end, $seq_region_strand, $hit_start, $hit_end, $hit_name,
$hit_strand, $cigar_line, $evalue, $perc_ident, $score,
$external_db_id, $hcoverage, $extra_data, $external_db_name, $external_display_db_name );
$external_db_id, $hcoverage, $extra_data, $pair_dna_align_feature_id,
$external_db_name, $external_display_db_name);
$sth->bind_columns(
\$dna_align_feature_id, \$seq_region_id, \$analysis_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand, \$hit_start, \$hit_end, \$hit_name,
\$hit_strand, \$cigar_line, \$evalue, \$perc_ident, \$score,
\$external_db_id, \$hcoverage, \$extra_data, \$external_db_name, \$external_display_db_name );
\$external_db_id, \$hcoverage, \$extra_data, \$pair_dna_align_feature_id,
\$external_db_name, \$external_display_db_name);
my $asm_cs;
my $cmp_cs;
......@@ -460,7 +466,8 @@ sub _objs_from_sth {
'hcoverage' => $hcoverage,
'extra_data' => $extra_data ? $self->get_dumped_data($extra_data) : '',
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name
'db_display_name' => $external_display_db_name,
'pair_dna_align_feature_id' => $pair_dna_align_feature_id
} ) );
}
......
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