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Commit cf148465 authored by Patrick Meidl's avatar Patrick Meidl
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added score

parent 11ed8ac4
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modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+ 34
− 19
View file @ cf148465
......@@ -141,7 +141,8 @@ sub fetch_by_stable_id_version {
SELECT
m.new_db_name,
m.new_release,
m.new_assembly
m.new_assembly,
sie.score
FROM stable_id_event sie, mapping_session m
WHERE sie.mapping_session_id = m.mapping_session_id
AND sie.new_stable_id = "$stable_id"
......@@ -153,7 +154,7 @@ sub fetch_by_stable_id_version {
my $sth = $self->prepare($sql);
$sth->execute();
my ($db_name, $release, $assembly) = $sth->fetchrow_array();
my ($db_name, $release, $assembly, $score) = $sth->fetchrow_array();
$sth->finish();
# you might have missed a stable ID that was deleted in the very first
......@@ -163,7 +164,8 @@ sub fetch_by_stable_id_version {
SELECT
m.old_db_name,
m.old_release,
m.old_assembly
m.old_assembly,
sie.score
FROM stable_id_event sie, mapping_session m
WHERE sie.mapping_session_id = m.mapping_session_id
AND sie.old_stable_id = "$stable_id"
......@@ -175,7 +177,7 @@ sub fetch_by_stable_id_version {
$sth = $self->prepare($sql);
$sth->execute();
($db_name, $release, $assembly) = $sth->fetchrow_array();
($db_name, $release, $assembly, $score) = $sth->fetchrow_array();
$sth->finish();
}
......@@ -186,6 +188,7 @@ sub fetch_by_stable_id_version {
$arch_id->db_name($db_name);
$arch_id->release($release);
$arch_id->assembly($assembly);
$arch_id->score($score);
}
return $arch_id;
......@@ -325,6 +328,7 @@ sub fetch_predecessors_by_archive_id {
SELECT
sie.old_stable_id,
sie.old_version,
sie.score,
m.old_db_name,
m.old_release,
m.old_assembly
......@@ -339,8 +343,8 @@ sub fetch_predecessors_by_archive_id {
$sth->bind_param(2, $arch_id->db_name, SQL_VARCHAR);
$sth->execute();
my ($old_stable_id, $old_version, $old_db_name, $old_release, $old_assembly);
$sth->bind_columns(\$old_stable_id, \$old_version, \$old_db_name, \$old_release, \$old_assembly);
my ($old_stable_id, $old_version, $score, $old_db_name, $old_release, $old_assembly);
$sth->bind_columns(\$old_stable_id, \$old_version, \$score, \$old_db_name, \$old_release, \$old_assembly);
while( $sth->fetch() ) {
if( defined $old_stable_id ) {
......@@ -351,7 +355,8 @@ sub fetch_predecessors_by_archive_id {
-db_name => $old_db_name,
-release => $old_release,
-assembly => $old_assembly,
-adaptor => $self
-adaptor => $self,
-score => $score
);
_resolve_type( $old_arch_id );
push( @result, $old_arch_id );
......@@ -373,6 +378,7 @@ sub fetch_predecessors_by_archive_id {
SELECT
sie.new_stable_id,
sie.new_version,
sie.score,
m.new_db_name,
m.new_release,
m.new_assembly
......@@ -387,7 +393,7 @@ sub fetch_predecessors_by_archive_id {
$sth->bind_param(2,$prev_dbname, SQL_VARCHAR);
$sth->execute();
$sth->bind_columns(\$old_stable_id, \$old_version, \$old_db_name, \$old_release, \$old_assembly);
$sth->bind_columns(\$old_stable_id, \$old_version, \$score, \$old_db_name, \$old_release, \$old_assembly);
while( $sth->fetch() ) {
if (defined $old_stable_id) {
......@@ -398,7 +404,8 @@ sub fetch_predecessors_by_archive_id {
-db_name => $old_db_name,
-release => $old_release,
-assembly => $old_assembly,
-adaptor => $self
-adaptor => $self,
-score => $score
);
_resolve_type( $old_arch_id );
push( @result, $old_arch_id );
......@@ -444,6 +451,7 @@ sub fetch_successors_by_archive_id {
SELECT
sie.new_stable_id,
sie.new_version,
sie.score,
m.new_db_name,
m.new_release,
m.new_assembly
......@@ -458,8 +466,8 @@ sub fetch_successors_by_archive_id {
$sth->bind_param(2,$arch_id->db_name,SQL_VARCHAR);
$sth->execute();
my ($new_stable_id, $new_version, $new_db_name, $new_release, $new_assembly);
$sth->bind_columns(\$new_stable_id, \$new_version, \$new_db_name, \$new_release, \$new_assembly);
my ($new_stable_id, $new_version, $score, $new_db_name, $new_release, $new_assembly);
$sth->bind_columns(\$new_stable_id, \$new_version, \$score, \$new_db_name, \$new_release, \$new_assembly);
while( $sth->fetch() ) {
if( defined $new_stable_id ) {
......@@ -470,7 +478,8 @@ sub fetch_successors_by_archive_id {
-db_name => $new_db_name,
-release => $new_release,
-assembly => $new_assembly,
-adaptor => $self
-adaptor => $self,
-score => $score
);
_resolve_type($new_arch_id);
......@@ -493,6 +502,7 @@ sub fetch_successors_by_archive_id {
SELECT
sie.old_stable_id,
sie.old_version,
sie.score,
m.old_db_name,
m.old_release,
m.old_assembly
......@@ -507,7 +517,7 @@ sub fetch_successors_by_archive_id {
$sth->bind_param(2, $next_dbname, SQL_VARCHAR);
$sth->execute();
$sth->bind_columns(\$new_stable_id, \$new_version, \$new_db_name, \$new_release, \$new_assembly);
$sth->bind_columns(\$new_stable_id, \$new_version, \$score, \$new_db_name, \$new_release, \$new_assembly);
while( $sth->fetch() ) {
if (defined $new_stable_id) {
......@@ -518,7 +528,8 @@ sub fetch_successors_by_archive_id {
-db_name => $new_db_name,
-release => $new_release,
-assembly => $new_assembly,
-adaptor => $self
-adaptor => $self,
-score => $score
);
_resolve_type($new_arch_id);
......@@ -888,7 +899,8 @@ sub _lookup_version {
m.new_db_name,
m.new_release,
m.new_assembly,
sie.new_version
sie.new_version,
sie.score
FROM stable_id_event sie, mapping_session m
WHERE sie.mapping_session_id = m.mapping_session_id
AND new_stable_id = "@{[$arch_id->stable_id]}"
......@@ -903,7 +915,8 @@ sub _lookup_version {
m.old_db_name,
m.old_release,
m.old_assembly,
sie.old_version
sie.old_version,
sie.score
FROM stable_id_event sie, mapping_session m
WHERE sie.mapping_session_id = m.mapping_session_id
AND sie.old_stable_id = "@{[$arch_id->stable_id]}"
......@@ -914,7 +927,7 @@ sub _lookup_version {
my $sth = $self->prepare($sql);
$sth->execute();
my ($db_name, $release, $assembly, $version) = $sth->fetchrow_array();
my ($db_name, $release, $assembly, $version, $score) = $sth->fetchrow_array();
$sth->finish();
# you might have missed a stable ID that was deleted in the very first
......@@ -925,7 +938,8 @@ sub _lookup_version {
m.old_db_name,
m.old_release,
m.old_assembly,
sie.old_version
sie.old_version,
sie.score
FROM stable_id_event sie, mapping_session m
WHERE sie.mapping_session_id = m.mapping_session_id
AND old_stable_id = "@{[$arch_id->stable_id]}"
......@@ -937,7 +951,7 @@ sub _lookup_version {
$sth = $self->prepare($sql);
$sth->execute();
($db_name, $release, $assembly, $version) = $sth->fetchrow_array();
($db_name, $release, $assembly, $version, $score) = $sth->fetchrow_array();
$sth->finish();
}
......@@ -950,6 +964,7 @@ sub _lookup_version {
$arch_id->db_name($db_name);
$arch_id->release($release);
$arch_id->assembly($assembly);
$arch_id->score($score);
}
}
......
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