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Commit f5fb4964 authored by Kieron Taylor's avatar Kieron Taylor :angry: Committed by Magali Ruffier
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Refactor process_dependents() to give me a good starting position to make changes.

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misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
+ 71
− 38
View file @ f5fb4964
......@@ -259,12 +259,13 @@ SEQCP
sub process_dependents{
my ($self, $old_master_xref_id, $new_master_xref_id, $object_type, $best_ensembl_id) = @_;
# $best_ensembl_id = list of e! IDs from highest priority xref for this accession
# master xref IDs are entries for the current accession via different methods. We take dependent xrefs from the old and add to the new
# possible that $object_type does not correspond to all of the $best_ensembl_id, only some
# get $object_type from object_xref of new_master_xref instead of trusting calling code
# cache object-type to id mapping
my $dep_sth = $self->xref->dbc->prepare("select distinct dependent_xref_id, dx.linkage_annotation, dx.linkage_source_id from dependent_xref dx where dx.master_xref_id = ?");
my $insert_dep_x_sth = $self->xref->dbc->prepare("insert into dependent_xref(master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) values(?, ?, ?, ?)");
my $remove_dep_ox_sth = $self->xref->dbc->prepare("delete ix, g from object_xref ox left join identity_xref ix on ix.object_xref_id = ox.object_xref_id left join go_xref g on g.object_xref_id = ox.object_xref_id where master_xref_id = ? and ensembl_object_type = ? and xref_id = ? and ensembl_id = ?");
my $old_ens_id_sth = $self->xref->dbc->prepare("select distinct ensembl_id from object_xref where xref_id = ?");
my $update_dep_ox_sth = $self->xref->dbc->prepare("update ignore object_xref set ox_status = 'FAILED_PRIORITY' where master_xref_id = ? and ensembl_object_type = ? and xref_id = ? and ensembl_id = ? and ox_status = 'DUMP_OUT'");
my $clean_dep_ox_sth = $self->xref->dbc->prepare("delete from object_xref where master_xref_id = ? and ensembl_object_type = ? and xref_id = ? and ensembl_id = ? and ox_status = 'DUMP_OUT'");
my $insert_dep_ox_sth = $self->xref->dbc->prepare("insert ignore into object_xref(master_xref_id, ensembl_object_type, ensembl_id, linkage_type, ox_status, xref_id) values(?, ?, ?, 'DEPENDENT', 'DUMP_OUT', ?)");
my $dep_ox_sth = $self->xref->dbc->prepare("select object_xref_id from object_xref where master_xref_id = ? and ensembl_object_type = ? and ensembl_id = ? and linkage_type = 'DEPENDENT' AND ox_status = 'DUMP_OUT' and xref_id = ?");
my $insert_dep_go_sth = $self->xref->dbc->prepare("insert ignore into go_xref values(?, ?, ?)");
......@@ -272,57 +273,33 @@ sub process_dependents{
my @master_xrefs;
my @old_ensembl_ids;
my $old_ensembl_id;
my $recursive = 0;
$old_ens_id_sth->execute($old_master_xref_id);
$old_ens_id_sth->bind_columns(\$old_ensembl_id);
my $skip = 0;
while ($old_ens_id_sth->fetch()) {
$skip = 0;
foreach my $best_ensembl_id (@$best_ensembl_id) {
if ($old_ensembl_id eq $best_ensembl_id) {
$skip = 1;
last;
}
}
if ($skip) {
next;
}
push @old_ensembl_ids, $old_ensembl_id;
}
$old_ens_id_sth->finish();
my @old_ensembl_ids = _get_old_ensembl_ids_associated_with_xref($old_master_xref_id, $best_ensembl_id);
push @master_xrefs, $old_master_xref_id;
while(my $xref_id = pop(@master_xrefs)){
my ($dep_xref_id, $linkage_type, $new_object_xref_id, $linkage_source_id);
## Loop through all dependent xrefs of current master xref
$dep_sth->execute($xref_id);
$dep_sth->bind_columns(\$dep_xref_id, \$linkage_type, \$linkage_source_id);
## Loop through all dependent xrefs
while($dep_sth->fetch()){
## Add dependent to priority xref if it is the first master
if (!$recursive) {
## Add dependent to priority xref if it is the first in the chain.
unless ($recursive) {
$insert_dep_x_sth->execute($new_master_xref_id, $dep_xref_id, $linkage_type, $linkage_source_id);
foreach my $best_ensembl_id (@$best_ensembl_id) {
$remove_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $best_ensembl_id);
$update_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $best_ensembl_id);
$clean_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $best_ensembl_id);
}
_detach_object_xref($xref_id, $object_type, $dep_xref_id, $best_ensembl_id);
}
## object_xref for dismissed xref set to FAILED_PRIORITY
## object_xref for dismissed old xref set to FAILED_PRIORITY
## also delete any leftover identity or go xrefs
foreach my $old_id (@old_ensembl_ids) {
$remove_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $old_id);
$update_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $old_id);
$clean_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $old_id);
}
_detach_object_xref($xref_id, $object_type, $dep_xref_id, $@old_ensembl_ids);
## Loop through all ensembl ids mapped to priority xref
foreach my $best_ensembl_id (@$best_ensembl_id) {
## new object_xref for each transfered mapping
$insert_dep_ox_sth->execute($new_master_xref_id, $object_type, $best_ensembl_id, $dep_xref_id);
## If there is a linkage_type, it is a go xref
if ($linkage_type) {
## If there is a linkage_type, it is a go xref
## Fetch the newly created object_xref to add them to go_xref
$dep_ox_sth->execute($new_master_xref_id, $object_type, $best_ensembl_id, $dep_xref_id);
$dep_ox_sth->bind_columns(\$new_object_xref_id);
......@@ -340,12 +317,68 @@ sub process_dependents{
$dep_sth->finish();
$insert_dep_x_sth->finish();
$remove_dep_ox_sth->finish();
$clean_dep_ox_sth->finish();
$insert_dep_ox_sth->finish();
$dep_ox_sth->finish();
$insert_dep_go_sth->finish();
$insert_ix_sth->finish();
}
# broken out of process_dependents.
# Get a list of IDs that are not associated with the new xref
sub _get_old_ensembl_ids_associated_with_xref {
my $old_master_xref_id = shift;
my $new_ensembl_ids = shift;
my %new_id_lookup;
map { $new_id_lookup{$_} = 1 } @$new_ensembl_ids;
my $old_ensembl_id;
my @old_ensembl_ids;
my $old_ens_id_sth = $self->xref->dbc->prepare("select distinct ensembl_id from object_xref where xref_id = ?");
$old_ens_id_sth->execute($old_master_xref_id);
$old_ens_id_sth->bind_columns(\$old_ensembl_id);
my $skip = 0;
while ($old_ens_id_sth->fetch()) {
unless (exists $new_id_lookup{$old_ensembl_id}) {
push @old_ensembl_ids, $old_ensembl_id;
}
}
$old_ens_id_sth->finish();
return @old_ensembl_ids;
}
sub _detach_object_xref {
my ($xref_id, $object_type, $dep_xref_id, $ids) = @_;
my $remove_dep_ox_sth = $self->xref->dbc->prepare(
"DELETE ix, g FROM object_xref ox \
LEFT JOIN identity_xref ix ON ix.object_xref_id = ox.object_xref_id \
LEFT JOIN go_xref g ON g.object_xref_id = ox.object_xref_id \
WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ?"
);
my $update_dep_ox_sth = $self->xref->dbc->prepare(
"UPDATE IGNORE object_xref SET ox_status = 'FAILED_PRIORITY' \
WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ? AND ox_status = 'DUMP_OUT'"
);
my $clean_dep_ox_sth = $self->xref->dbc->prepare(
"DELETE FROM object_xref \
WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ? AND ox_status = 'DUMP_OUT'"
);
foreach my $id (@$ids) {
$remove_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $id);
# change status of object_xref to FAILED_PRIORITY for record keeping
$update_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $id);
# delete the duplicates.
$clean_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $id);
}
$remove_dep_ox_sth->finish();
$update_dep_ox_sth->finish();
$clean_dep_ox_sth->finish();
}
1;
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