Raw content of XrefMapper::ProcessPrioritys
<![CDATA[package XrefMapper::ProcessPrioritys;
use vars '@ISA';
@ISA = qw{ XrefMapper::BasicMapper };
use strict;
use warnings;
use XrefMapper::BasicMapper;
use Cwd;
use DBI;
use File::Basename;
use IPC::Open3;
# Process the priority xrefs.
#
# 1) create a list of source "names" that are priority xrefs
#
# 2) Just to be sure set all ox_status in object_xref to 'DUMP_OUT'
# set dumped in xref to NULL
#
# 3) for each of the source names
# set ox_status to 'FAILED_PRIORITY' for those not the best match
# Also do this fro its depenedents
#
sub new {
my($class, $mapper) = @_;
my $self ={};
bless $self,$class;
# $self->core($mapper->core);
$self->xref($mapper->xref);
$self->verbose($mapper->verbose);
return $self;
}
sub get_priority_names{
my ($self) = @_;
my $psth = $self->xref->dbc->prepare("select s.priority_description, s.name from source s, xref x where x.source_id = s.source_id group by s.priority_description, s.name order by s.name") || die "prepare failed";
$psth->execute() || die "execute failed";
my @names;
my %seen;
my $last_name = "rubbish";
my ($desc,$name);
$psth->bind_columns(\$desc,\$name);
while($psth->fetch()){
if($name eq $last_name and !defined($seen{$name})){
push @names, $name;
$seen{$name} = 1;
}
$last_name = $name;
}
return @names;
}
sub process {
my ($self) = @_;
my @names = $self->get_priority_names();
print "The foillowing will be processed as priority xrefs\n" if($self->verbose);
foreach my $name (@names){
print "\t$name\n" if($self->verbose);
}
my $update_ox_sth = $self->xref->dbc->prepare('update object_xref set ox_status = "FAILED_PRIORITY" where object_xref_id = ?');
my $update_x_sth = $self->xref->dbc->prepare('update xref set dumped = 100 where xref_id = ?');
#
# Change of tact here to make the sql easier...
#
# 1) Set to failed all those that have no object xrefs.
my $f_sql =(<<FSQL);
SELECT x.xref_id
FROM source s, xref x
LEFT JOIN object_xref ox ON ox.xref_id = x.xref_id
WHERE x.source_id = s.source_id
AND s.name = ?
AND ox.object_xref_id is null
FSQL
my $f_sth = $self->xref->dbc->prepare($f_sql);
foreach my $name (@names){
$f_sth->execute($name);
my ($xref_id);
$f_sth->bind_columns(\$xref_id);
while($f_sth->fetch()){
$update_x_sth->execute($xref_id);
}
}
$f_sth->finish;
#
# Now ALL object_xrefs have an identity_xref :-)
# So we can do a straight join and treat all info_types the same way.
#
my $new_sql =(<<NEWS);
SELECT ox.object_xref_id, x.accession, x.xref_id, (ix.query_identity + ix.target_identity) as identity
FROM object_xref ox, xref x, source s, identity_xref ix
WHERE ox.object_xref_id = ix.object_xref_id
AND ox.xref_id = x.xref_id
AND s.source_id = x.source_id
AND ox.ox_status = "DUMP_OUT"
AND s.name = ?
ORDER BY x.accession DESC, s.priority ASC , identity DESC, x.xref_id DESC
NEWS
my $sth = $self->xref->dbc->prepare($new_sql);
foreach my $name (@names){
$sth->execute($name);
my ($object_xref_id, $acc, $xref_id, $identity);
$sth->bind_columns(\$object_xref_id, \$acc, \$xref_id, \$identity);
my $last_acc = "";
my $best_xref_id = undef;
while($sth->fetch){
if($last_acc eq $acc){
if($xref_id != $best_xref_id){
$update_x_sth->execute($xref_id);
$update_ox_sth->execute($object_xref_id);
}
}
else{ # NEW
$last_acc = $acc;
$best_xref_id = $xref_id;
}
}
}
$sth->finish;
$update_ox_sth->finish;
$update_x_sth->finish;
$sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('prioritys_flagged',now())");
$sth->execute();
$sth->finish;
}
1;
]]>