XrefMapper::XrefLoader Class Reference
Public Member Functions | |
| public | new () |
| public | mapper () |
| public | update () |
| public | get_single_analysis () |
| public | add_xref () |
| public | add_object_xref () |
Detailed Description
Definition at line 7 of file XrefLoader.pm.
Member Function Documentation
◆ add_object_xref()
| public XrefMapper::XrefLoader::add_object_xref | ( | ) |
Undocumented method
Code:
click to view
sub add_object_xref {
my ($self, $offset, $object_xref_id, $ensembl_id, $ensembl_object_type, $xref_id, $analysis_id, $dbc) = @_;
my $select_sth = $dbc->prepare("select object_xref_id from object_xref where xref_id = ? and ensembl_object_type = ? and ensembl_id = ? and analysis_id = ?");
my $insert_sth = $dbc->prepare("insert ignore into object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id, analysis_id) values (?, ?, ?, ?, ?)");
my $new_object_xref_id;
$select_sth->execute($xref_id, $ensembl_object_type, $ensembl_id, $analysis_id);
$select_sth->bind_columns(\$new_object_xref_id);
$select_sth->fetch();
if (!$new_object_xref_id) {
$insert_sth->execute(($object_xref_id+$offset), $ensembl_id, $ensembl_object_type, $xref_id, $analysis_id);
return $object_xref_id;
} else {
return $new_object_xref_id - $offset;
}
}
◆ add_xref()
| public XrefMapper::XrefLoader::add_xref | ( | ) |
Undocumented method
Code:
click to view
sub add_xref {
my ($self, $offset, $xref_id, $external_db_id, $dbprimary_acc, $display_label, $version, $description, $info_type, $info_text, $dbc) = @_;
my $select_sth = $dbc->prepare("select xref_id from xref where dbprimary_acc = ? and external_db_id = ? and info_type = ? and info_text = ? and version = ?");
my $insert_sth = $dbc->prepare("insert into xref (xref_id, external_db_id, dbprimary_acc, display_label, version, description, info_type, info_text) values (?, ?, ?, ?, ?, ?, ?, ?)");
my $new_xref_id;
$select_sth->execute($dbprimary_acc, $external_db_id, $info_type, $info_text, $version);
$select_sth->bind_columns(\$new_xref_id);
$select_sth->fetch();
if (!$new_xref_id) {
$insert_sth->execute(($xref_id+$offset), $external_db_id, $dbprimary_acc, $display_label, $version, $description, $info_type, $info_text);
return $xref_id;
} else {
return $new_xref_id - $offset;
}
}
◆ get_single_analysis()
| public XrefMapper::XrefLoader::get_single_analysis | ( | ) |
Undocumented method
Code:
click to view
sub get_single_analysis {
my ($self, $logic_name) = @_;
my $h = $self->core->dbc()->sql_helper();
my $analysis_ids = $h->execute_simple(
-SQL => 'SELECT analysis_id FROM analysis WHERE logic_name=?',
-PARAMS => [$logic_name]
);
my $analysis_id;
if(@{$analysis_ids}) {
$analysis_id = $analysis_ids->[0];
}
else {
print "No analysis with logic_name $logic_name found, creating ...\n" if ($self->verbose);
# TODO - other fields in analysis table
$self->core()->dbc()->sql_helper()->execute_update(
-SQL => 'INSERT INTO analysis (logic_name, created) VALUES (?,NOW())',
-PARAMS => [$logic_name],
-CALLBACK => sub {
my ($sth) = @_;
$analysis_id = $sth->{'mysql_insertid'};
return;
}
);
}
return $analysis_id;
}
◆ mapper()
| public XrefMapper::XrefLoader::mapper | ( | ) |
Undocumented method
Code:
click to view
sub mapper{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_mapper} = $arg );
return $self->{_mapper};
}
◆ new()
| public XrefMapper::XrefLoader::new | ( | ) |
Undocumented method
Code:
click to view
sub new {
my($class, $mapper) = @_;
my $self ={};
bless $self,$class;
$self->core($mapper->core);
$self->xref($mapper->xref);
$self->mapper($mapper);
return $self;
}
◆ update()
| public XrefMapper::XrefLoader::update | ( | ) |
Undocumented method
Code:
click to view
sub update{
my ($self, $arg) = @_;
# remove xref, object_xref, identity_xref, depenedent_xref, unmapped_object, external_synonym, projections.
my $verbose = $self->mapper->verbose;
my $core_dbi = $self->core->dbc;
my $xref_dbi = $self->xref->dbc;
#####################################
# first remove all the projections. #
#####################################
print "Deleting all PROJECTIONs from this database\n" if $verbose;
my $sql = "TRUNCATE table ontology_xref";
my $sth = $core_dbi->prepare($sql);
$sth->execute();
print "\tDeleted all ontology_xref rows\n" if $verbose;
$sql = "UPDATE gene g INNER JOIN xref x ON g.display_xref_id=x.xref_id SET g.display_xref_id=NULL,g.description=NULL WHERE x.info_type='PROJECTION'";
$sth = $core_dbi->prepare($sql);
my $affected_rows = $sth->execute();
print "\tSet display_xref_id and description to NULL in $affected_rows gene row(s) relating to PROJECTED xrefs\n" if $verbose;
$sql = "DELETE es FROM xref x, external_synonym es WHERE x.xref_id = es.xref_id and x.info_type = 'PROJECTION'";
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
print "\tDeleted $affected_rows PROJECTED external_synonym row(s)\n" if $verbose;
$sql = "DELETE dx FROM dependent_xref dx, xref x, external_db ed WHERE x.xref_id = dx.dependent_xref_id AND x.external_db_id = ed.external_db_id and ed.db_name = 'GO'";
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
print "\tDeleted $affected_rows GO dependent_xref row(s)\n" if $verbose;
$sql = "DELETE ox FROM object_xref ox, xref x, external_db e WHERE x.xref_id = ox.xref_id AND x.external_db_id =e.external_db_id and e.db_name = 'GO'";
$sth = $core_dbi->prepare($sql);
$sth->execute();
$sql = "DELETE dx FROM dependent_xref dx, xref x WHERE x.xref_id = dx.dependent_xref_id AND x.info_type = 'PROJECTION'";
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
print "\tDeleted $affected_rows PROJECTED dependent_xref row(s)\n" if $verbose;
$sql = "DELETE object_xref FROM object_xref, xref WHERE object_xref.xref_id = xref.xref_id AND xref.info_type = 'PROJECTION'";
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
print "\tDeleted $affected_rows PROJECTED object_xref row(s)\n" if $verbose;
$sql = "DELETE xref FROM xref WHERE xref.info_type = 'PROJECTION'";
$sth = $core_dbi->prepare($sql);
$affected_rows = $sth->execute();
print "\tDeleted $affected_rows PROJECTED xref row(s)\n" if $verbose;
$sth->finish;
#########################################
# Get source_id to external_db_id #
#########################################
my %name_to_external_db_id;
$sql = "select external_db_id, db_name from external_db";
$sth = $core_dbi->prepare($sql);
$sth->execute();
my ($id, $name);
$sth->bind_columns(\$id, \$name);
while($sth->fetch()){
$name_to_external_db_id{$name} = $id;
}
$sth->finish;
my %source_id_to_external_db_id;
$sql = 'select s.source_id, s.name from source s, xref x where x.source_id = s.source_id group by s.source_id'; # only get those of interest
$sth = $xref_dbi->prepare($sql);
$sth->execute();
$sth->bind_columns(\$id, \$name);
while($sth->fetch()){
if(defined($name_to_external_db_id{$name})){
$source_id_to_external_db_id{$id} = $name_to_external_db_id{$name};
}
elsif( $name =~ /notransfer$/){
}
else{
die "ERROR: Could not find $name in external_db table please add this too continue";
}
}
$sth->finish;
$sth = $xref_dbi->prepare("update xref set dumped = null where dumped != 'NO_DUMP_ANOTHER_PRIORITY'"); # just incase this is being ran again
$sth->execute;
$sth->finish;
######################################
# For each external_db to be updated #
# Delete the existing ones #
######################################
my ($count);
$sth = $xref_dbi->prepare('select s.name, count(*) from xref x, object_xref ox, source s where ox.xref_id = x.xref_id and x.source_id = s.source_id group by s.name');
$sth->execute();
$sth->bind_columns(\$name,\$count);
my $synonym_sth = $core_dbi->prepare('DELETE external_synonym FROM external_synonym, xref WHERE external_synonym.xref_id = xref.xref_id AND xref.external_db_id = ?');
my $identity_sth = $core_dbi->prepare('DELETE identity_xref FROM identity_xref, object_xref, xref WHERE identity_xref.object_xref_id = object_xref.object_xref_id AND object_xref.xref_id = xref.xref_id AND xref.external_db_id = ?');
my $object_sth = $core_dbi->prepare('DELETE object_xref FROM object_xref, xref WHERE object_xref.xref_id = xref.xref_id AND xref.external_db_id = ?');
my $master_sth = $core_dbi->prepare('DELETE ox, d FROM xref mx, xref x, dependent_xref d LEFT JOIN object_xref ox ON ox.object_xref_id = d.object_xref_id WHERE mx.xref_id = d.master_xref_id AND dependent_xref_id = x.xref_id AND mx.external_db_id = ?');
my $dependent_sth = $core_dbi->prepare('DELETE d FROM dependent_xref d, xref x WHERE d.dependent_xref_id = x.xref_id and x.external_db_id = ?');
my $xref_sth = $core_dbi->prepare('DELETE FROM xref WHERE xref.external_db_id = ?');
my $unmapped_sth = $core_dbi->prepare('DELETE FROM unmapped_object WHERE type="xref" and external_db_id = ?');
my $gene_reset_sth = $core_dbi->prepare('UPDATE gene g INNER JOIN xref x ON g.display_xref_id=x.xref_id SET g.display_xref_id=NULL,g.description=NULL WHERE x.external_db_id=?');
my $transaction_start_sth = $core_dbi->prepare('start transaction');
my $transaction_end_sth = $core_dbi->prepare('commit');
#
# ?? Is it faster to delete them all in one go with a external_db_id in (....) ???
# alternative load ottt etc that are not obtained from xrefs into xref table and then delete tables fully??
#
# my $test =1; # Can take a while so make optional when testing
# if(!$test){
$transaction_start_sth->execute();
while($sth->fetch()){
if(!defined($name_to_external_db_id{$name})){
next; #must end in notransfer
}
my $ex_id = $name_to_external_db_id{$name};
print "Setting display_xref_id and description to NULL if it refers to xrefs that are to be deleted\n" if ($verbose);
$affected_rows = $gene_reset_sth->execute($ex_id);
print "\tSet display_xref_id=NULL and description=NULL for $affected_rows gene row(s)\n" if ($verbose);
print "Deleting data for $name from core before updating from new xref database\n" if ($verbose);
$affected_rows = $synonym_sth->execute($ex_id);
print "\tDeleted $affected_rows external_synonym row(s)\n" if $verbose;
$affected_rows = $identity_sth->execute($ex_id);
print "\tDeleted $affected_rows identity_xref row(s)\n" if $verbose;
$affected_rows = $object_sth->execute($ex_id);
print "\tDeleted $affected_rows object_xref row(s)\n" if $verbose;
$affected_rows = $master_sth->execute($ex_id);
print "\tDeleted $affected_rows xref, object_xref and dependent_xref row(s)\n" if $verbose;
$affected_rows = $dependent_sth->execute($ex_id);
print "\tDeleted $affected_rows dependent_xref row(s)\n" if $verbose;
$affected_rows = $xref_sth->execute($ex_id);
print "\tDeleted $affected_rows xref row(s)\n" if $verbose;
$affected_rows = $unmapped_sth->execute($ex_id);
print "\tDeleted $affected_rows unmapped_object row(s)\n" if $verbose;
}
$sth->finish;
$transaction_end_sth->execute();
$synonym_sth->finish;
$identity_sth->finish;
$object_sth->finish;
$dependent_sth->finish;
$xref_sth->finish;
$unmapped_sth->finish;
##########################################
# Get the offsets for object_xref, xref #
##########################################
$sth = $core_dbi->prepare('select MAX(xref_id) from xref');
my $xref_offset;
$sth->execute;
$sth->bind_columns(\$xref_offset);
$sth->fetch();
$sth->finish;
$xref_offset = 0 if(!defined($xref_offset));
$self->add_meta_pair("xref_offset", $xref_offset);
$sth = $core_dbi->prepare('select MAX(object_xref_id) from object_xref');
my $object_xref_offset;
$sth->execute;
$sth->bind_columns(\$object_xref_offset);
$sth->fetch();
$sth->finish;
$object_xref_offset = 0 if(!defined($object_xref_offset));
$self->add_meta_pair("object_xref_offset", $object_xref_offset);
####################
# Get analysis id's
####################
my %analysis_ids = $self->get_analysis();
my $checksum_analysis_id; #do not populate until we know we need this
print "xref offset is $xref_offset, object_xref offset is $object_xref_offset\n" if ($verbose);
#####################################
# Now add the new ones #
#####################################
###########################
# SQL to get data from xref
###########################
my $seq_sql =(<<DIRS);
SELECT x.xref_id, x.accession, x.label, x.version, x.description, x.info_text,
ox.object_xref_id, ox.ensembl_id, ox.ensembl_object_type,
i.query_identity, i.target_identity, i.hit_start, i.hit_end,
i.translation_start, i.translation_end, i.cigar_line, i.score, i.evalue
FROM xref x, object_xref ox, identity_xref i
WHERE ox.ox_status = "DUMP_OUT" AND
i.object_xref_id = ox.object_xref_id AND
ox.xref_id = x.xref_id AND
x.source_id = ? AND
x.info_type = ? order by x.xref_id
DIRS
my $seq_sth = $xref_dbi->prepare($seq_sql);
###########################
# SQL to get data from xref without identity xref
###########################
my $dir_sql =(<<DIRS);
SELECT x.xref_id, x.accession, x.label, x.version, x.description, x.info_text,
ox.object_xref_id, ox.ensembl_id, ox.ensembl_object_type
FROM xref x, object_xref ox
WHERE ox.ox_status = "DUMP_OUT" AND
ox.xref_id = x.xref_id AND
x.source_id = ? AND
x.info_type = ? order by x.xref_id
DIRS
my $dir_sth = $xref_dbi->prepare($dir_sql);
# $dependent_sth = $xref_dbi->prepare('select x.xref_id, x.accession, x.label, x.version, x.description, x.info_text, ox.object_xref_id, ox.ensembl_id, ox.ensembl_object_type, d.master_xref_id from xref x, object_xref ox, dependent_xref d where ox.ox_status = "DUMP_OUT" and ox.xref_id = x.xref_id and d.object_xref_id = ox.object_xref_id and x.source_id = ? and x.info_type = ? order by x.xref_id, ox.ensembl_id');
my $dep_sql =(<<DSQL);
SELECT x.xref_id, x.accession, x.label, x.version, x.description, x.info_text,
ox.object_xref_id, ox.ensembl_id, ox.ensembl_object_type, ox.master_xref_id
FROM xref x, object_xref ox, xref mx, source s
WHERE ox.ox_status = "DUMP_OUT" and
ox.xref_id = x.xref_id and
ox.master_xref_id = mx.xref_id and
mx.source_id = s.source_id and
x.source_id = ? and
x.info_type = ?
ORDER BY x.xref_id, ox.ensembl_id, s.ordered
DSQL
$dependent_sth = $xref_dbi->prepare($dep_sql);
# SQL to add data to core
#########################
my $add_identity_xref_sth = $core_dbi->prepare('insert ignore into identity_xref (object_xref_id, xref_identity, ensembl_identity, xref_start, xref_end, ensembl_start, ensembl_end, cigar_line, score, evalue) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)');
my $add_dependent_xref_sth = $core_dbi->prepare('insert ignore into dependent_xref (object_xref_id, master_xref_id, dependent_xref_id) values (?, ?, ?)');
my $add_syn_sth = $core_dbi->prepare('insert ignore into external_synonym (xref_id, synonym) values (?, ?)');
my $add_release_info_sth = $core_dbi->prepare('update external_db set db_release = ? where external_db_id = ?');
$sth = $xref_dbi->prepare('select s.name, s.source_id, count(*), x.info_type, s.priority_description, s.source_release from xref x, object_xref ox, source s where ox.xref_id = x.xref_id and x.source_id = s.source_id and ox_status = "DUMP_OUT" group by s.name, s.source_id, x.info_type');
$sth->execute();
my ($type, $source_id, $where_from, $release_info);
$sth->bind_columns(\$name,\$source_id, \$count, \$type, \$where_from, \$release_info);
$transaction_start_sth->execute();
while($sth->fetch()){
next if(!defined($name_to_external_db_id{$name}));
if(defined($where_from) and $where_from ne ""){
$where_from = "Generated via $where_from";
}
my $ex_id = $name_to_external_db_id{$name};
print "updating ($source_id) $name in core (for $type xrefs)\n" if ($verbose);
my @xref_list=(); # process at end. Add synonyms and set dumped = 1;
# dump SEQUENCE_MATCH, DEPENDENT, DIRECT, COORDINATE_OVERLAP, INFERRED_PAIR, (MISC?? same as direct come from official naming)
### If DIRECT , xref, object_xref, (order by xref_id) # maybe linked to more than one?
### if INFERRED_PAIR xref, object_xref
### if MISC xref, object_xref
if($type eq "DIRECT" or $type eq "INFERRED_PAIR" or $type eq "MISC"){
my $count = 0;
$seq_sth->execute($source_id, $type);
my ($xref_id, $acc, $label, $version, $desc, $info, $object_xref_id, $ensembl_id, $ensembl_type);
my ( $query_identity, $target_identity, $hit_start, $hit_end, $translation_start, $translation_end, $cigar_line, $score, $evalue);
$seq_sth->bind_columns(\$xref_id, \$acc, \$label, \$version, \$desc, \$info, \$object_xref_id, \$ensembl_id, \$ensembl_type,
\$query_identity, \$target_identity, \$hit_start, \$hit_end, \$translation_start, \$translation_end, \$cigar_line, \$score, \$evalue);
my $last_xref = 0;
while($seq_sth->fetch){
if($last_xref != $xref_id){
push @xref_list, $xref_id;
$count++;
$xref_id = $self->add_xref($xref_offset, $xref_id, $ex_id, $acc, $label, $version, $desc, $type, $info || $where_from, $core_dbi);
$last_xref = $xref_id;
}
$object_xref_id = $self->add_object_xref($object_xref_offset, $object_xref_id, $ensembl_id, $ensembl_type, ($xref_id+$xref_offset), $analysis_ids{$ensembl_type}, $core_dbi);
$add_identity_xref_sth->execute( ($object_xref_id+$object_xref_offset), $query_identity, $target_identity, $hit_start, $hit_end,
$translation_start, $translation_end, $cigar_line, $score, $evalue) if $translation_start;
}
print "DIRECT $count\n" if ($verbose);
}
### IF CHECKSUM, xref, object_xref
# 1:m mapping between object & xref
elsif($type eq 'CHECKSUM') {
#If we had a checksum then get the analysis. Avoids unecessary analysis entries
if(! defined $checksum_analysis_id) {
$checksum_analysis_id = $self->get_single_analysis('xrefchecksum');
}
my $count = 0;
$dir_sth->execute($source_id, $type);
my $last_xref = 0;
while(my $row = $dir_sth->fetchrow_arrayref()) {
my ($xref_id, $acc, $label, $version, $desc, $info, $object_xref_id, $ensembl_id, $ensembl_type) = @{$row};
if($last_xref != $xref_id) {
push @xref_list, $xref_id;
$count++;
$xref_id = $self->add_xref($xref_offset, $xref_id, $ex_id, $acc, $label, $version, $desc, $type, $info || $where_from, $core_dbi);
$last_xref = $xref_id;
}
$object_xref_id = $self->add_object_xref($object_xref_offset, $object_xref_id, $ensembl_id, $ensembl_type, ($xref_id+$xref_offset), $checksum_analysis_id, $core_dbi);
}
print "CHECKSUM $count\n" if ($verbose);
}
### If DEPENDENT, xref, object_xref , dependent_xref (order by xref_id) # maybe linked to more than one?
elsif($type eq "DEPENDENT"){
my $count = 0;
my $ox_count = 0;
my @master_problems;
my $err_master_count=0;
$dependent_sth->execute($source_id, $type);
my ($xref_id, $acc, $label, $version, $desc, $info, $object_xref_id, $ensembl_id, $ensembl_type, $master_xref_id);
$dependent_sth->bind_columns(\$xref_id, \$acc, \$label, \$version, \$desc, \$info, \$object_xref_id, \$ensembl_id, \$ensembl_type, \$master_xref_id);
my $last_xref = 0;
my $last_ensembl = 0;
while($dependent_sth->fetch){
if($last_xref != $xref_id){
push @xref_list, $xref_id;
$count++;
$xref_id = $self->add_xref($xref_offset, $xref_id, $ex_id, $acc, $label || $acc, $version, $desc, $type, $info || $where_from, $core_dbi);
}
if($last_xref != $xref_id or $last_ensembl != $ensembl_id){
$object_xref_id = $self->add_object_xref($object_xref_offset, $object_xref_id, $ensembl_id, $ensembl_type, ($xref_id+$xref_offset), $analysis_ids{$ensembl_type}, $core_dbi);
if (defined($master_xref_id)){ # need to sort this out for FlyBase since there are EMBL direct entries from the GFF and dependent xrefs from Uniprot
$add_dependent_xref_sth->execute(($object_xref_id+$object_xref_offset), ($master_xref_id+$xref_offset), ($xref_id+$xref_offset) );
}
else{
if($err_master_count < 10){
push @master_problems, $acc;
}
$err_master_count++;
}
$ox_count++;
}
$last_xref = $xref_id;
$last_ensembl = $ensembl_id;
}
if(@master_problems){
print "WARNING:: for $name $err_master_count problem master xrefs\nExamples are :-\t";
print join ", ",@master_problems;
print "\n";
}
print "DEP $count xrefs, $ox_count object_xrefs\n" if ($verbose);
}
### If SEQUENCE_MATCH xref, object_xref, identity_xref (order by xref_id) # maybe linked to more than one?
elsif($type eq "SEQUENCE_MATCH"){
my $count = 0;
$seq_sth->execute($source_id, $type);
my ($xref_id, $acc, $label, $version, $desc, $info, $object_xref_id, $ensembl_id, $ensembl_type);
my ( $query_identity, $target_identity, $hit_start, $hit_end, $translation_start, $translation_end, $cigar_line, $score, $evalue);
$seq_sth->bind_columns(\$xref_id, \$acc, \$label, \$version, \$desc, \$info, \$object_xref_id, \$ensembl_id, \$ensembl_type,
\$query_identity, \$target_identity, \$hit_start, \$hit_end, \$translation_start, \$translation_end, \$cigar_line, \$score, \$evalue);
my $last_xref = 0;
while($seq_sth->fetch){
if($last_xref != $xref_id){
push @xref_list, $xref_id;
$count++;
$xref_id = $self->add_xref($xref_offset, $xref_id, $ex_id, $acc, $label, $version, $desc, $type, $info || $where_from, $core_dbi);
$last_xref = $xref_id;
}
$object_xref_id = $self->add_object_xref ($object_xref_offset, $object_xref_id, $ensembl_id, $ensembl_type, ($xref_id+$xref_offset), $analysis_ids{$ensembl_type}, $core_dbi);
$add_identity_xref_sth->execute( ($object_xref_id+$object_xref_offset), $query_identity, $target_identity, $hit_start, $hit_end,
$translation_start, $translation_end, $cigar_line, $score, $evalue);
}
print "SEQ $count\n" if ($verbose);
}
else{
print "PROBLEM:: what type is $type\n";
}
# Transfer data for synonym and set xref database xrefs to dumped.
if(@xref_list){
my $syn_count = 0;
my $syn_sql = "select xref_id, synonym from synonym where xref_id in(".join(", ",@xref_list).")";
my $syn_sth = $xref_dbi->prepare($syn_sql);
$syn_sth->execute();
my ($xref_id, $syn);
$syn_sth->bind_columns(\$xref_id, \$syn);
while($syn_sth->fetch()){
$add_syn_sth->execute(($xref_id+$xref_offset), $syn);
$syn_count++;
}
$syn_sth->finish;
print "\tadded $syn_count synonyms\n" if($syn_count);
my $xref_dumped_sth = $xref_dbi->prepare("update xref set dumped = 'MAPPED' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute() || die "Could not set dumped status";
$xref_dumped_sth->finish;
}
# Update the core databases release in for source form the xref database
if(defined($release_info) and $release_info ne "1"){
$add_release_info_sth->execute($release_info, $ex_id) || die "Failed to add release info **$release_info** for external source $ex_id\n";
}
}
$sth->finish;
$seq_sth->finish;
$dir_sth->finish;
$transaction_end_sth->execute();
#######################################
# Remember to do unmapped entries
########################################
##########
# DIRECT #
##########
$sql =(<<DIR);
UPDATE source s,xref x
LEFT JOIN object_xref ox ON ox.xref_id = x.xref_id
SET dumped = 'UNMAPPED_NO_STABLE_ID'
WHERE x.source_id = s.source_id
AND x.dumped is null
AND ox.ox_status != 'FAILED_PRIORITY'
AND x.info_type = 'DIRECT'
DIR
my $direct_unmapped_sth = $xref_dbi->prepare($sql);
$direct_unmapped_sth->execute();
########
# MISC #
########
$sql =(<<MIS);
UPDATE xref x, source s
SET dumped = 'UNMAPPED_NO_MAPPING'
WHERE x.source_id = s.source_id
AND x.dumped is null
AND x.info_type = 'MISC'
MIS
my $misc_unmapped_sth = $xref_dbi->prepare($sql);
$misc_unmapped_sth->execute();
#############
# DEPENDENT #
#############
$sql = (<<DEP);
UPDATE xref mx, source s, xref x
LEFT JOIN dependent_xref dx ON dx.dependent_xref_id = x.xref_id
LEFT JOIN object_xref ox ON ox.xref_id = x.xref_id
SET x.dumped = 'UNMAPPED_MASTER_FAILED'
WHERE x.source_id = s.source_id
AND dx.master_xref_id = mx.xref_id
AND x.dumped is null
AND ox.ox_status != 'FAILED_PRIORITY'
AND x.info_type = 'DEPENDENT'
DEP
my $dep_unmapped_sth = $xref_dbi->prepare($sql);
$dep_unmapped_sth->execute();
##################
# SEQUENCE_MATCH #
##################
$sql = (<<SEQ);
UPDATE source s, primary_xref px, xref x
LEFT JOIN object_xref ox ON ox.xref_id = x.xref_id
LEFT JOIN identity_xref ix ON ix.object_xref_id = ox.object_xref_id
SET x.dumped = 'UNMAPPED_NO_MAPPING'
WHERE x.source_id = s.source_id
AND px.xref_id = x.xref_id
AND x.dumped is null
AND x.info_type = 'SEQUENCE_MATCH'
SEQ
my $seq_unmapped_sth = $xref_dbi->prepare($sql);
$seq_unmapped_sth->execute();
###########################
# WEL (What ever is left).#
###########################
# These are those defined as dependent but the master never existed and the xref and their descriptions etc are loaded first
# with the dependencys added later so did not know they had no masters at time of loading.
# (e.g. EntrezGene, WikiGene, MIN_GENE, MIM_MORBID)
$sql = (<<WEL);
UPDATE source s, xref x
SET dumped = 'UNMAPPED_NO_MASTER'
WHERE x.source_id = s.source_id
AND x.dumped is null
AND x.info_type = 'DEPENDENT'
WEL
my $wel_unmapped_sth = $xref_dbi->prepare($sql);
$wel_unmapped_sth->execute();
my $sth_stat = $xref_dbi->prepare("insert into process_status (status, date) values('core_loaded',now())");
$sth_stat->execute();
$sth_stat->finish;
}
sub get_analysis{
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
