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Commit 442eb3fa authored by Ian Longden's avatar Ian Longden
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changed the dumped databases entrys from int to enum so changed the values... 

changed the dumped databases entrys from int to enum so changed the values here to match those in the database
parent 64f3338c
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misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
+ 26
− 16
View file @ 442eb3fa
......@@ -89,8 +89,7 @@ sub update{
$sth->finish;
# 100 is the dumped status for the dumpoed status for the "FAILED_PRIORIY"'s do not clear these.
$sth = $self->xref->dbc->prepare("update xref set dumped = null where dumped != 100"); # just incase this is being ran again
$sth = $self->xref->dbc->prepare("update xref set dumped = null where dumped != 'NO_DUMP_ANOTHER_PRIORITY'"); # just incase this is being ran again
$sth->execute;
$sth->finish;
......@@ -206,7 +205,18 @@ sub update{
# $dependent_sth = $self->xref->dbc->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');
$dependent_sth = $self->xref->dbc->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, ox.master_xref_id 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, 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
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, ox.ensembl_id
DSQL
$dependent_sth = $self->xref->dbc->prepare($dep_sql);
my $go_sql =(<<GSQL);
......@@ -374,7 +384,7 @@ GSQL
}
$syn_sth->finish;
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 2 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->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;
}
......@@ -489,7 +499,7 @@ GSQL
$set_unmapped_sth->finish;
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 3 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_INTERPRO' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......@@ -549,7 +559,7 @@ DIR
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 4 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_NO_STABLE_ID' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......@@ -585,7 +595,7 @@ MIS
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 5 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_NO_MAPPING' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......@@ -631,8 +641,9 @@ DEP
$dep_unmapped_sth->finish;
$set_unmapped_sth->finish;
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 6 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_MASTER_FAILED' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......@@ -645,7 +656,7 @@ DEP
SELECT x.xref_id, x.accession, x.version, x.label, x.description, x.info_type, x.info_text,
s.name, px.sequence_type,
ox.ensembl_object_type, ox.ensembl_id,
ix.query_identity, ix.target_identity
ix.query_identity, ix.target_identity, ox.ox_status
FROM 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
......@@ -653,16 +664,15 @@ DEP
AND px.xref_id = x.xref_id
AND x.dumped is null
AND x.info_type = 'SEQUENCE_MATCH'
AND ox.ox_status != 'FAILED_PRIORITY'
ORDER BY x.xref_id
SEQ
# removed AND ox.ox_status != 'FAILED_PRIORITY'
my $seq_unmapped_sth = $self->xref->dbc->prepare($sql);
$seq_unmapped_sth->execute();
my ($ensembl_object_type, $ensembl_id, $q_id, $t_id, $seq_type) ;
$seq_unmapped_sth->bind_columns(\$xref_id, \$acc, \$version, \$label, \$desc, \$type, \$info, \$dbname, \$seq_type, \$ensembl_object_type, \$ensembl_id, \$q_id, \$t_id);
my ($ensembl_object_type, $ensembl_id, $q_id, $t_id, $seq_type, $status) ;
$seq_unmapped_sth->bind_columns(\$xref_id, \$acc, \$version, \$label, \$desc, \$type, \$info, \$dbname, \$seq_type, \$ensembl_object_type, \$ensembl_id, \$q_id, \$t_id,\$status);
my $set_unmapped_no_sth = $self->core->dbc->prepare("insert into unmapped_object (type, analysis_id, external_db_id, identifier, unmapped_reason_id, ensembl_object_type ) values ('xref', ?, ?, ?, '".$reason_id{"FAILED_MAP"}."', ?)");
my $set_unmapped_failed_sth = $self->core->dbc->prepare("insert into unmapped_object (type, analysis_id, external_db_id, identifier, unmapped_reason_id, query_score, target_score, ensembl_id, ensembl_object_type ) values ('xref', ?, ?, ?, '".$reason_id{"FAILED_THRESHOLD"}."',?,?,?,?)");
......@@ -672,7 +682,7 @@ SEQ
my $last_xref = 0;
while($seq_unmapped_sth->fetch()){
my $ex_id = $name_to_external_db_id{$dbname};
if(!defined($ex_id)){
if(!defined($ex_id) or (defined($status) and $status eq "FAILED_PRIORITY") ){
next;
}
if($last_xref != $xref_id){
......@@ -701,7 +711,7 @@ SEQ
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 7 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_NO_MAPPING' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......@@ -744,7 +754,7 @@ WEL
$set_unmapped_sth->finish;
if(@xref_list){
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 8 where xref_id in (".join(", ",@xref_list).")");
my $xref_dumped_sth = $self->xref->dbc->prepare("update xref set dumped = 'UNMAPPED_NO_MASTER' where xref_id in (".join(", ",@xref_list).")");
$xref_dumped_sth->execute();
$xref_dumped_sth->finish;
}
......
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