From 442eb3faa46b432108c173721db08b8971209afa Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 11 Apr 2011 08:41:47 +0000
Subject: [PATCH] changed the dumped databases entrys from int to enum so
changed the values here to match those in the database
---
.../xref_mapping/XrefMapper/XrefLoader.pm | 42 ++++++++++++-------
1 file changed, 26 insertions(+), 16 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
index 4ea8ad9067..e4dad106c9 100644
--- a/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/XrefLoader.pm
@@ -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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