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Commit d2da46d2 authored by Ian Longden's avatar Ian Longden
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more tests

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misc-scripts/xref_mapping/XrefMapper/TestMappings.pm
+ 211
− 5
View file @ d2da46d2
......@@ -18,6 +18,7 @@ use IPC::Open3;
##### Unlinked entries ##############
# ERRORS
# dependent_xref and xref
# primary_xref and xref
# transcript_direct_xref and xref
......@@ -32,14 +33,12 @@ use IPC::Open3;
# gene_transcript_translation and transcript_stable_id
# gene_transcript_translation and translation_stable_id
##### if human or mouse check the number of gene name changes.
##### All go_xref have a linkage_type
# All object_xref of type go have a go_xref entry
##### All object_xref of type go have a go_xref entry
##### Numbers between xref and core (xref and object_xref) are similar
##### if human or mouse check the number of gene name changes.
sub new {
my($class, $mapper) = @_;
......@@ -85,6 +84,7 @@ sub unlinked_entries{
$count_sql = "select count(1) from dependent_xref d left join xref x on d.dependent_xref_id = x.xref_id where x.xref_id is null";
$sql = "select distinct(d.dependent_xref_id) from dependent_xref d left join xref x on d.dependent_xref_id = x.xref_id where x.xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
......@@ -94,7 +94,7 @@ sub unlinked_entries{
$sth->finish;
if($count){
$failed = 0;
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
......@@ -105,7 +105,213 @@ sub unlinked_entries{
$sth->finish;
}
$count_sql = "select count(1) from primary_xref d left join xref x on d.xref_id = x.xref_id where x.xref_id is null";
$sql = "select distinct(d.xref_id) from primary_xref d left join xref x on d.xref_id = x.xref_id where x.xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with primary xref $xref_id\n";
}
$sth->finish;
}
foreach my $type (qw(transcript translation gene)){
$count_sql = "select count(1) from ".$type."_direct_xref d left join xref x on d.general_xref_id = x.xref_id where x.xref_id is null";
$sql = "select distinct(d.xref_id) from ".$type."_direct_xref d left join xref x on d.general_xref_id = x.xref_id where x.xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with ".$type."_direct_xref $xref_id\n";
}
$sth->finish;
}
}
$count_sql = "select count(1) from synonym d left join xref x on d.xref_id = x.xref_id where x.xref_id is null";
$sql = "select distinct(d.xref_id) from synonym d left join xref x on d.xref_id = x.xref_id where x.xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with synonym $xref_id\n";
}
$sth->finish;
}
$count_sql = "select count(1) from identity_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null";
$sql = "select distinct(d.object_xref_id) from identity d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with object_xref $xref_id\n";
}
$sth->finish;
}
$count_sql = "select count(1) from go_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null";
$sql = "select distinct(d.object_xref_id) from go_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with object_xref $xref_id\n";
}
$sth->finish;
}
foreach my $type (qw(transcript translation gene)){
$count_sql = "select count(1) from gene_transcript_translation d left join ".$type."_stable_id x on d.".$type."_id = x.internal_id where x.internal_id is null and d.".$type."_id is not null";
$sql = "select distinct(d.".$type."_id) from gene_transcript_translation d left join ".$type."_stable_id x on d.".$type."_id = x.internal_id where x.internal_id is null and d.".$type."_id is not null limit 10";
$sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with ".$type."_id $xref_id\n";
}
$sth->finish;
}
}
$count_sql = "select count(1) from xref x, source s, object_xref o left join go_xref g on o.object_xref_id = g.object_xref_id where x.xref_id = o.xref_id and s.source_id = x.source_id and s.name like 'GO' and g.object_xref_id is null";
$sql = "select distinct(o.object_xref_id) from xref x, source s, object_xref o left join go_xref g on o.object_xref_id = g.object_xref_id where x.xref_id = o.xref_id and s.source_id = x.source_id and s.name like 'GO' and g.object_xref_id is null limit 10";
my $sth = $self->xref->dbc->prepare($count_sql);
$sth->execute();
$sth->bind_columns(\$count);
$sth->fetch();
$sth->finish;
if($count){
$failed = 1;
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$xref_id);
print "SQL QUERY: $sql\n";
while($sth->fetch){
print "Problem with object_xref $xref_id which is linked to a GO source but has no go_xref reference\n";
}
$sth->finish;
}
return $failed;
}
sub entry_number_check{
my ($self) = @_;
# No point doing xrefs object_xrefs are more important and gives a better indication of wether things went okay.
my %old_object_xref_count;
my %new_object_xref_count;
my $sth = $self->xref->dbc->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 and ox_status = "DUMP_OUT" group by s.name');
$sth->execute();
my ($name, $count);
$sth->bind_columns(\$name,\$count);
while($sth->fetch()){
$new_object_xref_count{$name} = $count;
}
$sth->finish;
$sth = $self->core->dbc->prepare('select e.db_name, count(*) from xref x, object_xref ox, external_db e where ox.xref_id = x.xref_id and x.external_db_id = e.external_db_id group by e.db_name');
$sth->execute();
$sth->bind_columns(\$name,\$count);
while($sth->fetch()){
my $change = 0;
if(defined($new_object_xref_count{$name})){
$change = (($new_object_xref_count{$name} - $count)/$new_object_xref_count{$name}) * 100;
if($change > 5){ # increase of 5%
print "WARNING: $name has increased by $change\% was $count now ". $new_object_xref_count{$name}. "\n";
}
elsif($change < -5){ # decrease by 5%
print "WARNING: $name has decreased by $change\% was $count now ". $new_object_xref_count{$name}. "\n";
}
}
}
$sth->finish;
return;
}
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