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to debug .loadTRNAScan step failure #58

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to debug .loadTRNAScan step failure #58

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32 changes: 25 additions & 7 deletions Load/plugin/perl/LoadTRNAScan.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ use GUS::Model::SRes::ExternalDatabase;
use GUS::Model::SRes::ExternalDatabaseRelease;
use GUS::Model::ApiDB::GeneFeatureProduct;
use GUS::Supported::Util;
use GUS::Supported::OntologyLookup;

# ----------------------------------------------------------
# Load Arguments
Expand Down Expand Up @@ -84,6 +85,13 @@ sub getArgsDeclaration {
reqd => 1,
isList => 0,
}),
stringArg({ name => 'soGusConfigFile',
descr => 'The gus config file for database containing SO term info',
constraintFunc => undef,
reqd => 0,
mustExist => 0,
isList => 0,
}),
stringArg({ name => 'prefix',
descr => 'prefix needed to construct source_id, prefix_trna_xxxx',
constraintFunc => undef,
Expand Down Expand Up @@ -215,22 +223,32 @@ sub fetchSequenceOntologyId {
my ($self, $name) = @_;

my $soExternalDatabaseSpec=$self->getArg('soExternalDatabaseSpec');
my ($soExtDbName, $soExtDbVer) = split ('\|', $soExternalDatabaseSpec);


my $soDbRlsId =
$self->getExtDbRlsId($soExternalDatabaseSpec);
($self->getExtDbRlsId($soExternalDatabaseSpec)) ? $self->getExtDbRlsId($soExternalDatabaseSpec) : $self->getOrCreateExtDbAndDbRls($soExtDbName, $soExtDbVer);

my $SOTerm = GUS::Model::SRes::OntologyTerm->new({'name' => $name,'external_database_release_id' => $soDbRlsId});

$SOTerm->retrieveFromDB;
if($SOTerm->retrieveFromDB) {
my $soId = $SOTerm->getId();
$self->undefPointerCache();
return $soId;

my $soId = $SOTerm->getId();
} else {
$self->log("Can't find SO term '$name' in database. adding...\n");

$self->undefPointerCache();
my $soGusConfigFile = $self->getArg('soGusConfigFile') if ($self->getArg('soGusConfigFile'));
$soGusConfigFile = $self->getArg('gusConfigFile') unless ($soGusConfigFile);
my $soLookup = GUS::Supported::OntologyLookup->new($soExternalDatabaseSpec, $soGusConfigFile);
my $soSourceId = $soLookup->getSourceIdFromName($name);

return $soId;
my $newSOTerm = GUS::Model::SRes::OntologyTerm->new({'name' => $name, 'source_id' => $soSourceId, 'external_database_release_id' => $soDbRlsId});
$newSOTerm->submit();
return ($newSOTerm->getId());

if (! $SOTerm->getId()) {
warn "Error: Can't find SO term '$name' in database.";
$self->undefPointerCache();
}
}

Expand Down