Commit de87e27e authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Remove '()' on subroutine names in their declarations.

Minor formatting.
parent 614c708b
......@@ -1028,31 +1028,32 @@ sub submit_depend_job {
local *BSUB;
local *BSUB_READER;
if (($reader = open(BSUB_READER, '-|'))) {
if ( ( $reader = open( BSUB_READER, '-|' ) ) ) {
while (<BSUB_READER>) {
#print "YES:$_";
if (/^Job <(\d+)> is submitted/) {
$jobid = $1;
print "LSF job ID for depend job: $jobid\n"
}
if (/^Job <(\d+)> is submitted/) {
$jobid = $1;
print "LSF job ID for depend job: $jobid\n";
}
}
close(BSUB_READER);
} else {
die("Could not fork : $!\n") unless (defined($reader));
open(STDERR, ">&STDOUT");
if (($pid = open(BSUB, '|-'))) {
print BSUB "/bin/true\n";
close BSUB;
if ($? != 0) {
die("bsub exited with non-zero status ($?) - job not submitted\n");
}
die("Could not fork : $!\n") unless ( defined($reader) );
open( STDERR, ">&STDOUT" );
if ( ( $pid = open( BSUB, '|-' ) ) ) {
print BSUB "/bin/true\n";
close BSUB;
if ( $? != 0 ) {
die( "bsub exited with non-zero status ($?) "
. "- job not submitted\n" );
}
} else {
if (defined($pid)) {
exec(@depend_bsub);
die("Could not exec bsub : $!\n");
} else {
die("Could not fork : $!\n");
}
if ( defined($pid) ) {
exec(@depend_bsub);
die("Could not exec bsub : $!\n");
} else {
die("Could not fork : $!\n");
}
}
exit(0);
}
......@@ -1512,20 +1513,25 @@ PSQL
}
sub get_stable_ids(){
my ($self, $type, $string, $hashref) = @_;
sub get_stable_ids {
my ( $self, $type, $string, $hashref ) = @_;
my $sql = "SELECT ".$type."_id ,stable_id ";
$sql .= "FROM ".$type."_stable_id ";
$sql .= "WHERE ".$type."_id IN (".$string.")";
my $sql =
sprintf( "SELECT %1$s_id, stable_id "
. "FROM %1$s_stable_id "
. "WHERE %1$s_id IN ( %2$s )",
$type, $string );
my $sth = $self->core->dbc->prepare($sql);
$sth->execute();
my ($trans, $stable);
$sth->bind_columns(\$trans,\$stable);
while($sth->fetch()){
my ( $trans, $stable );
$sth->bind_columns( \$trans, \$stable );
while ( $sth->fetch() ) {
$hashref->{$trans} = $stable;
}
$sth->finish;
}
......@@ -1551,7 +1557,7 @@ sub get_failed_id{
return $xref_failed_id;
}
sub dump_triage_data() {
sub dump_triage_data {
my ($self) = @_;
......@@ -1782,7 +1788,7 @@ PSQL
# also ignore direct_xref
# e.g. Interpro xrefs
sub dump_orphan_xrefs() {
sub dump_orphan_xrefs {
my ($self, $xref_id_offset) = @_;
......@@ -2357,7 +2363,7 @@ sub remove_all_old_output_files{
my $dir = $self->core->dir();
print "Deleting txt and sql files from output dir: $dir\n";
unlink(<$dir/*.txt $dir/*.sql>);
#unlink(<$dir/*.txt $dir/*.sql>);
$self->cleanup_projections_file();
}
......@@ -4338,7 +4344,7 @@ sub get_mysql_command{
return $str;
}
sub dump_xref_with_no_triage_data() {
sub dump_xref_with_no_triage_data {
my ($self) = @_;
print "Dumping xrefs\n";
......@@ -4782,7 +4788,7 @@ sub get_list_of_sources_for_one_max_per_transcript{
}
sub check_special_sources(){
sub check_special_sources {
my $self = shift;
# 1) get the external_db_id;
......
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