Commit 0f52588c authored by Steve Trevanion's avatar Steve Trevanion
Browse files

removed blank lines

parent a9deebf1
......@@ -108,106 +108,63 @@ if($support->param('prune')){
if(check_for_backup_table()){
# backup table present
if($support->user_proceed("Replace the current table 'repeat_consensus' with the backup table 'repeat_consensus_backup'?")){
if($dbh->do("drop table repeat_consensus")){
if($dbh->do("create table repeat_consensus select * from repeat_consensus_backup")){
$support->log("prune (undo) was successful\n");
if($support->user_proceed("Replace the current table 'repeat_consensus' with the backup table 'repeat_consensus_backup'?")){
if($dbh->do("drop table repeat_consensus")){
if($dbh->do("create table repeat_consensus select * from repeat_consensus_backup")){
$support->log("prune (undo) was successful\n");
$support->log_stamped("Done.\n");
# finish logfile
$support->finish_log;
exit(0);
}
else{
$support->log_error("prune failed\n");
$support->finish_log;
exit(0);
}
}
else{
$support->log_error("prune failed\n");
else {
$support->log_error("prune failed\n");
}
}
else {
$support->log_error("prune failed\n");
}
}
else{
#user is aborting
print "aborting...\n";
$support->log_error("aborting...\n");
}
$support->log_error("aborting...\n");
}
}
else{
else{
print "Cannot do prune, as no backup table\n";
$support->log_error("Cannot do prune, as no backup table\n");
$support->log_error("Cannot do prune, as no backup table\n");
}
}
else{
# normal run
# check to see if the backup table 'repeat_consensus_backup' already exists
# check to see if the backup table 'repeat_consensus_backup' already exists
if(check_for_backup_table()){
#table already exists: ask user if OK to overwrite it
#table already exists: ask user if OK to overwrite it
if ($support->user_proceed("The backup table 'repeat_consensus_backup' already exists, OK to delete?")) {
if($dbh->do("drop table 'repeat_consensus_backup'")){
$support->log("deleted previous backup table\n");
make_backup_table();
}
else{
$support->log_error("tried but failed to delete previous backup table\n");
}
}
else{
# user won't allow removing the backup table
print "Aborting ...\n";
$support->log_error("User won't allow removal of backup table ... aborting program\n");
}
}else{
# table doesn't exist, therefore we can create it
make_backup_table();
}
}
# mouse fixes
if ($support->species eq 'Mus_musculus') {
$support->log("Making Vega mouse specific changes...\n");
......@@ -299,15 +256,11 @@ $support->finish_log;
sub make_backup_table{
if($dbh->do("create table repeat_consensus_backup select * from repeat_consensus")){
$support->log("backup table 'repeat_consensus_backup was created successfully\n");
$support->log("backup table 'repeat_consensus_backup was created successfully\n");
}
else{
$support->log_error("failed to create backup table 'repeat_consensus_backup'\n");
}
}
sub check_for_backup_table{
......@@ -318,18 +271,10 @@ sub check_for_backup_table{
foreach my $table(@tables){
#print "$table\n";
if($table eq '`repeat_consensus_backup`'){
if($table eq '`repeat_consensus_backup`'){
$found=1;
last;
}
last;
}
}
return $found;
}
\ No newline at end of file
}
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