#79 DBD::Pg::st execute failed

[Brandon King]

I was trying to upload an array design xml file, that I
created from GPR files when I ran into the /tmp/genex
not writable error... I just created a writable
/tmp/genex directory to bypass it. I then got the
following error after select 'Load Array Designs' from
the GeneX DB Array Design Loader Page:

error: DBD::Pg::st execute failed: server closed the
connection unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65.
context:
...
61:
62: $self->{update_sth}->bind_param(1,
$session->{serialized});
63: $self->{update_sth}->bind_param(2,
$session->{data}->{_session_id});
64:
65: $self->{update_sth}->execute;
66:
67: $self->{update_sth}->finish;
68: }
69:
...
code stack:
/usr/share/perl5/Apache/Session/Store/DBI.pm:65
/usr/share/perl5/Apache/Session.pm:508
/usr/share/perl5/Apache/Session.pm:462
/usr/share/perl5/HTML/Mason/Request.pm:1050
/var/www/genex/mason/syshandler:1
raw error

DBD::Pg::st execute failed: server closed the
connection unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65.

Trace begun at
/usr/share/perl5/HTML/Mason/Exceptions.pm line 128
HTML::Mason::Exceptions::rethrow_exception('DBD::Pg::st
execute failed: server closed the connection
unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line
65.^J') called at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65
Apache::Session::Store::DBI::update('Bio::Genex::StorePostgres=HASH(0x958e6bc)',
'Bio::Genex::SessionPostgres=HASH(0x958e6c8)') called
at /usr/share/perl5/Apache/Session.pm line 508
Apache::Session::save('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/Apache/Session.pm line 462
Apache::Session::DESTROY('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/HTML/Mason/Request.pm line 1050
eval
{...}('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/HTML/Mason/Request.pm line 1050
HTML::Mason::Request::comp(undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 746
HTML::Mason::Request::call_next('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /var/www/genex/mason/syshandler line 1
HTML::Mason::Commands::__ANON__('write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Component.pm line 134
HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH(0x94bc07c)',
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 1051
eval
{...}('HTML::Mason::Component::FileBased=HASH(0x94bc07c)',
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 1050
HTML::Mason::Request::comp(undef, undef, undef,
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 331
eval {...}(undef, undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 331
eval {...}(undef, undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 290
HTML::Mason::Request::exec('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 134
eval
{...}('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 134
HTML::Mason::Request::ApacheHandler::exec('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 792
HTML::Mason::ApacheHandler::handle_request('HTML::Mason::ApacheHandler=HASH(0x80fc94c)',
'Apache=SCALAR(0x81f6678)') called at
/usr/local/genex/etc/genex-handler.pl line 28
Bio::Genex::ApacheHandler::genex::handler('Apache=SCALAR(0x81f6678)')
called at /dev/null line 0
eval {...}('Apache=SCALAR(0x81f6678)') called at
/dev/null line 0

[Jason E. Stewart]

Logged In: YES
user_id=85550

Hey Brandon,

This is a wierd timing issue that is hard to solve.

Whenever this happens, simply refresh the page, and you will
get the correct status output. I want to fix this
eventually, but since it is harmless once you know what to
do, it's going to have to wait

[Jason E. Stewart]

Logged In: YES
user_id=85550

the timing issue was fixed a long time ago by reading the
mod_perl guide.

for the curious it has to do with properly handling fork()
under mod_perl