Re: [Catalyst] Postgresql database with non default -public- schema
On 20/10/10 18:40, Hetényi Csaba wrote: The automatic schema generation is a very convenient feature -especially in developing phase, when table structures often change. I hear you!... I have the exact same issue. So far writing my own script that harnesses the power of DBIX::Class::Schema::Loader to run over each schema in my DB seems to be working out well... althou, due to some horrific column naming my dbic objects have a some ugly accessor names... I feel I 'might' start manually managing my ::Result:: files :( ___ List: Catalyst@lists.scsys.co.uk Listinfo: http://lists.scsys.co.uk/cgi-bin/mailman/listinfo/catalyst Searchable archive: http://www.mail-archive.com/catalyst@lists.scsys.co.uk/ Dev site: http://dev.catalyst.perl.org/
[Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run
I have a Catalyst model that runs a system command as part of a search facility. The system call only takes a fraction of a second so is processed inline and this all works fine when tested outside of Catalyst and when called under the Catalyst standalone server. However, when I deploy it to my FastCGI environment I have problems - everything seems to work fine apart from the results of the system call. The system call is (give or take): IPC::Cmd::run( command = [qw/ blastall -d sequences.db -i input.fa -o output.results /], verbose = 0, timeout = 10, ); When run under the test server the file 'output.results' contains the results of the search: gi|5524211|gb|AAD441661|pdb|3cx5C00 45.26 285 154 1 1 283 91 375 4e-73267 gi|5524211|gb|AAD441661|pdb|2e74A00 33.33 99 65 1 21 118 117 215 9e-16 77.0 gi|5524211|gb|AAD441661|pdb|2ih2A01 34.78 23 15 0 115 137 85 107 4.0 25.0 ... When the same application is being run under FastCGI the file is created but is empty. The system call was originally being wrapped with IPC::Cmd (via MooseX::Role::Cmd). I checked what happened when I explicitly used IPC::Run my ($in, $out, $err); my $success = IPC::Run::run [qw/ blastall -d sequences.db -i input.fa -o output.results /], \$in, \$out, \$err, IPC::Run::timeout( 10 ); This works under the test server, but throws the following error under FastCGI: Can't locate object method FILENO via package FCGI::Stream at /home/ian/perl5/lib/perl5/IPC/Run.pm line 1115. If I bypass IPC::* and run the system command with backticks then it seems to work fine under both the test server and FastCGI. However the system call is happening a long way away from Catalyst - I don't really want to hard code this with backticks just to get it working under FastCGI. There seems to be a few different things going on here - I'm not sure exactly where the problem lies or what might be a red herring - would be grateful if anyone can help point me in the right direction. Cheers, Ian Running FastCGI server on my desktop on port 3001: script/my_app_fastcgi.pl -l bsmlx53:3001 -n 3 -p my-app.pid -d Forwarding requests there from external facing server with the following config: VirtualHost *:80 ServerName test.foo.com DocumentRoot/home/ian/My-App/trunk/ ErrorLoglogs/test.foo.com-error_log FastCgiExternalServer /tmp/my-app.fcgi -host bsmlx53:3001 Alias /static /home/ian/My-App/trunk/root/static Alias / /tmp/my-app.fcgi/ /VirtualHost Modules: Catalyst::Runtime (5.80029) IPC::Run (0.89) FCGI (0.67) ___ List: Catalyst@lists.scsys.co.uk Listinfo: http://lists.scsys.co.uk/cgi-bin/mailman/listinfo/catalyst Searchable archive: http://www.mail-archive.com/catalyst@lists.scsys.co.uk/ Dev site: http://dev.catalyst.perl.org/
Re: [Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run
You may want to check your version of FCGI. There are previous reports of related issues, which seem to be an interaction between IPC::* modules expectations of standard input/output/error, and FCGI, which fakes them. See http://www.mail-archive.com/po...@openbsd.org/msg16948.html for an example. In my FCGI, the FILENO method is present, but this appears to have been added in version 0.67_01 on 20 Dec 2009 - this is pretty recent and your Perl may not include it. --S Stuart Watt ARM Product Developer Information Balance On 10/21/2010 2:43 PM, Ian Sillitoe wrote: I have a Catalyst model that runs a system command as part of a search facility. The system call only takes a fraction of a second so is processed inline and this all works fine when tested outside of Catalyst and when called under the Catalyst standalone server. However, when I deploy it to my FastCGI environment I have problems - everything seems to work fine apart from the results of the system call. The system call is (give or take): IPC::Cmd::run( command = [qw/ blastall -d sequences.db -i input.fa -o output.results /], verbose = 0, timeout = 10, ); When run under the test server the file 'output.results' contains the results of the search: gi|5524211|gb|AAD441661|pdb|3cx5C00 45.26 285 154 1 1 283 91 375 4e-73267 gi|5524211|gb|AAD441661|pdb|2e74A00 33.33 99 65 1 21 118 117 215 9e-16 77.0 gi|5524211|gb|AAD441661|pdb|2ih2A01 34.78 23 15 0 115 137 85 107 4.0 25.0 ... When the same application is being run under FastCGI the file is created but is empty. The system call was originally being wrapped with IPC::Cmd (via MooseX::Role::Cmd). I checked what happened when I explicitly used IPC::Run my ($in, $out, $err); my $success = IPC::Run::run [qw/ blastall -d sequences.db -i input.fa -o output.results /], \$in, \$out, \$err, IPC::Run::timeout( 10 ); This works under the test server, but throws the following error under FastCGI: |Can't locate object method FILENO via package FCGI::Stream at /home/ian/perl5/lib/perl5/IPC/Run.pm line 1115. | If I bypass IPC::* and run the system command with backticks then it seems to work fine under both the test server and FastCGI. However the system call is happening a long way away from Catalyst - I don't really want to hard code this with backticks just to get it working under FastCGI. There seems to be a few different things going on here - I'm not sure exactly where the problem lies or what might be a red herring - would be grateful if anyone can help point me in the right direction. Cheers, Ian Running FastCGI server on my desktop on port 3001: script/my_app_fastcgi.pl http://my_app_fastcgi.pl -l bsmlx53:3001 -n 3 -p my-app.pid -d Forwarding requests there from external facing server with the following config: VirtualHost *:80 ServerName test.foo.com http://test.foo.com DocumentRoot/home/ian/My-App/trunk/ ErrorLoglogs/test.foo.com-error_log FastCgiExternalServer /tmp/my-app.fcgi -host bsmlx53:3001 Alias /static /home/ian/My-App/trunk/root/static Alias / /tmp/my-app.fcgi/ /VirtualHost Modules: Catalyst::Runtime (5.80029) IPC::Run (0.89) FCGI (0.67) -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://antispam.infobal.com/cgi-bin/learn-msg.cgi?id=7751128072.AE451 ___ List: Catalyst@lists.scsys.co.uk Listinfo: http://lists.scsys.co.uk/cgi-bin/mailman/listinfo/catalyst Searchable archive: http://www.mail-archive.com/catalyst@lists.scsys.co.uk/ Dev site: http://dev.catalyst.perl.org/ ___ List: Catalyst@lists.scsys.co.uk Listinfo: http://lists.scsys.co.uk/cgi-bin/mailman/listinfo/catalyst Searchable archive: http://www.mail-archive.com/catalyst@lists.scsys.co.uk/ Dev site: http://dev.catalyst.perl.org/
Re: [Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run
I've run into this problem with FCGI too. Our solution at the time, since the
fileno call was in an internal API, was to skip it when STDOUT was tied.
Getting an updated FCGI instead sounds like a happier thing.
I notice this in current FCGI comments:
# Some things (e.g. IPC::Run) use fileno to determine if a filehandle is open,
# so we return a defined, but meaningless value. (-1 being the error return
# value from the syscall in c, meaning it can never be a valid fd no)
# Probably a better alternative would be to return the fcgi stream fd.
sub FILENO { -1 }
On Oct 21, 2010, at 12:29 PM, Stuart Watt wrote:
You may want to check your version of FCGI. There are previous reports of
related issues, which seem to be an interaction between IPC::* modules
expectations of standard input/output/error, and FCGI, which fakes them. See
http://www.mail-archive.com/po...@openbsd.org/msg16948.html for an example.
In my FCGI, the FILENO method is present, but this appears to have been added
in version 0.67_01 on 20 Dec 2009 - this is pretty recent and your Perl may
not include it.
--S
Stuart Watt
ARM Product Developer
Information Balance
On 10/21/2010 2:43 PM, Ian Sillitoe wrote:
I have a Catalyst model that runs a system command as part of a search
facility. The system call only takes a fraction of a second so is processed
inline and this all works fine when tested outside of Catalyst and when
called under the Catalyst standalone server. However, when I deploy it to my
FastCGI environment I have problems - everything seems to work fine apart
from the results of the system call.
The system call is (give or take):
IPC::Cmd::run(
command = [qw/ blastall -d sequences.db -i input.fa -o
output.results /],
verbose = 0,
timeout = 10,
);
When run under the test server the file 'output.results' contains the
results of the search:
gi|5524211|gb|AAD441661|pdb|3cx5C00 45.26 285 154 1
1 283 91 375 4e-73267
gi|5524211|gb|AAD441661|pdb|2e74A00 33.33 99 65 1
21 118 117 215 9e-16 77.0
gi|5524211|gb|AAD441661|pdb|2ih2A01 34.78 23 15 0
115 137 85 107 4.0 25.0
...
When the same application is being run under FastCGI the file is created but
is empty.
The system call was originally being wrapped with IPC::Cmd (via
MooseX::Role::Cmd). I checked what happened when I explicitly used IPC::Run
my ($in, $out, $err);
my $success = IPC::Run::run [qw/ blastall -d sequences.db -i input.fa -o
output.results /], \$in, \$out, \$err, IPC::Run::timeout( 10 );
This works under the test server, but throws the following error under
FastCGI:
Can't locate object method FILENO via package FCGI::Stream at
/home/ian/perl5/lib/perl5/IPC/Run.pm line 1115.
If I bypass IPC::* and run the system command with backticks then it seems
to work fine under both the test server and FastCGI. However the system call
is happening a long way away from Catalyst - I don't really want to hard
code this with backticks just to get it working under FastCGI.
There seems to be a few different things going on here - I'm not sure
exactly where the problem lies or what might be a red herring - would be
grateful if anyone can help point me in the right direction.
Cheers,
Ian
Running FastCGI server on my desktop on port 3001:
script/my_app_fastcgi.pl -l bsmlx53:3001 -n 3 -p my-app.pid -d
Forwarding requests there from external facing server with the following
config:
VirtualHost *:80
ServerName test.foo.com
DocumentRoot/home/ian/My-App/trunk/
ErrorLoglogs/test.foo.com-error_log
FastCgiExternalServer /tmp/my-app.fcgi -host bsmlx53:3001
Alias /static /home/ian/My-App/trunk/root/static
Alias / /tmp/my-app.fcgi/
/VirtualHost
Modules:
Catalyst::Runtime (5.80029)
IPC::Run (0.89)
FCGI (0.67)
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Re: [Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run
heidi brandenburg wrote on 10/21/2010 03:02 PM:
I've run into this problem with FCGI too. Our solution at the time, since the
fileno call was in an internal API, was to skip it when STDOUT was tied.
Getting an updated FCGI instead sounds like a happier thing.
I notice this in current FCGI comments:
# Some things (e.g. IPC::Run) use fileno to determine if a filehandle is open,
# so we return a defined, but meaningless value. (-1 being the error return
# value from the syscall in c, meaning it can never be a valid fd no)
# Probably a better alternative would be to return the fcgi stream fd.
sub FILENO { -1 }
In addition, you may want to look at SVN::Class, which does some fileno
hackery for this same reason.
http://cpansearch.perl.org/src/KARMAN/SVN-Class-0.16/lib/SVN/Class.pm
--
Peter Karman . http://peknet.com/ . pe...@peknet.com
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Re: [Catalyst] Running system commands under FastCGI with IPC::Cmd / IPC::Run
On 22 October 2010 05:43, Ian Sillitoe i...@sillit.com wrote: I have a Catalyst model that runs a system command as part of a search facility. The system call only takes a fraction of a second so is processed inline and this all works fine when tested outside of Catalyst and when called under the Catalyst standalone server. However, when I deploy it to my FastCGI environment I have problems - everything seems to work fine apart from the results of the system call. The system call is (give or take): IPC::Cmd::run( command = [qw/ blastall -d sequences.db -i input.fa -o output.results /], verbose = 0, timeout = 10, ); I recall that IPC::Run certainly has known-issues when used under FastCGI, and I'm guessing they extend to IPC::Cmd too. Have a look at IPC::Run::SafeHandles which I think got around it. Toby ___ List: Catalyst@lists.scsys.co.uk Listinfo: http://lists.scsys.co.uk/cgi-bin/mailman/listinfo/catalyst Searchable archive: http://www.mail-archive.com/catalyst@lists.scsys.co.uk/ Dev site: http://dev.catalyst.perl.org/
