2009/07/17 15:45:56 BioMart.Web:449:INFO> Restoring existing session
5b5d2aef618096f01d122bd0a82f7fe6
2009/07/17 15:45:56 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 15:45:56 BioMart.QueryRunner:179:WARN> NO FILTERS
2009/07/17 15:45:56 BioMart.Dataset.TableSet:852:INFO> MAIN TABLE:
kermits__emi_clone__main and i IS 0
2009/07/17 15:45:56 BioMart.Dataset.TableSet:906:INFO> COUNT SQL:
SELECT COUNT(*) FROM htgt_mart_alt.kermits__emi_clone__main main
2009/07/17 15:45:56 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 15:45:56 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits status_code main
2009/07/17 15:45:56 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits centre main
2009/07/17 15:45:56 BioMart.Dataset.TableSet:834:INFO> KEY: id_101_key
2009/07/17 15:45:56 BioMart.Dataset.TableSet:836:INFO> KEY TO MATCH:
id_103_key
2009/07/17 15:45:56 BioMart.Dataset.TableSet:834:INFO> KEY: id_103_key
2009/07/17 15:45:56 BioMart.Dataset.TableSet:836:INFO> KEY TO MATCH:
id_103_key
2009/07/17 15:45:56 BioMart.Dataset.TableSet:852:INFO> MAIN TABLE:
kermits__emi_event__main and i IS 1
2009/07/17 15:45:56 BioMart.Dataset.TableSet:906:INFO> COUNT SQL:
SELECT COUNT(DISTINCT main.id_102_key) FROM
htgt_mart_alt.kermits__emi_event__main main WHERE (main.status_code =
'GC') AND (main.centre = 'WTSI')
2009/07/17 15:45:56 martview:142:ERROR> ERROR: caught
BioMart::Exception: non-BioMart die(): Can't use an undefined value as
an ARRAY reference at /software/team87/biomart/biomart-0_7-prod/lib/
BioMart/Dataset/TableSet.pm line 917.
Stacktrace:
Exception::Class::Base::new /software/team87/biomart/biomart-0_7-
prod/cgi-bin/martview:125
ModPerl
::ROOT
::ModPerl
::Registry
::software_team87_biomart_biomart_2d0_7_2dprod_cgi_2dbin_martview
::handler /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-linux-
thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-linux-
thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /software/team87/HTGT/perl/lib/
site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /software/team87/HTGT/
perl/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:
31
ModPerl::Registry::handler -e:0
(eval) -e:0
2009/07/17 15:45:56 BioMart.Web:264:INFO> START PROCESSING TEMPLATE
error.tt
2009/07/17 15:45:56 BioMart.Web:271:INFO> !!!! 0 to get process
template error.tt and print to string
On 17 Jul 2009, at 15:42, Damian Smedley wrote:
so its cycling through the tables and keys in the correct reverse
order but somehow not picking up the fact that status uses
id_101_key. It should be bailing out of the loop at that stage. Can
you put in one more logger statement in the nested loop (see below)
- sorry, should have got you to do that straight away.
OUTER:foreach my $key (reverse @$keys){
$logger->info("KEY: $key");
foreach my $join_table (keys %joinTables){
$logger->info("KEY TO MATCH: $joinTables{$join_table}");
if (uc($joinTables{$join_table}) eq uc($key)){
last OUTER;
}
}
$i--;
On Fri, Jul 17, 2009 at 7:34 AM, Darren Oakley <[email protected]>
wrote:
Hi Damian,
Here's the output:
2009/07/17 15:33:21 BioMart.Web:271:INFO> !!!! 0.07 to get process
template main.tt and print to SCALAR
2009/07/17 15:33:31 BioMart.Web:449:INFO> Restoring existing session
c572e58e911da4fc2a47d5e28c8f437c
2009/07/17 15:33:31 BioMart.Web:449:INFO> Restoring existing session
c572e58e911da4fc2a47d5e28c8f437c
2009/07/17 15:33:31 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 15:33:31 BioMart.QueryRunner:179:WARN> NO FILTERS
2009/07/17 15:33:31 BioMart.Dataset.TableSet:851:INFO> MAIN TABLE:
kermits__emi_clone__main and i IS 0
2009/07/17 15:33:31 BioMart.Dataset.TableSet:905:INFO> COUNT SQL:
SELECT COUNT(*) FROM htgt_mart_alt.kermits__emi_clone__main main
2009/07/17 15:33:31 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 15:33:31 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits status_code main
2009/07/17 15:33:31 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits centre main
2009/07/17 15:33:31 BioMart.Dataset.TableSet:834:INFO> KEY:
id_101_key
2009/07/17 15:33:31 BioMart.Dataset.TableSet:834:INFO> KEY:
id_103_key
2009/07/17 15:33:31 BioMart.Dataset.TableSet:851:INFO> MAIN TABLE:
kermits__emi_event__main and i IS 1
2009/07/17 15:33:31 BioMart.Dataset.TableSet:905:INFO> COUNT SQL:
SELECT COUNT(DISTINCT main.id_102_key) FROM
htgt_mart_alt.kermits__emi_event__main main WHERE (main.status_code
= 'GC') AND (main.centre = 'WTSI')
2009/07/17 15:33:31 martview:142:ERROR> ERROR: caught
BioMart::Exception: non-BioMart die(): Can't use an undefined value
as an ARRAY reference at /software/team87/biomart/biomart-0_7-prod/
lib/BioMart/Dataset/TableSet.pm line 916.
Stacktrace:
Exception::Class::Base::new /software/team87/biomart/biomart-0_7-
prod/cgi-bin/martview:125
ModPerl
::ROOT
::ModPerl
::Registry
::software_team87_biomart_biomart_2d0_7_2dprod_cgi_2dbin_martview
::handler /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-
linux-thread-multi/ModPerl/RegistryCooker.pm:204
(eval) /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-
linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /software/team87/HTGT/perl/lib/
site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:
170
ModPerl::RegistryCooker::default_handler /software/team87/HTGT/
perl/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/
Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0
2009/07/17 15:33:31 BioMart.Web:264:INFO> START PROCESSING TEMPLATE
error.tt
2009/07/17 15:33:31 BioMart.Web:271:INFO> !!!! 0 to get process
template error.tt and print to string
On 17 Jul 2009, at 15:12, Damian Smedley wrote:
in the code in TableSet.pm around like 822 (in the _getCount
function) you need to add a couple of extra logger calls to sort
this out. Let us know what output you get
# identify the lowest key and set main accordingly
my $keys = $self->get('keys');
if (%joinTables){
$i = scalar @$keys - 1;
OUTER:foreach my $key (reverse @$keys){
$logger->info("KEY: $key");
foreach my $join_table (keys %joinTables){
if (uc($joinTables{$join_table}) eq uc($key)){
last OUTER;
}
}
$i--;
}
}
else{
$i = 0;# for when no join tables
}
my $mains = $self->get('mains');
$main = $$mains[$i];
$logger->info("MAIN TABLE: $main and i IS $i");
On Fri, Jul 17, 2009 at 5:30 AM, Darren Oakley <[email protected]>
wrote:
Hmmm,
This is strange... Running
SELECT COUNT(DISTINCT main.id_102_key) FROM
htgt_mart.kermits__emi_event__main main WHERE (main.status_code =
'GC') AND (main.centre = 'WTSI')
on the database actually throws an error:
Unknown column 'main.status_code' in 'where clause'
as the mart is looking at the wrong table. The attribute
'status_code' is only on the last table in the sequence
'kermits__emi_attempt__main' (the main tables in our mart go: clone
-> event -> attempt). Why would it be looking at the wrong table?
I've attached my MartEditor xmls for this dataset in case this
might help...
-- The Wellcome Trust Sanger Institute is operated by Genome
Research Limited, a charity registered in England with number
1021457 and a company registered in England with number 2742969,
whose registered office is 215 Euston Road, London, NW1 2BE.
The primary keys for the main tables are:
clone -> id_102_key
event -> id_103_key
attempt -> id_101_key
Cheers,
Daz
On 17 Jul 2009, at 12:39, Damian Smedley wrote:
Hi Darren,
What does that SQL do when you run it direct on the server - it
looks fine but seems like $ret = ${$sth->fetchrow_arrayref}[0]; is
giving the error i.e. no rows are coming back
Cheers
Damian
On Fri, Jul 17, 2009 at 4:10 AM, Darren Oakley <[email protected]>
wrote:
Hi Syed,
Here's the dump from my log file:
2009/07/17 12:07:53 BioMart.Web:449:INFO> Restoring existing
session d2e13b828c9c73a18e2b0d1808c66e8c
2009/07/17 12:07:53 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 12:07:53 BioMart.QueryRunner:179:WARN> NO FILTERS
2009/07/17 12:07:53 BioMart.Dataset.TableSet:900:INFO> COUNT SQL:
SELECT COUNT(*) FROM htgt_mart.kermits__emi_clone__main main
2009/07/17 12:07:53 BioMart.QueryRunner:169:WARN> NO ATTRIBUTES
2009/07/17 12:07:53 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits status_code main
2009/07/17 12:07:53 BioMart.QueryRunner:174:WARN> FILTER TABLE:
kermits centre main
2009/07/17 12:07:53 BioMart.Dataset.TableSet:900:INFO> COUNT SQL:
SELECT COUNT(DISTINCT main.id_102_key) FROM
htgt_mart.kermits__emi_event__main main WHERE (main.status_code
= 'GC') AND (main.centre = 'WTSI')
2009/07/17 12:07:53 martview:142:ERROR> ERROR: caught
BioMart::Exception: non-BioMart die(): Can't use an undefined
value as an ARRAY reference at /software/team87/biomart/bio
mart-0_7-prod/lib/BioMart/Dataset/TableSet.pm line 911.
Stacktrace:
Exception::Class::Base::new /software/team87/biomart/biomart-0_7-
prod/cgi-bin/martview:125
ModPerl
::ROOT
::ModPerl
::Registry
::software_team87_biomart_biomart_2d0_7_2dprod_cgi_2dbin_martview
::handler /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-
linux-threa
d-multi/ModPerl/RegistryCooker.pm:204
(eval) /software/team87/HTGT/perl/lib/site_perl/5.8.8/x86_64-
linux-thread-multi/ModPerl/RegistryCooker.pm:204
ModPerl::RegistryCooker::run /software/team87/HTGT/perl/lib/
site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/
RegistryCooker.pm:170
ModPerl::RegistryCooker::default_handler /software/team87/HTGT/
perl/lib/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/
Registry.pm:31
ModPerl::Registry::handler -e:0
(eval) -e:0
2009/07/17 12:07:53 BioMart.Web:264:INFO> START PROCESSING
TEMPLATE error.tt
2009/07/17 12:07:53 BioMart.Web:271:INFO> !!!! 0.03 to get process
template error.tt and print to string
Cheers,
Daz
On 17 Jul 2009, at 11:30, Syed Haider wrote:
Hi Darren,
when you hit the count button, please see what goes in the
error_log. you would need to switch on the logging to INFO from
FATAL in conf/log4perl.conf and reconfigure/restart.
Cheers
Syed
Darren Oakley wrote:
Hi All,
Sorry to disturb, but I'm getting an error which I just can't
figure out when doing a count on one of our Marts...
Here's the URL for the search:
http://www.sanger.ac.uk/htgt/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=kermits.default.attributes.sponsor
|kermits.default.attributes.marker_symbol|
kermits
.default
.attributes
.status&FILTERS=kermits.default.filters.status_code."GC"|
kermits.default.filters.centre."WTSI"&VISIBLEPANEL=resultspanel
The search works fine and returns results, but when I try to get a
count from this search (I'd like to know the number of genes with
this criteria), the mart throws the following error (both in
MartView and through the APIs):
Query ERROR: caught BioMart::Exception: non-BioMart die(): Can't
use an undefined value as an ARRAY reference at /software/team87/
biomart/biomart-0_7-prod/lib/BioMart/Dataset/TableSet.pm line 911.
To get the count, I'm hitting it via the rest api with the
following xml:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0"
uniqueRows="1" count="1" datasetConfigVersion="0.6">
<Dataset name="kermits" interface="default">
<Filter name="status_code" value="GC"/>
<Filter name="centre" value="WTSI"/>
</Dataset>
</Query>
Any idea what could be the issue here?
Thanks,
Daz
P.S. Forgot to let you all know - our new (preview) Mouse portal
at the Sanger is now running off Biomart: http://www.sanger.ac.uk/mouseportal/
(well, several biomarts really...) It's still in development,
and things can be flaky every now and then, so be gentle! ;)
--
The Wellcome Trust Sanger Institute is operated by Genome
ResearchLimited, a charity registered in England with number
1021457 and acompany registered in England with number 2742969,
whose registeredoffice is 215 Euston Road, London, NW1 2BE.
-- The Wellcome Trust Sanger Institute is operated by Genome
Research Limited, a charity registered in England with number
1021457 and a company registered in England with number 2742969,
whose registered office is 215 Euston Road, London, NW1 2BE.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
