Hi Thomas,
you do not have any meta tables in your mart. You must run MartEditor on
your mart, which creates these tables. Only then you can connect to the
mart through biomart-perl. Please see MartEditor section in docs. In
order to get going, run martj/bin/marteditor.sh
connect your mart, run 'Naive', run 'Export'.
Then try biomart-perl and it should work..
cheers
syed
On Thu, 2008-07-10 at 00:37 -0700, Thomas Juettemann wrote:
> mysql> show tables;
>
> +----------------------+
> | Tables_in_pdb |
> +----------------------+
> | bischet__links__main |
> +----------------------+
> 1 row in set (0.00 sec)
>
> the table contains more than 8000 entries.
> I removed the virtual scheme tags, no change.
>
> 2 rows in set (0.01 sec)
>
> mysql> describe bischet__links__main;
> +-------------------+-------------+------+-----+---------+----------------+
> | Field | Type | Null | Key | Default | Extra |
> +-------------------+-------------+------+-----+---------+----------------+
> | id_key | int(11) | NO | PRI | NULL | auto_increment |
> | uniprotID1 | varchar(50) | NO | PRI | | |
> | pdbID1 | char(4) | NO | PRI | | |
> | chainID1 | char(1) | NO | PRI | | |
> | eValue1 | double | NO | | | |
> | length1 | int(11) | NO | | | |
> | percentIdentity1 | float | NO | | | |
> | uniprotID2 | varchar(50) | NO | PRI | | |
> | pdbID2 | char(4) | NO | PRI | | |
> | chainID2 | char(1) | NO | PRI | | |
> | eValue2 | double | NO | | | |
> | length2 | int(11) | NO | | | |
> | percentIdentity2 | float | NO | | | |
> | experiments | mediumtext | NO | | | |
> | organismMT1 | varchar(50) | NO | | | |
> | organismMT2 | varchar(50) | NO | | | |
> | organismTP1 | varchar(50) | NO | | | |
> | organismTP2 | varchar(50) | NO | | | |
> | scop1 | varchar(50) | NO | | | |
> | scop2 | varchar(50) | NO | | | |
> | sequenceMT1 | mediumtext | NO | | | |
> | sequenceMT2 | mediumtext | NO | | | |
> | sequenceSeqResTP1 | mediumtext | NO | | | |
> | sequenceSeqResTP2 | mediumtext | NO | | | |
> | sequenceAtomTP1 | mediumtext | NO | | | |
> | sequenceAtomTP2 | mediumtext | NO | | | |
> | fastaCommentLine1 | mediumtext | NO | | | |
> | fastaCommentLine2 | mediumtext | NO | | | |
> +-------------------+---------
>
>
> Cheers,
> Thomas
>
>
> On Thu, Jul 10, 2008 at 00:23, Syed Haider <[EMAIL PROTECTED]> wrote:
> > Hi Thomas,
> >
> > Please try things,
> > 1- remove <virtaulSchema> tags and see if it works.
> >
> > 2- could you check if there are meta tables in your mart ? and if the
> > meta tables are present, any data in them ? Also if your __main table
> > has at least one data row in the mart.
> >
> >
> > cheers
> > syed
> >
> >
> > On Thu, 2008-07-10 at 00:21 -0700, Thomas Juettemann wrote:
> >> I tried these parameters from different servers, it worked fine. Are
> >> you spotting any stupid error there?
> >>
> >> I tried
> >>
> >>
> >> and the connection works fine.
> >>
> >> Any more ideas?
> >>
> >> Many thanks,
> >> Thomas
> >>
> >> On Thu, Jul 10, 2008 at 00:07, Syed Haider <[EMAIL PROTECTED]> wrote:
> >> > Hi Thomas,
> >> >
> >> > it looks ok already.
> >> > now the problem seems to be with your connection parameters in you
> >> > registry.
> >> >
> >> >
> >> > I would first try and configure with the registry martDBLocation.xml
> >> >
> >> > cheers
> >> > syed
> >> >
> >> > On Wed, 2008-07-09 at 16:27 -0700, Thomas Juettemann wrote:
> >> >> Hi Syed,
> >> >>
> >> >> many thanks for the answer.
> >> >>
> >> >> I check for the modules, I could not find any problems. I checked for
> >> >> the version, all have 2.011, I also used them in a script, no error
> >> >> from Perl.
> >> >> Do you want me to run a specific test?
> >> >>
> >> >> apxs2 is now installed
> >> >>
> >> >> just in case, the updated error:
> >> >>
> >> >> Do you want to install in API only mode [y/n] [n]:
> >> >>
> >> >> Checking prerequisites ...[Looks good]
> >> >>
> >> >> APACHE: /usr/sbin/httpd
> >> >> HOST: localhost
> >> >> PORT: 9002
> >> >> PROXY:
> >> >> LOCATION: biomart
> >> >>
> >> >> You can change the above configuration by editing
> >> >> "biomart-perl/conf/settings.conf"
> >> >>
> >> >> Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
> >> >> configuration
> >> >> Have Apache DSO-support and ModPerl library file present, configuring
> >> >> ModPerl in httpd.conf.
> >> >> Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
> >> >>
> >> >> Cached Registry Unavailable...
> >> >>
> >> >> Running Complete Clean...
> >> >>
> >> >> Optional setting for martUser in MartDBLocation location:bischet not
> >> >> defined - setting to default values
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >> >>
> >> >> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS
> >> >>
> >> >>
> >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >> >>
> >> >>
> >> >>
> >> >> ERROR something wrong with your registry: Problems with the retrieval
> >> >> of dataset configuration
> >> >> Please check:
> >> >> that your mart Registry files contains correct
> >> >> connection params,
> >> >> that you are using the correct version on XML::Simple,
> >> >> that BioMart databases contain a populated meta_conf
> >> >> tables and
> >> >> that you have set martUser correctly if you are running
> >> >> in restricted data
> >> >> access mode (populated meta_conf__user__dm)
> >> >>
> >> >> Trace begun at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> line 254
> >> >> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xa9348b8)',
> >> >> 'registryFile',
> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> line 377
> >> >> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xa9348b8)',
> >> >> 'registryFile',
> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> line 328
> >> >> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xa9348b8)',
> >> >> 'registryFile',
> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> line 168
> >> >> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xa9348b8)',
> >> >> 'registryFile',
> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
> >> >> line 64
> >> >> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> line 328
> >> >> eval {...} at
> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> line 327
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Jul 9, 2008 at 15:48, Syed Haider <[EMAIL PROTECTED]> wrote:
> >> >> > Thomas,
> >> >> > please test if the following CPAN modules are functional and do not
> >> >> > have broken or multiple installations:
> >> >> >
> >> >> > Compress::Zlib;
> >> >> > Compress::Raw::Zlib;
> >> >> > IO::Compress::Gzip;
> >> >> >
> >> >> >
> >> >> > Furthermore, you need to get apxs or apxs2. For details please see
> >> >> > docs.
> >> >> >
> >> >> > cheers
> >> >> > syed
> >> >> >
> >> >> >
> >> >> > On Wed, 2008-07-09 at 14:13 -0700, Thomas Juettemann wrote:
> >> >> >> Dear all,
> >> >> >>
> >> >> >> I am failing at the very begining, when running configure.pl:
> >> >> >>
> >> >> >> [camano] ~/compbio/programs/biomart/biomart-perl: perl
> >> >> >> bin/configure.pl -r conf/myRegistry.xml
> >> >> >>
> >> >> >> Do you want to install in API only mode [y/n] [n]:
> >> >> >>
> >> >> >> Checking prerequisites ...[Looks good]
> >> >> >> Subroutine BioMart::Web::Zlib::adler32 redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::crc32 redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::ZLIB_VERNUM redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at
> >> >> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> >> >> at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> >> >> line 20
> >> >> >> Use of uninitialized value in string ne at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 110.
> >> >> >> Use of uninitialized value in regexp compilation at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 112.
> >> >> >>
> >> >> >> rm
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/conf/templates/default/*.ttcrm:
> >> >> >> cannot remove
> >> >> >> `/projects/compbio/programs/biomart/biomart-perl/conf/templates/default/*.ttc':
> >> >> >> No such file or directory
> >> >> >>
> >> >> >> APACHE: /usr/sbin/httpd
> >> >> >> HOST: localhost
> >> >> >> PORT: 9002
> >> >> >> PROXY:
> >> >> >> LOCATION: biomart
> >> >> >>
> >> >> >> You can change the above configuration by editing
> >> >> >> "biomart-perl/conf/settings.conf"
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
> >> >> >> configuration
> >> >> >> Can't exec "/usr/sbin/apxs2": No such file or directory at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 173.
> >> >> >> Use of uninitialized value in scalar chomp at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 174.
> >> >> >> Use of uninitialized value in concatenation (.) or string at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 176.
> >> >> >> Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
> >> >> >> Libdir /projects/compbio/programs/biomart/biomart-perl/lib is not in
> >> >> >> @INC, adding to @INC
> >> >> >>
> >> >> >> Cached Registry Unavailable...
> >> >> >>
> >> >> >> Running Complete Clean...
> >> >> >>
> >> >> >>
> >> >> >> Optional setting for martUser in MartDBLocation location:bischet not
> >> >> >> defined - setting to default values
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >> >> >>
> >> >> >> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS
> >> >> >>
> >> >> >>
> >> >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >> >> >>
> >> >> >>
> >> >> >> ERROR something wrong with your registry: Problems with the
> >> >> >> retrieval
> >> >> >> of dataset configuration
> >> >> >> Please check:
> >> >> >> that your mart Registry files contains correct
> >> >> >> connection params,
> >> >> >> that you are using the correct version on XML::Simple,
> >> >> >> that BioMart databases contain a populated meta_conf
> >> >> >> tables and
> >> >> >> that you have set martUser correctly if you are
> >> >> >> running
> >> >> >> in restricted data
> >> >> >> access mode (populated meta_conf__user__dm)
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> Trace begun at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> >> line 254
> >> >> >> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xb1d3f48)',
> >> >> >> 'registryFile',
> >> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> >> line 377
> >> >> >> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xb1d3f48)',
> >> >> >> 'registryFile',
> >> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> >> line 328
> >> >> >> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xb1d3f48)',
> >> >> >> 'registryFile',
> >> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> >> >> line 168
> >> >> >> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xb1d3f48)',
> >> >> >> 'registryFile',
> >> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
> >> >> >> line 64
> >> >> >> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> >> >> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> >> >> 'action', 'cached', 'mode', 'memory') called at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 328
> >> >> >> eval {...} at
> >> >> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> >> >> line 327
> >> >> >>
> >> >> >>
> >> >> >> [camano] ~/compbio/programs/biomart/biomart-perl: perl -MXML::Simple
> >> >> >> -e 'print "$XML::Simple::VERSION\n"'
> >> >> >> 2.18
> >> >> >>
> >> >> >> Registry with user and password blanked:
> >> >> >> [camano] ~/compbio/programs/biomart/biomart-perl: cat
> >> >> >> conf/myRegistry.xml
> >> >> >> <?xml version="1.0" encoding="UTF-8"?>
> >> >> >> <!DOCTYPE MartRegistry>
> >> >> >> <MartRegistry>
> >> >> >> <virtualSchema name = "default">
> >> >> >> <MartDBLocation
> >> >> >> name = "bischet"
> >> >> >> displayName = "BISC-Het"
> >> >> >> databaseType = "mysql"
> >> >> >> host = "magnet.cse.ucsc.edu"
> >> >> >> port = "3306"
> >> >> >> database = "pdb"
> >> >> >> schema = ""
> >> >> >> user = "XXXX"
> >> >> >> password = "XXXXX"
> >> >> >> visible = "1"
> >> >> >> default = ""
> >> >> >> includeDatasets = ""
> >> >> >> />
> >> >> >> </virtualSchema>
> >> >> >> </MartRegistry>
> >> >> >>
> >> >> >> The connection connection works fine from the command line from any
> >> >> >> server. I tried it with schema = "pdb" and blank (like in example)
> >> >> >> There is no meta_conf table yet
> >> >> >>
> >> >> >> Any help greatly appreciated!
> >> >> >>
> >> >> >> Many thanks,
> >> >> >> Thomas
> >> >> > --
> >> >> > ======================================
> >> >> > Syed Haider.
> >> >> > EMBL-European Bioinformatics Institute
> >> >> > Wellcome Trust Genome Campus, Hinxton,
> >> >> > Cambridge CB10 1SD, UK.
> >> >> > ======================================
> >> >> >
> >> >> >
> >> > --
> >> > ======================================
> >> > Syed Haider.
> >> > EMBL-European Bioinformatics Institute
> >> > Wellcome Trust Genome Campus, Hinxton,
> >> > Cambridge CB10 1SD, UK.
> >> > ======================================
> >> >
> >> >
> > --
> > ======================================
> > Syed Haider.
> > EMBL-European Bioinformatics Institute
> > Wellcome Trust Genome Campus, Hinxton,
> > Cambridge CB10 1SD, UK.
> > ======================================
> >
> >
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
