On Tue, 2007-08-07 at 10:09 +0200, [EMAIL PROTECTED]
wrote:
>
> hi Syed,
>
> the output of ls -lh biomart-perl/conf/templates/cached/ is:
> total 636K
> -rw-r--r-- 1 ensembl users 56K Aug 6 17:01
> attributepanel_default.msd.tt
> -rw------- 1 ensembl users 149K Aug 6 17:01
> attributepanel_default.msd.ttc
> -rw-r--r-- 1 ensembl users 40K Aug 6 17:01
> attributepanel_default.uniprot.tt
> -rw------- 1 ensembl users 102K Aug 6 17:01
> attributepanel_default.uniprot.ttc
> -rw-r--r-- 1 ensembl users 36K Aug 6 17:01
> filterpanel_default.msd.tt
> -rw------- 1 ensembl users 70K Aug 6 17:01
> filterpanel_default.msd.ttc
> -rw-r--r-- 1 ensembl users 56K Aug 6 17:01
> filterpanel_default.uniprot.tt
> -rw------- 1 ensembl users 95K Aug 6 17:01
> filterpanel_default.uniprot.ttc
> Maybe ensembl-related entries are missing?
>
This looks fine, as your templates are being compiled correctly.
> > From your installation process what I can remotely guess is some
> paths
> > not being correctly mapped to the directory containing templates of
> your
> > datasets.
> in /lib/BioMart/Web.pm I see this:
> $tt_processor = Template->new({ INCLUDE_PATH => [
> $self->get_cached_tt_dir,
>
> $self->get_custom_tt_dir,
>
> $self->get_default_tt_dir ],
> DEFAULT =>
> 'notfound.tt',
> RELATIVE => 1,
>
> and $self->get_*_tt_dir seems to be correct too (conf/templates/...).
>
> > and see if all your directories have permissions assigned to
> apache.
>
> This is the case.
>
> > In addition, the problem seems to be an ENSEMBL integration problem
> and
> > you need to contact 'ensembl help desk' to get the best help on the
> > matter.
>
> I already wrote the helpdesk about this. They say they cannot help me
> unless I set up biomart standalone.
> (which I've done now, but the error does not appear there).
>
> Maybe you can help me in finding the problem because you know
> something about the biomart source-code?
I am willing to offer my best, but its good to ask ensembl help desk and
web team as well. They have carried out the integration and they know
their system quite well.
>
> Can you say something about these warnings:
> Use of uninitialized value in concatenation (.) or string
> at /u1/ET/ensembl/ensembl/biomart-perl/lib/BioMart/Web.pm line 1787.
> Use of uninitialized value in split
> at /u1/ET/ensembl/ensembl/biomart-perl/lib/BioMart/Web.pm line 1788.
> ?
> this is line 1787 in my Web.pm:
> $logger->debug("Got outputformats ".$atttree." for attpage
> $attributepage, in dataset $dataset_name");
The above warnings are normal, so dont worry about these :)
> I get this error: ERROR: requested template missing. Is there a way to
> find out which template is missing?
try using the following debug statements, might help
biomart/lib/Biomart/Web.pm:
find the following line:
# NOTE TO SELF: check if dirs exist & can be used
and add this afterwards.
print "<br/>", $self->get_cached_tt_dir," --- ",
$self->get_custom_tt_dir, " --- ",$self->get_default_tt_dir, " --- ";
also edit the file log4perl.conf under conf, and set the
log4perl.threshold = FATAL
to
log4perl.threshold = WARN
once done, kill and restart the server. your error_log should now have
detailed logging. and the print statement above should print the paths
to browser. hopefully this would help.
All the best.
syed
> Thanks and Best Regards,
>
> Felix Natter
> _________________________________________
>
> Bayer HealthCare AG
> BHC-PK
> Elberfeld, 0500
> Phone:
> Fax:
> E-mail: [EMAIL PROTECTED]
> Web: http://www.bayerhealthcare.com
>
> Vorstand: Arthur Higgins, Vorsitzender | Werner Baumann, Hartmut
> Klusik, Lykele van der Broek, Gunnar Riemann
> Vorsitzender des Aufsichtsrats: Richard Pott
> Sitz der Gesellschaft: Leverkusen | Eintragung: Amtsgericht Köln,
> HRB 49894
>
>
> ================================
> Die vorangehende e-mail inkl. jeglicher Anhänge beinhaltet
> Informationen, die vertraulich oder nicht für die Öffentlichkeit
> bestimmt sein könnten. Sie ist nur für den/die designierten Empfänger
> bestimmt. Sollten Sie nicht der designierte Empfänger sein,
> informieren Sie bitte den Absender und löschen Sie die Nachricht aus
> Ihrem System. Gebrauch, Verbreitung, Verteilung oder Reproduktion
> dieser Nachricht sind untersagt und können rechtswidrig sein.
>
>
> ================================
> The preceding e-mail message (including any attachments) contains
> information that may be confidential, or constitute non-public
> information. It is intended to be conveyed only to the designated
> recipient(s). If you are not an intended recipient of this message,
> please notify the sender by replying to this message and then delete
> it from your system. Use, dissemination, distribution, or
> reproduction of this message by unintended recipients is not
> authorized and may be unlawful.
>
>
>
> Syed Haider <[EMAIL PROTECTED]>
>
> 06.08.2007 19:20
>
>
> An
> [EMAIL PROTECTED]
> Kopie
> [email protected], [EMAIL PROTECTED], Arek Kasprzyk <[EMAIL PROTECTED]>
> Thema
> Re: Antwort: Re:
> [mart-dev]
> Problems with
> biomart 0.6 as
> part
> ofensembl
>
>
>
>
>
>
>
>
> Hi Felix
> nice to know that your biomart independent installation works fine.
> What
> >From your installation process what I can remotely guess is some
> paths
> not being correctly mapped to the directory containing templates of
> your
> datasets.
>
> please check whats in the following directory:
>
> ls -lh biomart-perl/conf/templates/cached/
>
> and see if all your directories have permissions assigned to apache.
> In addition, the problem seems to be an ENSEMBL integration problem
> and
> you need to contact 'ensembl help desk' to get the best help on the
> matter.
>
> Kind Regards
> Syed
>
>
> On Mon, 2007-08-06 at 18:43 +0200, [EMAIL PROTECTED]
> wrote:
> >
> > hello Syed,
> >
> > I just installed biomart 0.6 standalone and it is working. But
> > unfortunately I still get "ERROR: requested template missing" when
> > running biomart in ensembl.
> >
> > here is the output of configure.pl:
> > [EMAIL PROTECTED]:/u1/ET/ensembl/ensembl/biomart-perl> perl
> > bin/configure.pl -r
> > conf/registryURLPointer.xml --clean
> >
> > Do you want to install in API only mode [y/n] [n]:
> >
> > Checking prerequisites ...[Looks good]
> >
> > APACHE: /u1/ET/ensembl/ensembl/apache2/bin/httpd
> > HOST: localhost
> > PORT: 9002
> > Use of uninitialized value in print at
> >
> > /u1/ET/ensembl/branch-ensembl-45/biomart-perl/bin/configureBioMart.pl
> > line 116.
> > PROXY:
> > LOCATION: biomart
> >
> > You can change the above configuration by editing
> > "biomart-perl/conf/settings.conf"
> >
> >
> >
> > Got usable Apache in /u1/ET/ensembl/ensembl/apache2/bin/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
> > Libdir /u1/ET/ensembl/branch-ensembl-45/biomart-perl/lib is not in
> > @INC, adding to
> >
> > @INC
> >
> > Connection parameters of [UNIPROT PROTOTYPE (EBI)] [ OK ]
> > Connection parameters of [MSD PROTOTYPE (EBI)] [ OK ]
> >
> >
> >
> >
> > [NEW CONFIGURATION] .... WITH MEMORY [default]
> > default ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location
> >
> > .......................... (WEB) www.biomart.org:80 ............ ->
> > upgrading to
> >
> > 0.6 ... OK
> > default ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence
> >
> > .......................... (WEB) www.biomart.org:80 ............ ->
> > upgrading to
> >
> > 0.6 ... OK
> > default ... UNIPROT PROTOTYPE (EBI) .. 003/006 ...
> > uniprot_cell_component
> >
> > .................... (WEB) www.biomart.org:80 ............ ->
> > upgrading to 0.6 ...
> >
> > OK
> > default ... UNIPROT PROTOTYPE (EBI) .. 004/006 ...
> > uniprot_biol_process
> >
> > ...................... (WEB) www.biomart.org:80 ............ ->
> > upgrading to 0.6
> >
> > ... OK
> > default ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot
> >
> > ................................... (WEB)
> > www.biomart.org:80 ............ ->
> >
> > upgrading to 0.6 ... OK
> > default ... UNIPROT PROTOTYPE (EBI) .. 006/006 ...
> > uniprot_mol_function
> >
> > ...................... (WEB) www.biomart.org:80 ............ ->
> > upgrading to 0.6
> >
> > ... OK
> > default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd
> >
> > ....................................... (WEB)
> > www.biomart.org:80 ............ ->
> >
> > upgrading to 0.6 ... OK
> > Setting possible links between datasets
> > ....(scanning) 100%
> > ....(linking) 100%
> > ....(sorting) 100%
> > ....(clustering) 7/7
> > ....(resolving) 100%
> > Building templates for visible datasets
> > .... 100%
> > Compiling templates for visible datasets
> > [1/2] Attribute Panel of Dataset.. :uniprot
> > [1/2] Filter Panel of Dataset..... :uniprot
> > [2/2] Attribute Panel of Dataset.. :msd
> > [2/2] Filter Panel of Dataset..... :msd
> >
> > ========================================
> > this is the content of conf/settings.conf:
> > #########################################################
> > ################ httpd.conf settings ####################
> >
> > [httpdSettings]
> > #apacheBinary=/usr/sbin/httpd
> > apacheBinary=/u1/ET/ensembl/ensembl/apache2/bin/httpd
> > #serverHost=test.biomart.org
> > serverHost=localhost
> > port=9002
> > #port=3128
> > # to use proxying set the proxy port below (even if its 80) and set
> > serverHost as
> >
> > your proxy host
> > #proxy=3128
> > location=biomart
> >
> >
> > # Colours settings for MARTVIEW
> > # A good online tool help with picking a palette is;
> > # http://slayeroffice.com/tools/color_palette/
> > [cssSettings]
> >
> > # The default theme, based on a 6-level grey scale from black to
> > white.
> > colour_saturation0=black
> > colour_saturation20=black
> > colour_saturation40=#666666
> > colour_saturation60=#CCCCCC
> > colour_saturation80=#E5E5E5
> > colour_saturation100=white
> >
> > # The blue theme used for WormMart
> > #colour_saturation0=black
> > #colour_saturation20=#5870A3
> > #colour_saturation40=#8294BA
> > #colour_saturation60=#D5DBE8
> > #colour_saturation80=#EFF1F6
> > #colour_saturation100=white
> >
> > font_colour_top_bottom_menubar = #000
> > font_colour_rest = #000
> > summary_panel_bgcolour = #ffffdd
> > main_panel_bgcolour = #fff
> > top_bottom_menubar_bgcolour = #efefef
> > blocks_outline_colour = #efefef
> > summary_panel_highlight_border_colour = #ffd9af
> > summary_panel_highlight_bgcolour = #ffd9af
> >
> >
> > # These settings relate to the text displayed in the interface drop
> > downs
> >
> > [aliases]
> > Schema=- CHOOSE SCHEMA -
> > Database=- CHOOSE DATABASE -
> > Dataset=- CHOOSE DATASET -
> >
> >
> > # If an attribute URL is specified relatively such as '/geneview/?=%
> > s'
> > # then by default this will be used relative to the current host
> > # However if you set exturl below then this will be prefixed
> > # to these URLs
> >
> > [urlPrefixes]
> > exturl=http://byzvse:1235
> >
> >
> > # These settings are used to control how the background
> > # results jobs are managed.
> > #
> > # Set resultsDirCount to the number of results directories
> > # you want to use. Then, use resultsDir1, resultsDir2 etc.
> > # to assign names for these directories, up to resultsDirN
> > # where N is the value of resultsDirCount. Background jobs
> > # will be assigned to each of these resultsDir locations
> > # by a hash function which is intended to distribute them
> > # evenly.
> > #
> > # Use resultsDir to specify where
> > # files containing results from background jobs are stored.
> > # This folder must (a) exist and (b) be writable by the
> > # owner of the web server process.
> > #
> > # The enable setting should have a value of 'yes'
> > # if you want background jobs to be available to the user.
> > # Any other value, including non-lowercase versions of 'yes'
> > # will turn background jobs off.
> >
> > [background]
> > resultsDirCount=1
> > #resultsDir1=/ebi/www/biomart/test/files
> > resultsDir1=/u1/ET/ensembl/ensembl/biomart-results
> > enable=yes
> >
> > # Mail settings are used for informing users when their
> > # background tasks are finished. The mailerType defines
> > # the way in which mail is sent, as understood by
> > # Mail::Mailer. For details of how to control this, see:
> > #
> > # http://search.cpan.org/dist/MailTools/Mail/Mailer.pm
> > #
> > # The from address is the address that messages will
> > # appear to be from.
> >
> > [mailSettings]
> > mailerType=sendmail
> > subject=Your BioMart results are ready
> > [EMAIL PROTECTED]
> >
> > # These settings relate to sessions.
> > #
> > # The expire setting relates to how long sessions will live
> > # on disk for. If not accessed for a period of time longer than
> > # this, then the session will be dropped. Aliases are:
> > #
> > # +-----------+---------------+
> > # | alias | meaning |
> > # +-----------+---------------+
> > # | s | Second |
> > # | m | Minute |
> > # | h | Hour |
> > # | d | Day |
> > # | w | Week |
> > # | M | Month |
> > # | y | Year |
> > # +-----------+---------------+
> > #
> > # Driver could have values based on where you want the session to
> be
> > # stored. default or no value assigned is set to Berkeley DB
> > implementation.
> > # All possible values could be:
> > # driver=
> > # driver=default
> > # driver=files
> > # driver=mysql
> > # driver=oracle
> > # a database table must already exist with any name but with strict
> > columnName/Types
> > # EXAMPLES
> > # ========== MySQL ============
> > # first create the table as
> > # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session
> > LONGTEXT NOT NULL )
> >
> > ;
> > # then the following settings should follow under [sessions]
> > # driver=mysql
> > # dsn=DBI:mysql:database=YOU_DATABASE_NAME;host=127.0.0.1;port=3306
> > # user=root
> > # pass=
> > # ========== ORACLE ============
> > # first create the table as
> > # CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session
> CLOB
> > NOT NULL ) ;
> > # then the following settings should follow under [sessions]
> > # driver=oracle
> > # dsn=dbi:Oracle:host=172.22.70.89;sid=XE;port=1521
> > # user=root
> > # pass=
> >
> >
> > [sessions]
> > expire=12h
> > driver=default
> >
> > # Web Service Logging options
> > [webserviceLogging]
> > mode=ON
> > log_query=ON
> > log_IP=ON
> >
> > =====================================================
> > biomart-perl/conf/error_log does not exist as I am using the ensembl
> > web server.
> > Here is the relevant part of the ensembl apache2 error log:
> >
> > [Mon Aug 06 18:31:52 2007] [notice] Apache/2.2.4 (Unix)
> mod_perl/2.0.3
> > Perl/v5.8.5 configured -- resuming normal operations
> > INIT WEB MODULE...
> >
> at /u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/PageStub.pm
> line 27.
> > Use of uninitialized value in concatenation (.) or string
> > at /u1/ET/ensembl/ensembl/biomart-perl/lib/BioMart/Web.pm line 1784
> \
> > .
> > INIT WEB MODULE...
> >
> at /u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/PageStub.pm
> line 27.
> >
> > These are the relevant lines in Web.pm:
> > my $allAttributeTrees =
> > $registry->getConfigTreeForDataset($dataset_name, $schema_nam\
> > e, 'default')->getAllAttributeTrees();
> > my $atttree =
> > $allAttributeTrees->[0]; # first one is supposed to be the default
> > one
> > $logger->debug("Got
> > outputformats ".$atttree." for attpage $attributepage, in dataset\
> > $dataset_name");
> >
> > Thanks for your help and Best Regards,
> >
> > Felix Natter
> > _________________________________________
> >
> > Bayer HealthCare AG
> > BHC-PK
> > Elberfeld, 0500
> > Phone:
> > Fax:
> > E-mail: [EMAIL PROTECTED]
> > Web: http://www.bayerhealthcare.com
> >
> > Vorstand: Arthur Higgins, Vorsitzender | Werner Baumann, Hartmut
> > Klusik, Lykele van der Broek, Gunnar Riemann
> > Vorsitzender des Aufsichtsrats: Richard Pott
> > Sitz der Gesellschaft: Leverkusen | Eintragung: Amtsgericht
> Köln,
> > HRB 49894
> >
> >
> > ================================
> > Die vorangehende e-mail inkl. jeglicher Anhänge beinhaltet
> > Informationen, die vertraulich oder nicht für die Öffentlichkeit
> > bestimmt sein könnten. Sie ist nur für den/die designierten
> Empfänger
> > bestimmt. Sollten Sie nicht der designierte Empfänger sein,
> > informieren Sie bitte den Absender und löschen Sie die Nachricht aus
> > Ihrem System. Gebrauch, Verbreitung, Verteilung oder Reproduktion
> > dieser Nachricht sind untersagt und können rechtswidrig sein.
>
> >
> >
> > ================================
> > The preceding e-mail message (including any attachments) contains
> > information that may be confidential, or constitute non-public
> > information. It is intended to be conveyed only to the designated
> > recipient(s). If you are not an intended recipient of this message,
> > please notify the sender by replying to this message and then delete
> > it from your system. Use, dissemination, distribution, or
> > reproduction of this message by unintended recipients is not
> > authorized and may be unlawful.
> >
> >
> >
> > Syed Haider <[EMAIL PROTECTED]>
> > Gesendet von:
> > [EMAIL PROTECTED]
> >
> > 03.08.2007 12:00
> >
> >
> > An
> > [EMAIL PROTECTED]
> > Kopie
> > [email protected]
> > Thema
> > Re: [mart-dev]
> > Problems with
> > biomart 0.6 as
> > part ofensembl
> >
> >
> >
> >
> >
> >
> >
> >
> > Hi Felix
> >
> > could you please forward me
> >
> > - the onscreen response once you execute
> >
> > perl bin/configure.pl -r conf/registryURLPointer.xml --clean
> >
> > - your biomart-perl/conf/settings.conf
> >
> > - conf/error_log
> >
> > and most important of all, have you tried installing biomart
> > independently first and see if it works for you, then we can take a
> > step
> > forward to get this to work with Ensembl.
> > for instructions about how to install biomart independently, follow
> > DOCS
> > tab on www.biomart.org
> >
> > for any further help, free to write back.
> >
> > kind regards
> > syed
> >
> >
> >
> >
> > On Fri, 2007-08-03 at 11:51 +0200, [EMAIL PROTECTED]
> > wrote:
> > > perl bin/configure.pl -r conf/registryURLPointer.xml
> > --
> > ======================================
> > 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.
======================================
