On Wed, 2007-02-14 at 16:18 +0200, Etai Jacob wrote: > Hi, > > It didn't help. > > Below is the log file.
Hi Etai, Try executing the following code as an independent perl script, and let me know what you get. #===================================== use strict; use warnings; use English; my $result_string = ""; open(my $result_buffer, '>', \$result_string); print $result_buffer "\n ======= BIOMART ======== \n"; close($result_buffer); print $result_string; #===================================== Regards Syed > Thanks, > Etai > > BioMart.Dataset.TableSet:891:WARN> COUNT SQL: SELECT COUNT(*) FROM > DGV.variation__variation__main main > BioMart.QueryRunner:132:WARN> ATTRIBUTE: variation start main > BioMart.QueryRunner:132:WARN> ATTRIBUTE: variation stop main > BioMart.QueryRunner:132:WARN> ATTRIBUTE: variation variationtype main > BioMart.QueryRunner:150:WARN> NO FILTERS > BioMart.Dataset.TableSet:733:WARN> QUERY SQL: SELECT main.start, > main.stop, main.variationtype FROM DGV.variation__variation__main main > LIMIT 200 > Can't open a reference at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 1852. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 248. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 225. > print() on closed filehandle $result_buffer at > /home/etai/.html/biomart/biomart-perl/lib/BioMart/QueryRunner.pm line > 269. > > > On 2/14/07, Syed Haider <[EMAIL PROTECTED]> wrote: > > On Wed, 2007-02-14 at 09:02 +0000, Richard Holland wrote: > > > -----BEGIN PGP SIGNED MESSAGE----- > > > Hash: SHA1 > > > > > > I think in this case though that this is the cause of the user not > > > seeing any results? > > > > > > > > > Syed Haider wrote: > > > > I am confused. > > > > > > > > (To SYED...: do you have any ideas? MartView/MartService on this user's > > > > own server is throwing exceptions like this: Can't open a reference at > > > > <blah blah>/lib/BioMart/Web.pm line 1850.) > > > > > > > > > > > >> Yeah, I know whats this all about. Its a warning not causing any harm > > > >> due > > > >> passing a string to a file which sometimes is not assigned a value. > > > >> Will > > > >> be fixed soon. I dont sense if this should cause any serious troubles. > > > >> Cheers > > > >> Syed > > > > > > > > Hi Etai > > > > Could you add the following line just above your line 1850 of Web.pm > > > > $result_string = ""; > > > > just for reference, line 1850: > > > > open(my $result_buffer, '>', \$result_string); > > > > and see if results panel turns up. > > > > Cheers > > Syed > > > > > > > > > > > > > > > > > > > cheers, > > > > Richard > > > > > > > > Etai Jacob wrote: > > > >>>> Yes we have, the last version:( > > > >>>> > > > >>>> On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: > > > >>>> Hmm. Well it must be a CPAN module then... not sure exactly as I've > > > >>>> not > > > >>>> seen this problem before. The line I quoted is definitely the line > > > >>>> that > > > >>>> is causing your results to be blank though. > > > >>>> > > > >>>> You could check to see if you have IO::Stringy installed from CPAN. > > > >>>> It > > > >>>> provides the functions that back up the open() method. Let me know > > > >>>> if it > > > >>>> is installed or not - if not, install it and retry the request > > > >>>> (you'll > > > >>>> have to restart the MartView server after installing it). > > > >>>> > > > >>>> cheers, > > > >>>> Richard > > > >>>> > > > >>>> Etai Jacob wrote: > > > >>>>> We have perl 5.85 installed. > > > >>>>> Thanks, > > > >>>>> Etai > > > >>>>> On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: > > > >>>>> This line of the log indicates the problem: > > > >>>>> Can't open a reference at > > > >>>>> /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 1850. > > > >>>>> This is a Perl version incompatibility. It is trying to open a > > > >>>>> filehandle over a string then write the results to that string. > > > >>>>> This is > > > >>>>> not possible in versions of Perl older than 5.8. > > > >>>>> You need to upgrade your Perl to at least 5.8 for this to work. > > > >>>>> cheers, > > > >>>>> Richard > > > >>>>> Etai Jacob wrote: > > > >>>>>> Attached. > > > >>>>>> On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: > > > >>>>>>> On 13 Feb 2007, at 11:49, Etai Jacob wrote: > > > >>>>>>>> No errors. > > > >>>> > > > >>>>>>> I meant ... could you send us the contents > > > >>>>>>> of this file while you are doing your query? > > > >>>>>>> we need to see what comes back from the > > > >>>>>>> database or webserver when you do it > > > >>>> > > > >>>>>>> cheers, > > > >>>>>>> a. > > > >>>> > > > >>>> > > > >>>> > > > >>>>>>>> On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: > > > >>>>>>>>> On 13 Feb 2007, at 11:23, Etai Jacob wrote: > > > >>>>>>>>> > > > >>>>>>>>>> Hi, > > > >>>>>>>>>> > > > >>>>>>>>>> My answers below. > > > >>>>>>>>> Hi Etai, > > > >>>>>>>>> maybe we need a little bit more debugging there. > > > >>>>>>>>> Could you change the > > > >>>>>>>>> > > > >>>>>>>>> log4perl.threshold = FATAL > > > >>>>>>>>> > > > >>>>>>>>> to > > > >>>>>>>>> > > > >>>>>>>>> log4perl.threshold = WARN > > > >>>>>>>>> > > > >>>>>>>>> in biomart-perl/conf/log4perl.conf > > > >>>>>>>>> > > > >>>>>>>>> restart the server and see what you get > > > >>>>>>>>> in the error_log? > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> cheers, > > > >>>>>>>>> a. > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>>>> What do you mean by not seeing any results? Do you mean that > > > >>>> you > > > >>>>>>>>> get > > > >>>>>>>>>>> an error message? > > > >>>>>>>>>> I don't get any error messages, not on the web browser > > > >>>>> (firefox or > > > >>>>>>>>>> explorer) and not in the error log file of the httpd. > > > >>>>>>>>>> > > > >>>>>>>>>> Or you see the results page but the table only has > > > >>>>>>>>>>> headings? > > > >>>>>>>>>> No heading. > > > >>>>>>>>>> > > > >>>>>>>>>> What happens exactly? > > > >>>>>>>>>> When pressing the "results" it waits a second and then when > > > >>>>> "Done" > > > >>>>>>>>> the > > > >>>>>>>>>> page stays blank (except the default GUI of the martview on > > > >>>>> the left > > > >>>>>>>>>> side of the page). > > > >>>>>>>>>> > > > >>>>>>>>>>> Could you try a query with no filters at all and just one or > > > >>>> two > > > >>>>>>>>>>> attributes to see if you get results? > > > >>>>>>>>>> Yes I tried with many combinations. Nothing. > > > >>>>>>>>>> > > > >>>>>>>>>> I tried other biomart web interface, > > > >>>>>>>>>> http://www.dictybase.org/biomart/martview/, to see whether I > > > >>>>> have a > > > >>>>>>>>>> problem with the browser or JVM but it works fine. > > > >>>>>>>>>> > > > >>>>>>>>>> Thanks, > > > >>>>>>>>>> Etai > > > >>>>>>>>>> > > > >>>>>>>>>> > > > >>>>>>>>>>> Etai Jacob wrote: > > > >>>>>>>>>>>> Hi, > > > >>>>>>>>>>>> > > > >>>>>>>>>>>> I am trying to execute few basic queries using the biomart > > > >>>> web > > > >>>>>>>>>>>> interface with the default configurations (as instructed in > > > >>>>> the > > > >>>>>>>>>>>> installation guide). > > > >>>>>>>>>>>> I don't get to see any results on the browser even though > > > >>>>> at the > > > >>>>>>>>>>> count > > > >>>>>>>>>>>> stage I see that there are relevant entries (i.e. 1/3967). > > > >>>>>>>>>>>> > > > >>>>>>>>>>>> What could be the problem? > > > >>>>>>>>>>>> Thanks, > > > >>>>>>>>>>>> Etai > > > >>>>>>>>>>>> > > > >>>> > > > >>>> > > > >> > > > > > > > ====================================== > > > > Syed Haider. > > > > EMBL-European Bioinformatics Institute > > > > Wellcome Trust Genome Campus, Hinxton, > > > > Cambridge CB10 1SD, UK. > > > > ====================================== > > > > > > -----BEGIN PGP SIGNATURE----- > > > Version: GnuPG v1.4.2.2 (GNU/Linux) > > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > > > > > iD8DBQFF0tAV4C5LeMEKA/QRAlx0AJ9CWHlRwxfcEOkklOfHxRsnaJDNyACeK6as > > > FKa6LW0dRQtxk6hKD9UmkQ4= > > > =jTFK > > > -----END PGP SIGNATURE----- > > -- > > ====================================== > > 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. ======================================
