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. ======================================
