Hi Syed, I did the following:
Changed Web.pm line ~1850 to: $result_string = "xxx"; open(my $result_buffer, '>', $result_string); and it is working. Nevertheless, it writes "xxx" on the browser below the UI. Could you please elaborate what is the purpose of these lines when there is no assignment of a string to result_string? Should I leave it as "xxx" or something? Thanks, Etai On 2/14/07, Syed Haider <[EMAIL PROTECTED]> wrote:
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. ======================================
