I get all the results with no errors when running it manually.
On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote:
On 13 Feb 2007, at 12:23, Etai Jacob wrote: > Attached. > \ Hi Etai, can you run this in your db 'manually' and see if you are getting any results: SELECT main.start, main.stop, main.positionmb, main.pubmedid, main.method, main.comment, main.cytoband, main.hasdup, main.individual, main.knowngenes, main.landmark, main.literaturereference, main.locusid, main.variationid, main.variationtype FROM DGV.variation__variation__main main LIMIT 200 cheers, a. > 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 >> >> >> > >> >> >> -----BEGIN PGP SIGNATURE----- >> >> >> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >> >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >> >> >> >> >> iD8DBQFF0YZf4C5LeMEKA/QRAnfjAJ4ryJaiBgNwabuiZNFijhNEvTsz8wCfa9bu >> >> >> 1QBsgL/hNLndGODDdK9wmu8= >> >> >> =Ro2C >> >> >> -----END PGP SIGNATURE----- >> >> >> >> >> >> >> >> >> >> >> >> >> ---------------------------------------------------------------------- >> >> -- >> >> ------- >> >> Arek Kasprzyk >> >> EMBL-European Bioinformatics Institute. >> >> Wellcome Trust Genome Campus, Hinxton, >> >> Cambridge CB10 1SD, UK. >> >> Tel: +44-(0)1223-494606 >> >> Fax: +44-(0)1223-494468 >> >> >> ---------------------------------------------------------------------- >> >> -- >> >> ------- >> >> >> >> >> >> >> >> >> >> >> >> >> ---------------------------------------------------------------------- >> -- >> ------- >> Arek Kasprzyk >> EMBL-European Bioinformatics Institute. >> Wellcome Trust Genome Campus, Hinxton, >> Cambridge CB10 1SD, UK. >> Tel: +44-(0)1223-494606 >> Fax: +44-(0)1223-494468 >> ---------------------------------------------------------------------- >> -- >> ------- >> >> >> >> > <error.log> ------------------------------------------------------------------------ ------- Arek Kasprzyk EMBL-European Bioinformatics Institute. Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44-(0)1223-494606 Fax: +44-(0)1223-494468 ------------------------------------------------------------------------ -------
