Hi Jim, At a guess this was likely related to an issue with the new UniProt.org web site, which caused some UniProtKB data formats to be unavailable via dbfetch/WSDbfetch. The disappearance of the problem would be due to us deploying an updated dbfetch/WSDbfetch service which contains a workaround for the problem, thus restoring access to the UniProtKB data.
All the best, Hamish On 08/09/14 13:49, Dr JB Procter wrote: > Hello Ipek. > > I found I had the same problem as you - and then, strangely, I stopped > getting the error. > > Could you close Jalview then open it again and try retrieving sequences > once more ? > > Jim. > > On 08/09/2014 12:48, Ipek Birced wrote: >> >> Dear Dr Procter, >> >> >> >> Thank you so much for your help. I did what you indicated and it did >> not work once again… Here is the text from the console: >> >> >> >> Jalview Desktop 2.8.1 >> >> Build Date: 04 June 2014 >> >> Java version: 1.7.0_65 >> >> x86 Windows 7 6.1 >> >> INFO - Not enabling Google Tracking. >> >> INFO - Constructing news reader. >> >> INFO - Completed construction of reader. >> >> INFO - Saved last read date as 02-Sep-2014 09:27:08 >> >> INFO - Saved last read date as 02-Sep-2014 09:27:08 >> >> INFO - Saved last read date as 02-Sep-2014 09:27:08 >> >> INFO - Loading mapping descriptors from >> jar:http://www.jalview.org/webstart/jalview.jar!/uniprot_mapping.xml >> >> Error getUniprotEntries() Content is not allowed in prolog.{File: [not >> available]; line: 1; column: 1} >> >> Error getUniprotEntries() Content is not allowed in prolog.{File: [not >> available]; line: 1; column: 1} >> >> >> >> Many thanks and kind regards, >> >> >> >> Ipek >> >> >> >> *From:*James Procter >> *Sent:* 08 September 2014 12:34 >> *To:* Ipek Birced >> *Subject:* Re: Jalview bug report >> >> >> >> Hello Ipek - I'm very sorry to hear you are having problems ! >> On 08/09/2014 11:52, Ipek Birced wrote: >> >> >> >> I am writing to you to report a bug on Jalview. I tried emailing >> the jalview-discuss mailing list but although I subscribed my >> emails were not going through >> >> that's worrying in itself. I'll check that you're properly subscribed >> and confirm in a separate email. >> >> >> I am sorry to bother you with such a small thing, but I am quite >> pressed since I need Jalview for my project. >> >> no problem.. it's part of my role here in Dundee! >> >> The issue is that when I try to fetch sequences from Uniprot, a >> message pops up saying that it was not possible to fetch the >> sequence (for instance p00519). I have been working with JalView >> and doing the same routine for about a month, so I am not sure >> what is happening now. I have tried restarting the computer and >> uninstalling the desktop application, but nothing seems to work. >> My memory is also free (above 66%). >> >> >> OK. If you start Jalview again, then enable the Jalview Java Console >> (from the Tools menu). That will open a window showing some text >> output from the program. Then - try retrieving the Uniprot sequence >> again - if it doesn't work, cut and paste the text from the console >> window into an email and send it to me! >> >> Hear from you soon.. >> Jim -- ============================================================ Mr Hamish McWilliam, Web Production, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD United Kingdom URL: http://www.ebi.ac.uk/ ============================================================ _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
