<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Liam<div class=""><div class=""><div class=""><br class=""></div><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On 10 Oct 2016, at 14:44, Liam Thompson <<a href="mailto:dejmail@gmail.com" class="">dejmail@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Anne<br class=""><br class="">Thank you for looking at that. I can't confirm that it has been fixed as my bed file still doesn't validate. I am still getting "There was a problem uploading your data: File did not validate as format BED.<br class="">Please try again."<br class=""><br class="">The file seems to work fine on Genoverse, although UCSC is now giving me hassles.<br class=""><br class="">I have left a modified version at <a href="http://textuploader.com/d5ry1" class="">http://textuploader.com/d5ry1</a><br class=""></div></div></blockquote><div><br class=""></div><div>Sorry about that - I got called into a meeting and didn’t have a chance to reboot the servers to pick up the code fix. You should find that your files work now.</div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">It would be really helpful if the validation logic could output what it is about the validation that has failed, because as it stands I am just fiddling around in the dark. However I don't know how easy that is to do on your system.<br class=""></div></div></blockquote><div><br class=""></div><div>That’s a great suggestion, and one we’d like to implement, but at the moment we don’t have full validation across all formats so it would be of limited functionality. I will however put it into a development ticket, to be addressed in due course.</div><div><br class=""></div><div><br class=""></div><div><div>Cheers</div><div><br class=""></div><div>Anne</div></div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">Many thanks<br class="">Liam<br class=""></div></div></blockquote><div><br class=""></div><div><br class=""></div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class=""><br class=""><br class=""><br class="">On 2016-10-10 14:54, Anne Lyle wrote:<br class=""><blockquote type="cite" class="">Hi Liam<br class=""><br class="">As I suspected, there was a logic error in the validation code. I’m just pushing the fix out to our servers this afternoon.<br class=""><br class="">Regards<br class=""><br class="">Anne<br class=""><br class=""><br class=""><br class="">Anne Lyle<br class="">Senior Ensembl Web Developer<br class="">EMBL-EBI, Wellcome Trust Genome Campus<br class="">Cambridge CB10 1SD, UK<br class="">Tel: +44-(0)1223-494178<br class=""><br class=""><br class=""><br class=""><blockquote type="cite" class="">On 6 Oct 2016, at 14:29, Liam Thompson <<a href="mailto:dejmail@gmail.com" class="">dejmail@gmail.com</a>> wrote:<br class=""><br class="">Hi Anne<br class=""><br class="">I retried the GFF file on the Genoverse browser, and it loads fine and displays correctly (albeit in need of some tweaking), but still no luck on Ensembl.<br class=""><br class="">I have uploaded the file in case you want to see what is different with it, compared to the validator does.<br class=""><br class=""><a href="http://textuploader.com/dabl6" class="">http://textuploader.com/dabl6</a><br class=""><br class="">Kind regards<br class="">Liam<br class=""><br class="">On 2016-10-06 11:36, Anne Lyle wrote:<br class=""><blockquote type="cite" class="">Hi Liam<br class=""><br class="">BED should be fine - I’ll have a look at your file and see if there’s some reason it’s breaking our validator. The validation is quite new code, so there may be an error in its logic.<br class=""><br class="">Cheers<br class=""><br class="">Anne<br class=""><br class=""><br class=""><blockquote type="cite" class="">On 5 Oct 2016, at 19:01, Liam Thompson <dejmail@gmail.com> wrote:<br class=""><br class="">Hi Anne<br class=""><br class="">Thanks for the reply. I'm working from a Linux system, but not sure that<br class="">makes any difference.<br class=""><br class="">I have just tried it on Firefox v. 49, and the uploader just doesn't<br class="">seem to go anywhere, so I can confirm that behaviour. It also happens in<br class="">Private mode, so it's not a plugin.<br class=""><br class="">I tried in Google Chrome (53.0.2785.143 (64-bit)) normal and<br class="">Private/Incognito mode and the same thing happens.<br class=""><br class="">Is there another file format you would recommend that I can use to<br class="">display short sequences of interest in a track in the genome browser ?<br class=""><br class="">Kind regards<br class="">Liam<br class=""><br class=""><br class=""><blockquote type="cite" class="">------------------------------<br class=""><br class="">Message: 2<br class="">Date: Wed, 5 Oct 2016 17:14:57 +0100<br class="">From: Anne Lyle <annelyle@ebi.ac.uk><br class="">Subject: Re: [ensembl-dev] BED file format on custom track<br class="">To: Ensembl developers list <dev@ensembl.org><br class="">Message-ID: <3FBA2DBE-8EB3-4317-9785-A1FD61902772@ebi.ac.uk><br class="">Content-Type: text/plain; charset=utf-8<br class=""><br class="">Hi Liam<br class=""><br class="">Are you using Firefox (version 49) by any chance? We?ve seen some upload issues in this browser, so it could be related. If not, I?ll have a look at your file and see if there?s any reason why our parser isn?t reading it correctly.<br class=""><br class="">Cheers<br class=""><br class="">Anne<br class=""></blockquote><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""><br class=""></blockquote><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""><br class=""></blockquote><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>