<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Paolo,<div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 26 May 2016, at 13:59, Paolo Cozzi <<a href="mailto:paolo.cozzi@itb.cnr.it" class="">paolo.cozzi@itb.cnr.it</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><br class="">Dear Kieron,<br class=""><br class="">I've performed some test on the Info Species endpoint and now it seems to me consistent, thank you. For the Ld endpoints I will wait for your updates.<br class=""><br class="">Regarding biomart services, I found problem running biomart script locally: by using a registry downloaded at <a href="http://www.ensembl.org/biomart/martservice?type=registry" class="">http://www.ensembl.org/biomart/martservice?type=registry</a> I couldn't cache local data, and I got "Problems with the web server: 500 read timeout" error. Could you check also biomart server status?<br class=""></div></div></blockquote>I am afraid that we had some issues with our BioMart servers on Thursday, could you please try again?</div><div>If you still have issues, could you please share your BioMart Perl script with me so that I can have a look.<br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">I found on the documentation that the version of biomart-perl scripts is 0.7. Are any recent updates of biomart perl API available? and where I could find them?<br class=""></div></div></blockquote>In Ensembl, we are still using biomart version 0.7 so I would stick to this version when you are querying the Ensembl marts with the Biomart Perl API. </div><div>You can find the most recent updates of Biomart Perl API (biomart 0.9) on the following page: <a href="http://www.biomart.org/download.html" class="">http://www.biomart.org/download.html</a></div><div><br class=""></div><div>Hope this helps,</div><div>Best Regards,</div><div>Thomas<br class=""><blockquote type="cite" class=""><div class=""><div class=""><br class="">Many thanks,<br class=""><br class="">Best regards,<br class=""><br class="">Paolo<br class=""><br class=""><br class="">Il 26/05/2016 12:52, Kieron Taylor ha scritto:<br class=""><blockquote type="cite" class="">Dear Paolo,<br class=""><br class="">Thank you for reporting your troubles. The LD endpoint is rather fragile but we are working to improve it in future releases. The style and scope of the LD computation does not lend itself to our web architecture, so we're trying hard to make it reliable. We've been forced to drop the LD window size limits, but you can still trigger occasional 400 errors. Keep an eye on our changelog and do keep reporting bugs.<br class=""><br class="">Regarding getting different results for the same query, some patches have been applied to the servers this morning. Can you attempt to reproduce your differing species results? I believe one of the servers was out of step with the others.<br class=""><br class="">Regards,<br class=""><br class="">Kieron<br class=""><br class=""><br class="">Kieron Taylor PhD.<br class="">Ensembl Developer<br class=""><br class="">EMBL, European Bioinformatics Institute<br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><br class=""><blockquote type="cite" class="">On 25 May 2016, at 14:38, Paolo Cozzi <<a href="mailto:paolo.cozzi@itb.cnr.it" class="">paolo.cozzi@itb.cnr.it</a>> wrote:<br class=""><br class=""><br class="">Dear all,<br class=""><br class="">When accessing some endpoint of ensembl REST server I got some transient errors, for example by doing the sample request using the three Linkage Disequilibrium endpoints I may find a 400 Status code and "Something went wrong while fetching from LDFeatureContainerAdaptor" message or "something bad has happened" message.<br class=""><br class="">Other times, by querying info/species endpoint with "curl '<a href="http://rest.ensembl.org/info/species?division=ensembl'" class="">http://rest.ensembl.org/info/species?division=ensembl'</a> -H 'Content-type:application/json'" I can obtain almost indentical results, for example for c.savignyi (inside the whole response) I could have:<br class=""><br class="">{u'accession': None,<br class=""> u'aliases': [u'ciosav',<br class=""> u'51511',<br class=""> u'ciona savignyi',<br class=""> u'csavignyi',<br class=""> u'c.savignyi',<br class=""> u'csav',<br class=""> u'sea squirt ciona savignyi'],<br class=""> u'assembly': u'CSAV2.0',<br class=""> u'common_name': u'Sea squirt Ciona savignyi',<br class=""> u'display_name': u'C.savignyi',<br class=""> u'division': u'Ensembl',<br class=""> u'groups': [u'core', u'otherfeatures'],<br class=""> u'name': u'ciona_savignyi',<br class=""> u'release': 84,<br class=""> u'taxon_id': u'51511'}<br class=""><br class="">And<br class="">{u'accession': None,<br class=""> u'aliases': [u'ciosav',<br class=""> u'51511',<br class=""> u'ciona savignyi',<br class=""> u'csavignyi',<br class=""> u'c.savignyi',<br class=""> u'csav',<br class=""> u'sea squirt ciona savignyi',<br class=""> u'ciona_savignyi csav2.0'],<br class=""> u'assembly': u'CSAV2.0',<br class=""> u'common_name': u'Sea squirt Ciona savignyi',<br class=""> u'display_name': u'C.savignyi',<br class=""> u'division': u'Ensembl',<br class=""> u'groups': [u'core', u'otherfeatures'],<br class=""> u'name': u'ciona_savignyi',<br class=""> u'release': 84,<br class=""> u'taxon_id': u'51511'}<br class="">(The second result has the 'ciona_savignyi csav2.0' alias added). Could you give me some suggestions?<br class=""><br class="">Best Regards,<br class=""><br class="">Paolo<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=""></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=""></blockquote><br class=""><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=""></div></div></blockquote></div><br class=""><div class="">
<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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