<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="">Dear Julien,<div class=""><br class=""></div><div class=""><div class="">Please note that we have moved to a new system this release to generate and populate the ensembl marts filters/attributes. As a result, we have improved the consistency of our mart across the vertebrate and other ensembl divisions. The following filters and attributes names have changed and will affect script using the BiomaRt package.</div><div class="">Please find the full list below or on our FTP site: <a href="ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt" class="">ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt</a></div><div class=""><br class=""></div><div class="">If you replace “zfin_id” with “zfin_id_id” in your script, it should work again.</div><div class=""><div class=""><div class="">Also please make sure to set the $action variable from “cached” to “clean”, your script will then re-generate the cache using our newly released 88 version.</div><div class=""><br class=""></div></div></div><div class="">Kind Regards,</div><div class="">Thomas</div></div><div><blockquote type="cite" class=""><div class="">On 3 Apr 2017, at 13:35, Julien Fumey <<a href="mailto:julien.fumey@i2bc.paris-saclay.fr" class="">julien.fumey@i2bc.paris-saclay.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear ensembl team,<br class=""><br class="">I'm trying to get data from Zv10 using the BioMart Perl API. When I try to build the registry, I obtain the following error.<br class=""><br class="">Problems with the web server: 500 Server closed connection without sending any data back. No datasets available with given parameters for Location: ENSEMBL_MART_ENSEMBL<br class=""><br class=""> Problems with the retrieval of dataset configuration<br class=""> Please check:<br class=""> that your mart Registry files contains correct connection params,<br class=""> that you are using the correct version on XML::Simple,<br class=""> that BioMart databases contain a populated meta_conf tables and<br class=""> that you have set martUser correctly if you are running in restricted data<br class=""> access mode (populated meta_conf__user__dm)<br class=""><br class=""><br class="">I copy paste the registry from here : <a href="http://www.ensembl.org/biomart/martservice?type=registry" class="">http://www.ensembl.org/biomart/martservice?type=registry</a><br class=""><br class="">Is there a problem with the server ? Or maybe I did something wrong ?<br class=""><br class="">Cheers,<br class=""><br class="">-- <br class="">Julien Fumey, Ph.D.<br class=""><a href="mailto:julien.fumey@i2bc.paris-saclay.fr" class="">julien.fumey@i2bc.paris-saclay.fr</a><br class="">I2BC High Throughput Sequencing Platform<br class="">CNRS Gif Bat 26<br class="">Avenue de la Terrasse<br class="">91198 Gif-sur-Yvette<br class="">France<br class="">+33.(0)1.69.82.31.90<br class="">platform mail: sequencage-i2bc@i2bc.paris-saclay.fr<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=""></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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