<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></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="">We think that you might have a proxy that is getting in the way here.</div><div class="">If you run the following command:</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class="">perl -MLWP::UserAgent -e 'print LWP::UserAgent->new()->get("<a href="http://www.ensembl.org/biomart/martservice?type=registry" class="">http://www.ensembl.org/biomart/martservice?type=registry</a>")->code()'</div></blockquote><div class="">You should get back “200” which mean that all is working fine. If you get back “500”, this mean that your proxy setting might be wrong or something is going on with your proxy server. Usually the proxy url is set up in the following variable “http_proxy”.</div><div class=""><br class=""></div><div class="">Hope this helps,</div><div class="">Kind Regards,</div><div class="">Thomas<br class=""><div><blockquote type="cite" class=""><div class="">On 3 Apr 2017, at 15:58, 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="">
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type" class="">
<div bgcolor="#FFFFFF" text="#000000" class=""><p class="">Thanks Thomas for your answer.</p><p class="">I already changed "zfin_id" to "zfin_id_id" and re-generate the
cache to use version 88. But I still get the error when generating
the cache.</p><p class="">I previously had this error with the cache already generated when
querying version 87.</p><p class="">Best,</p><p class="">Julien<br class="">
</p>
<pre class="moz-signature" cols="72">Julien Fumey, Ph.D.
<a class="moz-txt-link-abbreviated" href="mailto:julien.fumey@i2bc.paris-saclay.fr">julien.fumey@i2bc.paris-saclay.fr</a>
I2BC High Throughput Sequencing Platform
CNRS Gif Bat 26
Avenue de la Terrasse
91198 Gif-sur-Yvette
France
+33.(0)1.69.82.31.90
platform mail: <a class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a></pre>
<div class="moz-cite-prefix">Le 03/04/2017 à 16:54, Thomas Maurel a
écrit :<br class="">
</div>
<blockquote cite="mid:DDE0D70C-49E9-404C-B15F-5E2C4D64551A@ebi.ac.uk" type="cite" class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" 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 moz-do-not-send="true" 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 class="">
<blockquote type="cite" class="">
<div class="">On 3 Apr 2017, at 13:35, Julien Fumey <<a moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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: <a class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a><br class="">
<br class="">
_______________________________________________<br class="">
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br class="">
Posting guidelines and subscribe/unsubscribe info:
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">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>
</div>
<br class="">
<br class="">
<fieldset class="mimeAttachmentHeader"></fieldset>
<br class="">
<pre wrap="" class="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br class="">
</div>
_______________________________________________<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></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>
</div>
<br class=""></div></body></html>