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<p>Thanks Thomas for your answer.</p>
<p>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>I previously had this error with the cache already generated when
querying version 87.</p>
<p>Best,</p>
<p>Julien<br>
</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>
</div>
<blockquote
cite="mid:DDE0D70C-49E9-404C-B15F-5E2C4D64551A@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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>
<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:
<a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">
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>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
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