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<p>Thanks Thomas,</p>
<p>I tried your command on my computer and I get 500. I tried on
another computer and I get 200.</p>
<p>Then I checked the 'http_proxy' and the 'https_proxy' env
variables, and they are the same on both computers.</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 04/04/2017 à 14:29, Thomas Maurel a
écrit :<br>
</div>
<blockquote
cite="mid:4BEB7407-6FA0-45EA-B8A3-1A2025CC8AF3@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="">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 moz-do-not-send="true"
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
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 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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=""> 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 moz-do-not-send="true"
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="">
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class="moz-txt-link-abbreviated"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br
class="">
Posting guidelines and subscribe/unsubscribe
info: <a moz-do-not-send="true"
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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="">
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<br class="">
<pre class="" wrap="">_______________________________________________
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Ensembl Blog: <a moz-do-not-send="true" 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 moz-do-not-send="true"
href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br
class="">
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
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class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br
class="">
Ensembl Blog: <a moz-do-not-send="true"
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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
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