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<p>I'm quite sure I don't have any problem with my proxy. There is
no proxy in my institute and I never configured one.</p>
<p>I tried a wget on the registry file with two computers. I can get
the file from any computer except the one on which I have problem
with biomart. <br>
</p>
<p>But I'm connected to the server. And then the server close the
connection without sending any data.</p>
<p>wget <a class="moz-txt-link-freetext" href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a><br>
--2017-04-04 16:56:37--
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a><br>
Resolving <a class="moz-txt-link-abbreviated" href="http://www.ensembl.org">www.ensembl.org</a> (<a class="moz-txt-link-abbreviated" href="http://www.ensembl.org">www.ensembl.org</a>)… 193.62.203.138,
193.62.203.137, 2001:630:206:4::137, ...<br>
Connection to <a class="moz-txt-link-abbreviated" href="http://www.ensembl.org">www.ensembl.org</a>
(<a class="moz-txt-link-abbreviated" href="http://www.ensembl.org">www.ensembl.org</a>)|193.62.203.138|:80… connected.<br>
HTTP request sent, awaiting response… No data received.<br>
Retrying.</p>
<p>Is it possible that this computer is blacklisted from the mart
server ?<br>
</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 15:28, Thomas Maurel a
écrit :<br>
</div>
<blockquote
cite="mid:A7DE1838-364F-4792-A6C9-915747B7BCC2@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="">I am afraid that I can’t help you further here as
something seems to be wrong with the proxy set up on your
computer. </div>
<div class="">Hopefully someone from your IT department will be
able to help from here. </div>
<div class=""><br class="">
</div>
<div class="">Kind Regards,</div>
<div class="">Thomas<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 4 Apr 2017, at 14:19, 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,</p>
<p class="">I tried your command on my computer and I
get 500. I tried on another computer and I get 200.</p>
<p class="">Then I checked the 'http_proxy' and the
'https_proxy' env variables, and they are the same on
both computers.</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 04/04/2017 à 14:29,
Thomas Maurel a écrit :<br class="">
</div>
<blockquote
cite="mid:4BEB7407-6FA0-45EA-B8A3-1A2025CC8AF3@ebi.ac.uk"
type="cite" 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
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 class="">
<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="">
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</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>
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<br class="">
<br class="">
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<br class="">
<pre class="" wrap="">_______________________________________________
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</pre>
</blockquote>
<br class="">
</div>
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Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br
class="">
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<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>
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<pre class="" wrap="">_______________________________________________
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</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
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class="">
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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>
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<br class="">
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<br>
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<br>
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