[ensembl-dev] Error 500 using BioMart perl API
Julien Fumey
julien.fumey at i2bc.paris-saclay.fr
Tue Apr 4 16:10:11 BST 2017
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.
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.
But I'm connected to the server. And then the server close the
connection without sending any data.
wget http://www.ensembl.org/biomart/martservice?type=registry
--2017-04-04 16:56:37--
http://www.ensembl.org/biomart/martservice?type=registry
Resolving www.ensembl.org (www.ensembl.org)… 193.62.203.138,
193.62.203.137, 2001:630:206:4::137, ...
Connection to www.ensembl.org (www.ensembl.org)|193.62.203.138|:80…
connected.
HTTP request sent, awaiting response… No data received.
Retrying.
Is it possible that this computer is blacklisted from the mart server ?
Julien
Julien Fumey, Ph.D.
julien.fumey at i2bc.paris-saclay.fr
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: sequencage-i2bc at i2bc.paris-saclay.fr
Le 04/04/2017 à 15:28, Thomas Maurel a écrit :
> Dear Julien,
>
> 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.
> Hopefully someone from your IT department will be able to help from here.
>
> Kind Regards,
> Thomas
>> On 4 Apr 2017, at 14:19, Julien Fumey
>> <julien.fumey at i2bc.paris-saclay.fr
>> <mailto:julien.fumey at i2bc.paris-saclay.fr>> wrote:
>>
>> Thanks Thomas,
>>
>> I tried your command on my computer and I get 500. I tried on another
>> computer and I get 200.
>>
>> Then I checked the 'http_proxy' and the 'https_proxy' env variables,
>> and they are the same on both computers.
>>
>> Julien
>>
>> Julien Fumey, Ph.D.
>> julien.fumey at i2bc.paris-saclay.fr
>> 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:sequencage-i2bc at i2bc.paris-saclay.fr
>> Le 04/04/2017 à 14:29, Thomas Maurel a écrit :
>>> Dear Julien,
>>>
>>> We think that you might have a proxy that is getting in the way here.
>>> If you run the following command:
>>>
>>> perl -MLWP::UserAgent -e 'print
>>> LWP::UserAgent->new()->get("http://www.ensembl.org/biomart/martservice?type=registry")->code()'
>>>
>>> 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”.
>>>
>>> Hope this helps,
>>> Kind Regards,
>>> Thomas
>>>> On 3 Apr 2017, at 15:58, Julien Fumey
>>>> <julien.fumey at i2bc.paris-saclay.fr
>>>> <mailto:julien.fumey at i2bc.paris-saclay.fr>> wrote:
>>>>
>>>> Thanks Thomas for your answer.
>>>>
>>>> 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.
>>>>
>>>> I previously had this error with the cache already generated when
>>>> querying version 87.
>>>>
>>>> Best,
>>>>
>>>> Julien
>>>>
>>>> Julien Fumey, Ph.D.
>>>> julien.fumey at i2bc.paris-saclay.fr
>>>> 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:sequencage-i2bc at i2bc.paris-saclay.fr
>>>> Le 03/04/2017 à 16:54, Thomas Maurel a écrit :
>>>>> Dear Julien,
>>>>>
>>>>> 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.
>>>>> Please find the full list below or on our FTP site:
>>>>> ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt
>>>>>
>>>>> If you replace “zfin_id” with “zfin_id_id” in your script, it
>>>>> should work again.
>>>>> 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.
>>>>>
>>>>> Kind Regards,
>>>>> Thomas
>>>>>> On 3 Apr 2017, at 13:35, Julien Fumey
>>>>>> <julien.fumey at i2bc.paris-saclay.fr
>>>>>> <mailto:julien.fumey at i2bc.paris-saclay.fr>> wrote:
>>>>>>
>>>>>> Dear ensembl team,
>>>>>>
>>>>>> 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.
>>>>>>
>>>>>> 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
>>>>>>
>>>>>> Problems with the retrieval of dataset configuration
>>>>>> Please check:
>>>>>> that your mart Registry files contains correct
>>>>>> connection params,
>>>>>> that you are using the correct version on XML::Simple,
>>>>>> that BioMart databases contain a populated
>>>>>> meta_conf tables and
>>>>>> that you have set martUser correctly if you are
>>>>>> running in restricted data
>>>>>> access mode (populated meta_conf__user__dm)
>>>>>>
>>>>>>
>>>>>> I copy paste the registry from here :
>>>>>> http://www.ensembl.org/biomart/martservice?type=registry
>>>>>>
>>>>>> Is there a problem with the server ? Or maybe I did something wrong ?
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> --
>>>>>> Julien Fumey, Ph.D.
>>>>>> julien.fumey at i2bc.paris-saclay.fr
>>>>>> <mailto:julien.fumey at i2bc.paris-saclay.fr>
>>>>>> 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: sequencage-i2bc at i2bc.paris-saclay.fr
>>>>>>
>>>>>> _______________________________________________
>>>>>> Dev mailing list Dev at ensembl.org
>>>>>> Posting guidelines and subscribe/unsubscribe info:
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>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>>> --
>>>>> Thomas Maurel
>>>>> Bioinformatician - Ensembl Production Team
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>> European Molecular Biology Laboratory
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridge CB10 1SD
>>>>> United Kingdom
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing listDev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>
>>>> _______________________________________________
>>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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>>>
>>> --
>>> Thomas Maurel
>>> Bioinformatician - Ensembl Production Team
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
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