[ensembl-dev] Error 500 using BioMart perl API

Julien Fumey julien.fumey at i2bc.paris-saclay.fr
Tue Apr 4 14:19:04 BST 2017


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
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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/
>>
>> _______________________________________________
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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 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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