[ensembl-dev] Error 500 using BioMart perl API

[Julien Fumey]

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
>>
>> _______________________________________________
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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
>
>
>
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