[ensembl-dev] Error 500 using BioMart perl API

[Thomas Maurel]

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 <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> 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
> 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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