[ensembl-dev] Error 500 using BioMart perl API
Thomas Maurel
maurel at ebi.ac.uk
Tue Apr 4 14:28:07 BST 2017
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> 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 <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 <mailto: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 <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 <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 <mailto: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 <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 <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 <mailto:sequencage-i2bc at i2bc.paris-saclay.fr>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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>>>>> Ensembl Blog: http://www.ensembl.info/ <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 <mailto:Dev at ensembl.org>
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>>>
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>>> Ensembl Blog: http://www.ensembl.info/ <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 <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev <http://lists.ensembl.org/mailman/listinfo/dev>
>> Ensembl Blog: http://www.ensembl.info/ <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
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