[ensembl-dev] Querying BioMart with XML

[Jerry Vinokurov]

Hi,

I raised this issue a few months ago and I checked back today and it's
still happening. I continue receiving the error that tells me that the
upstream_flank filter was not found.

thanks,
Jerry

On Wed, Apr 8, 2020 at 5:26 AM Thomas Maurel <maurel at ebi.ac.uk> wrote:

> Dear Jerry,
>
> I think it will be best to wait until the maintenance period is over. If
> you still get the error in few days, we will investigate further.
>
> Kind Regards,
> Thomas
>
> On 7 Apr 2020, at 16:44, Jerry Vinokurov <jvinokurov at flatironinstitute.org>
> wrote:
>
> Hi Thomas,
>
> Thanks for the quick reply. Should I just wait another few days until the
> maintenance period is over and then retry? I've been giving it a shot every
> few days and have always received this error, which makes me think that
> this is not an intermittent issue.
>
> thanks,
> Jerry
>
> On Tue, Apr 7, 2020 at 8:56 AM Thomas Maurel <maurel at ebi.ac.uk> wrote:
>
>> Dear Jerry,
>>
>> I am happy to report that your mart xml query is still valid and working.
>> I am afraid that we have experienced some intermittent issues with
>> BioMart recently so I am sorry about this. Please note that our website is
>> still working with reduced functionality, please see more information here:
>> http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/
>> .
>>
>> Hope this helps,
>> Kind Regards,
>> Thomas
>>
>> On 7 Apr 2020, at 03:43, Jerry Vinokurov <
>> jvinokurov at flatironinstitute.org> wrote:
>>
>> Hello all,
>>
>> I am a software engineer at the Flatiron Institute, where I inherited
>> some code from a predecessor that obtained data from BioMart. From the
>> code, it appears that the following query was being sent in XML format
>> appended to the URL as a query parameter:
>>
>>
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <!DOCTYPE Query>
>>> <Query  virtualSchemaName = "default" formatter = "FASTA" header = "0"
>>> uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
>>>   <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
>>>     <Filter name = "upstream_flank" value = "1000"/>
>>>     <Filter name = "with_entrezgene" excluded = "0"/>
>>>     <Attribute name = "ensembl_gene_id" />
>>>     <Attribute name = "gene_flank" />
>>>     <Attribute name = "ensembl_transcript_id" />
>>>   </Dataset>
>>>   </Query>
>>>
>>
>> This is a verbatim copy/paste from the code that was used by the person
>> working on the project before me. Apparently at some point it worked, and I
>> had even managed to download some data using this query, but lately it has
>> been failing for me with the following error:
>>
>> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
>>>
>>> Has something changed which renders the upstream_flank filter no longer
>> valid? Could someone offer some guidance for what I should do to replicate
>> the expected results of the query?
>>
>> thanks,
>> Jerry
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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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>>
> _______________________________________________
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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:
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>
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