[ensembl-dev] Querying BioMart with XML

[Jerry Vinokurov]

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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