[ensembl-dev] Querying BioMart with XML

[Thomas Maurel]

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 <mailto: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/ <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 <mailto: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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--
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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