<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Jerry,<div class=""><br class=""></div><div class="">I am happy to report that your mart xml query is still valid and working. I am afraid that we have <span style="font-variant-ligatures: normal; orphans: 2; white-space: pre-wrap; widows: 2;" class="">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: </span><a href="http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/" class="">http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/</a>.</div><div class=""><span style="orphans: 2; white-space: pre-wrap; widows: 2;" class=""><br class=""></span></div><div class=""><span style="orphans: 2; white-space: pre-wrap; widows: 2;" class="">Hope this helps,</span></div><div class=""><span style="orphans: 2; white-space: pre-wrap; widows: 2;" class="">Kind Regards,</span></div><div class=""><span style="orphans: 2; white-space: pre-wrap; widows: 2;" class="">Thomas </span></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 7 Apr 2020, at 03:43, Jerry Vinokurov <<a href="mailto:jvinokurov@flatironinstitute.org" class="">jvinokurov@flatironinstitute.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hello all,</div><div class=""><br class=""></div><div class="">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:</div><div class=""><br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><br class=""><?xml version="1.0" encoding="UTF-8"?><br class=""><!DOCTYPE Query><br class=""><Query  virtualSchemaName = "default" formatter = "FASTA" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><br class="">  <Dataset name = "hsapiens_gene_ensembl" interface = "default" ><br class="">    <Filter name = "upstream_flank" value = "1000"/><br class="">    <Filter name = "with_entrezgene" excluded = "0"/><br class="">    <Attribute name = "ensembl_gene_id" /><br class="">    <Attribute name = "gene_flank" /><br class="">    <Attribute name = "ensembl_transcript_id" /><br class="">  </Dataset><br class="">  </Query></div></blockquote><div class=""><br class=""></div><div class="">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:</div><div class=""><br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><pre class="">Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND</pre></div></blockquote><div class="">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?</div><div class=""><br class=""></div><div class="">thanks,</div><div class="">Jerry<br class=""></div></div>
_______________________________________________<br class="">Dev mailing list    <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" class="">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""><div class="">
<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>

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