This SQL doesn't look correct, something is missing right before the 'AND' for the part that is joined with 'OR', with the exception of the last item as below:
((pathway__referencepeptidesequence__dm.referencedatabase_uniprot = 'P49327') AND (pathway__referencednasequence__dm.referencedatabase_ensembl = 'ENSG00000169710')) It looks like the original query involves join between two datasets. Usually that is not a problem when the link defined as an exportable/importable pair, in which exportable contains one attribute (eg, ensembl_gene) and importable contains one filter (eg, ensembl_gene). The piece of SQL statement shown above makes me thinking that the link you defined seemed to have two attributes and two filters (ensembl gene and uniprot id) for its exportable and importable. Although it is legitimate to create such a link, but I am afraid it is not going to work in most of the cases. It works only when *one* pair of the values is exported from one dataset and imported to the other dataset. The 'band' filter works exactly like this in Ensembl gene mart, user specifies *one* band to a hidden dataset which exports *one* pair (ie, one row) of 'chromosome' and 'coordinate' value (eg, 1, 10000303), and ensembl_gene dataset imports this pair and stick it in to SQL that queries against it's own db. The confirm this, you can double check the exportable/importable settings in your configuration. Hope this helps. Let us know if you have any further questions. Best regards, Junjun On 11-09-26 9:47 AM, "[email protected]" <[email protected]> wrote: >Hi, >I am getting an error from one of my queries along the lines of SQL syntax >being the cause, am not sure what the real problem is though. I set the >log4perl.conf to debug mode and I got back a more elaborate error report >http://pastebin.com/9rqKBfWR >Anyone know what the problem is? >Thanks, >Nelson > >Serious Error: Error during query execution: You have an error in your SQL >syntax; check the manual that corresponds to your MySQL server version for >the right syntax to use near 'AND >(pathway__referencednasequence__dm.referencedatabase_ensembl = >'ENSG00000166' at line 1 > >ERROR: caught BioMart::Exception::Database: Error during query execution: >You have an error in your SQL syntax; check the manual that corresponds to >your MySQL server version for the right syntax to use near 'AND >(pathway__referencednasequence__dm.referencedatabase_ensembl = >'ENSG00000166' at line 1 > >_______________________________________________ >Users mailing list >[email protected] >https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
