Hi Lance, Not really a direct answer to your question but ... a different question ;)
are you using something like martj 0.7 MExplorer to query ensembl? you maybe be better of using 0.8 rc6. This is a new version of BioMart entirely java based complete with the BioMart web server. a On Tue, Nov 1, 2011 at 4:13 PM, Lance Frohman <[email protected]> wrote: > I am usgin the martj 0.7 code from the user docs, using the > igisMartRegistry.xml, and I get a: > > org.ensembl.mart.lib.config.ConfigurationException: Caught SQL Exception > during fetch of requested digest: 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 'ensembl_mart_62.meta_conf__xml__dm mx WHERE > md.dataset_id_key=mi.dataset_id_key ' at line 1 > > on the adaptor.getDatasetConfigByDatasetInternalName() method. > > the sql statement is > > SELECT interface, display_name, dataset, description, message_digest, > type, visible, version,md.dataset_id_key, modified FROM > ensembl_mart_62.meta_conf__interface__dm mi, > ensembl_mart_62.meta_conf__dataset__main md > ensembl_mart_62.meta_conf__xml__dm mx WHERE > md.dataset_id_key=mi.dataset_id_key AND > md.dataset_id_key=mx.dataset_id_key AND visible = 1 > > but it is missing a comma between the "md" and "ensembl_mart_62." > > Has anyone seen this? > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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