Thanks, I am using the code from section "6.5.2 Examples" from the biomart-user-docs.pdf file. The admin for the project said that our biomart database was set up for 0.7 so I could not use 0.8.
On Tue, Nov 1, 2011 at 1:32 PM, Arek Kasprzyk <[email protected]>wrote: > 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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