Hi Lance, the problem with the 0.7 code is that is not maintained very much anymore. I hope maybe someone else can chip in and answer your 0.7 question. I would however encourage you to try to see if you can 'import' your 0.7 source using 0.8 code and deploy BioMart server. This should work ok if your 0.7 set up is not too fancy. There is a chance that it could make your life easier in the long run
a On Tue, Nov 1, 2011 at 4:38 PM, Lance Frohman <[email protected]> wrote: > 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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