Hi Ronald, there are certain rules when creating marts with multiple mains. You are probably aware of this, I just want to make sure that we exclude any potential problems with those:
Each 'submain' must 'inherit' all the columns from the the previous main up including the keys eg. if the first main is 'gene__main' that has three columns including 'gene_key', then the next submain e.g transcript__main needs to have all the three columns from 'gene__main' plus any additional columns let's say 5 from transcript and its own key let's say 'transcript_key'. The next submain let's say 'protein__main would than have to have 8 columns including two keys 'gene_key' and 'transcript_key' plus its own key let's say 'protein_key' and any addtitional columns for protein__main. hope this helps, a On Tue, Dec 20, 2011 at 4:57 PM, Greenman, Ronald (NIH/CIT) [C] < [email protected]> wrote: > I’m extending the existing pride mart. Double underscores are used for > table names, single underscores for keys. My attributes were added later: > the ones on existing main tables worked fine, but this new main table > didn’t.**** > > ** ** > > I’ve actually made some progress since my last message: I needed to > explicitly add pride__spectrum__main to the list of main tables and > spectrum_id_key to the list of primary keys. This causes queries on that > table to show up normally, as long as I only use only attributes and > filters involving that table. However, if I use attributes or filters > involving BOTH that table AND another table (say, pride__experiment__main), > I get similar errors, only this time it says it can’t find “main” when > referring to fields on the tables that worked before. Queries involving > those old tables still work, as long as I don’t try to mix them with the > old tables.**** > > ** ** > > Single table, old: > OK > **** > > Multiple tables, old only: OK**** > > Single table, new: OK**** > > Multiple tables, old and new: FAILED**** > > (I only have one new table, do I can’t test what happens with multiple new > tables)**** > > ** ** > > For example, let’s say I have a query that filters on > pride__sequence__main.ms_level and returns pride__sequence__main.ms_level, > pride__sequence__main.range_start, and pride__sequence__main.range_stop. > This works fine. If I add pride__experiment__main.experiment_ac, however, > then martview says that it can’t find the column ‘main.experiment_ac’ in > ‘field list’. This also happens in martexplorer.**** > > ** ** > > *From:* Arek Kasprzyk [mailto:[email protected]] > *Sent:* Tuesday, December 20, 2011 11:50 AM > *To:* Greenman, Ronald (NIH/CIT) [C] > *Cc:* [email protected] > *Subject:* Re: [BioMart Users] Adding a new attribute set to an existing > mart**** > > ** ** > > Hi Ronald, > A few questions to help me with a 'diagnosis' of the problem: > Are you creating your mart from scratch or are you extending the existing > pride mart? > Do you use double underscores for table names and single underscores for > 'key' names? > Did your attributes show up in the naive configuration or did you add them > manually later? > > a**** > > On Tue, Dec 20, 2011 at 9:24 AM, Greenman, Ronald (NIH/CIT) [C] < > [email protected]> wrote:**** > > I'm running a mart (based on the one used by PRIDE), but I need to add a > new table to it. I'm currently calling it pride__spectrum__main, and I > don't think I need to add any dimension tables for now. I'm having some > trouble getting the API to recognize it, though. Although the filters and > attributes I created show up in martview, attempting to use them results in > a critical error: it says that it can't find the table 'main', which > doesn't sound like it falls into the BioMart naming scheme. > > I made a pride__spectrum__main table, with a primary key as the column > 'spectrum__id__key', and added spectrum_id_ref columns in other tables as > needed. I used marteditor to create an attribute set keyed to that table as > well as a set of filters for it. Is there something else I need to do to > make this work? > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users**** > > ** ** >
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