Hi Ellen, I understand now. Here is what you have to do:
1. Create separate database for each dataset (e.g hs_130, hs_137, etc) 2. Make sure the table names are identical in each database (eg ... marker__main). 3. Open MConfigurator 'add source' (eg 'hs_130) 4. Right panel, 'data source management'. 'add' (eg hs_137) 5. Update data source 6. Add access point 7. Start the server. I checked it properly this time (inserting different values to different databases) and everything seemed to be querying ok Below are examples that I used (please do not get confused with the use of 'marker_130' table names in both databases, I was just too lazy to edit it properly but principle remains the same: identical names) +-------------------------------+ | Tables_in_ellen_130 | +-------------------------------+ | hs_dbsnp130__markers__main | | hs_dbsnp130__markers_func__dm | +-------------------------------+ +-------------------------------+ | Tables_in_ellen_137 | +-------------------------------+ | hs_dbsnp130__markers__main | | hs_dbsnp130__markers_func__dm | +-------------------------------+ 2 rows in set (0.00 sec) (I am sending an example XML working with these tables in a separate email) Please let me know if this solves the problem Merry Xmas :) a On Thu, Dec 20, 2012 at 11:10 AM, Ellen Schofield < [email protected]> wrote: > Hi Arek, > > Many thanks for your help, sorry I've not got back to you before now, > other work took over :-) > > I have loaded up your xml, tweaked to point at my db to see how it works. > All starts ok etc, but when I select the dbSNP137 dataset, it is still > searching against the dbSNP130 data. > > An example from the BioMart Portal could be the ensembl one. There is a > single starting point (ensembl) and then multiple datasets (humna, mouse > etc) that you can choose, all, I guess witht he same structure behind the > scenes and the same queries etc. > > Thanks, > > Ellen. > > -- [email protected] > JDRF/WT Diabetes and Inflammation Laboratory (DIL) > Cambridge Institute for Medical Research (CIMR) > Wellcome Trust/MRC Building > Addenbrooke's Hospital Hills Road Cambridge CB2 0XY > Tel: 01223 763215 > > On 12/12/12 17:40, Arek Kasprzyk wrote: > > Hi Ellen, > I am sending my XML file. Please let me know if this is what you need or > your problem is different > > a > > > On Wed, Dec 12, 2012 at 2:33 PM, Arek Kasprzyk <[email protected]>wrote: > >> Hi Ellen, >> perhaps I did not understand what you are after. If you partition a table >> it will create many more smaller tables. I assumed that you were looking >> for the opposite effect to somehow "group" your tables? How do you want >> your datasets to look through GUI? Could you give me an example either from >> the BioPortal or from CancerPortal? >> >> cheers, >> a >> >> >> On Wed, Dec 12, 2012 at 12:02 PM, Ellen Schofield < >> [email protected]> wrote: >> >>> Hi Arek, >>> >>> Many thanks for your time. Good to know that the structure is OK. >>> >>> These are the steps that I did... >>> Imported as a relation mart >>> Select a main table and then ticked "Partition Table" at bottom of >>> wizard screen >>> Finish -> Java error & stack trace.... >>> >>> So I didn't get even as far as you :-( >>> >>> Does the above make sense? >>> >>> >>> Ellen. >>> >>> -- [email protected] >>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>> Cambridge Institute for Medical Research (CIMR) >>> Wellcome Trust/MRC Building >>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>> Tel: 01223 763215 >>> >>> On 12/12/12 10:30, Arek Kasprzyk wrote: >>> >>> Hi Ellen, >>> I have now had an opportunity to try your file and it seemed to have >>> produced the correct config structure (if I understood your problem >>> correctly) >>> >>> This is what I did: >>> >>> 1. Imported your schema >>> 2. Added data source with one main table >>> 3. Invoked 'data source management' window >>> 4. Added second dataset >>> 5. Updated both datasets >>> 6. Created a config >>> 7. Started the server >>> >>> I was able to query it through GUI (did not get any results bc the >>> schema was empty but did not get any errors either) >>> >>> >>> a >>> >>> >>> >>> >>> >>> >>> >>> On Thu, Dec 6, 2012 at 2:19 PM, Ellen Schofield < >>> [email protected]> wrote: >>> >>>> Hi Arek, >>>> >>>> Sent to you directly. >>>> >>>> Many thanks, >>>> >>>> Ellen. >>>> >>>> -- [email protected] >>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>> Cambridge Institute for Medical Research (CIMR) >>>> Wellcome Trust/MRC Building >>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>> Tel: 01223 763215 >>>> >>>> On 06/12/12 14:10, Arek Kasprzyk wrote: >>>> >>>> Hi Ellen, >>>> would you mind sending me your schema so I can double check here? >>>> >>>> >>>> cheers, >>>> a >>>> >>>> >>>> >>>> On Thu, Dec 6, 2012 at 10:25 AM, Ellen Schofield < >>>> [email protected]> wrote: >>>> >>>>> Hi All, >>>>> >>>>> I hope somebody is able to help me as I'm struggling with this. I am >>>>> using BioMart 0.8rc6 and MartConfigurator as part of that. I have a db >>>>> with 5 different datasets, all of which have the same structure (one main >>>>> table and one dm table). I can use MartConfigurator with one dataset to >>>>> create a working mart for the main/dm table in that dataset, suggesting >>>>> that the structure is correct. However, if I try building a mart on one >>>>> of >>>>> the main tables (with it's dimension table) and request building it with a >>>>> partition table causes a java null pointer exception (MartController.java >>>>> line 1315). Building the same partition-based mart without the dm tables >>>>> present works. >>>>> >>>>> Am really hoping somebody can point out what I'm doing wrong? >>>>> >>>>> Many thanks. >>>>> Ellen. >>>>> >>>>> -- >>>>> [email protected] >>>>> JDRF/WT Diabetes and Inflammation Laboratory (DIL) >>>>> Cambridge Institute for Medical Research (CIMR) >>>>> Wellcome Trust/MRC Building >>>>> Addenbrooke's Hospital Hills Road Cambridge CB2 0XY >>>>> Tel: 01223 763215 <01223%20763215> >>>>> >>>>> _______________________________________________ >>>>> Users mailing list >>>>> [email protected] >>>>> https://lists.biomart.org/mailman/listinfo/users >>>>> >>>> >>>> >>>> >>> > > > >
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