Hi Ellen, 'yes' to both of your questions :)
(Your datasets are already 'conceptually partitioned' ei conforming to the same model, so they do not require any further partitioning) a On Fri, Dec 21, 2012 at 11:55 AM, Ellen Schofield < [email protected]> wrote: > Thank you for your help Arek. > > So to get this to work, the datasets must be in different databases? > > And by the looks of your XML I don't get any of these (pc05) etc > pointers? Is there because it's not a partition now? Sorry for questions, > just trying to understand. > > Cheers & Merry Xmas to you too :-) > > > 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 21/12/12 11:38, Arek Kasprzyk wrote: > > 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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