Re: [XMLPipeDB-developer] System table subquery

[Richard B. <rbr...@gm...>]

OK, going to commit my changes to UniProtDatabaseProfile:
getSystemTableManager()

Here is some logging info to confirm result.next() within the while loop is
both id and species name:

3070712 [Thread-4] INFO
 edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
 - getSystemTableManager(): while loop: ID:: IPR006314  Species::
Staphylococcus aureus (strain MRSA252)
3070712 [Thread-4] INFO
 edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
 - getSystemTableManager(): while loop: ID:: IPR013840  Species::
Staphylococcus aureus (strain MRSA252)
3070728 [Thread-4] INFO
 edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
 - getSystemTableManager(): while loop: ID:: IPR015887  Species::
Pseudomonas aeruginosa
3070728 [Thread-4] INFO
 edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
 - getSystemTableManager(): while loop: ID:: IPR016148  Species::
Pseudomonas aeruginosa

Richard

On Wed, Sep 14, 2011 at 3:20 PM, Richard Brous <rbr...@gm...> wrote:

> Solid progress made and I now have a compilable working copy.
>
> I'm now working through how to plug the results of the query into the
> proper slots under the while loop. I had stumbled on an error where I was
> supplying the column name instead of the actual data from the tuple. Solved
> that and am hoping the current export will be the last before I commit to
> sourceforge.
>
> Richard
>
>
> On Mon, Sep 12, 2011 at 10:59 PM, Richard Brous <rbr...@gm...>wrote:
>
>> Spent the weekend reviewing sql and I have achieved some clarity.
>>
>> I'm still working through things but not at least I have better context
>> and can ask intelligent questions.
>>
>> The sub query was a big help, I'm not sure how long it would have taken me
>> to do all the joins using ON to return "hjid | species name"
>>
>> Dondi - I'll stop by after theory tomorrow to discuss further.
>>
>> Thanks.
>>
>> Richard
>>
>>
>> On Thu, Sep 8, 2011 at 5:24 PM, John David N. Dionisio <do...@lm...>wrote:
>>
>>> Hi Rich,
>>>
>>> As discussed in our meeting, here is a first step toward the new system
>>> table query:
>>>
>>>        SELECT entrytype.hjid, organismnametype.value FROM entrytype INNER
>>> JOIN organismtype ON (entrytype.organism = organismtype.hjid) inner join
>>> organismnametype on (organismtype.hjid =
>>> organismnametype.organismtype_name_hjid) INNER JOIN dbreferencetype
>>> ON(dbreferencetype.organismtype_dbreference_hjid = organismtype.hjid) WHERE
>>> dbreferencetype.type = 'NCBI Taxonomy' and (id = '90371');
>>>
>>> (substitute the "id = " clause accordingly)
>>>
>>> John David N. Dionisio, PhD
>>> Associate Professor, Computer Science
>>> Associate Director, University Honors Program
>>> Loyola Marymount University
>>>
>>>
>>>
>>>
>>>
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>>
>>
>