Re: [XMLPipeDB-developer] System table subquery

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

I'm hung up on the last else if conditional within
getRelationshipTableManager()

This is the "Species-X or X-Species" conditional, excluding GeneOntology

The original single species conditional is:

else if
((selectedSpeciesProfiles.get(0).getSpeciesSpecificSystemTables().containsKey(stp.systemTable1)
||

selectedSpeciesProfiles.get(0).getSpeciesSpecificSystemTables().containsKey(
stp.systemTable2)) &&
            !stp.systemTable2.equals("GeneOntology")) {

Now it needs to be multispecies aware obviously so...

Can I add a for loop within the else if and change the following
tablemanager creation logic , such as:

else if(
          for(SpeciesProfile species : selectedSpeciesProfiles) {

  (species.getSpeciesSpecificSystemTables().containsKey(stp.systemTable1)
||

 species.getSpeciesSpecificSystemTables().containsKey(stp.systemTable2)) &&
       !stp.systemTable2.equals("GeneOntology") }
) {


adding the for loop is wrought with syntax errors, but the real question is
... am I missing a much simpler solution to solve this?

Richard


On Sun, Sep 25, 2011 at 9:20 PM, Richard Brous <rbr...@gm...> wrote:

> Worked on the code during the past few days and have committed some changes
> tonight.
> Also successfully exported without error.
>
>
> UniProtDatabaseProfile.java
>
>    - clean up of some comments and old code
>    - cleaned up logging code for getSystemTableManager()
>    - Worked on getRelationshipTableManager()
>     - [Uniprot - X conditional]
>        - rewrote SQL programmatically
>          - used looping to create correct setStrings
>          - added logging to surface details
>          - -[X - X conditional]
>        - rewrite of programmatic SQL is in progress (created stringbuilder
>          etc. in preparation)
>          - added logging
>          - -[Species - X or X - Species]
>        - added minimal logging to be expanded upon
>
> DatabaseProfile.java
>
>
>    - cleaned up comments
>    - reviewed getRelationsTableManager() and added some logging to it
>
> ExportToGenMAPP.java
>
>    - cleaned up code and comments for readability
>
>
>
>
> Appreciate any feedback as usual =D
>
> Richard
>
>
> On Mon, Sep 19, 2011 at 6:22 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> Very cool; looks like we can move on now.  Dr. Dahlquist and I suspect
>> that the relationship tables may not actually be as hard as they seem; just
>> a matter of tweaking the initial queries (which you're more comfortable
>> doing now!) so that they return the corresponding records for all of the
>> requested species.  Onward we go  :)
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>>
>>
>>
>>  On Sep 19, 2011, at 11:09 AM, Kam Dahlquist wrote:
>>
>> > Hi,
>> >
>> > LMU can accept 20 MB attachments now; I don't know how big your file is
>> zipped, but that's an option.  You could also use LionShare.
>> >
>> > Glad to see success!
>> >
>> > Kam
>> >
>> > At 06:05 PM 9/18/2011, you wrote:
>> >> Tried to post my latest gdb export to the biodb wiki but receiving log
>> in error (per separate email)
>> >>
>> >> But, I wanted to let you know I verified that each improper system
>> table does in fact contain the id and species name (samples of each):
>> >>
>> >>
>> >> Pfam
>> >> ID Species Date
>> >> PF02866 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> PF07050 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> PF03479 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> PF02317 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> PF03279 |Pseudomonas aeruginosa| 9/14/2011
>> >> PF09922 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> PF04205 |Pseudomonas aeruginosa| 9/14/2011
>> >> PF03379 |Pseudomonas aeruginosa| 9/14/2011
>> >> PF05389 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >>
>> >>
>> >> RefSeq
>> >> ID Species Date
>> >> YP_039973 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> YP_040411 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> YP_039521 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> NP_253798 |Pseudomonas aeruginosa| 9/14/2011
>> >> NP_254101 |Pseudomonas aeruginosa| 9/14/2011
>> >> NP_248930 |Pseudomonas aeruginosa| 9/14/2011
>> >> NP_251503 |Pseudomonas aeruginosa| 9/14/2011
>> >> NP_249960 |Pseudomonas aeruginosa| 9/14/2011
>> >> NP_253220 |Pseudomonas aeruginosa| 9/14/2011
>> >> YP_040877 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> NP_253802 |Pseudomonas aeruginosa| 9/14/2011
>> >>
>> >>
>> >> GeneId
>> >> ID Species Date
>> >> 879140 |Pseudomonas aeruginosa| 9/14/2011
>> >> 2859243 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 879337 |Pseudomonas aeruginosa| 9/14/2011
>> >> 2860668 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 881899 |Pseudomonas aeruginosa| 9/14/2011
>> >> 882312 |Pseudomonas aeruginosa| 9/14/2011
>> >> 2860009 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 881520 |Pseudomonas aeruginosa| 9/14/2011
>> >> 2861152 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 881596 |Pseudomonas aeruginosa| 9/14/2011
>> >>
>> >>
>> >> InterPro
>> >> ID Species Date
>> >> IPR022522 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR003538 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR016379 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR016920 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR000477 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR008948 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR005415 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR009651 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> IPR007895 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR008231 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR004558 |Pseudomonas aeruginosa| 9/14/2011
>> >> IPR011067 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> IPR006358 |Pseudomonas aeruginosa| 9/14/2011
>> >>
>> >>
>> >> PDB
>> >> ID Species Date
>> >> 2ZWS |Pseudomonas aeruginosa| 9/14/2011
>> >> 2F9I |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 2EXV |Pseudomonas aeruginosa| 9/14/2011
>> >> 3L34 |Pseudomonas aeruginosa| 9/14/2011
>> >> 1EZM |Pseudomonas aeruginosa| 9/14/2011
>> >> 2WYB |Pseudomonas aeruginosa| 9/14/2011
>> >> 2F1L |Pseudomonas aeruginosa| 9/14/2011
>> >> 1D7L |Pseudomonas aeruginosa| 9/14/2011
>> >> 1Y12 |Pseudomonas aeruginosa| 9/14/2011
>> >> 2IXH |Pseudomonas aeruginosa| 9/14/2011
>> >> 1XAG |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> 2IXI |Pseudomonas aeruginosa| 9/14/2011
>> >>
>> >>
>> >> EMBL
>> >> ID Species Date
>> >> AJ003006 |Pseudomonas aeruginosa| 9/14/2011
>> >> BX571856 |Staphylococcus aureus (strain MRSA252)| 9/14/2011
>> >> AJ633619 |Pseudomonas aeruginosa| 9/14/2011
>> >> AJ633602 |Pseudomonas aeruginosa| 9/14/2011
>> >> U07359 |Pseudomonas aeruginosa| 9/14/2011
>> >> X54201 |Pseudomonas aeruginosa| 9/14/2011
>> >> AY899300 |Pseudomonas aeruginosa| 9/14/2011
>> >> AB085582 |Pseudomonas aeruginosa| 9/14/2011
>> >> AB075926 |Pseudomonas aeruginosa| 9/14/2011
>> >> AF306766 |Pseudomonas aeruginosa| 9/14/2011
>> >> X99471 |Pseudomonas aeruginosa| 9/14/2011
>> >> M21093 |Pseudomonas aeruginosa| 9/14/2011
>> >>
>> >>
>> >> Richard
>> >>
>> >> On Wed, Sep 14, 2011 at 6:50 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> >> 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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>> >>
>> >>
>> >>
>> >>
>> >>
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
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