Re: [XMLPipeDB-developer] Info table

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

OK, have moved onto getRelationsTableManager() ... this one seems pretty
complicated...

Have reviewed the method and submethods called and have the following
questions:

1. What are the RelationshipTables that are stored in relationshipTables?

aren't they species dependent? Can't seem to find where they were created?

If not, then:

2. How should the if/else conditional be handled?

*

if* (speciesProfile.getSpeciesSpecificSystemTables().containsKey(stp.
systemTable1) |

speciesProfile.getSpeciesSpecificSystemTables().containsKey(stp.systemTable2))
{

tableManager = speciesProfile.getRelationsTableManagerCustomizations(stp.
systemTable1,

stp.systemTable2, *templateDefinedSystemToSystemCode*, tableManager);

This obviously needs to be made aware of Lists of SpeciesProfiles... to
build the correct tableManager, do I need this conditional to run through
every species or should we enclose all the code (if and else) within a loop
through each species?

Thanks.

Richard


On Tue, Aug 16, 2011 at 11:02 AM, Richard Brous <rbr...@gm...> wrote:

> Sorry I typed and sent that out too quickly before getting my thoughts
> completely together...
>
> First off i thought that the array[][] portion of the submit needed to be
> in the following format: { "Species", speciesName1 }, { "Species",
> speciesName2 }, { "Species", speciesName3 },...
> but I see you specified it as: { "Species", speciesName1 | speciesName2 |
> speciesName3 }, ... OR'ing each of the species names?
>
> I see what you did regarding the date object... yes no reason to recreate a
> second object...
>
> As mentioned previously I will continue through the next methods,
> submitting (well thought out) changes and emailing out updates...
>
> Richard
>   On Tue, Aug 16, 2011 at 10:36 AM, Richard Brous <rbr...@gm...>wrote:
>
>> Took a look at your code and realized what I had done wrong. I should have
>> just broken out the loop as the second argument of the 3 in the submit
>> method. That was a rookie move on my part.
>>
>> I am moving on to the next method and will keep my mind on the syntactic
>> solution that I'm not thinking through prior to moving forward with an
>> implementation.
>>
>> Richard
>>
>>   On Mon, Aug 15, 2011 at 1:30 AM, John David N. Dionisio <do...@lm...>wrote:
>>
>>> OK, everything is committed.  I got up to the tweaks on the second panel
>>> in the wizard (Save As/GO Aspects), as well as the query change for
>>> exporting any combination of C, F, or P.
>>>
>>> I still have to do the GO OBO format check, plus the UI work on the
>>> remaining two wizard panels.  But meanwhile, hope these latest changes work
>>> out well.
>>>
>>> John David N. Dionisio, PhD
>>> Associate Professor, Computer Science
>>> Loyola Marymount University
>>>
>>>
>>>
>>>  On Aug 14, 2011, at 7:31 PM, Richard Brous wrote:
>>>
>>> > OK, using option 2 I have made changes to DatabaseProfile.java to allow
>>> for all species names to be included in the submit argument.
>>> > But I'm stuck on how to change my StringBuilder object to a type that
>>> submit wants. Help please!!
>>> >
>>> > Submitted the above and some comment changes to SourceForge this
>>> evening.
>>> >
>>> > Richard
>>> >
>>> > On Fri, Aug 12, 2011 at 12:08 PM, Kam Dahlquist <kda...@lm...>
>>> wrote:
>>> > Hi,
>>> >
>>> > I think we had better leave the info table with only one record
>>> > (option 2).  The species names can be separated by pipes " | " as
>>> > they are in the Systems table where there are multiple species.  To
>>> > my knowledge, the only time GenMAPP needs to access the info table is
>>> > for the "DisplayOrder" field, I don't know what would happen if there
>>> > were multiple records there. I know that the spec for the table says
>>> > that it should only be one record, but I don't know if it would crash
>>> > if there were multiple records.  To be on the safe side, I think we
>>> > should just keep it to the one record.
>>> >
>>> > Best,
>>> > Kam
>>> >
>>> > At 09:45 PM 8/10/2011, John David N. Dionisio wrote:
>>> > >Greetings,
>>> > >
>>> > >I think we have to turn to Dr. Dahlquist's GenMAPP knowledge here to
>>> > >get the definitive answer.  I see two choices:
>>> > >
>>> > >- The Info table should have one record for each species that the
>>> > >.gdb holds, in which case the change you need is to wrap that single
>>> > >submit call inside a loop, so that submit is called once for each
>>> > >chosen species.
>>> > >
>>> > >- The Info table should always have one record, and if the .gdb
>>> > >holds multiple species, the "Species" column should be some
>>> > >concatenation of multiple species names.  In this case, you would
>>> > >still call submit only once, but the value you send into the
>>> > >"Species" column is some accumulation of all chosen species names.
>>> > >
>>> > >Admittedly I don't know which way is right (I assumed the former as
>>> > >of our Tuesday meeting, but on further examination I'm no longer
>>> > >quite so sure).
>>> > >
>>> > >For Kam --- what does GenMAPP expect to see in the Info table if the
>>> > >opened .gdb contains multiple species?
>>> > >
>>> > >John David N. Dionisio, PhD
>>> > >Associate Professor, Computer Science
>>> > >Loyola Marymount University
>>> > >
>>> > >
>>> > >On Aug 10, 2011, at 9:36 PM, Richard Brous wrote:
>>> > >
>>> > > > OK, continued to review ExportToGenMAPP and dug into the creation
>>> > > of the first TableManager tmA on line 118.
>>> > > >
>>> > > > In reading through the method, my understanding is that it
>>> > > creates a new TableManager based on the selectedDatabaseProfile
>>> > > (which is UniProt).
>>> > > >
>>> > > > This is performed by the method getInfoTableManager() which then
>>> > > calls method submit(String tableName, QueryType queryType,
>>> > > String[][] columnNamesToValues);
>>> > > >
>>> > > > the code is as follows:
>>> > > >
>>> > > > tableManager.submit("Info", QueryType.insert, new String[][] { {
>>> > > "Owner", owner }, { "Version", new
>>> > > SimpleDateFormat("yyyyMMdd").format(version) }, { "MODSystem",
>>> > > modSystem }, { "Species", speciesProfile.getSpeciesName() }, {
>>> > > "Modify", new SimpleDateFormat("yyyyMMdd").format(modify) }, {
>>> > > "DisplayOrder", displayOrder }, { "Notes", notes } });
>>> > > >
>>> > > >
>>> > > > The modification of this line centers on { "Species",
>>> > > speciesProfile.getSpeciesName() }, since it originally processed a
>>> > > single species.
>>> > > >
>>> > > > So now I need to populate the arguments with the species
>>> > > contained within selectedDatabaseprofile.selectedSpeciesProfiles.
>>> > > >
>>> > > > I think I'll start with the baseArgument up to MODSystem, then
>>> > > append as many species as necessary, and then cap off the end with
>>> > > the rest starting at Modify. (similar to your approach in
>>> > > ExportGoData, populateUniprotGoTableFromSQL(char chosenAspect,
>>> > > List<Integer> taxonIds) line 513
>>> > > >
>>> > > > Please let me know if this approach or analysis is off track.
>>> > > >
>>> > > > Thanks!
>>> > > >
>>> > > > Richard
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > >
>>> > > > On Wed, Aug 10, 2011 at 5:50 PM, Richard Brous <rbr...@gm...>
>>> wrote:
>>> > > > Updated repository to include all Gene Ontology changes discussed
>>> > > during our meeting yesterday.
>>> > > >
>>> > > > Digging into TableManager next.
>>> > > >
>>> > > > Richard
>>> > > >
>>> > > > On Fri, Aug 5, 2011 at 10:06 AM, Richard Brous <rbr...@gm...>
>>> wrote:
>>> > > > whew... thanks for the detailed reply. I will digest this a bit
>>> > > and get back to you with further questions.
>>> > > >
>>> > > > rb
>>> > > >
>>> > > > On Thu, Aug 4, 2011 at 11:18 PM, John David N. Dionisio
>>> > > <do...@lm...> wrote:
>>> > > > Greetings,
>>> > > >
>>> > > > Sorry for the delay.  I wasn't able to walk through the relevant
>>> > > code until this evening.
>>> > > >
>>> > > > As Kam said, GOA serves as the link between the UniProt and GO
>>> > > IDs.  It essentially determines which GO IDs get exported by using
>>> > > GOA to see which GO IDs are associated with an exported UniProt
>>> > > ID.  The populateUniprotGoTableFromSQL, in its current form,
>>> > > extracts the GO association records that match the given taxon ID
>>> > > then exports, as UniProt-GO pairs, the GO and UniProt IDs
>>> > > referenced within that GO association record.  Processing that
>>> > > follows this is then based on the GO IDs that got exported --- and
>>> > > that's how the current code avoids exporting the entire list of GO
>>> terms.
>>> > > >
>>> > > > The operative query is on the second line of
>>> populateUniprotGoTableFromSQL:
>>> > > >
>>> > > >        String uniProtAndGOIDSQL = "select db_object_id, go_id,
>>> > > evidence_code, with_or_from from goa where db like '%UniProt%' and
>>> > > taxon = 'taxon:" + taxon + "'";
>>> > > >
>>> > > > In plain English, this selects the GOA records whose database is
>>> > > UniProt and whose taxon ID is the given taxon.  An additional
>>> > > condition is added for the "aspect" (All, Component, Function, or
>>> > > Process) that is to be exported.  This is another reduction filter,
>>> > > to further shrink the number of exported GO terms and thus avoid
>>> > > MAPPFinder issues later on.
>>> > > >
>>> > > > Given this, the proper expansion here is to change the taxon
>>> > > predicate to a multiple predicate.  That is, this method can be
>>> > > changed to now accept a collection or array of taxon IDs, and the
>>> > > base query should then be changed so that it accepts any taxon from
>>> > > that collection.  More or less, you want:
>>> > > >
>>> > > >    private void populateUniprotGoTableFromSQL(char chosenAspect,
>>> > > int[] taxons) throws SQLException {
>>> > > >
>>> > > > ...then, instead of the single string, you want to iterate
>>> > > through the taxon IDs:
>>> > > >
>>> > > >    StringBuilder baseQueryBuilder = new StringBuilder("select
>>> > > db_object_id, go_id, evidence_code, with_or_from from goa where db
>>> > > like '%UniProt%'");
>>> > > >    boolean first = true;
>>> > > >    for (int taxon: taxons) {
>>> > > >        baseQueryBuilder.append(first ? " and (" : " or ");
>>> > > >        baseQueryBuilder
>>> > > >            .append("taxon = 'taxon:")
>>> > > >            .append(taxon).append("'");
>>> > > >        first = false;
>>> > > >    }
>>> > > >    baseQueryBuilder.append(")");
>>> > > >
>>> > > > ...and so on.  I just sort of rattled this off so there may be
>>> > > little glitches, but anyway this is just to give you an overall idea.
>>> > > >
>>> > > > Put another way, no, you do not need to iterate this method for
>>> > > each taxon ID.  Instead, you can still call this method once, with
>>> > > the multiplicity of taxon IDs emerging in terms of the actual
>>> > > condition used for selecting the GO terms to be exported (based on
>>> > > the available GOA records, which as you may recall are loaded from
>>> .goa files).
>>> > > >
>>> > > > As a side note, right here you have an opportunity for a little
>>> > > sanity check regarding the content of the relational database: GO
>>> > > terms will only be exported if GOA records for the desired taxon
>>> > > IDs have been imported into the database.  So, as a pre-flight
>>> > > check, one can see if there are any GOA records at all for each
>>> > > chosen taxon ID.  If there are none, then the .goa file for that
>>> > > species needs to be imported into the relational database.
>>> > > >
>>> > > > Hope this helps...
>>> > > >
>>> > > > John David N. Dionisio, PhD
>>> > > > Associate Professor, Computer Science
>>> > > > Loyola Marymount University
>>> > > >
>>> > > >
>>> > > > On Aug 4, 2011, at 1:00 PM, Kam Dahlquist wrote:
>>> > > >
>>> > > > > Hi,
>>> > > > >
>>> > > > > Dondi will have to chime in on this, but I think this is where
>>> > > things are going to get tricky.
>>> > > > >
>>> > > > > The final gdb does not actually contain the entire GO, it gets
>>> > > trimmed somehow based on the GO associations for a particular
>>> > > species.  This is because MAPPFinder cannot handle loading the
>>> > > entire GO.  Since there is some type of species-specific trimming
>>> > > going on, it's quite possible that this will need to iterate.
>>> > > > >
>>> > > > > However, I don't have the foggiest idea of how this works, so
>>> > > Dondi will have to chime in.
>>> > > > >
>>> > > > > Best,
>>> > > > > Kam
>>> > > > >
>>> > > > > At 12:09 AM 8/4/2011, you wrote:
>>> > > > >> Wednesday 8/3/11 progress:
>>> > > > >>
>>> > > > >> 1. After following the ExportPanel1.java ground zero code of:
>>> > > databaseProfile.setSelectedSpeciesProfile( selectedProfile );
>>> > > > >>
>>> > > > >> I found the method in DatabaseProfile.java plus a getter method;
>>> > > > >> SpeciesProfile setSelectedSpeciesProfile( speciesProfile ) and
>>> > > SpeciesProfile getSelectedSpeciesProfile( speciesProfile )
>>> > > > >>
>>> > > > >> I created two new methods that each handle List<Object> of
>>> > > SpeciesProfiles argument instead of a single SpeciesProfile;
>>> > > setSelectedSpeciesProfiles and getSelectedSpeciesProfiles.
>>> > > > >>
>>> > > > >> This enabled the ExportPanel1 ground zero code to become:
>>> > > databaseProfile.setSelectedSpeciesProfiles(selectedSpecies);
>>> > > > >>
>>> > > > >> 2. public static void export() on line 104 in
>>> ExportToGenMAPP.java
>>> > > > >>
>>> > > > >> On line 107 ExportGoData is instantiated which I found in
>>> > > ExportGoData.java and calls a method: public void export(char
>>> > > chosenAspect, int taxon).
>>> > > > >>
>>> > > > >> Within export, taxon id is required for another method:
>>> > > private void populateGoTables(char chosenAspect, int taxon).
>>> > > > >>
>>> > > > >> Within populateGoTables, taxon id is required for another
>>> > > method: private void populateUniprotGoTableFromSQL( char
>>> > > chosenAspect, int taxon).
>>> > > > >>
>>> > > > >> But, if the export to GDB process starts off with exporting GO
>>> > > data, doesn't it only need to do that once no matter how many
>>> > > species are selected? As you probably realize, I'm leading towards
>>> > > not having to iterate through this for each taxon id if possible.
>>> > > > >>
>>> > > > >> Also, how does the export actually work? How are GO ids and
>>> > > UniProt ids related within the table?
>>> > > > >>
>>> > > > >> Thanks!
>>> > > > >>
>>> > > > >> Richard
>>> > > > >>
>>> > > > >>
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