Re: [XMLPipeDB-developer] Info table
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Re: [XMLPipeDB-developer] Info table
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From: Richard B. <rbr...@gm...> - 2011-08-15 02:31:23
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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
> > > >>
> > > >>
> > > > <ATT00001..txt><ATT00002..txt>
> > >
> > >
> > >
> >
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> > > <ATT00001..txt><ATT00002..txt>
> >
> >
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