Re: [XMLPipeDB-developer] Multispecies implementation:getSystemTableManager changes

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

In case your workspace is perfectly fine, here are some of the errors i'm
seeing:


DatabaseProfile.java

*

public* *abstract* *class* DatabaseProfile *extends* *Profile* {  Error here
says: Profile cannot be resolved to a type.

-------------------------------------------------------------------

*

public* String getProfileName() {

*return* *getName*();  Error here says: Method is undefined

}

/**

* Returns the profile description.

*

* *@return
*

*/

*public* String getProfileDescription() {

*return* *getDescription*(); Error here says: Method is undefined

}

 I then check Profile.java and the class constructor and methods are in fact
defined....

more unusual stuff...

springutilities can't be resolved on exportpanel1
ExportToGenMAPP can't resolve TableCoordinator


I really don't get this. What could I have possibly done to my config?

Richard


On Mon, Aug 22, 2011 at 7:40 PM, Richard Brous <rbr...@gm...> wrote:

> OK, I'll add some logging to that loop and change that last ? to
> OrderedLocusNames ( I think thats what it should be )
>
> I do have another odd problem tho...
>
> I'm not sure what I did but I now have errors throughout some of the class
> files:
> ExportPanel1.java
> DatabaseProfile.java
> SpeciesProfile.java
> and many more...
>
> I'm not sure what I did but doing a resync to the repository did not bring
> me back to a non-error state.
>
> I don't know what to do to fix it. When you sync to sourceforge do you get
> source files without error?
>
> Help please =/
>
> Richard
>
>
> On Mon, Aug 22, 2011 at 4:30 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> Greetings,
>>
>> The plan sounds good, all around.
>>
>> Regarding the "type = ?" clause in our SQL, recall that the "?"s in the
>> query are placeholders for actual parameter values.  If you follow where
>> that last setString call (which thus sets the right side of the "type = ?"
>> clause) gets its value, you'll see where that comes from (and what it leads
>> to in the GDB).  Hint: "GeneId" is one of the values that this clause takes.
>>  :)
>>
>> The doubling up of Sa is interesting.  Either there is a bug in your
>> Species column string building code, or there are multiple taxon IDs that
>> actually have the same species name.  I think some judicious debug logging
>> will resolve that.
>>
>> Once these GDBs have been duly vetted, I think we can move on to the
>> relationship tables.
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>>
>>  On Aug 22, 2011, at 10:03 AM, Richard Brous wrote:
>>
>> > OK, I have exported single species Sa and Pa GDBs from the current
>> working build and from the pre-multispecies build (all from my existing Pa
>> and Sa postgres databases.
>> >
>> > Then exported a multipspecies Sa and Pa gdb from the current working
>> build from my existing Sa/Pa multispecies postrgres database.
>> >
>> > I will post all GDB exports to the db wiki shortly...
>> >
>> >
>> -----------------------------------------------------------------------------------------------------------------------------------------------
>> > getSystemTableManager()
>> >
>> >
>> > So in effort to check the correctness of the multispecies changes to the
>> System table I was going to run the SQL commands from within PGAdmin then
>> compare the results to those within the multispecies GDB.
>> >
>> > Is my method correct?
>> >
>> >
>> -----------------------------------------------------------------------------------------------------------------------------------------------
>> > would use sql command (with errors =/):
>> >
>> > SELECT distinct id FROM dbreferencetype
>> > INNER JOIN (SELECT entrytype.hjid FROM entrytype
>> >      INNER JOIN organismtype ON (entrytype.organism = organismtype.hjid)
>> >      INNER JOIN dbreferencetype
>> ON(dbreferencetype.organismtype_dbreference_hjid = organismtype.hjid)
>> >      WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or id =
>> 282458))
>> >      as species_entry on dbreferencetype.entrytype_dbreference_hjid =
>> species_entry.hjid where type = ?;
>> >
>> >
>> > But I get an error for the = signs on line 5 and I'm not sure what the ?
>> is at the end of the last line... I thought it was taxonID but then thought
>> maybe it was something else.
>> >
>> >
>> ---------------------------------------------------------------------------------------------------------------------------------------------
>> >
>> > getInfoTableManager()
>> >
>> > To check the Info Table I opened the multispecies GDB in Access and did
>> a visual check.
>> >
>> > All colums looked ok (when compared to single species exports) except
>> for the Species column which had one too many entries. Will have to
>> determine why Sa is listed twice but a quick review of the loop didn't
>> reveal any issues.
>> > Info
>> > Species
>> > Pseudomonas aeruginosa|Staphylococcus aureus (strain
>> MRSA252)|Staphylococcus aureus (strain MRSA252)
>> >
>> >
>> >
>> > Richard
>> >
>> >
>> > On Sat, Aug 20, 2011 at 9:37 AM, John David N. Dionisio <do...@lm...>
>> wrote:
>> > Hi Rich,
>> >
>> > The JDBC mention was meant mainly to help with your use of
>> PreparedStatement.  If you've gotten that working, it's fine to move along.
>>  I think it would be good now to see how the system and info table code does
>> with multiple species (if you haven't already done so).  I prefer this way
>> before going into the relationship tables, just so we know that the work
>> done so far is OK for the full case, and because the relationship code will
>> be tougher to navigate.
>> >
>> > The main thing about the old-school loop when dealing solely with the
>> count was just that I prefer not to declare variables that I don't use (in
>> this case, the iterated object).  Plus, with the use of an index, you also
>> obviate the need for that boolean first variable.  Admittedly not an issue
>> of correctness here (as you said, your original code ran fine), but more of
>> a refinement/"best fit" choice.
>> >
>> >
>> > John David N. Dionisio, PhD
>> > Associate Professor, Computer Science
>> > Loyola Marymount University
>> >
>> >
>> > On Aug 20, 2011, at 9:17 AM, Richard Brous <rbr...@gm...> wrote:
>> >
>> >> also, I have compiled and run a new export.
>> >>
>> >> the GDB looks good for single species so which method should I go to
>> next OR do you want me to read JDBC before proceeding?
>> >>
>> >> richard
>> >>
>> >> On Sat, Aug 20, 2011 at 9:07 AM, Richard Brous <rbr...@gm...>
>> wrote:
>> >> Interesting about the looping through species profiles vs old-school
>> int loop:
>> >>
>> >> My choice of looping through the species still provided the correct
>> count, but what I think you are saying is that it is more appropriate to use
>> int looping because i'm not actually using the species profile objects for
>> anything?
>> >>
>> >>
>> >> I'll check out the JDBC portion shortly... I'm still working on the
>> details surrounding question #1 on the syllabus. I have been reading the
>> text in time slots avail when awaiting your feedback but honestly attempting
>> to prioritize GM builder coding. I have finished digesting E/R and am
>> working through UML...
>> >>
>> >> Richard
>> >> On Sat, Aug 20, 2011 at 12:02 AM, John David N. Dionisio <
>> do...@lm...> wrote:
>> >> Hi Rich,
>> >>
>> >> Having now taken a closer look at the code, I definitely recommended
>> that you do what was suggested in the previous reply, which is to form and
>> issue the SQL query directly before coding it up.  More details have been
>> committed in comments, so go ahead and take a look.
>> >>
>> >> You are also now getting further exposure to the JDBC (Java Database
>> Connectivity) API.  There is a section in the textbook that provides a brief
>> introduction to JDBC, and there are extensive tutorials and references
>> available on the web.  If you haven't already done so, it might be
>> worthwhile to glance at these.  Looking at the PreparedStatement class in
>> particular may help solidify your understanding of the code in question.
>> >>
>> >> Happy querying  :)
>> >>
>> >> John David N. Dionisio, PhD
>> >> Associate Professor, Computer Science
>> >> Loyola Marymount University
>> >>
>> >>
>> >>
>> >> On Aug 19, 2011, at 8:47 PM, Richard Brous wrote:
>> >>
>> >> > Fatal error during export which was related to "as" which I suspect I
>> left out a right parens when building the ps string.
>> >> >
>> >> > Rerunning export now but must head to bed.
>> >> >
>> >> > Will commit the changes I have and look for email comments in the
>> morn.
>> >> >
>> >> > Richard
>> >> >
>> >> > On Fri, Aug 19, 2011 at 8:04 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> >> > OK, made changes to getSystemTableManager() based on your comments
>> below.
>> >> >
>> >> > The ps string is programmatically created by adding "id = ?" for each
>> species profile within selectedSpeciesProfiles
>> >> >
>> >> > also added for loops below to cycle through the ps.set...
>> >> >
>> >> > and a for loop to grab each species customization.
>> >> >
>> >> > Running an export now which will be done in an hour or so to review
>> prior to submitting changes to sourceforge.
>> >> >
>> >> > Richard
>> >> >
>> >> > On Thu, Aug 18, 2011 at 11:19 PM, John David N. Dionisio <
>> do...@lm...> wrote:
>> >> > Greetings,
>> >> >
>> >> > OK, the transitional prep code (i.e., using the get(0) trick) looks
>> good.  Looks like we can safely hunker down now, starting with
>> getSystemTableManager.
>> >> >
>> >> > I agree that the clause:
>> >> >
>> >> >        WHERE dbreferencetype.type = 'NCBI Taxonomy' and id = ?
>> >> >
>> >> > ...where "?" becomes the single taxon ID to be exported should now
>> become:
>> >> >
>> >> >        WHERE dbreferencetype.type = 'NCBI Taxonomy' and (id = ? or id
>> = ? or id = ? ......)
>> >> >
>> >> > ...where the "?"s each get a taxon ID.  This requires that this
>> single large string must be built programmatically before being passed into
>> prepareStatement.  Plus, the ps.set.... calls now change from a single
>> statement into a loop.
>> >> >
>> >> > On a side note, you can change ps.setString to ps.setLong, thus
>> avoiding the concatenation with the empty string.
>> >> >
>> >> > I traced where that speciesCustomizeTextField value leads and found
>> that it ultimately goes into the getSpeciesName property of the species
>> profile, which is in turn what is used in the Species column of the ID
>> tables.  It appears that the purpose of speciesCustomizeTextField was to
>> allow the user to modify the species name; seeing as we hardly (if ever)
>> made use of this customization, I propose that we just auto-set this
>> property in the species profiles to the actual species name stored in the
>> UniProt records.
>> >> >
>> >> > John David N. Dionisio, PhD
>> >> > Associate Professor, Computer Science
>> >> > Loyola Marymount University
>> >> >
>> >> >
>> >> >
>> >> > On Aug 18, 2011, at 8:17 PM, Richard Brous wrote:
>> >> >
>> >> > > Posted new working copy to the db wiki
>> >> > > Committed changes to SourceForge
>> >> > >
>> >> > > On Thu, Aug 18, 2011 at 7:41 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> >> > > getRelationsTableManager()
>> >> > > Interim changes complete using selectedSpeciesProfiles.get(0)
>> >> > > we skipped this one as its pretty complex. Need to discuss how I
>> need to tackle this.
>> >> > >
>> >> > > getSystemTableManager()
>> >> > > Interim changes complete using selectedSpeciesProfiles.get(0)
>> >> > > After reviewing the code I think the way to update this method is
>> to loop through each selected species profile prior to if conditional at
>> line 525?
>> >> > > Seem sound?
>> >> > >
>> >> > > getRelationshipTableManager()
>> >> > > Interim changes complete using selectedSpeciesProfiles.get(0)
>> >> > > Not quite sure how to make method aware of multispecies. Use
>> looping or a single command vs actually changing the sql table commands?
>> >> > >
>> >> > > getSecondPassTableManager()
>> >> > > Interim change complete using selectedSpeciesProfiles.get(0)
>> >> > > I think we need to loop through each species profile here, to add
>> the customizations for each species
>> >> > >
>> >> > >
>> -------------------------------------------------------------------------------------------------------------------------------------
>> >> > >
>> >> > > Attempted another Ms export and this time figured out what was
>> going on.
>> >> > >
>> >> > > As Dr. D noted, no IDs existed in the previous GDB attempt and this
>> is related to the speciesCustomizeTextField which we had commented out a few
>> weeks ago. I changed it to
>> speciesCustomizeTextField.setText(selectedSpecies.get(0).getName()); to
>> ensure the field was populated with something and that did the trick. Now
>> exports are nearly identical for Ms for pre-multispecies build and the
>> current working build.
>> >> > >
>> >> > > I'm going to place my current working multispecies build (which
>> only exports a single species still) up on the db class wiki for your
>> review.
>> >> > >
>> >> > > Look for SourceForge changes soonish...
>> >> > >
>> >> > > Richard
>> >> > >
>> >> > >
>> >> > >
>> >> > > On Thu, Aug 18, 2011 at 11:40 AM, Kam Dahlquist <
>> kda...@lm...> wrote:
>> >> > > Hi,
>> >> > >
>> >> > > That's good news.  Let me know when there's a build that I can run.
>> >> > >
>> >> > > Also, would you guys mind changing the subject line to more closely
>> >> > > reflect the task being described in the message?
>> >> > >
>> >> > > Thanks,
>> >> > > Kam
>> >> > >
>> >> > > At 10:29 AM 8/18/2011, you wrote:
>> >> > > >Greetings,
>> >> > > >
>> >> > > >FYI I've committed some changes to the GO import handling.  The
>> most
>> >> > > >recent "breakage" in GO importing was caused by GO's addition of
>> an
>> >> > > ><ontology> element to the <header>.  Interestingly, the text in
>> this
>> >> > > >element was simply "go" --- an interesting change, implying that
>> >> > > >other ontologies may be accommodated.
>> >> > > >
>> >> > > >In any case, I've updated the GO database libraries and source
>> code,
>> >> > > >and I did a successful test import on a daily OBO file downloaded
>> >> > > >yesterday.  So, it looks like we can use the latest OBO files
>> again,
>> >> > > >at least until another element gets added to the schema.
>> >> > > >
>> >> > > >John David N. Dionisio, PhD
>> >> > > >Associate Professor, Computer Science
>> >> > > >Loyola Marymount University
>> >> > >
>> >> > >
>> >> > >
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