xmlpipedb-developer Mailing List for XMLPipeDB (Page 6)
Brought to you by:
kdahlquist,
zugzugglug
Menu
▾
▴
xmlpipedb-developer — Mailing list for XMLPipeDB software development questions and discussions.
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
(16) |
Sep
|
Oct
(9) |
Nov
(3) |
Dec
(6) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
(2) |
Feb
(8) |
Mar
|
Apr
(22) |
May
(1) |
Jun
|
Jul
|
Aug
(3) |
Sep
(32) |
Oct
(2) |
Nov
|
Dec
|
| 2011 |
Jan
|
Feb
(60) |
Mar
(42) |
Apr
(35) |
May
(17) |
Jun
(2) |
Jul
(23) |
Aug
(72) |
Sep
(15) |
Oct
(10) |
Nov
(14) |
Dec
(4) |
| 2012 |
Jan
(6) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
(11) |
Dec
|
| 2014 |
Jan
(1) |
Feb
(12) |
Mar
(14) |
Apr
(8) |
May
|
Jun
(14) |
Jul
(2) |
Aug
|
Sep
(5) |
Oct
(6) |
Nov
|
Dec
|
| 2015 |
Jan
|
Feb
(5) |
Mar
(2) |
Apr
|
May
|
Jun
(2) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Richard B. <rbr...@gm...> - 2011-08-31 19:52:14
|
Submitted changes to UniProtDatabaseProfile based on the logical corrections from yesterdays convo with Dondi. These do not yet include the discussed optimizations, just wanted to get it working and do some test exports... which completed successfully. I also added a for loop under the while loop in getSystemTableManager() to ensure each query result is processed for each selected species profile. The loop is on line 587 and I added it because it seemed a solution to have each species profile included... is this correct or should I be submitting all at once versus each species? Richard |
|
From: John D. N. D. <do...@lm...> - 2011-08-25 18:40:53
|
Hi Rich,
Alrighty, sounds like a plan. Have a good rest-of-the-week!
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Aug 25, 2011, at 7:14 AM, Richard Brous wrote:
> Ok will work on this during my next quiet moment. Have some ideas which I will try to code out and incorporate into the existing code (which you are strongly suggesting I do heh).
>
> I synced your changes down and they look good in respect to the the ui and will run a single species export to confirm that still works.
>
> Today is our last full day and tomorrow we head from Nantucket to Boston then the next day from Boston to LA so I will not have an opportunity to code much after this eve. I will restablish communications once back in LA and settled.
>
> Richard
>
> On Thu, Aug 25, 2011 at 1:35 AM, John David N. Dionisio <do...@lm...> wrote:
> Greetings,
>
> Hope the sleep has done you well, and given you some fresh energy toward that PreparedStatement code. I can assure you, there is no switch statement involved. In your prospective code, you start looping through selectedSpeciesProfiles. That alone is already around 20% of the code that you need to write. 25% if you tweak the loop initialization a little bit.
>
> Meanwhile, I have completed my revamping of the wizard UI. The main change is that the last two panels --- the one where you select the system tables to export, and the one where you select relationship tables to export --- are gone. As discussed before, we never make use of these customizations. The export code now automatically sets these to everything, period. Thus, those two panels are no longer needed.
>
> I looked into providing a better user interface for the display order string, but concluded that this is a lot more coding that it is currently worth. So, for now, the customization has been removed, and the default order is always used.
>
> I could not find a way to change the label on the Next button, so I just added a message at the bottom of the second panel which says that clicking Next starts the export.
>
> Hope the changes are what we had in mind.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Aug 24, 2011, at 9:07 PM, Richard Brous wrote:
>
> > I was thinking switch in this way:
> >
> > for
> >
> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> > switch (numOfSpecies)
> >
> > case 1 : ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, systemTable.getKey());
> >
> > break;
> >
> > case 2 : ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(3, systemTable.getKey());
> >
> > break;
> >
> > case 3 :
> >
> > case 4 :
> >
> > case 5:
> >
> > result = ps.executeQuery();
> >
> > I hadn't implemented it yet so never found out if it would work or not.
> >
> > ----------------------------------------------------------------------------------------------------------------------------------
> >
> > In thinking about how to do this programatically I started getting hung up on how to do it for multiple lines.
> >
> > I understand how to do it for a submit now which needs multiple arguments (and not a string like I tried previously)... but its still only creating the arguments for a single line.
> >
> > Essentially I want to trigger based off selectedSpeciesProfiles.getSize() to provide the number of ps.setString(?, Integer.toString()(selected.getTaxon())) lines that are needed. Then cap it off with ps.setString(?, systemTable.getkey() )
> >
> > Maybe I'm overthinking it by trying to create multiple lines simultaneously instead of one by one....
> >
> > Going to sleep on this since its midnight and pick it up in the morning.
> >
> > Thanks as always!
> >
> > Richard
> >
> > On Wed, Aug 24, 2011 at 8:47 PM, John David N. Dionisio <do...@lm...> wrote:
> > Hi Rich,
> >
> > Actually, I don't see how switch would help at all. It's...hm, I really don't know how much would be right to say pedagogically. I daresay you might be overthinking this, or else misunderstanding some part of this whole process.
> >
> > You have a collection of species profiles. You have to form a query that is based on that collection. Really, there is no additional information (nor programming construct) to include.
> >
> > The ability to convert data structures into appropriate, corresponding queries is a key element of database programming, I'd say, so I think I prefer to let you mull over this a bit more. :)
> >
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> > On Aug 24, 2011, at 8:26 PM, Richard Brous <rbr...@gm...> wrote:
> >
> >> Understood, we are on the same page.
> >>
> >> I have been contemplating how to do this (knowing that there will be a limit to the number of compared species) between using switch statement or using a more programmatic way.
> >>
> >> I'm leaning towards the switch at the moment because I know I can get it done that way although certainly not as elegant.
> >>
> >> Richard
> >>
> >> On Wed, Aug 24, 2011 at 7:44 PM, John David N. Dionisio <do...@lm...> wrote:
> >> Hi Rich,
> >>
> >> Your second sentence/paragraph is right --- for every selected species, there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding setString call, setting that parameter to the taxon ID.
> >>
> >> Implied, but not explicitly stated, is that *after* all of these clauses, you have one more clause, for "type = ?". The parameter to set for that is systemTable.getKey().
> >>
> >> And, yes, the code for this must be based solely on the current content of the selectedSpeciesProfiles collection.
> >>
> >> So, given what you are setting out to do (one clause per selected species profile, with corresponding parameter, followed by specification of the system type), here is what you have:
> >>
> >> - You have the collection of selected species profiles. ***For each element in this collection, you must have an "id = ?" clause, and you must set the parameter of that clause with the taxon ID of that element.***
> >>
> >> - You have the systemTable object from which you will grab the parameter for "type = ?".
> >>
> >> You have the (a) part down (that is, the concatenation of the correct number of "id = ?" clauses to the query). It looks like this:
> >>
> >> for (int i = 0; i < selectedSpeciesProfiles.size(); i++) {
> >> basePrepareStatement
> >> .append((i == 0) ? " and (" : " or ")
> >> .append("id = ?");
> >> }
> >>
> >> Now, when the PreparedStatement has been created, ***you need to call setString once for each "id = ?" clause that you appended in the code block above.*** Finally, for the *last* parameter in the query (self-test question: what is the index of that last parameter?), you must set that to systemTable.getKey().
> >>
> >> The translation of the above paragraph into Java is essentially what you are setting out to do.
> >>
> >> John David N. Dionisio, PhD
> >> Associate Professor, Computer Science
> >> Loyola Marymount University
> >>
> >>
> >> On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
> >>
> >> > OK, spent some time digging through it with an eye to that 3rd '?'
> >> >
> >> > I believe I simply need to add as many ps.setString(?, Integer.toString(selected.getTaxon())); as there are species selected.
> >> >
> >> > Exports for single species work fine but if I want to export 2 species I need the following (example is hardcoded):
> >> >
> >> >
> >> > ps = ConnectionManager.getRelationalDBConnection().prepareStatement( basePrepareStatement.toString() );
> >> >
> >> > for
> >> >
> >> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> >> >
> >> > ps.setString(1, Integer.toString(selected.getTaxon()));
> >> >
> >> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >> >
> >> > ps.setString(3, systemTable.getKey());
> >> >
> >> > result = ps.executeQuery();
> >> >
> >> > etc...
> >> >
> >> >
> >> > The solve is to programmatically build the ps.set... going forward.
> >> >
> >> > Richard
> >> >
> >> >
> >> >
> >> > On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...> wrote:
> >> >
> >> > Hi Rich,
> >> >
> >> > Sure, I don't think it will do any harm to give the method another once-over. What you have to see solidly are:
> >> >
> >> > - What information does this method extract from the relational database?
> >> > - What information does this method send to the Gene Database?
> >> >
> >> > As to the code --- no, I did not change anything. I only added comments. Not sure about the successful export then. What I thought was that you did execute the changes I described, and that is how you successfully exported the .gdb.
> >> >
> >> > John David N. Dionisio, PhD
> >> > Associate Professor, Computer Science
> >> > Loyola Marymount University
> >> >
> >> >
> >> >
> >> >
> >> > On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
> >> >
> >> > > Yes your comments make sense but I feel as though my understanding of this method is the weak link... I'll work through it again tomorrow.
> >> > >
> >> > > Also, in thinking back over our discussions regarding getSystemTableManager(), I read through the code again and saw your comments.
> >> > >
> >> > > Then I realized I may have assumed you corrected the method when you may only in fact had commented... Was this the case?
> >> > >
> >> > > But then how did I get a successful two species export yesterday?
> >> > >
> >> > > OK, my brain is starting to hurt...
> >> > >
> >> > > I'm going to head to bed and start fresh tomorrow.
> >> > >
> >> > > Richard
> >> > >
> >> > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...> wrote:
> >> > > Hi Rich,
> >> > >
> >> > > The key is this message:
> >> > >
> >> > > org.postgresql.util.PSQLException: No value specified for parameter 3.
> >> > >
> >> > > That means the third question mark in the query (which turns out to be type = ?) was never given a value. Check that method and make sure that the code invokes as many set's as there are question marks in the query. And for this particular query, the last set is for the gene database type.
> >> > >
> >> > > John David N. Dionisio, PhD
> >> > > Associate Professor, Computer Science
> >> > > Loyola Marymount University
> >> > >
> >> > >
> >> > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
> >> > >
> >> > >> org.postgresql.util.PSQLException: No value specified for parameter 3.
> >> > >
> >> > > ------------------------------------------------------------------------------
> >> > > EMC VNX: the world's simplest storage, starting under $10K
> >> > > The only unified storage solution that offers unified management
> >> > > Up to 160% more powerful than alternatives and 25% more efficient.
> >> > > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> > > _______________________________________________
> >> > > xmlpipedb-developer mailing list
> >> > > xml...@li...
> >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> > >
> >> > >
> >> >
> >> > > <ATT00001..txt><ATT00002..txt>
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > EMC VNX: the world's simplest storage, starting under $10K
> >> > The only unified storage solution that offers unified management
> >> > Up to 160% more powerful than alternatives and 25% more efficient.
> >> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> > _______________________________________________
> >> > xmlpipedb-developer mailing list
> >> > xml...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> >
> >> >
> >> >
> >> > <ATT00001..txt><ATT00002..txt>
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> EMC VNX: the world's simplest storage, starting under $10K
> >> The only unified storage solution that offers unified management
> >> Up to 160% more powerful than alternatives and 25% more efficient.
> >> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >> ------------------------------------------------------------------------------
> >> EMC VNX: the world's simplest storage, starting under $10K
> >> The only unified storage solution that offers unified management
> >> Up to 160% more powerful than alternatives and 25% more efficient.
> >> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> > ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
> <ATT00001..txt><ATT00002..txt>
|
|
From: Kam D. <kda...@lm...> - 2011-08-25 18:22:51
|
Hi, Looks good. Cheers, Kam At 01:35 AM 8/25/2011, John David N. Dionisio wrote: >Greetings, > >Hope the sleep has done you well, and given you some fresh energy >toward that PreparedStatement code. I can assure you, there is no >switch statement involved. In your prospective code, you start >looping through selectedSpeciesProfiles. That alone is already >around 20% of the code that you need to write. 25% if you tweak the >loop initialization a little bit. > >Meanwhile, I have completed my revamping of the wizard UI. The main >change is that the last two panels --- the one where you select the >system tables to export, and the one where you select relationship >tables to export --- are gone. As discussed before, we never make >use of these customizations. The export code now automatically sets >these to everything, period. Thus, those two panels are no longer needed. > >I looked into providing a better user interface for the display >order string, but concluded that this is a lot more coding that it >is currently worth. So, for now, the customization has been >removed, and the default order is always used. > >I could not find a way to change the label on the Next button, so I >just added a message at the bottom of the second panel which says >that clicking Next starts the export. > >Hope the changes are what we had in mind. > >John David N. Dionisio, PhD >Associate Professor, Computer Science >Loyola Marymount University > > > > > > |
|
From: Richard B. <rbr...@gm...> - 2011-08-25 14:14:28
|
Ok will work on this during my next quiet moment. Have some ideas which I
will try to code out and incorporate into the existing code (which you are
strongly suggesting I do heh).
I synced your changes down and they look good in respect to the the ui and
will run a single species export to confirm that still works.
Today is our last full day and tomorrow we head from Nantucket to Boston
then the next day from Boston to LA so I will not have an opportunity to
code much after this eve. I will restablish communications once back in LA
and settled.
Richard
On Thu, Aug 25, 2011 at 1:35 AM, John David N. Dionisio <do...@lm...>wrote:
> Greetings,
>
> Hope the sleep has done you well, and given you some fresh energy toward
> that PreparedStatement code. I can assure you, there is no switch statement
> involved. In your prospective code, you start looping through
> selectedSpeciesProfiles. That alone is already around 20% of the code that
> you need to write. 25% if you tweak the loop initialization a little bit.
>
> Meanwhile, I have completed my revamping of the wizard UI. The main change
> is that the last two panels --- the one where you select the system tables
> to export, and the one where you select relationship tables to export ---
> are gone. As discussed before, we never make use of these customizations.
> The export code now automatically sets these to everything, period. Thus,
> those two panels are no longer needed.
>
> I looked into providing a better user interface for the display order
> string, but concluded that this is a lot more coding that it is currently
> worth. So, for now, the customization has been removed, and the default
> order is always used.
>
> I could not find a way to change the label on the Next button, so I just
> added a message at the bottom of the second panel which says that clicking
> Next starts the export.
>
> Hope the changes are what we had in mind.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Aug 24, 2011, at 9:07 PM, Richard Brous wrote:
>
> > I was thinking switch in this way:
> >
> > for
> >
> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> > switch (numOfSpecies)
> >
> > case 1 : ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, systemTable.getKey());
> >
> > break;
> >
> > case 2 : ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(3, systemTable.getKey());
> >
> > break;
> >
> > case 3 :
> >
> > case 4 :
> >
> > case 5:
> >
> > result = ps.executeQuery();
> >
> > I hadn't implemented it yet so never found out if it would work or not.
> >
> >
> ----------------------------------------------------------------------------------------------------------------------------------
> >
> > In thinking about how to do this programatically I started getting hung
> up on how to do it for multiple lines.
> >
> > I understand how to do it for a submit now which needs multiple arguments
> (and not a string like I tried previously)... but its still only creating
> the arguments for a single line.
> >
> > Essentially I want to trigger based off selectedSpeciesProfiles.getSize()
> to provide the number of ps.setString(?,
> Integer.toString()(selected.getTaxon())) lines that are needed. Then cap it
> off with ps.setString(?, systemTable.getkey() )
> >
> > Maybe I'm overthinking it by trying to create multiple lines
> simultaneously instead of one by one....
> >
> > Going to sleep on this since its midnight and pick it up in the morning.
> >
> > Thanks as always!
> >
> > Richard
> >
> > On Wed, Aug 24, 2011 at 8:47 PM, John David N. Dionisio <do...@lm...>
> wrote:
> > Hi Rich,
> >
> > Actually, I don't see how switch would help at all. It's...hm, I really
> don't know how much would be right to say pedagogically. I daresay you
> might be overthinking this, or else misunderstanding some part of this whole
> process.
> >
> > You have a collection of species profiles. You have to form a query that
> is based on that collection. Really, there is no additional information
> (nor programming construct) to include.
> >
> > The ability to convert data structures into appropriate, corresponding
> queries is a key element of database programming, I'd say, so I think I
> prefer to let you mull over this a bit more. :)
> >
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> > On Aug 24, 2011, at 8:26 PM, Richard Brous <rbr...@gm...> wrote:
> >
> >> Understood, we are on the same page.
> >>
> >> I have been contemplating how to do this (knowing that there will be a
> limit to the number of compared species) between using switch statement or
> using a more programmatic way.
> >>
> >> I'm leaning towards the switch at the moment because I know I can get it
> done that way although certainly not as elegant.
> >>
> >> Richard
> >>
> >> On Wed, Aug 24, 2011 at 7:44 PM, John David N. Dionisio <do...@lm...>
> wrote:
> >> Hi Rich,
> >>
> >> Your second sentence/paragraph is right --- for every selected species,
> there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding
> setString call, setting that parameter to the taxon ID.
> >>
> >> Implied, but not explicitly stated, is that *after* all of these
> clauses, you have one more clause, for "type = ?". The parameter to set for
> that is systemTable.getKey().
> >>
> >> And, yes, the code for this must be based solely on the current content
> of the selectedSpeciesProfiles collection.
> >>
> >> So, given what you are setting out to do (one clause per selected
> species profile, with corresponding parameter, followed by specification of
> the system type), here is what you have:
> >>
> >> - You have the collection of selected species profiles. ***For each
> element in this collection, you must have an "id = ?" clause, and you must
> set the parameter of that clause with the taxon ID of that element.***
> >>
> >> - You have the systemTable object from which you will grab the parameter
> for "type = ?".
> >>
> >> You have the (a) part down (that is, the concatenation of the correct
> number of "id = ?" clauses to the query). It looks like this:
> >>
> >> for (int i = 0; i <
> selectedSpeciesProfiles.size(); i++) {
> >> basePrepareStatement
> >> .append((i == 0) ? " and (" : " or ")
> >> .append("id = ?");
> >> }
> >>
> >> Now, when the PreparedStatement has been created, ***you need to call
> setString once for each "id = ?" clause that you appended in the code block
> above.*** Finally, for the *last* parameter in the query (self-test
> question: what is the index of that last parameter?), you must set that to
> systemTable.getKey().
> >>
> >> The translation of the above paragraph into Java is essentially what you
> are setting out to do.
> >>
> >> John David N. Dionisio, PhD
> >> Associate Professor, Computer Science
> >> Loyola Marymount University
> >>
> >>
> >> On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
> >>
> >> > OK, spent some time digging through it with an eye to that 3rd '?'
> >> >
> >> > I believe I simply need to add as many ps.setString(?,
> Integer.toString(selected.getTaxon())); as there are species selected.
> >> >
> >> > Exports for single species work fine but if I want to export 2 species
> I need the following (example is hardcoded):
> >> >
> >> >
> >> > ps = ConnectionManager.getRelationalDBConnection().prepareStatement(
> basePrepareStatement.toString() );
> >> >
> >> > for
> >> >
> >> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> >> >
> >> > ps.setString(1, Integer.toString(selected.getTaxon()));
> >> >
> >> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >> >
> >> > ps.setString(3, systemTable.getKey());
> >> >
> >> > result = ps.executeQuery();
> >> >
> >> > etc...
> >> >
> >> >
> >> > The solve is to programmatically build the ps.set... going forward.
> >> >
> >> > Richard
> >> >
> >> >
> >> >
> >> > On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <
> do...@lm...> wrote:
> >> >
> >> > Hi Rich,
> >> >
> >> > Sure, I don't think it will do any harm to give the method another
> once-over. What you have to see solidly are:
> >> >
> >> > - What information does this method extract from the relational
> database?
> >> > - What information does this method send to the Gene Database?
> >> >
> >> > As to the code --- no, I did not change anything. I only added
> comments. Not sure about the successful export then. What I thought was
> that you did execute the changes I described, and that is how you
> successfully exported the .gdb.
> >> >
> >> > John David N. Dionisio, PhD
> >> > Associate Professor, Computer Science
> >> > Loyola Marymount University
> >> >
> >> >
> >> >
> >> >
> >> > On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
> >> >
> >> > > Yes your comments make sense but I feel as though my understanding
> of this method is the weak link... I'll work through it again tomorrow.
> >> > >
> >> > > Also, in thinking back over our discussions regarding
> getSystemTableManager(), I read through the code again and saw your
> comments.
> >> > >
> >> > > Then I realized I may have assumed you corrected the method when you
> may only in fact had commented... Was this the case?
> >> > >
> >> > > But then how did I get a successful two species export yesterday?
> >> > >
> >> > > OK, my brain is starting to hurt...
> >> > >
> >> > > I'm going to head to bed and start fresh tomorrow.
> >> > >
> >> > > Richard
> >> > >
> >> > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <
> do...@lm...> wrote:
> >> > > Hi Rich,
> >> > >
> >> > > The key is this message:
> >> > >
> >> > > org.postgresql.util.PSQLException: No value specified for parameter
> 3.
> >> > >
> >> > > That means the third question mark in the query (which turns out to
> be type = ?) was never given a value. Check that method and make sure that
> the code invokes as many set's as there are question marks in the query.
> And for this particular query, the last set is for the gene database type.
> >> > >
> >> > > John David N. Dionisio, PhD
> >> > > Associate Professor, Computer Science
> >> > > Loyola Marymount University
> >> > >
> >> > >
> >> > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...>
> wrote:
> >> > >
> >> > >> org.postgresql.util.PSQLException: No value specified for parameter
> 3.
> >> > >
> >> > >
> ------------------------------------------------------------------------------
> >> > > EMC VNX: the world's simplest storage, starting under $10K
> >> > > The only unified storage solution that offers unified management
> >> > > Up to 160% more powerful than alternatives and 25% more efficient.
> >> > > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> > > _______________________________________________
> >> > > xmlpipedb-developer mailing list
> >> > > xml...@li...
> >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> > >
> >> > >
> >> >
> >> > > <ATT00001..txt><ATT00002..txt>
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > EMC VNX: the world's simplest storage, starting under $10K
> >> > The only unified storage solution that offers unified management
> >> > Up to 160% more powerful than alternatives and 25% more efficient.
> >> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> > _______________________________________________
> >> > xmlpipedb-developer mailing list
> >> > xml...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> >
> >> >
> >> >
> >> > <ATT00001..txt><ATT00002..txt>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> EMC VNX: the world's simplest storage, starting under $10K
> >> The only unified storage solution that offers unified management
> >> Up to 160% more powerful than alternatives and 25% more efficient.
> >> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >>
> ------------------------------------------------------------------------------
> >> EMC VNX: the world's simplest storage, starting under $10K
> >> The only unified storage solution that offers unified management
> >> Up to 160% more powerful than alternatives and 25% more efficient.
> >> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-25 08:35:34
|
Greetings, Hope the sleep has done you well, and given you some fresh energy toward that PreparedStatement code. I can assure you, there is no switch statement involved. In your prospective code, you start looping through selectedSpeciesProfiles. That alone is already around 20% of the code that you need to write. 25% if you tweak the loop initialization a little bit. Meanwhile, I have completed my revamping of the wizard UI. The main change is that the last two panels --- the one where you select the system tables to export, and the one where you select relationship tables to export --- are gone. As discussed before, we never make use of these customizations. The export code now automatically sets these to everything, period. Thus, those two panels are no longer needed. I looked into providing a better user interface for the display order string, but concluded that this is a lot more coding that it is currently worth. So, for now, the customization has been removed, and the default order is always used. I could not find a way to change the label on the Next button, so I just added a message at the bottom of the second panel which says that clicking Next starts the export. Hope the changes are what we had in mind. John David N. Dionisio, PhD Associate Professor, Computer Science Loyola Marymount University |
|
From: Richard B. <rbr...@gm...> - 2011-08-25 04:07:34
|
I was thinking switch in this way:
*
for* ( SpeciesProfile selected : selectedSpeciesProfiles ) {
switch (numOfSpecies)
case 1 : ps.setString(1, Integer.*toString*(selected.getTaxon()));
ps.setString(2, systemTable.getKey());
break;
case 2 : ps.setString(1, Integer.*toString*(selected.getTaxon()));
ps.setString(2, Integer.*toString*(selected.getTaxon()));
ps.setString(3, systemTable.getKey());
break;
case 3 :
case 4 :
case 5:
result = ps.executeQuery();
I hadn't implemented it yet so never found out if it would work or not.
----------------------------------------------------------------------------------------------------------------------------------
In thinking about how to do this programatically I started getting hung up
on how to do it for multiple lines.
I understand how to do it for a submit now which needs multiple arguments
(and not a string like I tried previously)... but its still only creating
the arguments for a single line.
Essentially I want to trigger based off selectedSpeciesProfiles.getSize() to
provide the number of ps.setString(?,
Integer.toString()(selected.getTaxon())) lines that are needed. Then cap it
off with ps.setString(?, systemTable.getkey() )
Maybe I'm overthinking it by trying to create multiple lines simultaneously
instead of one by one....
Going to sleep on this since its midnight and pick it up in the morning.
Thanks as always!
Richard
On Wed, Aug 24, 2011 at 8:47 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> Actually, I don't see how switch would help at all. It's...hm, I really
> don't know how much would be right to say pedagogically. I daresay you
> might be overthinking this, or else misunderstanding some part of this whole
> process.
>
> You have a collection of species profiles. You have to form a query that
> is based on that collection. Really, there is no additional information
> (nor programming construct) to include.
>
> The ability to convert data structures into appropriate, corresponding
> queries is a key element of database programming, I'd say, so I think I
> prefer to let you mull over this a bit more. :)
>
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Aug 24, 2011, at 8:26 PM, Richard Brous <rbr...@gm...> wrote:
>
> Understood, we are on the same page.
>
> I have been contemplating how to do this (knowing that there will be a
> limit to the number of compared species) between using switch statement or
> using a more programmatic way.
>
> I'm leaning towards the switch at the moment because I know I can get it
> done that way although certainly not as elegant.
>
> Richard
>
> On Wed, Aug 24, 2011 at 7:44 PM, John David N. Dionisio <do...@lm...>wrote:
>
>> Hi Rich,
>>
>> Your second sentence/paragraph is right --- for every selected species,
>> there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding
>> setString call, setting that parameter to the taxon ID.
>>
>> Implied, but not explicitly stated, is that *after* all of these clauses,
>> you have one more clause, for "type = ?". The parameter to set for that is
>> systemTable.getKey().
>>
>> And, yes, the code for this must be based solely on the current content of
>> the selectedSpeciesProfiles collection.
>>
>> So, given what you are setting out to do (one clause per selected species
>> profile, with corresponding parameter, followed by specification of the
>> system type), here is what you have:
>>
>> - You have the collection of selected species profiles. ***For each
>> element in this collection, you must have an "id = ?" clause, and you must
>> set the parameter of that clause with the taxon ID of that element.***
>>
>> - You have the systemTable object from which you will grab the parameter
>> for "type = ?".
>>
>> You have the (a) part down (that is, the concatenation of the correct
>> number of "id = ?" clauses to the query). It looks like this:
>>
>> for (int i = 0; i < selectedSpeciesProfiles.size();
>> i++) {
>> basePrepareStatement
>> .append((i == 0) ? " and (" : " or ")
>> .append("id = ?");
>> }
>>
>> Now, when the PreparedStatement has been created, ***you need to call
>> setString once for each "id = ?" clause that you appended in the code block
>> above.*** Finally, for the *last* parameter in the query (self-test
>> question: what is the index of that last parameter?), you must set that to
>> systemTable.getKey().
>>
>> The translation of the above paragraph into Java is essentially what you
>> are setting out to do.
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>> On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
>>
>> > OK, spent some time digging through it with an eye to that 3rd '?'
>> >
>> > I believe I simply need to add as many ps.setString(?,
>> Integer.toString(selected.getTaxon())); as there are species selected.
>> >
>> > Exports for single species work fine but if I want to export 2 species I
>> need the following (example is hardcoded):
>> >
>> >
>> > ps = ConnectionManager.getRelationalDBConnection().prepareStatement(
>> basePrepareStatement.toString() );
>> >
>> > for
>> >
>> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
>> >
>> > ps.setString(1, Integer.toString(selected.getTaxon()));
>> >
>> > ps.setString(2, Integer.toString(selected.getTaxon()));
>> >
>> > ps.setString(3, systemTable.getKey());
>> >
>> > result = ps.executeQuery();
>> >
>> > etc...
>> >
>> >
>> > The solve is to programmatically build the ps.set... going forward.
>> >
>> > Richard
>> >
>> >
>> >
>> > On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...>
>> wrote:
>> >
>> > Hi Rich,
>> >
>> > Sure, I don't think it will do any harm to give the method another
>> once-over. What you have to see solidly are:
>> >
>> > - What information does this method extract from the relational
>> database?
>> > - What information does this method send to the Gene Database?
>> >
>> > As to the code --- no, I did not change anything. I only added
>> comments. Not sure about the successful export then. What I thought was
>> that you did execute the changes I described, and that is how you
>> successfully exported the .gdb.
>> >
>> > John David N. Dionisio, PhD
>> > Associate Professor, Computer Science
>> > Loyola Marymount University
>> >
>> >
>> >
>> >
>> > On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
>> >
>> > > Yes your comments make sense but I feel as though my understanding of
>> this method is the weak link... I'll work through it again tomorrow.
>> > >
>> > > Also, in thinking back over our discussions regarding
>> getSystemTableManager(), I read through the code again and saw your
>> comments.
>> > >
>> > > Then I realized I may have assumed you corrected the method when you
>> may only in fact had commented... Was this the case?
>> > >
>> > > But then how did I get a successful two species export yesterday?
>> > >
>> > > OK, my brain is starting to hurt...
>> > >
>> > > I'm going to head to bed and start fresh tomorrow.
>> > >
>> > > Richard
>> > >
>> > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <
>> do...@lm...> wrote:
>> > > Hi Rich,
>> > >
>> > > The key is this message:
>> > >
>> > > org.postgresql.util.PSQLException: No value specified for parameter 3.
>> > >
>> > > That means the third question mark in the query (which turns out to be
>> type = ?) was never given a value. Check that method and make sure that the
>> code invokes as many set's as there are question marks in the query. And
>> for this particular query, the last set is for the gene database type.
>> > >
>> > > John David N. Dionisio, PhD
>> > > Associate Professor, Computer Science
>> > > Loyola Marymount University
>> > >
>> > >
>> > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...>
>> wrote:
>> > >
>> > >> org.postgresql.util.PSQLException: No value specified for parameter
>> 3.
>> > >
>> > >
>> ------------------------------------------------------------------------------
>> > > EMC VNX: the world's simplest storage, starting under $10K
>> > > The only unified storage solution that offers unified management
>> > > Up to 160% more powerful than alternatives and 25% more efficient.
>> > > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> > > _______________________________________________
>> > > xmlpipedb-developer mailing list
>> > > xml...@li...
>> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >
>> > >
>> >
>> > > <ATT00001..txt><ATT00002..txt>
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > EMC VNX: the world's simplest storage, starting under $10K
>> > The only unified storage solution that offers unified management
>> > Up to 160% more powerful than alternatives and 25% more efficient.
>> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> > _______________________________________________
>> > xmlpipedb-developer mailing list
>> > xml...@li...
>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >
>> >
>> >
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> EMC VNX: the world's simplest storage, starting under $10K
>> The only unified storage solution that offers unified management
>> Up to 160% more powerful than alternatives and 25% more efficient.
>> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
>
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-25 03:46:38
|
Hi Rich,
Actually, I don't see how switch would help at all. It's...hm, I really don't know how much would be right to say pedagogically. I daresay you might be overthinking this, or else misunderstanding some part of this whole process.
You have a collection of species profiles. You have to form a query that is based on that collection. Really, there is no additional information (nor programming construct) to include.
The ability to convert data structures into appropriate, corresponding queries is a key element of database programming, I'd say, so I think I prefer to let you mull over this a bit more. :)
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Aug 24, 2011, at 8:26 PM, Richard Brous <rbr...@gm...> wrote:
> Understood, we are on the same page.
>
> I have been contemplating how to do this (knowing that there will be a limit to the number of compared species) between using switch statement or using a more programmatic way.
>
> I'm leaning towards the switch at the moment because I know I can get it done that way although certainly not as elegant.
>
> Richard
>
> On Wed, Aug 24, 2011 at 7:44 PM, John David N. Dionisio <do...@lm...> wrote:
> Hi Rich,
>
> Your second sentence/paragraph is right --- for every selected species, there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding setString call, setting that parameter to the taxon ID.
>
> Implied, but not explicitly stated, is that *after* all of these clauses, you have one more clause, for "type = ?". The parameter to set for that is systemTable.getKey().
>
> And, yes, the code for this must be based solely on the current content of the selectedSpeciesProfiles collection.
>
> So, given what you are setting out to do (one clause per selected species profile, with corresponding parameter, followed by specification of the system type), here is what you have:
>
> - You have the collection of selected species profiles. ***For each element in this collection, you must have an "id = ?" clause, and you must set the parameter of that clause with the taxon ID of that element.***
>
> - You have the systemTable object from which you will grab the parameter for "type = ?".
>
> You have the (a) part down (that is, the concatenation of the correct number of "id = ?" clauses to the query). It looks like this:
>
> for (int i = 0; i < selectedSpeciesProfiles.size(); i++) {
> basePrepareStatement
> .append((i == 0) ? " and (" : " or ")
> .append("id = ?");
> }
>
> Now, when the PreparedStatement has been created, ***you need to call setString once for each "id = ?" clause that you appended in the code block above.*** Finally, for the *last* parameter in the query (self-test question: what is the index of that last parameter?), you must set that to systemTable.getKey().
>
> The translation of the above paragraph into Java is essentially what you are setting out to do.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
>
> > OK, spent some time digging through it with an eye to that 3rd '?'
> >
> > I believe I simply need to add as many ps.setString(?, Integer.toString(selected.getTaxon())); as there are species selected.
> >
> > Exports for single species work fine but if I want to export 2 species I need the following (example is hardcoded):
> >
> >
> > ps = ConnectionManager.getRelationalDBConnection().prepareStatement( basePrepareStatement.toString() );
> >
> > for
> >
> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> >
> > ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(3, systemTable.getKey());
> >
> > result = ps.executeQuery();
> >
> > etc...
> >
> >
> > The solve is to programmatically build the ps.set... going forward.
> >
> > Richard
> >
> >
> >
> > On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...> wrote:
> >
> > Hi Rich,
> >
> > Sure, I don't think it will do any harm to give the method another once-over. What you have to see solidly are:
> >
> > - What information does this method extract from the relational database?
> > - What information does this method send to the Gene Database?
> >
> > As to the code --- no, I did not change anything. I only added comments. Not sure about the successful export then. What I thought was that you did execute the changes I described, and that is how you successfully exported the .gdb.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> >
> >
> > On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
> >
> > > Yes your comments make sense but I feel as though my understanding of this method is the weak link... I'll work through it again tomorrow.
> > >
> > > Also, in thinking back over our discussions regarding getSystemTableManager(), I read through the code again and saw your comments.
> > >
> > > Then I realized I may have assumed you corrected the method when you may only in fact had commented... Was this the case?
> > >
> > > But then how did I get a successful two species export yesterday?
> > >
> > > OK, my brain is starting to hurt...
> > >
> > > I'm going to head to bed and start fresh tomorrow.
> > >
> > > Richard
> > >
> > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...> wrote:
> > > Hi Rich,
> > >
> > > The key is this message:
> > >
> > > org.postgresql.util.PSQLException: No value specified for parameter 3.
> > >
> > > That means the third question mark in the query (which turns out to be type = ?) was never given a value. Check that method and make sure that the code invokes as many set's as there are question marks in the query. And for this particular query, the last set is for the gene database type.
> > >
> > > John David N. Dionisio, PhD
> > > Associate Professor, Computer Science
> > > Loyola Marymount University
> > >
> > >
> > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
> > >
> > >> org.postgresql.util.PSQLException: No value specified for parameter 3.
> > >
> > > ------------------------------------------------------------------------------
> > > EMC VNX: the world's simplest storage, starting under $10K
> > > The only unified storage solution that offers unified management
> > > Up to 160% more powerful than alternatives and 25% more efficient.
> > > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > >
> >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> > ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
|
|
From: Richard B. <rbr...@gm...> - 2011-08-25 03:27:00
|
Understood, we are on the same page.
I have been contemplating how to do this (knowing that there will be a limit
to the number of compared species) between using switch statement or using a
more programmatic way.
I'm leaning towards the switch at the moment because I know I can get it
done that way although certainly not as elegant.
Richard
On Wed, Aug 24, 2011 at 7:44 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> Your second sentence/paragraph is right --- for every selected species,
> there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding
> setString call, setting that parameter to the taxon ID.
>
> Implied, but not explicitly stated, is that *after* all of these clauses,
> you have one more clause, for "type = ?". The parameter to set for that is
> systemTable.getKey().
>
> And, yes, the code for this must be based solely on the current content of
> the selectedSpeciesProfiles collection.
>
> So, given what you are setting out to do (one clause per selected species
> profile, with corresponding parameter, followed by specification of the
> system type), here is what you have:
>
> - You have the collection of selected species profiles. ***For each
> element in this collection, you must have an "id = ?" clause, and you must
> set the parameter of that clause with the taxon ID of that element.***
>
> - You have the systemTable object from which you will grab the parameter
> for "type = ?".
>
> You have the (a) part down (that is, the concatenation of the correct
> number of "id = ?" clauses to the query). It looks like this:
>
> for (int i = 0; i < selectedSpeciesProfiles.size();
> i++) {
> basePrepareStatement
> .append((i == 0) ? " and (" : " or ")
> .append("id = ?");
> }
>
> Now, when the PreparedStatement has been created, ***you need to call
> setString once for each "id = ?" clause that you appended in the code block
> above.*** Finally, for the *last* parameter in the query (self-test
> question: what is the index of that last parameter?), you must set that to
> systemTable.getKey().
>
> The translation of the above paragraph into Java is essentially what you
> are setting out to do.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
>
> > OK, spent some time digging through it with an eye to that 3rd '?'
> >
> > I believe I simply need to add as many ps.setString(?,
> Integer.toString(selected.getTaxon())); as there are species selected.
> >
> > Exports for single species work fine but if I want to export 2 species I
> need the following (example is hardcoded):
> >
> >
> > ps = ConnectionManager.getRelationalDBConnection().prepareStatement(
> basePrepareStatement.toString() );
> >
> > for
> >
> > ( SpeciesProfile selected : selectedSpeciesProfiles ) {
> >
> > ps.setString(1, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(2, Integer.toString(selected.getTaxon()));
> >
> > ps.setString(3, systemTable.getKey());
> >
> > result = ps.executeQuery();
> >
> > etc...
> >
> >
> > The solve is to programmatically build the ps.set... going forward.
> >
> > Richard
> >
> >
> >
> > On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...>
> wrote:
> >
> > Hi Rich,
> >
> > Sure, I don't think it will do any harm to give the method another
> once-over. What you have to see solidly are:
> >
> > - What information does this method extract from the relational database?
> > - What information does this method send to the Gene Database?
> >
> > As to the code --- no, I did not change anything. I only added comments.
> Not sure about the successful export then. What I thought was that you did
> execute the changes I described, and that is how you successfully exported
> the .gdb.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> >
> >
> > On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
> >
> > > Yes your comments make sense but I feel as though my understanding of
> this method is the weak link... I'll work through it again tomorrow.
> > >
> > > Also, in thinking back over our discussions regarding
> getSystemTableManager(), I read through the code again and saw your
> comments.
> > >
> > > Then I realized I may have assumed you corrected the method when you
> may only in fact had commented... Was this the case?
> > >
> > > But then how did I get a successful two species export yesterday?
> > >
> > > OK, my brain is starting to hurt...
> > >
> > > I'm going to head to bed and start fresh tomorrow.
> > >
> > > Richard
> > >
> > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...>
> wrote:
> > > Hi Rich,
> > >
> > > The key is this message:
> > >
> > > org.postgresql.util.PSQLException: No value specified for parameter 3.
> > >
> > > That means the third question mark in the query (which turns out to be
> type = ?) was never given a value. Check that method and make sure that the
> code invokes as many set's as there are question marks in the query. And
> for this particular query, the last set is for the gene database type.
> > >
> > > John David N. Dionisio, PhD
> > > Associate Professor, Computer Science
> > > Loyola Marymount University
> > >
> > >
> > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
> > >
> > >> org.postgresql.util.PSQLException: No value specified for parameter 3.
> > >
> > >
> ------------------------------------------------------------------------------
> > > EMC VNX: the world's simplest storage, starting under $10K
> > > The only unified storage solution that offers unified management
> > > Up to 160% more powerful than alternatives and 25% more efficient.
> > > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > >
> >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-25 02:44:22
|
Hi Rich,
Your second sentence/paragraph is right --- for every selected species, there must be: (a) a corresponding "id = ?" clause, and (b) a corresponding setString call, setting that parameter to the taxon ID.
Implied, but not explicitly stated, is that *after* all of these clauses, you have one more clause, for "type = ?". The parameter to set for that is systemTable.getKey().
And, yes, the code for this must be based solely on the current content of the selectedSpeciesProfiles collection.
So, given what you are setting out to do (one clause per selected species profile, with corresponding parameter, followed by specification of the system type), here is what you have:
- You have the collection of selected species profiles. ***For each element in this collection, you must have an "id = ?" clause, and you must set the parameter of that clause with the taxon ID of that element.***
- You have the systemTable object from which you will grab the parameter for "type = ?".
You have the (a) part down (that is, the concatenation of the correct number of "id = ?" clauses to the query). It looks like this:
for (int i = 0; i < selectedSpeciesProfiles.size(); i++) {
basePrepareStatement
.append((i == 0) ? " and (" : " or ")
.append("id = ?");
}
Now, when the PreparedStatement has been created, ***you need to call setString once for each "id = ?" clause that you appended in the code block above.*** Finally, for the *last* parameter in the query (self-test question: what is the index of that last parameter?), you must set that to systemTable.getKey().
The translation of the above paragraph into Java is essentially what you are setting out to do.
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Aug 24, 2011, at 7:26 PM, Richard Brous wrote:
> OK, spent some time digging through it with an eye to that 3rd '?'
>
> I believe I simply need to add as many ps.setString(?, Integer.toString(selected.getTaxon())); as there are species selected.
>
> Exports for single species work fine but if I want to export 2 species I need the following (example is hardcoded):
>
>
> ps = ConnectionManager.getRelationalDBConnection().prepareStatement( basePrepareStatement.toString() );
>
> for
>
> ( SpeciesProfile selected : selectedSpeciesProfiles ) {
>
> ps.setString(1, Integer.toString(selected.getTaxon()));
>
> ps.setString(2, Integer.toString(selected.getTaxon()));
>
> ps.setString(3, systemTable.getKey());
>
> result = ps.executeQuery();
>
> etc...
>
>
> The solve is to programmatically build the ps.set... going forward.
>
> Richard
>
>
>
> On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...> wrote:
>
> Hi Rich,
>
> Sure, I don't think it will do any harm to give the method another once-over. What you have to see solidly are:
>
> - What information does this method extract from the relational database?
> - What information does this method send to the Gene Database?
>
> As to the code --- no, I did not change anything. I only added comments. Not sure about the successful export then. What I thought was that you did execute the changes I described, and that is how you successfully exported the .gdb.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
>
> On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
>
> > Yes your comments make sense but I feel as though my understanding of this method is the weak link... I'll work through it again tomorrow.
> >
> > Also, in thinking back over our discussions regarding getSystemTableManager(), I read through the code again and saw your comments.
> >
> > Then I realized I may have assumed you corrected the method when you may only in fact had commented... Was this the case?
> >
> > But then how did I get a successful two species export yesterday?
> >
> > OK, my brain is starting to hurt...
> >
> > I'm going to head to bed and start fresh tomorrow.
> >
> > Richard
> >
> > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...> wrote:
> > Hi Rich,
> >
> > The key is this message:
> >
> > org.postgresql.util.PSQLException: No value specified for parameter 3.
> >
> > That means the third question mark in the query (which turns out to be type = ?) was never given a value. Check that method and make sure that the code invokes as many set's as there are question marks in the query. And for this particular query, the last set is for the gene database type.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
> >
> >> org.postgresql.util.PSQLException: No value specified for parameter 3.
> >
> > ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
>
> > <ATT00001..txt><ATT00002..txt>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> <ATT00001..txt><ATT00002..txt>
|
|
From: Richard B. <rbr...@gm...> - 2011-08-25 02:26:55
|
OK, spent some time digging through it with an eye to that 3rd '?'
I believe I simply need to add as many ps.setString(?,
Integer.*toString*(selected.getTaxon()));
as there are species selected.
Exports for single species work fine but if I want to export 2 species I
need the following (example is hardcoded):
ps = ConnectionManager.*getRelationalDBConnection*().prepareStatement(
basePrepareStatement.toString() );
*
for* ( SpeciesProfile selected : selectedSpeciesProfiles ) {
ps.setString(1, Integer.*toString*(selected.getTaxon()));
ps.setString(2, Integer.*toString*(selected.getTaxon()));
ps.setString(3, systemTable.getKey());
result = ps.executeQuery();
etc...
The solve is to programmatically build the ps.set... going forward.
Richard
On Tue, Aug 23, 2011 at 8:53 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> Sure, I don't think it will do any harm to give the method another
> once-over. What you have to see solidly are:
>
> - What information does this method extract from the relational database?
> - What information does this method send to the Gene Database?
>
> As to the code --- no, I did not change anything. I only added comments.
> Not sure about the successful export then. What I thought was that you did
> execute the changes I described, and that is how you successfully exported
> the .gdb.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
>
> On Aug 23, 2011, at 8:41 PM, Richard Brous wrote:
>
> > Yes your comments make sense but I feel as though my understanding of
> this method is the weak link... I'll work through it again tomorrow.
> >
> > Also, in thinking back over our discussions regarding
> getSystemTableManager(), I read through the code again and saw your
> comments.
> >
> > Then I realized I may have assumed you corrected the method when you may
> only in fact had commented... Was this the case?
> >
> > But then how did I get a successful two species export yesterday?
> >
> > OK, my brain is starting to hurt...
> >
> > I'm going to head to bed and start fresh tomorrow.
> >
> > Richard
> >
> > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...>
> wrote:
> > Hi Rich,
> >
> > The key is this message:
> >
> > org.postgresql.util.PSQLException: No value specified for parameter 3.
> >
> > That means the third question mark in the query (which turns out to be
> type = ?) was never given a value. Check that method and make sure that the
> code invokes as many set's as there are question marks in the query. And
> for this particular query, the last set is for the gene database type.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Loyola Marymount University
> >
> >
> > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote:
> >
> >> org.postgresql.util.PSQLException: No value specified for parameter 3.
> >
> >
> ------------------------------------------------------------------------------
> > EMC VNX: the world's simplest storage, starting under $10K
> > The only unified storage solution that offers unified management
> > Up to 160% more powerful than alternatives and 25% more efficient.
> > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
>
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> EMC VNX: the world's simplest storage, starting under $10K
> The only unified storage solution that offers unified management
> Up to 160% more powerful than alternatives and 25% more efficient.
> Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-24 03:53:21
|
Hi Rich, Sure, I don't think it will do any harm to give the method another once-over. What you have to see solidly are: - What information does this method extract from the relational database? - What information does this method send to the Gene Database? As to the code --- no, I did not change anything. I only added comments. Not sure about the successful export then. What I thought was that you did execute the changes I described, and that is how you successfully exported the .gdb. John David N. Dionisio, PhD Associate Professor, Computer Science Loyola Marymount University On Aug 23, 2011, at 8:41 PM, Richard Brous wrote: > Yes your comments make sense but I feel as though my understanding of this method is the weak link... I'll work through it again tomorrow. > > Also, in thinking back over our discussions regarding getSystemTableManager(), I read through the code again and saw your comments. > > Then I realized I may have assumed you corrected the method when you may only in fact had commented... Was this the case? > > But then how did I get a successful two species export yesterday? > > OK, my brain is starting to hurt... > > I'm going to head to bed and start fresh tomorrow. > > Richard > > On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...> wrote: > Hi Rich, > > The key is this message: > > org.postgresql.util.PSQLException: No value specified for parameter 3. > > That means the third question mark in the query (which turns out to be type = ?) was never given a value. Check that method and make sure that the code invokes as many set's as there are question marks in the query. And for this particular query, the last set is for the gene database type. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Loyola Marymount University > > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote: > >> org.postgresql.util.PSQLException: No value specified for parameter 3. > > ------------------------------------------------------------------------------ > EMC VNX: the world's simplest storage, starting under $10K > The only unified storage solution that offers unified management > Up to 160% more powerful than alternatives and 25% more efficient. > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > <ATT00001..txt><ATT00002..txt> |
|
From: Richard B. <rbr...@gm...> - 2011-08-24 03:41:29
|
Yes your comments make sense but I feel as though my understanding of this method is the weak link... I'll work through it again tomorrow. Also, in thinking back over our discussions regarding getSystemTableManager(), I read through the code again and saw your comments. Then I realized I may have assumed you corrected the method when you may only in fact had commented... Was this the case? But then how did I get a successful two species export yesterday? OK, my brain is starting to hurt... I'm going to head to bed and start fresh tomorrow. Richard On Tue, Aug 23, 2011 at 8:18 PM, John David N. Dionisio <do...@lm...>wrote: > Hi Rich, > > The key is this message: > > org.postgresql.util.PSQLException: No value specified for parameter 3. > > That means the third question mark in the query (which turns out to be type > = ?) was never given a value. Check that method and make sure that the code > invokes as many set's as there are question marks in the query. And for > this particular query, the last set is for the gene database type. > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Loyola Marymount University > > > On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote: > > org.postgresql.util.PSQLException: No value specified for parameter 3. > > > > ------------------------------------------------------------------------------ > EMC VNX: the world's simplest storage, starting under $10K > The only unified storage solution that offers unified management > Up to 160% more powerful than alternatives and 25% more efficient. > Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > |
|
From: John D. N. D. <do...@lm...> - 2011-08-24 03:18:23
|
Hi Rich, The key is this message: org.postgresql.util.PSQLException: No value specified for parameter 3. That means the third question mark in the query (which turns out to be type = ?) was never given a value. Check that method and make sure that the code invokes as many set's as there are question marks in the query. And for this particular query, the last set is for the gene database type. John David N. Dionisio, PhD Associate Professor, Computer Science Loyola Marymount University On Aug 23, 2011, at 7:59 PM, Richard Brous <rbr...@gm...> wrote: > org.postgresql.util.PSQLException: No value specified for parameter 3. |
|
From: Richard B. <rbr...@gm...> - 2011-08-24 02:59:11
|
Thanks for the thoughts on the SQL issue - I should have picked up on the
single quotes for the id values =/
I'm back up and running as I mentioned, but i'm having difficulties
exporting from a multispecies Postgres db with two species selected.
I know I was able to get through the export process before (its how I knew
the info table had 3 species names instead of the expected 2) so I
dumped the last few changes and reverted back to the latest repository
version. I attempted a two species selected export again and it still failed
with the error logged below.
Now I'm running a single species export from the multispecies db to check
and see if I can at least get that without error.
Can you shed any light on this for me please?
Richard
------------------------------------------------------------------------------------------------------------------------------------------------------------
0 [main] INFO edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder - ***** GenMAPP
Builder started at: 6:25:55 PM PDT
69841 [AWT-EventQueue-0] WARN net.sf.ehcache.config.Configurator - No
configuration found. Configuring ehcache from ehcache-failsafe.xml found in
the classpath: ja
r:file:/C:/Users/rbrous/workspace/xmlpipedb-gmbuilder-brous-laptop/dist/lib/ehcache-1.1.jar!/ehcache-failsafe.xml
70980 [AWT-EventQueue-0] INFO edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder -
Getting DB column Pseudomonas aeruginosa
78530 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager - Using
database connection string: jdbc:odbc:Driver={Microsoft Access
Driver
(*.mdb)};DBQ=C:\Users\rbrous\workspace\xmlpipedb-gmbuilder-brous-laptop\dist\GeneMAPPBuilder.db;DriverID=22;READONLY=false}
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [Pfam] System Code: [Pf]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [RefSeq] System Code: [Q]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [GeneId] System Code: [L]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [InterPro] System Code: [I]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [PDB] System Code: [Pd]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Table: [EMBL] System Code: [Em]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- System Codes: [[S, T, N, Em, I, L, Pd, Pf, Q]]
137296 [AWT-EventQueue-0] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- Default Display Order: [|S|T|N|Em|I|L|Pd|Pf|Q|]
138450 [Thread-4] WARN
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Export
Started at: 6:28:13 PM PDT
138450 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Starting
GeneOntology export...
138466 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager - Using
database connection string: jdbc:odbc:Driver={Microsoft Access Driver
(*.mdb)};DBQ=C:\Users\rbrous\Desktop\Multispecies GDB compare\multispecies
testing\3 - both\Pa-Std_20110823.gdb;DriverID=22;READONLY=false}
138513 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating
UniProt-GO table...
138513 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating:
"UniProt-GeneOntology"
152506 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating
GeneOntology table...
152506 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating:
GeneOntology
216591 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating
GeneOntologyTree...
216591 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating:
GeneOntologyTree
366320 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating
GeneOntologyCount...
366320 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating:
GeneOntologyCount
367505 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - Populating
UniProt-GO count...
367802 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - creating:
"UniProt-GOCount"
2984800 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.go.ExportGoData - done!
2984800 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Finished
GeneOntology export...
2984800 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Starting first
pass table creation...
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Getting
first-pass table managers
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - Info table...
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getInfoTableManger()
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 1
rows
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count:
[1]
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count:
[0]
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing
tables...
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.size():: 1
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.toArray().length:: 1
2984816 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
successful passes through for loop: [1]
2984831 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getRelationsTableManager()
2984831 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - Relations table...
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 26
rows
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count:
[26]
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count:
[0]
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing
tables...
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.size():: 26
2984847 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.toArray().length:: 26
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
successful passes through for loop: [26]
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getOtherTableManager()
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - Other table...
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 0
rows
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count:
[0]
2984862 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count:
[0]
2984878 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing
tables...
2984878 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getSystemsTableManager()
2984878 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - Systems table...
2984878 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 10
rows
2984894 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count:
[0]
2984894 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count:
[10]
2984894 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing
tables...
2984894 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.size():: 10
2984894 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.toArray().length:: 10
2984909 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
successful passes through for loop: [10]
2984909 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getPrimarySystemTableManager()
2984909 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - Primary System table...
2985034 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
-
SQL Query: [SELECT entrytype_accession.entrytype_accession_hjid,
entrytype_accession.hjvalue FROM entrytype_accession INNER JOIN entrytype ON
(entrytype_accession.e
ntrytype_accession_hjid = entrytype.hjid) INNER JOIN organismtype ON
(entrytype.organism = organismtype.hjid) INNER JOIN dbreferencetype ON
(organismtype.hjid = dbr
eferencetype.organismtype_dbreference_hjid) WHERE
entrytype_accession_hjindex = 0 AND dbreferencetype.type LIKE '%NCBI
Taxonomy%' AND dbreferencetype.id = ?]
2990104 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- Total Records: [5558]
2990104 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- Step 1 - Number of rows in TM: [5558]
2990104 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
-
SQL Query: [SELECT hjvalue FROM entrytype_name WHERE entrytype_name_hjid =
?]
3054220 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- End of Method - Number of rows in TM: [5558]
3054220 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Create Table in
GDB. Table Name: [UniProt]
3054220 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Processing 5558
rows
3054251 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Insert Count:
[5558]
3054251 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Update Count:
[0]
3054251 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Flushing
tables...
3054251 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.size():: 5559
3054251 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
records to process: sqlBuffer.toArray().length:: 5559
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.Table - Number of
successful passes through for loop: [5559]
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP - Start
getSystemTableManager()
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportWizard - Preparing
tables - System tables...
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- systemTable.getKey(): Pfam
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- getSystemTableManager(): for loop: systemTable.getKey() = Pfa
m
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- getSystemTableManager(): for loop: Pfam is not in the list of
DatabaseSpecificSystemTables or SpeciesSpecificSystemTables.
3057512 [Thread-4] INFO
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile
- getSystemTableManager(): query used: SELECT distinct id FROM
dbreferencetype INNER JOIN (SELECT entrytype.hjid FROM entrytype INNER JOIN
organismtype ON (entrytype.organism = organismtype.hjid) INNER JOIN
dbreferencetype ON(d
breferencetype.organismtype_dbreference_hjid = organismtype.hjid) WHERE
dbreferencetype.type = 'NCBI Taxonomy' and (id = ? or id = ?)) as
species_entry on dbrefere
ncetype.entrytype_dbreference_hjid = species_entry.hjid where type = ?
3057512 [Thread-4] FATAL
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportPanel5Descriptor -
Export problem
org.postgresql.util.PSQLException: No value specified for parameter 3.
at
org.postgresql.core.v3.SimpleParameterList.checkAllParametersSet(SimpleParameterList.java:134)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:179)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257)
at
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtDatabaseProfile.getSystemTableManager(UniProtDatabaseProfile.java:587)
at
edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ExportToGenMAPP.export(ExportToGenMAPP.java:152)
at
edu.lmu.xmlpipedb.gmbuilder.gui.wizard.export.ExportPanel5Descriptor$1.run(ExportPanel5Descriptor.java:90)
On Tue, Aug 23, 2011 at 9:36 AM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> Good to hear that Clean worked! Keep that in mind in case Eclipse freaks
> again :)
>
> For SQL, check the table definition --- I believe id is actually a string
> (varchar). In that case, you need to enclose the values in quotes (i.e., id
> = '287'). (recall that the Java code used setString for these, not setInt
> nor setLong).
>
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
> On Aug 23, 2011, at 6:10 AM, Richard Brous <rbr...@gm...> wrote:
>
> Project > Clean worked like magic thank goodness!!!!
>
> I retraced my steps and was adding logging to DatabaseProfile.java when all
> went haywire.
>
> But I'm back on track and adding the logging back in again to try and catch
> that extra loop in Info table.
>
>
> ------------------------------------------------------------------------------------------------------
>
> Also I still need help with the sql:
>
>
> 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 = 'OrderedLocusNames';
>
>
> When I attempt to run this PGAdmin I get the following error:
>
> ERROR: operator does not exist: character varying = integer
> LINE 5: ...RE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or i...
>
> I'm not quite sure what this is telling me.
>
> Thanks!
>
> Richard
>
>
> On Mon, Aug 22, 2011 at 10:07 PM, John David N. Dionisio <do...@lm...>wrote:
>
>
>> Hi Rich,
>>
>> I'm all updated and compiling OK on my end. So my guess is that the
>> directory where Eclipse stores your build products (typically ./bin/) is
>> messed up somehow. Try cleaning your project to get it back in gear: choose
>> Project > Clean... then select the malfunctioning project(s). Wait a bit,
>> then see if things get better.
>>
>> Sorry couldn't get on early enough to help you address this sooner. Hope
>> this suggestion helps.
>>
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Loyola Marymount University
>>
>>
>>
>> On Aug 22, 2011, at 8:14 PM, Richard Brous wrote:
>>
>> > 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
>> > >> > >
>> > >> > >
>> > >> > >
>> ------------------------------------------------------------------------------
>> > >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > >> > > user administration capabilities and model configuration. Take
>> > >> > > the hassle out of deploying and managing Subversion and the
>> > >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > >> > > _______________________________________________
>> > >> > > xmlpipedb-developer mailing list
>> > >> > > xml...@li...
>> > >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >> > >
>> > >> > >
>> > >> > > <ATT00001..txt><ATT00002..txt>
>> > >> >
>> > >> >
>> > >> >
>> ------------------------------------------------------------------------------
>> > >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > >> > user administration capabilities and model configuration. Take
>> > >> > the hassle out of deploying and managing Subversion and the
>> > >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > >> > _______________________________________________
>> > >> > xmlpipedb-developer mailing list
>> > >> > xml...@li...
>> > >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >> >
>> > >> >
>> > >> > <ATT00001..txt><ATT00002..txt>
>> > >>
>> > >>
>> > >>
>> ------------------------------------------------------------------------------
>> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > >> user administration capabilities and model configuration. Take
>> > >> the hassle out of deploying and managing Subversion and the
>> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > >> _______________________________________________
>> > >> xmlpipedb-developer mailing list
>> > >> xml...@li...
>> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >>
>> > >>
>> > >>
>> ------------------------------------------------------------------------------
>> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > >> user administration capabilities and model configuration. Take
>> > >> the hassle out of deploying and managing Subversion and the
>> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > >> _______________________________________________
>> > >> xmlpipedb-developer mailing list
>> > >> xml...@li...
>> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >
>> > >
>> ------------------------------------------------------------------------------
>> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > > user administration capabilities and model configuration. Take
>> > > the hassle out of deploying and managing Subversion and the
>> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > > _______________________________________________
>> > > xmlpipedb-developer mailing list
>> > > xml...@li...
>> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> > >
>> > >
>> > > <ATT00001..txt><ATT00002..txt>
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > uberSVN's rich system and user administration capabilities and model
>> > configuration take the hassle out of deploying and managing Subversion
>> and
>> > the tools developers use with it. Learn more about uberSVN and get a
>> free
>> > download at: http://p.sf.net/sfu/wandisco-dev2dev
>> > _______________________________________________
>> > xmlpipedb-developer mailing list
>> > xml...@li...
>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >
>> >
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> user administration capabilities and model configuration. Take
>> the hassle out of deploying and managing Subversion and the
>> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>>
>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-23 16:36:10
|
Hi Rich,
Good to hear that Clean worked! Keep that in mind in case Eclipse freaks again :)
For SQL, check the table definition --- I believe id is actually a string (varchar). In that case, you need to enclose the values in quotes (i.e., id = '287'). (recall that the Java code used setString for these, not setInt nor setLong).
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Aug 23, 2011, at 6:10 AM, Richard Brous <rbr...@gm...> wrote:
> Project > Clean worked like magic thank goodness!!!!
>
> I retraced my steps and was adding logging to DatabaseProfile.java when all went haywire.
>
> But I'm back on track and adding the logging back in again to try and catch that extra loop in Info table.
>
> ------------------------------------------------------------------------------------------------------
>
> Also I still need help with the sql:
>
> 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 = 'OrderedLocusNames';
>
> When I attempt to run this PGAdmin I get the following error:
> ERROR: operator does not exist: character varying = integer
> LINE 5: ...RE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or i...
> I'm not quite sure what this is telling me.
>
> Thanks!
>
> Richard
>
>
> On Mon, Aug 22, 2011 at 10:07 PM, John David N. Dionisio <do...@lm...> wrote:
>
> Hi Rich,
>
> I'm all updated and compiling OK on my end. So my guess is that the directory where Eclipse stores your build products (typically ./bin/) is messed up somehow. Try cleaning your project to get it back in gear: choose Project > Clean... then select the malfunctioning project(s). Wait a bit, then see if things get better.
>
> Sorry couldn't get on early enough to help you address this sooner. Hope this suggestion helps.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Aug 22, 2011, at 8:14 PM, Richard Brous wrote:
>
> > 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
> > >> > >
> > >> > >
> > >> > > ------------------------------------------------------------------------------
> > >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> > > user administration capabilities and model configuration. Take
> > >> > > the hassle out of deploying and managing Subversion and the
> > >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> > > _______________________________________________
> > >> > > xmlpipedb-developer mailing list
> > >> > > xml...@li...
> > >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >> > >
> > >> > >
> > >> > > <ATT00001..txt><ATT00002..txt>
> > >> >
> > >> >
> > >> > ------------------------------------------------------------------------------
> > >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> > user administration capabilities and model configuration. Take
> > >> > the hassle out of deploying and managing Subversion and the
> > >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> > _______________________________________________
> > >> > xmlpipedb-developer mailing list
> > >> > xml...@li...
> > >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >> >
> > >> >
> > >> > <ATT00001..txt><ATT00002..txt>
> > >>
> > >>
> > >> ------------------------------------------------------------------------------
> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> user administration capabilities and model configuration. Take
> > >> the hassle out of deploying and managing Subversion and the
> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> _______________________________________________
> > >> xmlpipedb-developer mailing list
> > >> xml...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >>
> > >>
> > >> ------------------------------------------------------------------------------
> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> user administration capabilities and model configuration. Take
> > >> the hassle out of deploying and managing Subversion and the
> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> _______________________________________________
> > >> xmlpipedb-developer mailing list
> > >> xml...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > > ------------------------------------------------------------------------------
> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > > user administration capabilities and model configuration. Take
> > > the hassle out of deploying and managing Subversion and the
> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> > ------------------------------------------------------------------------------
> > uberSVN's rich system and user administration capabilities and model
> > configuration take the hassle out of deploying and managing Subversion and
> > the tools developers use with it. Learn more about uberSVN and get a free
> > download at: http://p.sf.net/sfu/wandisco-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
|
|
From: Richard B. <rbr...@gm...> - 2011-08-23 13:10:40
|
Project > Clean worked like magic thank goodness!!!!
I retraced my steps and was adding logging to DatabaseProfile.java when all
went haywire.
But I'm back on track and adding the logging back in again to try and catch
that extra loop in Info table.
------------------------------------------------------------------------------------------------------
Also I still need help with the sql:
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 = 'OrderedLocusNames';
When I attempt to run this PGAdmin I get the following error:
ERROR: operator does not exist: character varying = integer
LINE 5: ...RE dbreferencetype.type = 'NCBI Taxonomy' and (id = 287 or i...
I'm not quite sure what this is telling me.
Thanks!
Richard
On Mon, Aug 22, 2011 at 10:07 PM, John David N. Dionisio <do...@lm...>wrote:
> Hi Rich,
>
> I'm all updated and compiling OK on my end. So my guess is that the
> directory where Eclipse stores your build products (typically ./bin/) is
> messed up somehow. Try cleaning your project to get it back in gear: choose
> Project > Clean... then select the malfunctioning project(s). Wait a bit,
> then see if things get better.
>
> Sorry couldn't get on early enough to help you address this sooner. Hope
> this suggestion helps.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Aug 22, 2011, at 8:14 PM, Richard Brous wrote:
>
> > 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
> > >> > >
> > >> > >
> > >> > >
> ------------------------------------------------------------------------------
> > >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> > > user administration capabilities and model configuration. Take
> > >> > > the hassle out of deploying and managing Subversion and the
> > >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> > > _______________________________________________
> > >> > > xmlpipedb-developer mailing list
> > >> > > xml...@li...
> > >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >> > >
> > >> > >
> > >> > > <ATT00001..txt><ATT00002..txt>
> > >> >
> > >> >
> > >> >
> ------------------------------------------------------------------------------
> > >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> > user administration capabilities and model configuration. Take
> > >> > the hassle out of deploying and managing Subversion and the
> > >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> > _______________________________________________
> > >> > xmlpipedb-developer mailing list
> > >> > xml...@li...
> > >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >> >
> > >> >
> > >> > <ATT00001..txt><ATT00002..txt>
> > >>
> > >>
> > >>
> ------------------------------------------------------------------------------
> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> user administration capabilities and model configuration. Take
> > >> the hassle out of deploying and managing Subversion and the
> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> _______________________________________________
> > >> xmlpipedb-developer mailing list
> > >> xml...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >>
> > >>
> > >>
> ------------------------------------------------------------------------------
> > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > >> user administration capabilities and model configuration. Take
> > >> the hassle out of deploying and managing Subversion and the
> > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > >> _______________________________________________
> > >> xmlpipedb-developer mailing list
> > >> xml...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > >
> ------------------------------------------------------------------------------
> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > > user administration capabilities and model configuration. Take
> > > the hassle out of deploying and managing Subversion and the
> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > > _______________________________________________
> > > xmlpipedb-developer mailing list
> > > xml...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > >
> > >
> > > <ATT00001..txt><ATT00002..txt>
> >
> >
> >
> ------------------------------------------------------------------------------
> > uberSVN's rich system and user administration capabilities and model
> > configuration take the hassle out of deploying and managing Subversion
> and
> > the tools developers use with it. Learn more about uberSVN and get a free
> > download at: http://p.sf.net/sfu/wandisco-dev2dev
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: John D. N. D. <do...@lm...> - 2011-08-23 05:07:56
|
Hi Rich,
I'm all updated and compiling OK on my end. So my guess is that the directory where Eclipse stores your build products (typically ./bin/) is messed up somehow. Try cleaning your project to get it back in gear: choose Project > Clean... then select the malfunctioning project(s). Wait a bit, then see if things get better.
Sorry couldn't get on early enough to help you address this sooner. Hope this suggestion helps.
John David N. Dionisio, PhD
Associate Professor, Computer Science
Loyola Marymount University
On Aug 22, 2011, at 8:14 PM, Richard Brous wrote:
> 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
> >> > >
> >> > >
> >> > > ------------------------------------------------------------------------------
> >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> > > user administration capabilities and model configuration. Take
> >> > > the hassle out of deploying and managing Subversion and the
> >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >> > > _______________________________________________
> >> > > xmlpipedb-developer mailing list
> >> > > xml...@li...
> >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> > >
> >> > >
> >> > > <ATT00001..txt><ATT00002..txt>
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> > user administration capabilities and model configuration. Take
> >> > the hassle out of deploying and managing Subversion and the
> >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >> > _______________________________________________
> >> > xmlpipedb-developer mailing list
> >> > xml...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >> >
> >> >
> >> > <ATT00001..txt><ATT00002..txt>
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> user administration capabilities and model configuration. Take
> >> the hassle out of deploying and managing Subversion and the
> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> >> user administration capabilities and model configuration. Take
> >> the hassle out of deploying and managing Subversion and the
> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> > ------------------------------------------------------------------------------
> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> > user administration capabilities and model configuration. Take
> > the hassle out of deploying and managing Subversion and the
> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
> ------------------------------------------------------------------------------
> uberSVN's rich system and user administration capabilities and model
> configuration take the hassle out of deploying and managing Subversion and
> the tools developers use with it. Learn more about uberSVN and get a free
> download at: http://p.sf.net/sfu/wandisco-dev2dev
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
> <ATT00001..txt><ATT00002..txt>
|
|
From: Richard B. <rbr...@gm...> - 2011-08-23 03:14:21
|
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
>> >> > >
>> >> > >
>> >> > >
>> ------------------------------------------------------------------------------
>> >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> >> > > user administration capabilities and model configuration. Take
>> >> > > the hassle out of deploying and managing Subversion and the
>> >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> >> > > _______________________________________________
>> >> > > xmlpipedb-developer mailing list
>> >> > > xml...@li...
>> >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >> > >
>> >> > >
>> >> > > <ATT00001..txt><ATT00002..txt>
>> >> >
>> >> >
>> >> >
>> ------------------------------------------------------------------------------
>> >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> >> > user administration capabilities and model configuration. Take
>> >> > the hassle out of deploying and managing Subversion and the
>> >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> >> > _______________________________________________
>> >> > xmlpipedb-developer mailing list
>> >> > xml...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >> >
>> >> >
>> >> > <ATT00001..txt><ATT00002..txt>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> >> user administration capabilities and model configuration. Take
>> >> the hassle out of deploying and managing Subversion and the
>> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> >> _______________________________________________
>> >> xmlpipedb-developer mailing list
>> >> xml...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> >> user administration capabilities and model configuration. Take
>> >> the hassle out of deploying and managing Subversion and the
>> >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> >> _______________________________________________
>> >> xmlpipedb-developer mailing list
>> >> xml...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>> > user administration capabilities and model configuration. Take
>> > the hassle out of deploying and managing Subversion and the
>> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>> > _______________________________________________
>> > xmlpipedb-developer mailing list
>> > xml...@li...
>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> >
>> >
>> > <ATT00001..txt><ATT00002..txt>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> uberSVN's rich system and user administration capabilities and model
>> configuration take the hassle out of deploying and managing Subversion and
>> the tools developers use with it. Learn more about uberSVN and get a free
>> download at: http://p.sf.net/sfu/wandisco-dev2dev
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>
>
|
|
From: Richard B. <rbr...@gm...> - 2011-08-23 02:40:40
|
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 > >> > > > >> > > > >> > > > ------------------------------------------------------------------------------ > >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > >> > > user administration capabilities and model configuration. Take > >> > > the hassle out of deploying and managing Subversion and the > >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > >> > > _______________________________________________ > >> > > xmlpipedb-developer mailing list > >> > > xml...@li... > >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > >> > > > >> > > > >> > > <ATT00001..txt><ATT00002..txt> > >> > > >> > > >> > > ------------------------------------------------------------------------------ > >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > >> > user administration capabilities and model configuration. Take > >> > the hassle out of deploying and managing Subversion and the > >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > >> > _______________________________________________ > >> > xmlpipedb-developer mailing list > >> > xml...@li... > >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > >> > > >> > > >> > <ATT00001..txt><ATT00002..txt> > >> > >> > >> > ------------------------------------------------------------------------------ > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > >> user administration capabilities and model configuration. Take > >> the hassle out of deploying and managing Subversion and the > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > >> _______________________________________________ > >> xmlpipedb-developer mailing list > >> xml...@li... > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > >> > >> > >> > ------------------------------------------------------------------------------ > >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > >> user administration capabilities and model configuration. Take > >> the hassle out of deploying and managing Subversion and the > >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > >> _______________________________________________ > >> xmlpipedb-developer mailing list > >> xml...@li... > >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > ------------------------------------------------------------------------------ > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > user administration capabilities and model configuration. Take > > the hassle out of deploying and managing Subversion and the > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > > xmlpipedb-developer mailing list > > xml...@li... > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > <ATT00001..txt><ATT00002..txt> > > > > ------------------------------------------------------------------------------ > uberSVN's rich system and user administration capabilities and model > configuration take the hassle out of deploying and managing Subversion and > the tools developers use with it. Learn more about uberSVN and get a free > download at: http://p.sf.net/sfu/wandisco-dev2dev > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > |
|
From: John D. N. D. <do...@lm...> - 2011-08-22 23:30:21
|
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 >> > > >> > > >> > > ------------------------------------------------------------------------------ >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > > user administration capabilities and model configuration. Take >> > > the hassle out of deploying and managing Subversion and the >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > > _______________________________________________ >> > > xmlpipedb-developer mailing list >> > > xml...@li... >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > >> > > >> > > <ATT00001..txt><ATT00002..txt> >> > >> > >> > ------------------------------------------------------------------------------ >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > user administration capabilities and model configuration. Take >> > the hassle out of deploying and managing Subversion and the >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > _______________________________________________ >> > xmlpipedb-developer mailing list >> > xml...@li... >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > >> > <ATT00001..txt><ATT00002..txt> >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > <ATT00001..txt><ATT00002..txt> |
|
From: Richard B. <rbr...@gm...> - 2011-08-22 17:04:07
|
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
>>> > >
>>> > >
>>> > >
>>> ------------------------------------------------------------------------------
>>> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>>> > > user administration capabilities and model configuration. Take
>>> > > the hassle out of deploying and managing Subversion and the
>>> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>>> > > _______________________________________________
>>> > > xmlpipedb-developer mailing list
>>> > > xml...@li...
>>> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> > >
>>> > >
>>> > > <ATT00001..txt><ATT00002..txt>
>>> >
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>>> > user administration capabilities and model configuration. Take
>>> > the hassle out of deploying and managing Subversion and the
>>> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>>> > _______________________________________________
>>> > xmlpipedb-developer mailing list
>>> > xml...@li...
>>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> >
>>> >
>>> > <ATT00001..txt><ATT00002..txt>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
>>> user administration capabilities and model configuration. Take
>>> the hassle out of deploying and managing Subversion and the
>>> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>>> _______________________________________________
>>> xmlpipedb-developer mailing list
>>> xml...@li...
>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>
>>
>>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
>
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> ------------------------------------------------------------------------------
> Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
> user administration capabilities and model configuration. Take
> the hassle out of deploying and managing Subversion and the
> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
|
|
From: Richard B. <rbr...@gm...> - 2011-08-21 03:56:04
|
OK, ran a successful Ms export after attempting a fix for the speciesCustomizeTextField. (will commit my changes to ExportPanel1) Now I'm back to working with my multispecies postgres db containing Paeruginosa and Saureus. I plan to export 3 times from this db: 1. Paeruginosa alone 2. Saureus alone 3. both species selected I'll attempt a table comparison between the three to see how the system and info tables look and report back tomorrow. 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 >>> > > >>> > > >>> > > >>> ------------------------------------------------------------------------------ >>> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >>> > > user administration capabilities and model configuration. Take >>> > > the hassle out of deploying and managing Subversion and the >>> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >>> > > _______________________________________________ >>> > > xmlpipedb-developer mailing list >>> > > xml...@li... >>> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >>> > > >>> > > >>> > > <ATT00001..txt><ATT00002..txt> >>> > >>> > >>> > >>> ------------------------------------------------------------------------------ >>> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >>> > user administration capabilities and model configuration. Take >>> > the hassle out of deploying and managing Subversion and the >>> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >>> > _______________________________________________ >>> > xmlpipedb-developer mailing list >>> > xml...@li... >>> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >>> > >>> > >>> > <ATT00001..txt><ATT00002..txt> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >>> user administration capabilities and model configuration. Take >>> the hassle out of deploying and managing Subversion and the >>> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >>> _______________________________________________ >>> xmlpipedb-developer mailing list >>> xml...@li... >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >>> >> >> > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > |
|
From: John D. N. D. <do...@lm...> - 2011-08-20 16:37:08
|
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 > > > > > > > > > ------------------------------------------------------------------------------ > > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > > user administration capabilities and model configuration. Take > > > the hassle out of deploying and managing Subversion and the > > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > > _______________________________________________ > > > xmlpipedb-developer mailing list > > > xml...@li... > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > > > > <ATT00001..txt><ATT00002..txt> > > > > > > ------------------------------------------------------------------------------ > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > user administration capabilities and model configuration. Take > > the hassle out of deploying and managing Subversion and the > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > > xmlpipedb-developer mailing list > > xml...@li... > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > <ATT00001..txt><ATT00002..txt> > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
|
From: Richard B. <rbr...@gm...> - 2011-08-20 16:17:20
|
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 >> > > >> > > >> > > >> ------------------------------------------------------------------------------ >> > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > > user administration capabilities and model configuration. Take >> > > the hassle out of deploying and managing Subversion and the >> > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > > _______________________________________________ >> > > xmlpipedb-developer mailing list >> > > xml...@li... >> > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > >> > > >> > > <ATT00001..txt><ATT00002..txt> >> > >> > >> > >> ------------------------------------------------------------------------------ >> > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> > user administration capabilities and model configuration. Take >> > the hassle out of deploying and managing Subversion and the >> > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> > _______________________________________________ >> > xmlpipedb-developer mailing list >> > xml...@li... >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > >> > <ATT00001..txt><ATT00002..txt> >> >> >> >> ------------------------------------------------------------------------------ >> Get a FREE DOWNLOAD! and learn more about uberSVN rich system, >> user administration capabilities and model configuration. Take >> the hassle out of deploying and managing Subversion and the >> tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > |
|
From: Richard B. <rbr...@gm...> - 2011-08-20 16:07:43
|
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 > > > > > > > > > > ------------------------------------------------------------------------------ > > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > > user administration capabilities and model configuration. Take > > > the hassle out of deploying and managing Subversion and the > > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > > _______________________________________________ > > > xmlpipedb-developer mailing list > > > xml...@li... > > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > > > > <ATT00001..txt><ATT00002..txt> > > > > > > > ------------------------------------------------------------------------------ > > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > > user administration capabilities and model configuration. Take > > the hassle out of deploying and managing Subversion and the > > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > > _______________________________________________ > > xmlpipedb-developer mailing list > > xml...@li... > > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > > > > > > <ATT00001..txt><ATT00002..txt> > > > > ------------------------------------------------------------------------------ > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer > |
16 messages has been excluded from this view by a project administrator.
