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From: Richard B. <rbr...@gm...> - 2011-08-20 15:58:45
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sound advice... I'll keep it in mind going forward. added logging to getSystemTableManager() query richard On Fri, Aug 19, 2011 at 10:10 PM, John David N. Dionisio <do...@lm...>wrote: > Greetings, > > Ah yes, I know this type of bug well. :) This is how I avoid/deal with > it: before running the application, I formulate the query separately (some > combination of copy/paste and manual typing) then issue it directly in the > relational database first. This way, I can assure myself that the query is > correct on its own, and can fix problems with that query in that context > before embedding it in the application code. > > That way, when the application runs, you can attribute problems to the code > that processes the query results, or, in the case of dynamically generated > queries like this one, to the code that forms the query string. You can be > fairly confident that the query itself is right, because you have run it > independently beforehand and verified that it returns the results that you > want. > > It is also helpful to log the final query string prior to executing it. > That way, you can see the exact query that was issued, and can copy/paste > it directly into pgAdmin in case it requires some troubleshooting or > debugging. > > Hope this helps (in case query problems persist)... > > 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 > |
