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From: Richard B. <rbr...@gm...> - 2011-08-20 03:47:57
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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 >> > > |
