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From: Richard B. <rbr...@gm...> - 2011-08-20 16:17:20
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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 >> > > |
