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From: Richard B. <rbr...@gm...> - 2011-08-21 03:56:04
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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 > > |
