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From: Richard B. <rbr...@gm...> - 2011-08-23 02:40:40
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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. 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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 > |
