Re: [XMLPipeDB-developer] UniProtDatabaseProfile submits
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From: Richard B. <rbr...@gm...> - 2011-09-05 00:45:30
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ok, performed a two species export and the info table now contains only two species names in the form: species1|species2 Looks good. Richard On Sun, Sep 4, 2011 at 12:45 PM, Richard Brous <rbr...@gm...> wrote: > Thanks for sourcing this... I hadn't had any luck in doing so. > > Compiled and running a test export now before I head to the beach. > > Will let you know how it goes. > > Richard > > On Sun, Sep 4, 2011 at 12:25 AM, John David N. Dionisio <do...@lm...>wrote: > >> Hi Rich, >> >> I took a look at the getInfoTableManager code and may have located the >> problem. I committed the possible fix, with a comment above it explaining >> why. Next time you do an export, keep an eye on that species name when more >> than one species is selected and report back as needed. >> >> John David N. Dionisio, PhD >> Associate Professor, Computer Science >> Associate Director, University Honors Program >> Loyola Marymount University >> >> >> >> On Sep 2, 2011, at 11:21 AM, Richard Brous wrote: >> >> > roger, thanks. >> > >> > richard >> > >> > On Fri, Sep 2, 2011 at 11:10 AM, John David N. Dionisio <do...@lm...> >> wrote: >> > OK, thanks. I will look into issue #1 concurrently and will report >> back. Regarding issue #2, I confirmed with Kam that we do need the >> per-species value for each ID. As we are prioritizing database approaches >> first, here you have a distinct exercise in SQL formation that is relevant >> to the tutorial course: >> > >> > - Modify the formed query so that it returns, for each ID, the >> corresponding species name. If successful, you will then have both ID and >> species name to provide to tableManager.submit, and you will not need an >> outer loop for every species profile. >> > >> > The way I suggest you do this is to form a valid query directly in >> PostgreSQL (i.e., via pgAdmin or psql). That should be pretty easy to get >> since you are logging the final query string --- just copy and paste that. >> Experiment with the query directly within PostgreSQL until you have one >> that works. Then transplant that into the code. >> > >> > John David N. Dionisio, PhD >> > Associate Professor, Computer Science >> > Associate Director, University Honors Program >> > Loyola Marymount University >> > >> > >> > >> > On Sep 2, 2011, at 11:04 AM, Richard Brous wrote: >> > >> > > OK, so still two outstanding issues regarding the last 2 modified >> methods: >> > > >> > > 1. getInfoTableManager() >> > > >> > > Still returning 3 species names when only two are selected. Returns >> one species name when only one is selected. >> > > - I will review the loop again and see if I can determine what is >> going on here. >> > > >> > > 2. getSystemTableManager() >> > > >> > > I added a for loop within the while condition which after discussions >> we know is incorrect. Will pull that out but we need to determine how to >> move forward with the issue of determining which species each id belongs to. >> removed loop and submitted to SourceForge but now build is essentially >> broken till we figure out the wrinkle. Adding a for speciesprofile loop at >> the top was discussed as a solution of last resort. >> > > >> > > UniProtDatabaseProfile - while loop begins at line # 585 >> > > >> > > >> --------------------------------------------------------------------------------------------------------------- >> > > >> > > Also made modifications to getSystemsTableManager() which applies the >> species customizations for each species profile selected. Seems correct to >> me but please confirm. >> > > >> > > >> -------------------------------------------------------------------------------------------------------------- >> > > >> > > Discussions surrounding getPrimarySystemTableManager() assumed likely >> bad coding since it seems to call for a customized schema although it is >> identical to the default UniProt schema. >> > > >> > > It calls getPrimarySystemTableManagerCustomizations() which is >> specific to Arabidopsis thaliana and Ecoli only. >> > > >> > > Didn't want to dig into this yet until other higher priority >> modifications were done first plus I believe a discussion with Dr. D was >> going to occur as well. >> > > >> > > >> --------------------------------------------------------------------------------------------------------------- >> > > >> > > getRelationsTableManager() is the last method which remains untouched >> but I will start reviewing and come up with a plan of attack. >> > > >> > > >> -------------------------------------------------------------------------------------------------------------- >> > > >> > > These are all the loose ends I can think of to document. >> > > >> > > Thanks! >> > > >> > > Richard >> > > >> > > >> > > >> > > On Wed, Aug 31, 2011 at 12:52 PM, Richard Brous <rbr...@gm...> >> wrote: >> > > Submitted changes to UniProtDatabaseProfile based on the logical >> corrections from yesterdays convo with Dondi. >> > > >> > > These do not yet include the discussed optimizations, just wanted to >> get it working and do some test exports... which completed successfully. >> > > >> > > I also added a for loop under the while loop in >> getSystemTableManager() to ensure each query result is processed for each >> selected species profile. >> > > The loop is on line 587 and I added it because it seemed a solution to >> have each species profile included... is this correct or should I be >> submitting all at once versus each species? >> > > >> > > Richard >> > > >> > > <ATT00001..txt><ATT00002..txt> >> > >> > >> > >> ------------------------------------------------------------------------------ >> > Special Offer -- Download ArcSight Logger for FREE! >> > Finally, a world-class log management solution at an even better >> > price-free! And you'll get a free "Love Thy Logs" t-shirt when you >> > download Logger. Secure your free ArcSight Logger TODAY! >> > http://p.sf.net/sfu/arcsisghtdev2dev >> > _______________________________________________ >> > xmlpipedb-developer mailing list >> > xml...@li... >> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > >> > <ATT00001..txt><ATT00002..txt> >> >> >> >> ------------------------------------------------------------------------------ >> Special Offer -- Download ArcSight Logger for FREE! >> Finally, a world-class log management solution at an even better >> price-free! And you'll get a free "Love Thy Logs" t-shirt when you >> download Logger. Secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsisghtdev2dev >> _______________________________________________ >> xmlpipedb-developer mailing list >> xml...@li... >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer >> > > |