Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released
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From: John D. N. D. <do...@lm...> - 2011-11-07 06:31:35
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Greetings, Yes, the missed section (method) is UniProtDatabaseProfile.getPrimarySystemTableManager. If you look at the current commit, you will see that it still uses only the first species profile in the selected collection. The other methods have been duly tweaked, and as far as I can tell look largely OK. I've done a couple of exports at this point, and found some things to tweak with each one, but I think I am at a point where I can commit then release soon. I have just one more export in progress to verify the latest changes, then I'll stop there. John David N. Dionisio, PhD Associate Professor, Computer Science Associate Director, University Honors Program Loyola Marymount University On Nov 6, 2011, at 10:28 AM, Richard Brous wrote: > Interesting, what missed section??!! > > Look forward to the new build so I can do some testing on my own. > > > Richard > > On Sun, Nov 6, 2011 at 12:15 AM, John David N. Dionisio <do...@lm...> wrote: > Greetings, > > I just wanted to post an update that a new build (2.0b66) will be on its way in a day or so. I'm just waiting for a test export run to conclude then will proceed based on how that goes. > > This build will have the right taxon ID for S. cerevisiae, will supply a species name if the generic species profile is used (i.e., selected species does not have a custom profile), and, finally, may address the bug that Rich as reported about a single ID only appearing in a supposed multi-species export. > > The first two fixes are relatively straightforward and easy to confirm without doing a full export, but the last one needs the export for confirmation. The issue with this is that there was actually a step that got overlooked in the "multiple species" transition. I was in a holding pattern with that for so long because I had focused in the sections that Rich had changed, thinking that there may be a bug there, when it may turn out that the issue was in something that was actually *not* changed in his last round of commits (and thus it did not go under the microscope until I finally stepped a little further back to see what was going on through the overall export process). > > Anyway, we will see after this export whether I was barking up the right tree. Stay tuned :) > > John David N. Dionisio, PhD > Associate Professor, Computer Science > Associate Director, University Honors Program > Loyola Marymount University > > > On Nov 2, 2011, at 4:33 PM, Kam Dahlquist wrote: > > > Hi, > > > > Yes, sorry, that is the correct taxon ID and it should be changed. > > > > Best, > > Kam > > > > At 04:16 PM 11/2/2011, you wrote: > >> Yes, a query for the name should be doable. It will be a matter of > >> finding the right time/place to do it. > >> > >> Also, just to confirm, should the taxon ID be changed then to 559292? > >> > >> John David N. Dionisio, PhD > >> Associate Professor, Computer Science > >> Associate Director, University Honors Program > >> Loyola Marymount University > >> > >> > >> > >> On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote: > >> > >>> Hi, > >>> > >>> Ah. So I think what happened is the same thing with E. coli, they > >>> made an ID for a more specific strain (in this case S288c) because > >>> they are sequencing more substrains of yeast. > >>> > >>> I think option 1 below is the way to go. Can't we discover what the > >>> name is by reading the xml? > >>> > >>> Thanks, > >>> Kam > >>> > >>> At 10:53 PM 11/1/2011, John David N. Dionisio wrote: > >>>> Greetings, > >>>> > >>>> I checked the S. cerevisiae species profile in the code and its > >>>> Taxon ID is 4932. Thus, you were indeed seeing a generic species > >>>> profile being called up to do this export because the included yeast > >>>> profile did not have a matching Taxon ID. > >>>> > >>>> I can change the profile to use 559292 no problem. However, this > >>>> scenario still reveals a bug for when the generic species profile is > >>>> invoked: the species name becomes null, and code that processes this > >>>> name crashes on that condition. > >>>> > >>>> For this latter issue, there are two ways to fix it: > >>>> > >>>> - Make the generic species profile still provide some kind of > >>>> species name (or make the user enter one?). > >>>> - Make the export code more robust by not crashing in the case where > >>>> the species name is null. > >>>> > >>>> I'm thinking that the former is the right way to go (the species > >>>> name is used to offer a default filename for the GDB, as well as for > >>>> various columns in the GDB schema, so its being null or blank may > >>>> cause issues in that aspect). > >>>> > >>>> John David N. Dionisio, PhD > >>>> Associate Professor, Computer Science > >>>> Associate Director, University Honors Program > >>>> Loyola Marymount University > >>>> > >>>> > >>>> On Nov 1, 2011, at 4:32 PM, Kam Dahlquist wrote: > >>>> > >>>>> This time with attachments. > >>>>> > >>>>> At 04:31 PM 11/1/2011, Kam Dahlquist wrote: > >>>>>> Hi, > >>>>>> > >>>>>> I finally had a chance to try a yeast export wtih GMB2.0b65--I > >>>>>> didn't get very far: > >>>>>> > >>>>>> 1. I imported the UniProt, GO, and GOA all fine. When I started > >>>>>> the export, the Species panel listed "Taxon ID 559292, > >>>>>> null". That's the correct taxon ID for the species I am > >>>>>> importing/exporting, but shouldn't it also tell me the species name, > >>>>>> not just null? or is that what happens when the generic profile is > >>>>>> called. There should be a Saccharomyces cerevisiae profile in > >>>>>> GenMAPP Builder somewhere, even though we never finished it. > >>>>>> > >>>>>> 2. In the next window, I click on the box "Save GenMAPP Database > >>>>>> File As..." and nothing happens. Screenshots of the console window > >>>>>> (parts 1 and 2, could not fit into one screen) are attached. > >>>>>> > >>>>>> 3. The title bar and notes field of the export wizard did not get > >>>>>> updated to gmb2.0b65. > >>>>>> > >>>>>> Thanks, > >>>>>> Kam > >>>>>> > >>>>>> At 11:13 PM 10/14/2011, you wrote: > >>>>>>> GenMAPP Builder 2.0b65 Release Notes > >>>>>>> > >>>>>>> This release of GenMAPP Builder includes a preliminary > >>>>>>> implementation of multi-species Gene Database exports, as well as > >>>>>>> user interface changes to the export wizard. 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