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: Richard B. <rbr...@gm...> - 2011-11-06 18:28:50
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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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