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...> - 2011-11-06 07:15:43
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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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