I restarted OE and the problem below did not seem to appear again.
As I mentioned, I had had OE open for only a short time when I noticed
the problem yesterday, but I haven't been able to reproduce it today.
At any rate, after restarting OE, I have also renamed the perspectives
Should the problem occur again, I'll send you a detailed report.
Thanks and sorry for the bother,
On 1/9/12 10:34 PM, Nomi Harris wrote:
> On Jan 9, 2012, at 2:05 PM, Paola Roncaglia wrote:
>> Hi Nomi, thanks for your prompt reply.
>>> A few questions:
>>> - When you say you "couldn't see your changes", do you mean you made changes, clicked Commit, and your changes went away and the synonyms and dbxref reverted to how they looked before you made the changes?
>>> - I assume you're working with Autocommit off (so you have to click Commit to commit your changes)?
>>> - Did you try quitting and restarting OE and doing the edits again? If so, what happened?
>> I didn't try, because I didn't want to lose my "good" edits, but above all I wanted to figure out if the edits had been saved or not. I will certainly try that, if the problem occurs again.
>>> - The other thing I would suggest is renaming your ~/oboedit_config (renaming rather than removing, so you can restore it if desired) and restarting OBO-Edit. Because some things in oboedit_config (particularly the perspectives) are binary objects, they can cause unexpected problems when you switch to a new version of OBO-Edit. You can also try only removing or renaming your ~/oboedit_config/perspectives subdirectory. That usually works as well as removing the whole oboedit_config, and that way you only lose your preferred component layout and not any of your other personal settings.
>> Thanks for the tip. I'll certainly try that tomorrow, sorry but it's 10pm here :-}
>>> If you can find a repeatable instance where the commit is failing, please tell me and I will immediately investigate. I can't do anything with the nonspecific error report you sent (though of course it's still good that you sent it!).
>> Tomorrow I'll try adding some synonyms and report back with full details if the issue presents itself again. Apologies if my report today was not descriptive enough, I wanted to post it right away. On further thought, I think the oboedit_config directory suggestion may be the one to try out first. So I'll do that, then try adding some synonyms. I'll get back to you tomorrow. Thanks for your help.
> Suggestion: BEFORE you move your oboedit_config directory, restart OBO-Edit and see if you are still seeing the commit problem. THEN rename your oboedit_config and see if the problem goes away. If it doesn't go away, please give me specifics (which ontology you loaded, which term you changed, what exactly you did to it) and also send me your oboedit log file and I'll investigate.
>>> On Jan 9, 2012, at 1:38 PM, Paola Roncaglia wrote:
>>>> Hi Nomi,
>>>> I'm using the latest download of OE 2.1. Last week I seemed to notice a
>>>> fleeting behavior of edits not showing up after commit, but I wasn't
>>>> sure, and at any rate I could see my commits if I clicked on a different
>>>> term and then went back to the one I had edited. I remembered that that
>>>> behavior had already been noticed occasionally so it wasn't a new bug.
>>>> Today, however, the behavior occurred again and this time I could not
>>>> see my edits even if I moved to another term and then back. I tried to
>>>> do the same edits again and still they wouldn't show up. I had no way to
>>>> know if my changes had been recorded or not, so I went ahead and saved,
>>>> and updated the obo file in cvs. When I did a diff, I could indeed see
>>>> my changes. Has anyone else noticed this?
>>>> If it's any use, here's a summary of my edits:
>>>> I did all of them in a single (quick) session;
>>>> I added 2 new terms in - and these changes where recorded upon commit;
>>>> then I did some simple edits in the definition of 3 terms and added
>>>> synonyms and a Dbxref to these same terms; after working on each term, I
>>>> clicked Commit, and that's when I couldn't see any of my changes.
>>>> I had only had OE open for maybe an hour, and it was working fine otherwise.
>>>> Any advice what I may be doing wrong?
>>>> Dr Paola Roncaglia
>>>> GO Editorial Office
>>>> Wellcome Trust Genome Campus
>>>> Cambridgeshire, UK
>>>> CB10 1SD
>>>> p: +44 1223 492600
>>>> f: +44 1223 494468
>> Dr Paola Roncaglia
>> GO Editorial Office
>> Wellcome Trust Genome Campus
>> Cambridgeshire, UK
>> CB10 1SD
>> p: +44 1223 492600
>> f: +44 1223 494468
Dr Paola Roncaglia
GO Editorial Office
Wellcome Trust Genome Campus
p: +44 1223 492600
f: +44 1223 494468