OEWG 20110607

OBO-Edit Working Group Meeting: Tuesday, June 7, 2011, 8:30am PDT

Conference call numbers:
US: 1 866 953 9688
UK: 0808 238 6001
PIN: 801561

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Chris Mungall, Heiko Dietze, Karen Christie, Laurel Cooper, Paola Roncaglia, Ramona Walls

Bug and Feature Trackers

Is_a closure broken
- Filtered save with "is_a closure" checked not saving the right terms.
- There turned out to be multiple problems in the code, the most egregious of which was that the getAncestors methods had an erroneous "!" that was looking for terms that DIDN'T match the requested filter rather than those that did!
Made definitions of obsolete terms editable
Made titlebar of Text Editor say "(OBSOLETE TERM)" in red if it's showing a term that's obsolete.
Ontology Term Generation plugin fixed by its authors

Problem Running in Windows 7
- This bug has been reported multiple times, e.g. Unable to start oboedit 2.1.3 windows version
- Looks like the prescribed fix was to use a lower memory allocation than the one suggested by the installer. If that works for Alyona, I will add it to the user guide and maybe even to the text on the installer page that asks you to set the memory. (Not that people will actually read it, but at least we can then point them to the text when they complain.)
Bad handling of unrecognized relation (text editor et al.)
- I have started looking into this. Has to do with how dangling objects (e.g., unrecognized relations) are handled in different components. Each component (e.g., Text Editor, Parent Editor, etc.) will have to be debugged separately.
- Unrecognized relations in cross-products seem to behave differently from non-cross-product ones.

Action Item from last meeting: OEWG members will look at the bug and feature trackers (sorted in descending order by priority) and reprioritize where appropriate (or ask Nomi to reprioritize if they don't have permission to change priorities) and suggest to Nomi which bugs to look at next.
- Bugs with priority 6, Features with priority 6-7
- OEWG group members at this meeting didn't get a chance to look at these yet but will soon.
  - Ramona sent me comments and priority adjustments for several bugs
  - Paola said OE is working well for her so she doesn't have any priority adjustments
Karen C. said that the Graph Editor seems to have a strange/buggy way of counting relationship links--it will often have a menu item that says, say, "expand 5 children", and when you click it, it only shows three children. It must be double-counting some of the relationships (maybe cross-products). Karen will submit a bug report.
OEWG members should tell me if they're not satisfied with how I made definitions of obsolete terms editable and made the titlebar of the Text Editor say "OBSOLETE TERM" in red when it's showing a term that's obsolete.
Bad handling of unrecognized relation: Chris M. suggests handling this by creating dummy relations at load time for unrecognized relationships. Nomi will look into this.