OEWG 20120306

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OBO-Edit Working Group Meeting: Tuesday, March 6, 2012, 8:30am PST

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

Agenda/Chair: Nomi Harris
Minutes: Nomi
Attendees: Nomi, Midori, Heiko, Ramona, Karen

Bug and Feature Trackers

Fixed or newly added since last meeting

  • In compound ancestor/descendant queries, relation list bad
    Compound query
    Compound query
    • In a compound search with two aspects (see example on right), the relation pulldown lists didn't behave well. This turned out to be because of basically infinite refreshing of the lists.
  • quick save not working properly
    • Was letting you do Quick Save before you'd done Save As on that file.
    • Worked fine when I launched from the command line--bug appeared only when you launched via the OE icon.

Currently working on

  • Deleted differentia (in XP editor) sometimes reappear
    • Non-deterministic--you can load the same ontology file and delete the same differentium, and sometimes it will reappear whereas other times it will stay gone.
      • When the differentium comes back, console shows error message, "Couldn't delete non-existant [sic] relationship regulation of carbohydrate utilization ~~regulates~~> carbohydrate utilization)"
    • Seems to occur when there's a regular relation that's redundant with a cross-product, e.g.,
id: GO:0043610
name: regulation of carbohydrate utilization
is_a: GO:0050789 ! regulation of biological process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009758 ! carbohydrate utilization
relationship: regulates GO:0009758 ! carbohydrate utilization


  • OBO-Edit 2.1.1-b7 released on 28 February
  • Warn about possible stale config files when launching new version
    • Whenever you upgrade to a new version of OBO-Edit, there is the risk that out-of-date binary files in your ~/oboedit_config (mostly in oboedit_config/perspectives) will cause bad behavior of various unexpected sorts (perhaps even the relation-choosing issue above). Now a warning message pops up the first time you run a new OBO-Edit release (and it offers to rename oboedit_config/perspectives for you.)
      • Reworded warning. Added a popup message that appears if you say Yes to the move that tells you where the directory was moved to.
      • The consequences of not renaming/resetting your oboedit_config/perspectives can be serious enough that I'm considering just having it just move the perspectives directory automatically when you upgrade OE, tell you where it's moved to, and let power users restore it themselves if they want to. Opinions?
        • People agreed that it might be less confusing/intimidating to have OE rename your perspectives directory without asking first. It will tell you where it moved it to, and power users can restore it at their own risk.
        • Update: I decided NOT to have it move your perspectives without asking, mostly because it would be so extremely annoying to ME as I try to debug (I often run different versions to compare them).
  • Obo-edit control keys on windows 7
    • "I use obo edit(2.1 or 2.1.6beta) and installed it on windows 7. When I press any control key (shift, ctrl, alt) obo edit will delete loaded data and make some action. Dialog with title "Progress..." will pop up and in less than 1 sec will dissapear [sic]."
    • Another user (a student of Karen Eilbeck's) had a similar problem: "Whenever she goes to type/edit she gets a window that says 'do you want to proceed, etc etc', the same behavior you get when you go to file and click 'new ontology'. So basically any editing becomes a task of clicking away spurious windows. She is using java version 1.6 build 26.
    • The first user said, "Keyboard listener problem is better name for this problem. Any typing in search box cause this behavior. I have latest version of java 1.7.0_02. I deleted whole directory /oboedit_config and let OBO_edit to create a new one. But did not help. We have in office another windows, there it works fine. The problem on my notebook remains."
    • Several of us tested OE on Windows 7 and it worked fine for us, so I have no idea what the problem is or what else to try.
  • Next meeting April 3


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