OEWG 20120221

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OBO-Edit Working Group Meeting: Tuesday, February 21, 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, Heiko, Ramona, Midori, Laurel

Bug and Feature Trackers


  • Warn about possible stale config files when launching new version
    Warning about perspectives
    Warning about perspectives
    • Whenever you upgrade to a new version of OBO-Edit, there is the risk that out-of-date binary files in your ~/oboedit_config (mostly in oboedit_config/perspectives) will cause bad behavior of various unexpected sorts (perhaps even the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.
        • Midori and Ramona confirmed that they have frequently (and recently) observed OE "bugs" that are cured by removing their perspectives directory, so it's clearly still important.

Fixed or newly added since last meeting

  • Quick save lets you save the first time when it shouldn't
    • If you loaded via Advanced interface, you could then do a Quick Save the first time you saved (but it didn't actually know yet what file to save to, so it tried to save to null).
    • Ramona reported a bug in quick save--will submit bug report
  • 64bit JRE can not be used on windows 7
    • Windows apparently doesn't let you designate a preferred Java version, so the installer can do no better than using the first Java it comes across. The fix is that we will distribute two Windows installers: 32-bit and 64-bit, and let Windows users choose the appropriate one.

Currently working on

  • Query bug makes choosing relation impossible
    Compound query
    Compound query
    • David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."
    • It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.
    • The problem started in 2.1-b16 (released in July 2011). Before that, the ontology-specific relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.
  • 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


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