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:

Bug and Feature Trackers

Discussion

  • 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    • Whenever you upgrade to a new version of OBO-Edit, there is the risk that out-of-date binary files in your ~/oboedit_config (mostly in oboedit_config/perspectives) will cause bad behavior of various unexpected sorts (perhaps even the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.)
      • Added a popup message that tells you where the directory was moved
      • The consequences of not renaming/resetting your oboedit_config/perspectives are annoying 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?

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).
  • 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 to istribute two Windows installers: 32-bit and 64-bit, and let Windows users choose the appropriate one.

Currently working on

  • Graph Editor makes Text Editor show old version of term
    Graph Editor makes Text Editor show stale version of term
    Graph Editor makes Text Editor show stale version of term
    • This is not a new issue (2.0 has it), but it's going to be more of a problem with a workflow that involves making changes to ontology files both inside OBO-Edit and outside in other applications (e.g., Protege) running at the same time.
    • If you look at a term in the Text Editor, and then reload a changed-on-disk version of the current ontology file (with, for example, a changed term name) and look at the term again by reselecting it 'from the Graph Editor' you see, misleadingly, the OLD version of the term. (The Graph Editor itself correctly shows the new version of the term.) (See image at right.) If you instead select the term from the OTE, the new version shows up.
      • It looks as though the stale term is cached somewhere down in the Piccolo code that the Graph Editor uses. This is not going to be easy to fix.
    • Most people present today said they don't tend to click on the Graph Editor to look at terms in the Text Editor, so this bug probably wouldn't affect them much.
  • 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

Links

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