OEWG 20120207

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OBO-Edit Working Group Meeting: Tuesday, February 7, 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, Chris M., Harold, Midori, Heiko

Bug and Feature Trackers


  • Participants in the annotation workshop successfully used the latest (2.1.1-b4) OBO-Edit
  • Automatic detection of changed files/reload option
    Warning about file changing on disk
    • Added a new background thread that checks whether the file you're looking at has changed on disk since you last loaded or saved it.
    • Rather than trying to reload the file itself (which was problematic due to OE's control flow), it pops up a message that the file has changed on disk and advising you to reload it (see screenshot at right).
      • Some issues fixed. Is this working well for everyone?
      • Last time we met, Paola reported problems with it, but never sent Nomi screenshots. Does the new version (2.1.1-b4) work right?
  • quick save
    • For years, OE users have longed for a quick save (command-S) that just saves in the last-used file instead of making you go through the Save As GUI. I have now implemented this.
      • The FIRST time you save with a particular adapter (e.g., OBO or OWL) in an OE session, it makes you use the Save As interface (rather than trying to guess all the save configuration options). After the first save, you can do quick save, which will use the same save profile.
        • I decided to get rid of the popup telling you you have to Save As the first time you save--it had more potential to be annoying than useful.
      • Quick Save pops up a "Saved as foo.obo" message and then deletes it after 1.5 seconds.
  • Chris and Heiko got OBO<->OWL conversion working inside OE
    • Note: if Chris can't make it to the meeting today, we'll discuss this when he's available.
    • Documentation added; some issues fixed.
    • Fixed issue where file browser strips off .owl extension if you select an existing .owl file. (Can't fix problem in file browser itself, which is native, but the OWL adapter now restores the .owl extension after you select the file.)
    • Note that some things that are permissible in OWL (e.g., two definitions for one term, or external dependencies) are not in OBO, so there are legal OWL files that can't be converted to OBO.
      • Error reporting for this could be better.

Fixed or newly added since last meeting

  • Warn about possible stale config files when launching new version
    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 (for example, sometimes it makes Autocommit in the Text Editor not work). Now a warning message about it pops up the first time you run a new OBO-Edit release (and it offers to rename oboedit_config/perspectives for you.)
      • Harold asked what you lose if you get rid of your perspectives directory--do you, for example, lose load and save profiles? Nomi said no, all you lose is your layout. She will add text to the popup about this.
      • Midori asked where it moves your perspectives directory to. Nomi said it's still in your oboedit_config, now called perspectives_something. She will add a note about this to the popup (but we don't want it to get TOO verbose).
  • Can't delete genus in cross product tab -- if you erase the genus from the genus box and then commit, the genus comes back.
    • It turns out this broke around v2.1-b5 due to a fix that addressed a problem where the genus in the xp would disappear. If I commented out that fix, then you could delete the genus by erasing it, but then you get the problem where it goes away when you don't want it to!
    • After much work, I managed to fix this. You should now be able to delete the genus by simply erasing it in the genus field.
    • Midori said that this worked for her, but she found examples where an erased differentium returned from the dead. She will send examples to Nomi.
  • Minor fix: When user saves their work in a file, the titlebar changes to show the new filename--but don't do that if the save was an autosave.
  • Can't launch two (recent) OBO-Edits at the same time
    • Heiko was able to fix this by upgrading our InstallAnywhere (the software we use to build the installers for OBO-Edit and Oort)

Currently working on

  • Graph Editor makes Text Editor show old 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.
  • tree editor not displaying correctly with reasoner on
    • Ramona wrote, "Whenever I move a term to a new parent (by dragging and dropping in the tree editor) with the reasoner on, the term does not display in its proper place in the ree. If the term has no other parents, it just displays as a root term (even though the parent editor shows it has the correct is_a parent). If the term has another parent (like a part_of parent), it only shows that parent in the tree. If I do the same thing with the reasoner off, it renders correctly. Quitting OE and re-opening it fixes the problem."
    • I have now reproduced this problem and determined that it was introduced between release 2.1-beta6 and 2.1-beta7.
    • How important is this to fix (as compared with other old bugs)?
      • No one on the call today edits with the reasoner on (they turn it on just to check things after editing), so it's probably not a high priority.

Next bugs/feature requests to work on


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