OEWG 20120117

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OBO-Edit Working Group Meeting: Tuesday, January 17, 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, Harold, Ramona, Paola, Chris M.

Bug and Feature Trackers


  • GO Editors have switched to using 2.1.0, and it seems to be working well in general.
  • Harold thought that the latest version seemed to start up slower than the previous release candidate a few weeks ago. I'm not aware of any reason why this should happen--has anyone else observed this?
    • My tests show the startup time to be the same (it prints how long it takes to start up, so I'm not just going by my subjective impression).
    • You could try moving your oboedit_config to see if that helps.
    • You didn't add any new filters or anything, right? (Right.)
    • Maybe you just noticed the startup time more because you were paying attention because it was a new version?
  • Can't save cross products (in OE1 or OE2)
    • I haven't heard any more reports about this. Can I close this bug report? (Yes.)
  • Allow extended characters (except in dbxrefs) broken
    Warning about needing to restart OE after changing configuration
    Warning about needing to restart OE after changing configuration
    • As far as I can tell, this works fine. I wrote to the bug submitter (Ceri): "If you changed the "Allow extended characters" setting in the Configuration Manager, you must quit and restart OBO-Edit for that to take effect. Try that and try saving cell.edit.obo again and it should work. Please try it and let me know." (She hasn't replied yet.)
    • Does the Configuration Manager need to state more clearly that you have to quit and restart before your changes take effect? Maybe a popup message when you click "Save Configuration"? (See image to right)
  • Autocommit text edits not working
    • Alarming if true. In my tests, it works fine. I suspect she's encountering the problem of stale binary files in her oboedit_config, as Paola did last week. I suggested removing her ~/oboedit_config/perspectives directory. Haven't heard back yet.
    • A few other users said that Autocommit is working fine for them.
  • I am looking for a few users to test the new features we've added (see below) before doing a public release.

Fixed or newly added since last meeting

  • Chris and Heiko got OBO<->OWL conversion working inside OE
  • When you load a file, say foo.obo, and then edit it and save it as, say, bar.obo, the OE titlebar still says foo.obo. Would be nice if the title would change to the saved filename.
    • Fixed
  • Automatic detection of changed files/reload option
    Warning about file changing on disk
    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).
      • If you've loaded multiple files, it only checks the first one. I could (with some more work) make it check all of them.
    • cvs revision tag check Jane requested, "Can OE look at the cvs revision in the header of the file to see that the file it's saving over is the same as the one it loaded? And if not, give a warning. We occasionally lose changes this way if we cvs update before saving in OE - OE writes over the patched file when the save is then made."
      • This is a special case of checking whether the file has changed on disk, and will be covered by that (but OE will not specifically check cvs revision information)
    • This new feature (warning when your file has changed on disk) is not working right for Paola and Becky--something about the CVS version? It's claiming the file changed on disk *while* they're doing a save. I didn't understand their scenario--they see the CVS version in the Save GUI? Paola will send Nomi screenshots.
  • quick save
    Save warning
    Save warning
    • 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 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 quickly and silently use the same save profile.
        • Warn users so they're not confused by this behavior? (See popup warning at right) After you OK that warning, you get the Save As interface.
      • Should quick Save be totally silent, or should it pop up a "Saved as foo.obo" message (which it could then kill after a second or two)?
          • People liked that idea--it's nice to see *some* confirmation that the save happened.
          • Nomi had a cool idea that there could be some visual indicator whenever you have unsaved changes (perhaps a * in the OE titlebar or something), and then when you saved this indicator would go away, so you would know the save happened. Other people didn't seem to think this would be cool enough to be worth the work it would take.
  • The version number in the installed version was coming out as 2.1 instead of 2.1.0
    • Fixed

Currently working on

  • 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 comment out that fix, then you can delete the genus by erasing it, but then you get the problem where it goes away when you don't want it to!
    • I'm trying to fix this and/or to get the genus trashcan working in Autocommit mode

Next bugs/feature requests to work on


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