OEWG 20110208

OBO-Edit Working Group Meeting: Tuesday, February 8th, 2011, 8:30am PST

Conference call details: New GOC conference call numbers
US: 1 866 953 9688
UK: 0808 238 6001
pin: 801561

Agenda/Chair: Nomi Harris
Minutes:
Attendees:

Bug and Feature Tracker Updates

• OE Bug tracker
• OE Feature tracker

Discussion items

• Nomi will be away during our next scheduled meeting (22 Feb). Should we:
  • Skip that meeting and meet in four weeks (8 Mar)?
  • Meet in three weeks (1 Mar) and then every two weeks after that? (Would that confuse people?)
  • Meet some other day during the week of 22 Feb? (Any other day that week is ok with Nomi.)

Fixed since last meeting:

• hitting return just selects first term from dropdown list
  irritating selection bug in autocompletion-searches (b30)
  • Several similar bug reports were closed as fixed in 2.1-b7, but they weren't--it would still choose the first item in the list if you moused down in the list and then hit return. Now it's really fixed.
• Users with older Macs that don't have Java 1.6 (such as Ramona) couldn't launch OE--see also The JVM could not be started
  • Fixed--OE installer will now work even if you only have Java 1.5.
  • Pre-release available for those who need it--ask Nomi in email.

Issues and action items carried over from last meeting:

• Chris fixed the bug where OE was failing to exclude disjoint relationships when checking is_a complete.
  • Terry has question about is_a closure across different ontologies. He'll test beta8 and report any problems.
• Terry wrote instructors for configuring a renderer to color terms by namespace (Thanks, Terry!). Nomi needs to add this to user guide.
• Nomi will also add comments on reasoner + memory to user guide.
  • Marcus often gets out-of-memory warning. Nomi (and GO editors) also sees it with GO and the reasoner. Not an easy fix. Work-around: edit with reasoner off, then SAVE, then reason. Nomi will add note to user guide.
  • Brainstorming possible ways to remind users that reasoner is on/to turn off reasoner when quitting/etc.
• ID fixer: Chris thinks the ID fixer is buggy and that it needs to be fixed. However, I haven't seen any high-priority bugs posted about this (only a level-5 bug I posted myself several years ago). How important is this?
  • Most wg members don't even know what it does! Nomi will bring it up with Chris.

Currently working on:

• Obsolete terms appear in autocomplete dropdown lists.
  • Current status: implemented removal of obsolete terms from autocomplete lists for searches of "Any text field" (will implement for other types of searches.
    • This extra test slows down creation of autocomplete list.
    • Accordingly, Becky suggested making this a user-configurable option (whether or not to exclude obsolete terms from autocomplete lists). Will add to Configuration Manager.
    • I'm also looking into ways to speed up autocomplete.
• built in icons missing (Ramona)
  • I looked around and couldn't find H_UC.svg anywhere in any version. In all the versions I looked at, the built-in type icons (which live in src/org/oboedit/gui/resources/icons/typeicons) were the same 21 icons. I don't know where Becky got H_UC.svg from.

Next bugs to work on:

• Search term Filter returning wrong results
  Some filters give wrong answers unless reasoner turned on
  • Discussed with Chris. Agreed on short-term fix: "if an aspect of a search cannot be performed without the reasoner, then it should be greyed out or otherwise indicated."
  • Longer term possibilities--see discussion in Some filters give wrong answers unless reasoner turned on
• This issue is annoying me: Text icons for unknown relationships too small in Graph Ed. I'm thinking of trying to add a mouseover popup showing the whole relationship name (when you hover over the unreadable relationship icon)?
• Bad handling of unrecognized relation (text editor et al.)
  • I looked into this some--will not be simple to fix. Has to do with how dangling objects (e.g., unrecognized relations) are handled in different components.

Demo

none

Action Items

• Nomi to add Terry's instructions on how to use renderers to color terms by namespaces to the user guide.
• Nomi will add note about reasoner & memory to user guide.

Links

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