OEWG 20120417

OBO-Edit Working Group Meeting: Tuesday, April 17, 2012, 8:30am PDT

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

Bug and Feature Trackers

• OE Bug tracker
• OE Feature tracker

Fixed or newly added since last meeting

• Deleted differentia (in XP editor) sometimes reappear
  • This was the weird "nondeterministic" bug--sometimes the removal worked, sometimes it didn't.
  • Nomi will give Midori the latest release to test and make sure it really works

• allow obsolete term to have same name as live term
  • The issue here was that there were two terms with the same name but different IDs. Melissa wanted to be able to drag the live term onto the obsolete term and see the menu items for adding a consider or replaced_by relation between the two same-named terms, and it wasn't showing those menu items.
  • Ramona already tested the fix and said it works now.

Currently working on

• 'Select all' not working in Remove Redundant Links panel
  • Not a new problem.
  • Remove Redundant Links panel has other problems as well--how important is this component?
    • "Undo" doesn't undo enough in Remove Redundant Links (For example, if you use "Select All" and delete all the redundant links, Undo doesn't bring them back.)
    • Remove Redundant Links Panel doesn't refresh when it should (now fixed
  • Sometimes when you select a single redundant link and remove it, other links are removed as well--is this intentional? (Nomi will send Midori an example.)
  • Assert Implied Links panel also has similar (but not identical) problems. How important is this component?

Discussion

• Obo-edit control keys on windows 7
  • "I use obo edit(2.1 or 2.1.6beta) and installed it on windows 7. When I press any control key (shift, ctrl, alt) obo edit will delete loaded data and make some action. Dialog with title "Progress..." will pop up and in less than 1 sec will dissapear [sic]."
  • Another user (a student of Karen Eilbeck's) had a similar problem: "Whenever she goes to type/edit she gets a window that says 'do you want to proceed, etc etc', the same behavior you get when you go to file and click 'new ontology'. So basically any editing becomes a task of clicking away spurious windows. She is using java version 1.6 build 26.
  • The first user said, "Keyboard listener problem is better name for this problem. Any typing in search box cause this behavior. I have latest version of java 1.7.0_02. I deleted whole directory /oboedit_config and let OBO_edit to create a new one. But did not help. We have in office another windows, there it works fine. The problem on my notebook remains."
  • Several of us tested OE on Windows 7 and it worked fine for us, so I have no idea what the problem is or what else to try.
• "duplicate key" problem
  • "We are using OBO Edit () to manage vertebrate trait ontology development. When we port the OBO files from OBO Edit to Amigo for display, a small portion of the entries give rise to complains like:
    DBD::mysql::st execute failed: Duplicate entry '283-7-1' for key 1 at /usr/lib/perl5/site_perl/5.8.8/DBIx/DBStag.pm line 3314.
    I wonder if it is a real "duplicate key" problem, as I thought the "keys" within OBO Edit must be managed to be unique? Does similar problem happen to others? Thank you."
    • User asked to submit an example of a problematic OBO file; no response.
• "I am trying to install the latest version of OBO-Edit tool on a 64-bit windows 7 professional but the installation was not successful because of 64-bit JRE java installer. Please what do I need to do to ensure that the installation is successful?"
  • Heiko replied that the user most likely had a problem with the installed Java, and suggested installing a 64-bit Java. User did not reply.
• I create a root but all attempts to give it a name result in an error
  • Creating and naming roots seems to work fine. User asked for more information; no response.
• I would like to do another official release soon (2.1.1).

Links

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