OBO-Editv2.1beta12

Status

2.1-b12 released on 4/25/2011

Bugs Fixed

• parent/child search problem in 2.1-b11
  • Choosing "Parent" or "Children" from Aspect menu was causing Search component to freeze up.
• Configuration manager not opening (on some Linux machines)
  • Was throwing an exception while trying to read from oboedit.vmoptions, which isn't there on Laurel's Linux box
  • Still not sure why vmoptions isn't there (though it doesn't seem to hurt OE), but now it doesn't throw an exception, so Config manager comes up.
• The string "et al.," causes warning about whitespace
• Cycle over mixed relationship types -> infinite loop
  • Couldn't save fly_anatomy_XP.obo because OE goes into an infinite loop while running verification checks.
  • Two ways to fix the infinite loop (it now does both):
    • Before recursing on alt_id in the validation check, check whether it's the same as the primary ID.
    • When reading in ontology, check for alt_id == primary_id and refuse to add it.
• adding words to dictionary removes uncommitted text edits
  • Unfortunately, fixing this involved undoing a change I had made that fixed another, more minor bug:
    Words added to dictionary in unedited term don't turn black immediately.
    For now, we'll just have to live with the newly-added-to-dictionary word staying red until user does something that causes a commit (or moves to another term and then back).
• ID Profile Mismatch dialogue box and multiple ontologies
  • Loading multiple ontologies--PATO, GO, cell etc, Marcus gets message "ID profile mismatch--use profile loaded from the file"? Which ontology file is it referring to? It should say which.
  • This message now lists the two ID profiles, so at least it's somewhat clearer. However, it still seems a bit random which one it chooses as the new one if you have multiple ontologies loaded, and I have not yet added the new feature to let you select which of multiple ID profiles you want to use. (If there are only two, it does let you choose between the two.)

Features/Changes/Documentation

• Bogus warning messages during validation: if you have a URL in a comment or definition, you get complaints about there not being spaces between "sentences" and lack of capital letters. Not sure what's the best way to address this. URL is not parsed as a single "word" but rather as multiple "sentences".
  • This is somewhat improved, but not totally eliminated.

Future Work

• Search for children misses some (unless reasoner on)
  • If you turn on one of the reasoners, you find more children. But what do we really mean by "children"?
• Is_a closure broken
  • Filtered save with "is_a closure" checked doesn't save all the terms it should.

Links

OBO-Edit Wiki home page

OBO-Edit Working Group Meeting Agendas and Minutes