OEWG 20111004

OBO-Edit Working Group Meeting: Tuesday, October 4, 2011, 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, Paola, Harold, Laurel

Bug and Feature Trackers

Allow 64 bit to be chosen on install
- Heiko improved the installer so that if you have a 64-bit computer with 64-bit Java, the installer will install OBO-Edit so that it will launch in 64-bit mode. The installer tries to detect if you have a 64-bit machine, in which case it suggests a larger memory allocation, but it is (by necessity) conservative about this (because if it suggested a too-high memory setting you wouldn't be able to launch OE at all), so it may limit you to an 1860M setting. If this happens, you can hand-edit OBO-Edit.vmoptions and put a higher memory setting (up to the amount of physical memory on your computer), and then relaunch OE (twice, if you're on a Mac).
- Ramona (?) said this is working for her.

DBxref library: sort by description
- As requested, DBxref library entries are now sorted by description (if any) and then by db:ID.
- The sample dbxref libraries that I had didn't have any descriptions, so their sorted order is the same as before.

Verfication check for empty DBxrefs (ID:0)
- It was already checking for no ID in dbxrefs; now it also warns about "ID:O" or "<new xref>".

Verification manager 'quick-fixes' don't show up in Text Ed
- If you clicked on the "quick-fix" icons in the Verification Manager, the fixes didn't show up in the Text Editor automatically. Now they do.

Extended characters result in fatal error
- Fixed "Allow extended characters (except in dbxrefs)" configuration option.
- Default is false; user can now change it.
- Ramona said this is working for her (Japanese characters)

Release 2.1-b19 is the release candidate for official release 2.1. Please try it out and report any (new) problems.
- Several people have tried and said it looks good
- Paola noted that the name redundancy check is now taking a really long time (~5 min on GO). Nomi said that it's slower now because before it wasn't actually *doing* a name redundancy check, and now it has to do an O(n^2) check (every name against every other name--and synonyms as well), so this is going to take longer. She will look and see whether maybe it's doing more work than it needs to.