Re: [OBO-Edit Working Group] OBO-Edit 2.2 ready for testing

[Nomi H. <nlh...@lb...>]

Mike said 2.2-rc2 looked fine, and several other OEWG members also tried it and said it seemed fine (thanks for your help testing it!), so I went ahead and released it as 2.2.
Anyone who has been using 2.1 should be able to safely switch to 2.2 now.
	Nomi

On May 24, 2012, at 11:05 AM, Nomi Harris wrote:

> Hi Mike,
> 
> I have fixed a bunch of bugs since release 2.1 (see list below) and would like to do another official release. I am calling this release 2.2, even though it's not radically different from 2.1. I started out by calling it 2.1.1 but realized that that was too confusing.
> 
> Just about all of the fixes involve the GUI, so they shouldn't affect the pipeline. The only I/O fix was one Heiko made (Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date)).
> I ran the unit tests and the same ones pass and fail as before.
> 
> The 2.2 candidate can be downloaded from https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/2.2-rc2/
> Please try it out and let me know if you see any issues.
> 
> Thanks,
> 	Nomi
> 
> 
> ===============================
> What's New in OBO-Edit 2.2-rc2  (5/22/2012)
> ===============================
> Cycle Check fixed in Text Editor (warns you if the specific term is in a
> cycle). (The Cycle Check of all terms done by the Verification Manager was
> fixed in the previous release.)
> 
> 
> ===============================
> What's New in OBO-Edit 2.2-rc1 (aka v2.1.1-b10) (5/14/2012)
> ===============================
> [ geneontology-Bugs-3521387 ] link filter not working properly
> Regardless of what you selected in the first drop-down menu (self, type,
> parent, child), the only options offered in the "have a/don't have a" menu
> were those that apply to Self (Namespace, Is intersection, Is necessary, Is
> implied, and Is redundant), rather that the complete list that starts with
> "Any text field".
> 
> [ geneontology-Bugs-3521113 ] Cycle Check doesn't work
> (Note that this also fixes [ geneontology-Bugs-3323275 ] equivalent_to cycle
> not detected )
> - New cycle check method finds (possibly mixed-relationship) cycles by
> checking for objects that are descendants of one of their own children.
> - The check works whether or not you have the reasoner on, but it doesn't find
> cycles that involve implied links found by the reasoner.
> - The new cycle check is set by default to run on save and on manual
> verification; other times (e.g., on reasoner change) can be added by the user
> via the Verification Manager configuration panel.
> 
> [ geneontology-Bugs-3384594 ] Name redundancy check not working in Text Editor
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b9 (4/23/2012)
> ==============================
> [ geneontology-Bugs-3487351 ] Deleted differentia (in XP editor) sometimes reappear
> 
> [ geneontology-Feature Requests-3181194 ] allow obsolete term to have same name as live term
> The issue here is that there were two terms with the same name but different
> IDs. Ramona 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.
> 
> Remove Redundant Links panel:
> [ geneontology-Bugs-3520750 ] Remove Redundant Link doesn't always remove the right link
> [ geneontology-Bugs-3147642 ] 'Select all' not working in Remove Redundant Links panel
> [ geneontology-Bugs-3517323 ] Remove Redundant Links Panel doesn't refresh when it should
> [ geneontology-Bugs-3517324 ] Undo only restores last link removed in Remove Redundant Links
> The way links were being removed (by creating multiple(!) TermMacroHistoryItems)
> the removal couldn't be undone. If you deleted even a single link, Undo wouldn't
> restore it.
> I have improved this behavior--you can now undo single deletions. However, if you
> delete multiple links at a time, Undo only successfully undoes the last one. I'm
> not sure why. See https://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855
> As a beneficial side effect of improving the Undoableness, I expect link deletion
> to be faster than it was.
> 
> Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b7 (2/28/2012)
> ==============================
> Quick Save fixes:
> [ geneontology-Bugs-3487349 ] Quick save lets you save the first time when it shouldn't
> If you loaded via Advanced interface, you could then do a Quick Save the first
> time you saved (but it didn't actually know yet what file to save to, so it
> tried to save to null).
> [ geneontology-Bugs-3490963 ] quick save not working properly
> Was letting you do Quick Save before you'd done Save As on that file.
> 
> [ geneontology-Bugs-3486945 ] 64bit JRE can not be used on windows 7
> Windows apparently doesn't let you designate a preferred Java version, so the
> installer can do no better than using the first Java it comes across. The fix
> is to distribute two Windows installers: 32-bit and 64-bit, and let Windows
> users choose the appropriate one.
> 
> [ geneontology-Bugs-3487892 ] In compound ancestor/descendant queries, relation list bad
> In a compound search with two aspects, the relation pulldown lists didn't
> behave well. This turned out to be because of basically infinite refreshing of
> the lists.
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b6 (2/6/2012)
> ==============================
> - When user saves their work in a file, the titlebar changes to show the new
> filename--but don't do that if the save was an autosave.
> - [ geneontology-Bugs-3481225 ] Can't launch two (recent) OBO-Edits at the
> same time
> (Fixed by upgrading InstallAnywhere)
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b5
> ==============================
> TEMPORARY WORKAROUND for [ geneontology-Bugs-3481225 ] Can't launch two (recent) OBO-Edits at the same time
> [Fixed properly in 2.1.1-b6]
> 
> Minor change:
> Warn about possible stale config files when launching new version--but
> not when a user who's never installed OBO-Edit launches for the first
> time. (Existing users won't notice this change.)
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b4
> ==============================
> OWL Adapter:
> - Fixed issue where file browser strips off .owl extension if you select an
> existing .owl file. (Can't fix problem in file browser itself, which is
> native, but the OWL adapter now restores the .owl suffix after you select the file.)
> - Added user guide page about OWL adapter
> 
> New feature:
> [ geneontology-Feature Requests-3476913 ] Warn about possible stale config files when launching new version
> Whenever you upgrade to a new version of OBO-Edit, there is the risk that
> out-of-date binary files in your ~/oboedit_config (mostly in
> oboedit_config/perspectives) will cause bad behavior of various unexpected
> sorts (for example, sometimes it makes Autocommit in the Text Editor not
> work). Now a warning message about it pops up the first time you run a new
> OBO-Edit release (and it offers to rename oboedit_config/perspectives for you.)
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b3
> ==============================
> - I made the configuration option "Confirm on exit" say "Confirm on exit, even
> if there are no changes to be saved", and I made it default to false instead of true.
> 
> Fixed some issues with new Quick Save:
> - If you do quick save when you have unsaved changes in the text editor, it doesn't warn you (Save As does)
> - If you save as obo and then save as owl, quick save says you can't quick save yet, and also when it does
> the save as, it does it again after you hit ok.
> - [ geneontology-Bugs-3475532 ] 'Write ontology' box not dismissed upon save
> 
> Fixed the evil twin Cross Product Editor problems:
> [ geneontology-Bugs-3471901] can't delete cross products
> [ geneontology-Bugs-3303595] deleting genus relationship in cross product tab
> In an earlier version of OE, the genus would mysteriously disappear
> when you committed. Chris and Amina fixed this by caching the value of
> the genus field in AutocompleteBox and restoring it when it
> disappeared. However, this had the unwanted side effect of making it
> impossible to delete the genus by erasing the genus field--it would
> simply reappear, like a zombie returned from the dead, when you committed.
> Now you should be able to save OR delete your genus.
> 
> 
> ==============================
> What's New in OBO-Edit v2.1.1-b1 and b2
> ==============================
> New features:
> - [ geneontology-Feature Requests-3469108 ] Titlebar should show last saved-as filename
> - [ geneontology-Feature Requests-1604638 ] quick save
> After your first Save As, you can do a quick Save (command-S) to save the ontology again with the same save parameters.
> (A message window briefly appears letting you know the quick save worked.)
> - [ geneontology-Feature Requests-3375766 ] Automatic detection of changed files/reload option
> A new background thread checks whether the file you're looking at has changed on disk since you last loaded or saved it.
> If it changes, a popup advises you to save your work (if you've made changes) and reload.
> - Chris and Heiko got OBO<->OWL conversion working inside OBO-Edit, so you can load and/or save in OWL format.
> 
> Changes:
> - When you save your configuration in the Configuration Manager, you now get a
> popup message reminding you that you may need to quit and restart OE for your
> changes to take effect.  (If people find this annouying, I can take it out.)
>