OE Webex 15Apr08

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04/15/2008    09:28:42 AM    from midori:	Hi Nomi
04/15/2008    09:28:44 AM    from Nomi Harris:	Hello
04/15/2008    09:29:04 AM    from Nomi Harris:	You guys are so prompt!
04/15/2008    09:29:44 AM    from midori:	It's late afternoon here.
04/15/2008    09:31:09 AM    from Nomi Harris:	So?
04/15/2008    09:31:55 AM    from David OS:	I'm sad enough to have had the window open waiting fot the meeting to start.
04/15/2008    09:32:00 AM    from midori:	Long finished with the getting up and in to work thing, and ready to do something other thatn stare at SourceForge requests!
04/15/2008    09:32:03 AM    from Jen Deegan:	hello!
04/15/2008    09:32:07 AM    from Nomi Harris:	Hi, Jen!
04/15/2008    09:32:26 AM    from Jen Deegan:	how's it going?
04/15/2008    09:32:38 AM    from Nomi Harris:	I don't understand why my combobox fix didn't work on the reasoner manager.
04/15/2008    09:32:46 AM    from Jen Deegan:	yes that's very mysterious
04/15/2008    09:32:49 AM    from Nomi Harris:	 I did the same thing that fixed several other comboboxes.
04/15/2008    09:32:54 AM    from Nomi Harris:	Oh well, probably not worth spending a lot of time on.
04/15/2008    09:33:00 AM    from Jen Deegan:	must be an extra stretchy one
04/15/2008    09:33:29 AM    from Jen Deegan:	I could have a prod sometime since I have windows if it helps
04/15/2008    09:33:38 AM    from Nomi Harris:	So, are there any "must fix before GO meeting" issues that you've come up with?
04/15/2008    09:33:44 AM    from Jen Deegan:	nope
04/15/2008    09:33:49 AM    from Nomi Harris:	That's good!
04/15/2008    09:33:56 AM    from Nomi Harris:	Did anyone get a chance to try b37?
04/15/2008    09:33:59 AM    from Jen Deegan:	yes
04/15/2008    09:34:01 AM    from Jen Deegan:	very ncie
04/15/2008    09:34:03 AM    from Jen Deegan:	nice
04/15/2008    09:34:07 AM    from Nomi Harris:	Yay!
04/15/2008    09:34:09 AM    from midori:	I've done a little bit with it.
04/15/2008    09:34:13 AM    from Jen Deegan:	lovely icons
04/15/2008    09:34:27 AM    from Nomi Harris:	Yes, I was happy to finally get that problem fixed.
04/15/2008    09:34:34 AM    from Nomi Harris:	But what I spent the most time on was fixing delete.
04/15/2008    09:34:34 AM    from Jen Deegan:	I have even done a proper edit and commit with oboedit 2 now
04/15/2008    09:34:35 AM    from midori:	'regulates' stanzas roundtripping happily now.
04/15/2008    09:34:38 AM    from David OS:	I've been editing with it all afternoon. No probs so far!
04/15/2008    09:34:40 AM    from Nomi Harris:	I'm hoping that it works correctly now.
04/15/2008    09:34:46 AM    from Nomi Harris:	No crashes, David?
04/15/2008    09:34:58 AM    from Nomi Harris:	Are you working with an ontology that has dangling refs?
04/15/2008    09:34:59 AM    from David OS:	None
04/15/2008    09:35:11 AM    from midori:	I haven't checked what it does with a Graph Editor window open, though.
04/15/2008    09:35:23 AM    from midori:	... so it may still grind to a halt.
04/15/2008    09:35:25 AM    from Nomi Harris:	There are clearly still major issues with the Graph Editor.
04/15/2008    09:35:46 AM    from Nomi Harris:	I spent a lot of time fixing delete behavior in the Graph Editor,
04/15/2008    09:35:55 AM    from midori:	It seems to be fairly robust if I don't use the GE.
04/15/2008    09:36:01 AM    from Nomi Harris:	but I haven't been able to nail down its slowness/crashing problems.
04/15/2008    09:36:20 AM    from David OS:	No dangling refs. Need to sort out display issues before finally using these - and to be certain I can use oboedit2 for all my editing.
04/15/2008    09:36:25 AM    from Nomi Harris:	If you get a chance, please see if delete seems to be working well now
04/15/2008    09:36:25 AM    from Jen Deegan:	when I use it I always end up accidently opening hundreds of terms and then shutting them all piecemeal
04/15/2008    09:36:34 AM    from Nomi Harris:	and also other editing functionality, which I have not tested much.
04/15/2008    09:37:05 AM    from David OS:	Delete relation seems fine.  That's all I've used today.
04/15/2008    09:37:10 AM    from Nomi Harris:	Good.
04/15/2008    09:37:20 AM    from Nomi Harris:	And did it seem to be preserving your memory setting?
04/15/2008    09:37:27 AM    from midori:	I haven't tried to test systematically for a while now; I hope to do more after the GOC meetings.
04/15/2008    09:37:46 AM    from Jen Deegan:	would it be possible to quietly comment out the code that produces the date stamp on new terms while we are testing. We currently have to remove those pines before commit.
04/15/2008    09:37:50 AM    from Nomi Harris:	Jen, I hope this one made you happy: * Configuration setting for "End title of search results panel with" in Search panel is now saved between sessions.
04/15/2008    09:37:58 AM    from Jen Deegan:	fab!
04/15/2008    09:38:00 AM    from Jen Deegan:	thansk for that
04/15/2008    09:38:02 AM    from David OS:	yep.  Just checked - memory setting now remembered from installation.
04/15/2008    09:38:02 AM    from Jen Deegan:	it's a big help
04/15/2008    09:38:11 AM    from midori:	But the routine edits I've done (adding a few terms, relationships, synonyms) have been fine.
04/15/2008    09:38:14 AM    from Nomi Harris:	Date stamp:  sure, I can comment that out, but I will try to get that fixed in b38.
04/15/2008    09:38:28 AM    from Jen Deegan:	thanks
04/15/2008    09:38:31 AM    from Nomi Harris:	It needs to use the new date format in order to be readable by other tools--is that the issue?
04/15/2008    09:38:43 AM    from Jen Deegan:	there a user name line or something isn't there too/
04/15/2008    09:38:51 AM    from Nomi Harris:	Dunno
04/15/2008    09:38:53 AM    from Jen Deegan:	no it's just that we don't actually put a date stamp in the file
04/15/2008    09:39:00 AM    from Jen Deegan:	so to commit we have to delete those lines by hand
04/15/2008    09:39:00 AM    from Karen:	yes, a created_by line or something
04/15/2008    09:39:04 AM    from midori:	I think Jen means something like my latest feature request:
04/15/2008    09:39:19 AM    from Nomi Harris:	Oh, you mean when you commit the edited GO file?
04/15/2008    09:39:24 AM    from midori:	https://sourceforge.net/tracker/index.php?func=detail&aid=1942965&group_id=36855&atid=418260
04/15/2008    09:39:24 AM    from Jen Deegan:	yes
04/15/2008    09:39:58 AM    from Jen Deegan:	yes that's right
04/15/2008    09:40:05 AM    from Nomi Harris:	Ok.  So would that be a checkbox in the advanced save GUI?
04/15/2008    09:40:06 AM    from Jen Deegan:	I was thinking commenting out might be the quick fix
04/15/2008    09:40:11 AM    from Jen Deegan:	yes that's right
04/15/2008    09:40:31 AM    from Jen Deegan:	it just makes it a bit easier for us to test oboedit 2 on our edits
04/15/2008    09:40:34 AM    from Jen Deegan:	one less step
04/15/2008    09:40:38 AM    from Nomi Harris:	Yes, commenting out would be a quick fix!  I'll do that if it turns out to be tricky to add the option.
04/15/2008    09:40:44 AM    from Jen Deegan:	thanks :-)
04/15/2008    09:40:47 AM    from midori:	less risk of annoying users too  ;)
04/15/2008    09:41:02 AM    from Jen Deegan:	true
04/15/2008    09:41:21 AM    from Nomi Harris:	You mean, annoying them because they don't want to deal with yet another checkbox?
04/15/2008    09:41:28 AM    from Nomi Harris:	Or annoying them with the possibly unwanted date stamps?
04/15/2008    09:41:52 AM    from Jen Deegan:	b
04/15/2008    09:42:02 AM    from midori:	I mean the latter - some GO users haven't quite got the OBO format "tolerate new tags" philosophy
04/15/2008    09:42:03 AM    from Nomi Harris:	Here at the OBO-Edit headquarters, we are dedicated to annoying users in as many ways as possible!
04/15/2008    09:42:13 AM    from Jen Deegan:	quite right too
04/15/2008    09:42:42 AM    from Nomi Harris:	So now that the regulates definitions are round-tripping properly, does everything look good in terms of handling regulates?
04/15/2008    09:42:50 AM    from Nomi Harris:	Are we all happy with the regulates icons and colors?
04/15/2008    09:42:58 AM    from midori:	I haven't run into any problems yet ...
04/15/2008    09:43:21 AM    from Nomi Harris:	Is there anything I am expected to discuss and/or demo at the GO meeting?
04/15/2008    09:43:28 AM    from Jen Deegan:	I wondered about them being larger and black, but I suspect I'm splitting hairs.
04/15/2008    09:43:37 AM    from Karen:	I kind of think that the red icon doesn't show up very well against the purple... since there's no legacy from OE1 maybe we could just switch the purple and yellow for those types
04/15/2008    09:43:44 AM    from Jen Deegan:	I think we could all ust meet and enjoy the chance to talk in person and that would be good
04/15/2008    09:44:26 AM    from Nomi Harris:	I thought people were used to having yellow/orange for part_of links.
04/15/2008    09:44:41 AM    from Jen Deegan:	this is all pretty new to us
04/15/2008    09:44:45 AM    from midori:	Nomi - there'll be a time slot for OBO-Edit at the meeting, so it would be great to have an update on how it's going. Format is pretty flexible, and the other wg members who are there can chime in.
04/15/2008    09:44:49 AM    from Karen:	I think only from OE2 though, this panel didn't exist in OE1
04/15/2008    09:44:58 AM    from Nomi Harris:	I don't think purple is good for part_of links because it's too close to the part_of icon color, isn't it?
04/15/2008    09:45:22 AM    from midori:	I'm clinging fiercely to my color neutrality!
04/15/2008    09:45:38 AM    from David OS:	me too
04/15/2008    09:45:39 AM    from Nomi Harris:	midori, should the update include only future plans, or would it be appropriate to summarize recent OE improvements?  I know you guys are aware of those, but maybe other people aren't?
04/15/2008    09:45:46 AM    from Jen Deegan:	I'm quite keen on colour flexibility but it's beyond me to pick on ena stick to it just like that
04/15/2008    09:46:01 AM    from Karen:	and again, at one level, I don't care because I can change it for myself, I'm currently using green for regulates, because  I didn' think the purple/red constrast was good
04/15/2008    09:46:10 AM    from Jen Deegan:	I really like how the graphviz plugin is configuratble on colour but I know that's a tall order
04/15/2008    09:46:14 AM    from Nomi Harris:	But the up-regulates icons are green!
04/15/2008    09:46:24 AM    from Nomi Harris:	I have not yet played with the GraphViz plugin.
04/15/2008    09:46:29 AM    from Nomi Harris:	Does it do everything the Graph Editor does?
04/15/2008    09:46:43 AM    from Jen Deegan:	it's like the graph viewer
04/15/2008    09:46:47 AM    from Karen:	I'm using a light green relatinship color and it has much better contrast than the red on purple, I also tried something else
04/15/2008    09:46:49 AM    from Jen Deegan:	but uses the graphviz code
04/15/2008    09:46:56 AM    from midori:	re meeting: a brief summary of recent improvements won't go amiss - there will be quite a few people who haven't heard much lately.
04/15/2008    09:46:56 AM    from Jen Deegan:	the lines are less tangly too
04/15/2008    09:47:04 AM    from Jen Deegan:	it's just what I'm used to as it's the old version
04/15/2008    09:47:26 AM    from Nomi Harris:	Should we consider abandoning the Graph Editor and switching to the GraphViz plugin?
04/15/2008    09:47:39 AM    from Jen Deegan:	no I think they're both nice in their way
04/15/2008    09:47:50 AM    from Jen Deegan:	the grpah viewer shows individual relationship graphs
04/15/2008    09:48:02 AM    from Jen Deegan:	 while the graph viewer shows the whole thing with colour choise and untangle lines
04/15/2008    09:48:22 AM    from David OS:	"Should we consider abandoning the Graph Editor and switching to the GraphViz plugin?" No!
04/15/2008    09:48:26 AM    from Nomi Harris:	Perhaps we could extend GraphViz to do everything the Graph Editor does?
04/15/2008    09:48:36 AM    from Jen Deegan:	not sure
04/15/2008    09:48:40 AM    from Nomi Harris:	Since the Graph Editor seems deeply problematic in terms of memory/speed
04/15/2008    09:48:40 AM    from Jen Deegan:	maybe
04/15/2008    09:48:52 AM    from Nomi Harris:	Something to consider, anyway.
04/15/2008    09:48:54 AM    from Jen Deegan:	graph viewer couldn't be used for editing
04/15/2008    09:48:59 AM    from Jen Deegan:	I don't think , anyway
04/15/2008    09:49:01 AM    from David OS:	The advantage of the graph editor is that you can browse around a neighborhood.
04/15/2008    09:49:05 AM    from Nomi Harris:	"graph viewer" == GraphViz?
04/15/2008    09:49:14 AM    from Jen Deegan:	but the editor and viewer are very new concepts so there's not rush to get them perfect
04/15/2008    09:49:27 AM    from Jen Deegan:	graph viewer is the non graphviz viewer one
04/15/2008    09:49:29 AM    from Karen:	I really like the way the graph editor works, but haven't used the GraphViz viewer at all, so I can't really comment on the comparison
04/15/2008    09:49:30 AM    from David OS:	And filter on relations
04/15/2008    09:49:34 AM    from Nomi Harris:	Hey, did you all like the new config manager organization in b37?
04/15/2008    09:49:59 AM    from Jen Deegan:	I can't remember what the old one looked like but it seemed nice :-)
04/15/2008    09:50:07 AM    from midori:	I only looked at your screenshots, not at the actual config panel. But it looks fine.
04/15/2008    09:50:33 AM    from Jen Deegan:	it's split into more different tabs isn't it?
04/15/2008    09:50:37 AM    from Jen Deegan:	good idea
04/15/2008    09:50:40 AM    from Nomi Harris:	Same number of tabs
04/15/2008    09:50:42 AM    from Jen Deegan:	fits in a smaller space
04/15/2008    09:50:44 AM    from Nomi Harris:	but some have changed.
04/15/2008    09:50:46 AM    from Jen Deegan:	oh
04/15/2008    09:50:49 AM    from Jen Deegan:	really?
04/15/2008    09:50:50 AM    from Jen Deegan:	okay
04/15/2008    09:50:52 AM    from Nomi Harris:	Actually, it's possible there's one more.
04/15/2008    09:50:56 AM    from Nomi Harris:	But no more than that.
04/15/2008    09:51:04 AM    from Jen Deegan:	font and user settings used to be together didn't they?
04/15/2008    09:51:09 AM    from Jen Deegan:	oh good
04/15/2008    09:51:09 AM    from Nomi Harris:	Yes
04/15/2008    09:51:13 AM    from Nomi Harris:	And I thought that was confusing.
04/15/2008    09:51:14 AM    from Jen Deegan:	yes it seems nice
04/15/2008    09:51:18 AM    from Jen Deegan:	yes it was odd
04/15/2008    09:51:23 AM    from Jen Deegan:	also made it bgi
04/15/2008    09:51:25 AM    from Jen Deegan:	big
04/15/2008    09:51:28 AM    from Jen Deegan:	smaller is better
04/15/2008    09:51:29 AM    from Nomi Harris:	My main goal was to make the config directory path easier to find
04/15/2008    09:51:44 AM    from Jen Deegan:	excellent idea
04/15/2008    09:51:47 AM    from Nomi Harris:	My next step is to move that from .oboeditbeta to a system-appropriate directory
04/15/2008    09:51:51 AM    from Jen Deegan:	especially for windows
04/15/2008    09:52:05 AM    from Jen Deegan:	and for new users
04/15/2008    09:52:06 AM    from Nomi Harris:	but to make that nicer for current users, I want to make it copy your configuration from .oboeditbeta to the new directory
04/15/2008    09:52:13 AM    from Nomi Harris:	and I couldn't get that working in time to put it in b37.
04/15/2008    09:52:58 AM    from Karen:	Since it's still beta, and probably not that  many current users, maybe not such a big deal if it copies your configuration from .oboeditbeta to the new directory, I wouldn't mind doing it manually once
04/15/2008    09:53:16 AM    from Nomi Harris:	Yeah, I know it's not required, I just thought it would be nice.
04/15/2008    09:53:27 AM    from Jen Deegan:	could we just copy the file over?
04/15/2008    09:53:32 AM    from Jen Deegan:	folder I mean
04/15/2008    09:53:41 AM    from Nomi Harris:	Second best:  I can make it pop up a window saying, "You seem to have config files in .oboeditbeta.  You may want to copy them to [new directory] and restart OBO-Edit."
04/15/2008    09:53:50 AM    from Jen Deegan:	good idea
04/15/2008    09:53:55 AM    from Karen:	thanks for thinking of us, but if it's tricky maybe not worth the effort...
04/15/2008    09:54:00 AM    from Jen Deegan:	true
04/15/2008    09:54:00 AM    from Nomi Harris:	Yes, you could copy the stuff inside .oboeditbeta (not the folder itself).
04/15/2008    09:54:03 AM    from Jen Deegan:	we can just copy
04/15/2008    09:54:10 AM    from Nomi Harris:	I didn't think it would be tricky, but for some reason I was having trouble making it work.
04/15/2008    09:54:14 AM    from midori:	yep, fine with me
04/15/2008    09:54:23 AM    from Nomi Harris:	Ok, so should I go ahead and put that new config directory location in b38?
04/15/2008    09:54:32 AM    from Jen Deegan:	would it be okay if we have a central version of the verification data on repeatable words?
04/15/2008    09:54:42 AM    from Nomi Harris:	I wasn't sure all the existing users (who are used to looking in ~/.oboeditbeta) would be happy about the move.
04/15/2008    09:54:49 AM    from Jen Deegan:	I'm happy
04/15/2008    09:54:49 AM    from midori:	new directory location ok by me
04/15/2008    09:54:59 AM    from Nomi Harris:	"a central version of the verification data on repeatable words"--??
04/15/2008    09:55:05 AM    from Karen:	sounds good, as long as I know where to look I'm fine
04/15/2008    09:55:10 AM    from Jen Deegan:	you know when you run the verification check
04/15/2008    09:55:17 AM    from Jen Deegan:	 and it says you have repeated words
04/15/2008    09:55:21 AM    from Jen Deegan:	like kinase kinase
04/15/2008    09:55:24 AM    from Jen Deegan:	in a defintiion
04/15/2008    09:55:27 AM    from Nomi Harris:	ok...
04/15/2008    09:55:39 AM    from Jen Deegan:	it takes ages to teach it all the allowed ones
04/15/2008    09:55:41 AM    from Karen:	maybe we should handle "central version of the verification data on repeatable words" by having a file in GO  CVS, since that's ontology specific
04/15/2008    09:55:47 AM    from Jen Deegan:	yes
04/15/2008    09:55:52 AM    from Nomi Harris:	I see, so you want something like the dictionary file
04/15/2008    09:55:53 AM    from midori:	centralized for whom?
04/15/2008    09:55:56 AM    from Jen Deegan:	yes
04/15/2008    09:55:58 AM    from Nomi Harris:	for allowable repeated words?
04/15/2008    09:56:00 AM    from midori:	(crossed comments with Karen)
04/15/2008    09:56:01 AM    from Jen Deegan:	yes
04/15/2008    09:56:10 AM    from Jen Deegan:	anywhere is good
04/15/2008    09:56:10 AM    from Nomi Harris:	Ok, can you submit a feature request for that?
04/15/2008    09:56:13 AM    from Jen Deegan:	in cvs would be good
04/15/2008    09:56:15 AM    from Jen Deegan:	yes
04/15/2008    09:56:18 AM    from Jen Deegan:	will do
04/15/2008    09:56:23 AM    from Jen Deegan:	or should I just put it in cvs?
04/15/2008    09:56:25 AM    from Nomi Harris:	That will be doable but it is a new feature and I probably won't get that done immediately.
04/15/2008    09:56:25 AM    from Jen Deegan:	myself
04/15/2008    09:56:39 AM    from Nomi Harris:	Wait, does it already look in a file for these allowable repeats?
04/15/2008    09:56:42 AM    from Jen Deegan:	we wouldjust need to check out the file and put it in the config place
04/15/2008    09:56:46 AM    from Nomi Harris:	And you just want the file itself in svn?
04/15/2008    09:56:48 AM    from Jen Deegan:	I assume so
04/15/2008    09:56:55 AM    from Jen Deegan:	maybe
04/15/2008    09:56:57 AM    from Jen Deegan:	or somewhere
04/15/2008    09:57:10 AM    from Jen Deegan:	so I don't have to click okay a thousand times each time I delete the config folder
04/15/2008    09:57:17 AM    from Nomi Harris:	As Karen said, this is GO-specific.
04/15/2008    09:57:18 AM    from Jen Deegan:	if you see what I mean
04/15/2008    09:57:20 AM    from Jen Deegan:	yes
04/15/2008    09:57:22 AM    from Nomi Harris:	I see what you mean, yes.
04/15/2008    09:57:31 AM    from Jen Deegan:	I'm asking them rather than for a feature request
04/15/2008    09:57:35 AM    from Jen Deegan:	but since they're all here
04/15/2008    09:57:39 AM    from midori:	I have no idea where it looks for/stores  the allowable repeats ...
04/15/2008    09:57:47 AM    from Nomi Harris:	Since it's GO-specific, I'm not sure it should be in the OE distribution.
04/15/2008    09:57:49 AM    from Jen Deegan:	I guess in oboeditbeta
04/15/2008    09:58:02 AM    from Jen Deegan:	but cvs would be fine wouldn't it?
04/15/2008    09:58:10 AM    from Jen Deegan:	where do we keep the oboedit spelling dictionary?
04/15/2008    09:58:11 AM    from Nomi Harris:	But it should be possible to have a file in the GO CVS and we can tell GO users to stick it in their OE config directory
04/15/2008    09:58:38 AM    from Nomi Harris:	The dictionary is in the OE distribution
04/15/2008    09:58:49 AM    from Jen Deegan:	that's go specific isn't it?
04/15/2008    09:58:53 AM    from Karen:	maybe we should put the verification plugin in cvs too
04/15/2008    09:58:56 AM    from midori:	Swerving off topic: I have to leave a bit early this week.
04/15/2008    09:58:57 AM    from Nomi Harris:	but that's a little different, isn't it?  Words are words, and if a word is legal in GO, it presumably is not illegal in other ontologies.
04/15/2008    09:58:57 AM    from Jen Deegan:	yes
04/15/2008    09:59:08 AM    from Nomi Harris:	But it could be that "kinase kinase" is ok in GO but other ontologies would not want it.
04/15/2008    09:59:13 AM    from Jen Deegan:	unless they use different spelling conventions
04/15/2008    09:59:14 AM    from midori:	agreed
04/15/2008    09:59:23 AM    from Nomi Harris:	Ok, midori, anything else you want to discuss before you go?
04/15/2008    09:59:27 AM    from Jen Deegan:	if they used a uk dictionary then ours would be no use
04/15/2008    10:00:05 AM    from Jen Deegan:	so I guess I will check the verification data into go/doc
04/15/2008    10:00:06 AM    from midori:	Nothing else; I'll catch up with the transcript.
04/15/2008    10:00:07 AM    from Karen:	we mostly have to put both US and UK spellings in so that we don't get warnings on all the synonyms
04/15/2008    10:00:21 AM    from Jen Deegan:	congratulations to Erika on passing her viva!
04/15/2008    10:00:25 AM    from Nomi Harris:	Anyway, I still suggest you enter a Feature Request that OE allow you to have a file in your OE config directory that lists allowable repeated words.
04/15/2008    10:00:38 AM    from midori:	gotta run; bye all!
04/15/2008    10:00:39 AM    from Nomi Harris:	If that feature already exists, then it may need to be debugged and/or clarified to users.
04/15/2008    10:00:41 AM    from Nomi Harris:	Bye!
04/15/2008    10:00:41 AM    from Jen Deegan:	okay :-)
04/15/2008    10:00:43 AM    from Nomi Harris:	See you in SLC!
04/15/2008    10:00:49 AM    from Jen Deegan:	see ya
04/15/2008    10:00:53 AM    from David OS:	see ya
04/15/2008    10:01:23 AM    from Jen Deegan:	bye
04/15/2008    10:01:31 AM    from Nomi Harris:	Anything else?
04/15/2008    10:01:40 AM    from Nomi Harris:	I've been working with Chris this week on
04/15/2008    10:01:48 AM    from Nomi Harris:	testing obo file roundtripping
04/15/2008    10:01:54 AM    from Jen Deegan:	great
04/15/2008    10:02:00 AM    from Jen Deegan:	very important
04/15/2008    10:02:06 AM    from Nomi Harris:	I will be adding some JUnit tests (after the GO meeting)
04/15/2008    10:02:09 AM    from Jen Deegan:	that means spitting out all it read in right?
04/15/2008    10:02:14 AM    from Nomi Harris:	Right.
04/15/2008    10:02:17 AM    from Jen Deegan:	oh good
04/15/2008    10:02:24 AM    from Jen Deegan:	tests are good
04/15/2008    10:02:30 AM    from Nomi Harris:	We also should somehow test that edits are saved properly
04/15/2008    10:02:38 AM    from Jen Deegan:	that would be excellent
04/15/2008    10:02:38 AM    from Nomi Harris:	which is of course harder to construct tests for than simple roundtripping.
04/15/2008    10:02:43 AM    from Jen Deegan:	yes
04/15/2008    10:02:58 AM    from Nomi Harris:	Hi Chris
04/15/2008    10:03:02 AM    from Nomi Harris:	We were just about to wrap up.
04/15/2008    10:03:08 AM    from Jen Deegan:	we often get new terms with no namespece.
04/15/2008    10:03:12 AM    from Jen Deegan:	a test for that would be good
04/15/2008    10:03:26 AM    from Nomi Harris:	You often "get" new terms?  Or create them and their namespaces are erroneously not saved?
04/15/2008    10:03:29 AM    from Jen Deegan:	currently we make one in the verification manager
04/15/2008    10:03:34 AM    from Jen Deegan:	not sure
04/15/2008    10:03:43 AM    from Jen Deegan:	they just get given the default instead of the parent's one
04/15/2008    10:03:49 AM    from Nomi Harris:	Ah
04/15/2008    10:03:53 AM    from Jen Deegan:	then it causes chaos for users
04/15/2008    10:03:57 AM    from Jen Deegan:	in databases
04/15/2008    10:04:00 AM    from Nomi Harris:	That sounds like a bug.  So new terms should inherit the parent's namespace, and sometimes they don't
04/15/2008    10:04:05 AM    from Jen Deegan:	yes
04/15/2008    10:04:09 AM    from Jen Deegan:	that's right
04/15/2008    10:04:17 AM    from Nomi Harris:	If there's not a bug report about that in SF, I will add one.
04/15/2008    10:04:22 AM    from Jen Deegan:	great, thanks
04/15/2008    10:04:30 AM    from Chris Mungall:	Hi, think I have another meeting now anyway, just checking in to lurk
04/15/2008    10:04:39 AM    from Nomi Harris:	Not much more to lurk for, we're just about done.
04/15/2008    10:04:52 AM    from Jen Deegan:	I think a test that each term has the required bits would be good
04/15/2008    10:04:58 AM    from David OS:	I've never noticed obo-edit automatically adding NS of parent to new terms.  Think it should though.
04/15/2008    10:05:14 AM    from Jen Deegan:	a name, namespace, id etc.
04/15/2008    10:05:14 AM    from Nomi Harris:	Possibly that is a new feature request, then.  But definitely a reasonable one.
04/15/2008    10:05:22 AM    from Jen Deegan:	it almost always does for us
04/15/2008    10:05:27 AM    from Jen Deegan:	just not quite always
04/15/2008    10:05:29 AM    from Jen Deegan:	not sure why
04/15/2008    10:05:36 AM    from Jen Deegan:	like once in a blue moon though
04/15/2008    10:05:42 AM    from Jen Deegan:	just when you#re not expecting it
04/15/2008    10:05:48 AM    from Nomi Harris:	Yes, I need to make a JUnit test that creates a new child term and makes sure it inherits all the fields it should.
04/15/2008    10:05:56 AM    from Jen Deegan:	that would be great
04/15/2008    10:06:08 AM    from Jen Deegan:	that's always been a pitfall in editing
04/15/2008    10:06:44 AM    from Jen Deegan:	nothing else leaping to mind
04/15/2008    10:07:11 AM    from Nomi Harris:	When do you leave for SLC, Jen?
04/15/2008    10:07:19 AM    from Jen Deegan:	monday. You?
04/15/2008    10:07:24 AM    from Nomi Harris:	Monday as well.
04/15/2008    10:07:25 AM    from Alexander Diehl:	Can I ask a basic question?
04/15/2008    10:07:28 AM    from Jen Deegan:	yep
04/15/2008    10:07:28 AM    from Nomi Harris:	Of course!
04/15/2008    10:08:22 AM    from Alexander Diehl:	I just loaded OBOEdit B37 with the gene ontology "write" file and I don't see regulates relationships in the GE
04/15/2008    10:08:31 AM    from Jen Deegan:	:-)
04/15/2008    10:08:40 AM    from Alexander Diehl:	do I have to activate something?
04/15/2008    10:08:42 AM    from Jen Deegan:	that always happens
04/15/2008    10:08:44 AM    from Jen Deegan:	:-)
04/15/2008    10:09:12 AM    from Nomi Harris:	You may have the is_transitive filter set in your .oboeditbeta
04/15/2008    10:09:40 AM    from Nomi Harris:	That filter is now off by default, but it used to be on.
04/15/2008    10:09:46 AM    from Alexander Diehl:	I dumped the old .oboeditbeta folder before installing.
04/15/2008    10:09:50 AM    from Nomi Harris:	Try moving ~/.oboeditbeta/filter_prefs.xml out of the way and restarting OE
04/15/2008    10:09:57 AM    from Nomi Harris:	(Does this advice sound right to you, Jen?)
04/15/2008    10:10:03 AM    from Jen Deegan:	excellent!
04/15/2008    10:10:47 AM    from Jen Deegan:	suspense
04/15/2008    10:10:53 AM    from Nomi Harris:	Alex, please let me know if it works for you.
04/15/2008    10:11:01 AM    from Nomi Harris:	If so, perhaps I should mail those instructions to the whole OEWG
04/15/2008    10:11:04 AM    from Jen Deegan:	are you doing it now?
04/15/2008    10:11:10 AM    from Alexander Diehl:	Is there no way within the program to fix this?
04/15/2008    10:11:11 AM    from Nomi Harris:	and also add them to the appropriate userguide page.
04/15/2008    10:11:13 AM    from Jen Deegan:	yes everyone is hitting this one at a time.
04/15/2008    10:11:20 AM    from Nomi Harris:	Yes, there is.  Go to Global Filters
04/15/2008    10:11:22 AM    from Jen Deegan:	we get the same puzzled email from each person
04/15/2008    10:11:54 AM    from Alexander Diehl:	okay
04/15/2008    10:12:17 AM    from Nomi Harris:	In Link filters
04/15/2008    10:12:26 AM    from Nomi Harris:	Is there a filter that requires is_transitive?
04/15/2008    10:12:45 AM    from Alexander Diehl:	okay
04/15/2008    10:12:49 AM    from Alexander Diehl:	yes
04/15/2008    10:12:52 AM    from Nomi Harris:	Remove that filter
04/15/2008    10:13:12 AM    from Jen Deegan:	then restart? :)
04/15/2008    10:13:18 AM    from Nomi Harris:	There have been reports (from midori) that restarting is required
04/15/2008    10:13:24 AM    from Nomi Harris:	to activate global filter changes, though it shouldn't be.
04/15/2008    10:13:29 AM    from Nomi Harris:	I have not been able to recreate that bug.
04/15/2008    10:13:37 AM    from Jen Deegan:	tanya and I also had it
04/15/2008    10:13:39 AM    from Jen Deegan:	very odd
04/15/2008    10:13:48 AM    from Nomi Harris:	It must happen under certain circumstances.
04/15/2008    10:13:50 AM    from Jen Deegan:	alsodavid I think
04/15/2008    10:14:01 AM    from Nomi Harris:	Maybe we can look at it together at the GO meeting.
04/15/2008    10:14:03 AM    from Jen Deegan:	it senses the fear
04/15/2008    10:14:07 AM    from Nomi Harris:	:-)
04/15/2008    10:14:16 AM    from Alexander Diehl:	I removed the filter but no change -- will restart
04/15/2008    10:14:25 AM    from Jen Deegan:	drum roll.....
04/15/2008    10:14:28 AM    from Nomi Harris:	I should compile a list of "works for me" bug reports and get you guys to demo them for me in SLC.
04/15/2008    10:14:38 AM    from Jen Deegan:	good idea
04/15/2008    10:15:02 AM    from Jen Deegan:	there's a risk that you then have to work on them while you have out laptops
04/15/2008    10:15:12 AM    from Alexander Diehl:	it's busy reasoning at the moment
04/15/2008    10:15:20 AM    from Jen Deegan:	chug chug chug
04/15/2008    10:15:24 AM    from Alexander Diehl:	(after reatarting and reloading)
04/15/2008    10:15:28 AM    from Nomi Harris:	I usually don't test with reasoning on (unless that is specifically mentioned in the bug reports)
04/15/2008    10:15:33 AM    from Nomi Harris:	so it's possible that that's the difference.
04/15/2008    10:15:47 AM    from Alexander Diehl:	I just don't know any better.
04/15/2008    10:15:50 AM    from Nomi Harris:	I also usually test with small ontologies rather than GO.
04/15/2008    10:16:01 AM    from Jen Deegan:	that may be why we have such special bugs
04/15/2008    10:16:03 AM    from Nomi Harris:	What do you mean, you don't know any better?  You don't know how to turn reasoning off?
04/15/2008    10:16:12 AM    from Alexander Diehl:	Stress testing!
04/15/2008    10:16:24 AM    from Jen Deegan:	for the user or the computer? ;-)
04/15/2008    10:16:28 AM    from Nomi Harris:	Stress testing is good!  I just don't do it as a matter of course because it's too slow.
04/15/2008    10:16:35 AM    from Jen Deegan:	true
04/15/2008    10:16:39 AM    from Jen Deegan:	that's what we're here for
04/15/2008    10:16:42 AM    from Alexander Diehl:	I know how to turn reasoning off and on, I just left it on for good luck.
04/15/2008    10:16:46 AM    from Nomi Harris:	!
04/15/2008    10:16:49 AM    from Jen Deegan:	:-)
04/15/2008    10:17:07 AM    from Jen Deegan:	and because it's needed for th graph viewer and editor I believe
04/15/2008    10:17:10 AM    from Nomi Harris:	Perhaps I should send you a four-leaf clover and then you can turn reasoning off.
04/15/2008    10:17:18 AM    from Karen:	I haven't been turning it off either, mostly just because it actually hasn't been annoying me to have it on
04/15/2008    10:17:38 AM    from Jen Deegan:	any luck alex?
04/15/2008    10:17:41 AM    from Nomi Harris:	It has been annoying you--you just don't know it.  If you turn it off, you will find OE suddenly speedier and more responsive!
04/15/2008    10:17:44 AM    from David OS:	 I do plenty of browsing with the old reasoner on.  But only when I'm using our souped up Linux box.
04/15/2008    10:17:53 AM    from David OS:	Tend to avoid new reasoner though.
04/15/2008    10:18:07 AM    from Alexander Diehl:	Okay, the links are there now!
04/15/2008    10:18:11 AM    from Jen Deegan:	yay!!!!!!!!!
04/15/2008    10:18:12 AM    from Nomi Harris:	Enjoy the old one while it lasts; Chris has condemned it to die.
04/15/2008    10:18:20 AM    from Jen Deegan:	eep!
04/15/2008    10:18:26 AM    from Karen:	but it's probably good to know that the only time I find it annoyingly slow is the first search I do is slow to respond, after that it's fine
04/15/2008    10:18:30 AM    from Nomi Harris:	Oh, yay, Alex!  Ok, I will send the filter-removal instructions to the OEWG.
04/15/2008    10:18:39 AM    from Jen Deegan:	good idea
04/15/2008    10:18:44 AM    from Chris Mungall:	don't worry i wont ill it before its faster.
04/15/2008    10:18:58 AM    from Jen Deegan:	thanks :-)
04/15/2008    10:19:04 AM    from Nomi Harris:	(The second "it" refers to the new reasoner, in case that wasn't clear.)
04/15/2008    10:19:17 AM    from Alexander Diehl:	So the lesson is always reatart after filter changes?
04/15/2008    10:19:21 AM    from Jen Deegan:	yes
04/15/2008    10:19:24 AM    from Nomi Harris:	Probably best for now.
04/15/2008    10:19:33 AM    from Nomi Harris:	I want to debug that, but haven't been able to recreate the issue.
04/15/2008    10:19:41 AM    from Nomi Harris:	For me, the filter changes seem to work right away.
04/15/2008    10:19:51 AM    from Jen Deegan:	weird
04/15/2008    10:20:07 AM    from Jen Deegan:	we can have a try in slc
04/15/2008    10:20:12 AM    from Alexander Diehl:	I haven't been using OE in a while, so I am trying to catch up on the changes.
04/15/2008    10:20:18 AM    from Nomi Harris:	OE is scared to misbehave for me.  It knows I might punish it by ripping out pieces of code.  :-)
04/15/2008    10:20:22 AM    from Jen Deegan:	you can debug in my eclipse if you'd like
04/15/2008    10:20:37 AM    from Nomi Harris:	Thanks
04/15/2008    10:20:45 AM    from Nomi Harris:	Ok, are we done?
04/15/2008    10:20:48 AM    from Jen Deegan:	yep
04/15/2008    10:20:53 AM    from Nomi Harris:	Great--see you all next week!
04/15/2008    10:20:57 AM    from Jen Deegan:	see ya!
04/15/2008    10:20:59 AM    from Nomi Harris:	Bye!
04/15/2008    10:21:05 AM    from Alexander Diehl:	Thanks, bye