OE Webex 5Aug08
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08/05/2008 09:26:25 AM from Nomi Harris: Good morning 08/05/2008 09:26:47 AM from Jen Deegan: Morning! 08/05/2008 09:26:52 AM from Jen Deegan: How's it going? 08/05/2008 09:27:06 AM from Nomi Harris: Ok 08/05/2008 09:27:14 AM from Nomi Harris: Trying to figure out why OE2 is so slow. 08/05/2008 09:27:21 AM from Nomi Harris: I'll be right back, just getting a cup of tea. 08/05/2008 09:27:25 AM from Jen Deegan: ok 08/05/2008 09:28:40 AM from Jen Deegan: Hi Amina 08/05/2008 09:28:46 AM from Amina: Hi Jen 08/05/2008 09:28:53 AM from Jen Deegan: How's it going? 08/05/2008 09:29:05 AM from Amina: pretty good.. how are things on your side 08/05/2008 09:29:20 AM from Jen Deegan: good thanks. I'm getting on well with the graphviz fixing that I'm doing 08/05/2008 09:29:31 AM from Jen Deegan: Nicolas helped me today with getting object passing to work properly. 08/05/2008 09:29:40 AM from midori: hi 08/05/2008 09:29:41 AM from Nomi Harris: Hey, midori. 08/05/2008 09:29:41 AM from Amina: thats good news - let me know if I coud help 08/05/2008 09:29:50 AM from Jen Deegan: Thanks 08/05/2008 09:29:51 AM from Amina: Hi Midori 08/05/2008 09:29:59 AM from Nomi Harris: We may be a small group today. Harold said he can't come. 08/05/2008 09:30:11 AM from Jen Deegan: ok 08/05/2008 09:30:14 AM from Jen Deegan: shall we start then? 08/05/2008 09:30:16 AM from Nomi Harris: I sent out the meeting announcement kind of late. 08/05/2008 09:30:28 AM from Jen Deegan: Hi Karen 08/05/2008 09:30:30 AM from Nomi Harris: Chris Mungall is about to join. 08/05/2008 09:30:34 AM from Jen Deegan: great 08/05/2008 09:30:46 AM from Karen: Hi all 08/05/2008 09:30:52 AM from Nomi Harris: Hi, Karen. 08/05/2008 09:30:59 AM from Amina: hi Karen 08/05/2008 09:31:22 AM from Nomi Harris: Hey, Karen, you're at Stanford, aren't you? 08/05/2008 09:31:51 AM from Karen: Yes, I'm at STanford 08/05/2008 09:31:55 AM from Amina: I have something I'd like to chat about 08/05/2008 09:32:00 AM from Karen: OK 08/05/2008 09:32:24 AM from Amina: During our group meeting yesterday - Suzi mentioned setting a time frame for the next OE release 08/05/2008 09:32:25 AM from Nomi Harris: (I was just thinking, maybe some time you could visit us in Berkeley so we could watch you use OE to edit.) 08/05/2008 09:32:55 AM from Jen Deegan: Does Suzi expect us to be able to predict when it will be ready? 08/05/2008 09:33:03 AM from Amina: In order for us to have that time-frame - I'd like to outline the key features and bug fixes 08/05/2008 09:33:12 AM from Jen Deegan: good idea 08/05/2008 09:33:18 AM from Amina: define rather than outline - Chris suggested putting that on the wiki 08/05/2008 09:33:18 AM from Karen: I'd love to, I do like Berkeley, I'll check with Mike C to see if that's OK with him. 08/05/2008 09:34:00 AM from Amina: that way we can just check those off the list and hopefully have a release by end of september or early Oct before we go to montreal 08/05/2008 09:34:01 AM from Nomi Harris: Of course, ideally the bug/feature trackers already define that list for us, via priorities. 08/05/2008 09:34:08 AM from Amina: right 08/05/2008 09:34:20 AM from Nomi Harris: There are only a few items that are >5 priority. 08/05/2008 09:34:33 AM from Nomi Harris: Of course, some of them are big vague things like "OE is too slow" and "OE crashes sometimes". 08/05/2008 09:34:35 AM from midori: We have to allow time for a lot more testing too. 08/05/2008 09:34:39 AM from Nomi Harris: Yes. 08/05/2008 09:34:51 AM from Amina: Thats exactly why I'd like the Go-editors to define this list 08/05/2008 09:34:53 AM from Jen Deegan: we need to fix the lower priority ones too in many cases 08/05/2008 09:35:04 AM from Jen Deegan: good idea 08/05/2008 09:35:17 AM from Nomi Harris: Suzi said that she kept hearing that OE2 would be ready for a public release "real soon now", 08/05/2008 09:35:26 AM from Amina: Yeah because in some cases the low priority ones could be important to some folks too 08/05/2008 09:35:27 AM from Nomi Harris: to which Amina and Chris and I said, "Who's saying that? We didn't say that." 08/05/2008 09:35:28 AM from midori: I have a nasty suspicion that we haven't found all the bugs that are bad enough to need fixing before release -- 08/05/2008 09:35:29 AM from Jen Deegan: who said that?! 08/05/2008 09:35:37 AM from Karen: We should also make sure we check with Mike C on the time frame for making OE2 the official version since there are some file format changes/additions. 08/05/2008 09:35:47 AM from Nomi Harris: But I realized that before he left, John had been under the impression that OE2 was almost ready to release. 08/05/2008 09:35:57 AM from Amina: Karen it would be great to have to visit sometime this month if possible 08/05/2008 09:35:57 AM from Nomi Harris: I think he had no idea how far it really was, because it hadn't really been tested much yet. 08/05/2008 09:36:03 AM from midori: almost every time I use OE2 I find more bugs (tho the last few have mostly been minor) 08/05/2008 09:36:18 AM from Jen Deegan: I think that timeframe you're talking about is very unrealistic 08/05/2008 09:36:44 AM from midori: yeah, "Real Soon Now(tm)" (i.e. sarcastic) might be nearer the mark ... 08/05/2008 09:36:49 AM from Tanya: (Hi) 08/05/2008 09:36:52 AM from midori: hi tanya 08/05/2008 09:36:54 AM from Jen Deegan: Maybe if we give them a list then that will help get the point across 08/05/2008 09:36:54 AM from Amina: hi Tanya 08/05/2008 09:36:57 AM from Nomi Harris: Suzi feels like it should already have been released. I think she didn't realize how buggy it was. 08/05/2008 09:37:05 AM from Jen Deegan: we maybe need to tell her 08/05/2008 09:37:18 AM from Tanya: maybe we need to *show* her 08/05/2008 09:37:18 AM from Nomi Harris: Hopefully the list won't make it look like we're not doing our jobs. :-) 08/05/2008 09:37:18 AM from midori: Has she used it much? 08/05/2008 09:37:24 AM from Nomi Harris: I don't think she's used it at all. 08/05/2008 09:37:37 AM from Jen Deegan: We can tell her how hard you've been working too 08/05/2008 09:37:43 AM from midori: methinks that speaks volumes 08/05/2008 09:37:44 AM from Nomi Harris: I assured her that I'm knocking bugs off the tracker as fast as they're getting on there--but the list isn't getting much shorter. 08/05/2008 09:37:56 AM from Amina: Would be great of we had a list - it doesn't have to be comprehensive - could just list sourceforge bug/feature ids in some order 08/05/2008 09:37:58 AM from Jen Deegan: sounds like we need to talk to Suzi. 08/05/2008 09:38:02 AM from midori: see above re: every time I use it ... <sigh> 08/05/2008 09:38:32 AM from Jen Deegan: is there some way we can use SF to convey this so we don't waste time? 08/05/2008 09:38:56 AM from Jen Deegan: We could give a certain priority level to indicate things that need done before release. 08/05/2008 09:38:58 AM from Nomi Harris: Perhaps the priority score could be used to designate "blocking" bugs 08/05/2008 09:39:04 AM from Jen Deegan: yes 08/05/2008 09:39:09 AM from Nomi Harris: (i.e., things that need to be done before release, as Jen just said) 08/05/2008 09:39:15 AM from Jen Deegan: yes that would be good 08/05/2008 09:39:17 AM from midori: SF has some reporting features built in, tho they're not the most flexible or expressive 08/05/2008 09:39:30 AM from Nomi Harris: I kind of figured that >5 meant needs to be fixed before release 08/05/2008 09:39:33 AM from Chris: the majority of items are still priority 5 08/05/2008 09:39:45 AM from Karen: I don't have access to change the priority when I submit items to the feature tracker (though I do for the curator tracker) 08/05/2008 09:39:56 AM from Nomi Harris: but there are some reasoner bugs with >5 that although they need to be fixed at some point, probably shouldn't hold back the release. 08/05/2008 09:40:10 AM from Nomi Harris: Really, you don't have access to change the priority? I thought everyone who could submit a bug could set priorities. 08/05/2008 09:40:25 AM from Nomi Harris: That would explain why most of the items have priority 5! 08/05/2008 09:40:25 AM from Karen: doesn't seem so 08/05/2008 09:40:31 AM from midori: No, it depends on what permissions each person has within each tracker. 08/05/2008 09:40:41 AM from Nomi Harris: Huh. I will see if I can grant you that privilege. 08/05/2008 09:40:51 AM from Jen Deegan: I think we need to be very careful of releasing OBO-Edit when it is still problematic, as it used to have a terrible reputation for being bug-ridden and OBO-Edit1 has gone a long way to fixing that. 08/05/2008 09:41:04 AM from Karen: I completely agree wtih what Jen just said. 08/05/2008 09:41:10 AM from midori: I can give more people the permissions they'd need ... who should get? 08/05/2008 09:41:13 AM from Nomi Harris: We are under pressure to release it before the GO meeting. 08/05/2008 09:41:22 AM from Chris: We won 't release it before everyone has signed off on it 08/05/2008 09:41:26 AM from Jen Deegan: At the EBI they are just upgrading from DAG-Edit so we need to be aware that some people will be stuck with the released version for a long time. 08/05/2008 09:41:38 AM from midori: That. Is. Not. Going. To. Happen. ... unless you guys pull off a minor miracle. 08/05/2008 09:41:46 AM from Jen Deegan: not at all. 08/05/2008 09:41:58 AM from midori: Even if you could fix the bugs in time, there wouldn't be enough testing time. 08/05/2008 09:42:08 AM from Jen Deegan: very true 08/05/2008 09:42:13 AM from Jen Deegan: Suzi is kidding herself. 08/05/2008 09:42:18 AM from Nomi Harris: I think John convinced Suzi that OE2 was almost ready for prime time. 08/05/2008 09:42:21 AM from Nomi Harris: Because he believed it himself. 08/05/2008 09:42:25 AM from Jen Deegan: that's really bizarre. 08/05/2008 09:42:48 AM from Jen Deegan: it was so buggy we couldn't use it at all. 08/05/2008 09:42:50 AM from midori: She really has to sit down and try using OE2 for a good 2-4 hours editing something as big as GO ... or listen to those of us who do! 08/05/2008 09:42:54 AM from Nomi Harris: I remember asking John just before he left what the high-priority outstanding bugs were, and he said he'd fixed all the bugs that were reported! 08/05/2008 09:43:02 AM from Karen: John was always very optimistic about these things, sometimes overly so, but optimistic almost all the time. 08/05/2008 09:43:02 AM from Jen Deegan: ah 08/05/2008 09:43:14 AM from Jen Deegan: maybe he didn't realise how bad it was then 08/05/2008 09:43:16 AM from Chris: Let's make this more concrete and quantifiable 08/05/2008 09:43:17 AM from Tanya: probably because it hadn't been as extensively tested as it is now 08/05/2008 09:43:24 AM from Jen Deegan: I just assumed he'd fix the awful bugs if we waited a bit. 08/05/2008 09:43:30 AM from Amina: I agree with Chris 08/05/2008 09:43:31 AM from Nomi Harris: "She really has to sit down and try using OE2 for a good 2-4 hours editing something as big as GO"--yeah, but we should make her use b14, not b43. :-) 08/05/2008 09:43:33 AM from midori: Maybe, but then I tried using his last release and immediately plugged in a raft of new bug reports. 08/05/2008 09:43:39 AM from midori: <g> 08/05/2008 09:43:52 AM from Chris: action: someone will take charge of getting all items prioritised such that we know how many blocking and non-blocking bugs and features we have 08/05/2008 09:44:08 AM from Jen Deegan: shall we each do our own then? 08/05/2008 09:44:14 AM from Nomi Harris: That would be good. 08/05/2008 09:44:17 AM from Jen Deegan: great 08/05/2008 09:44:27 AM from midori: I'll give Karen SF permissions right now 08/05/2008 09:44:31 AM from Nomi Harris: Though I have noticed a tendency for each person to overstate the importance of his/her own bug reports. :-) 08/05/2008 09:44:35 AM from Jen Deegan: shoudl we discuss this with Suzi on the managers' call? 08/05/2008 09:44:45 AM from midori: I've got some that I put in at 1 ;) 08/05/2008 09:44:45 AM from Chris: unfortunately there is no way for a developer to indicate difficulty of a request, estimated time frame, other dependent issues etc 08/05/2008 09:44:51 AM from Jen Deegan: that's because we haven't got down to the unimportant ones yet :-) 08/05/2008 09:45:06 AM from Jen Deegan: I have a couple that don't matter. 08/05/2008 09:45:10 AM from Nomi Harris: I sometimes put in comments to that effect, Chris. 08/05/2008 09:45:12 AM from Chris: We could have a structured comment field in the tracker for this 08/05/2008 09:45:22 AM from Chris: but getting prioritised is the priority 08/05/2008 09:45:42 AM from Nomi Harris: I try to adjust priorities, but really only the editors can set them. 08/05/2008 09:45:49 AM from Jen Deegan: One of hte problems is that this version has so many new features that it is taking a long time to perfect and I already need new features that should be in the next one. 08/05/2008 09:46:20 AM from Jen Deegan: I think we need to decide what features to have in the release and comment out the others that are not perfected yet 08/05/2008 09:46:27 AM from Jen Deegan: that way we could get an earlier release. 08/05/2008 09:46:43 AM from Nomi Harris: Well, we had discussed making the Graph Editor not part of the default layout. 08/05/2008 09:46:53 AM from Jen Deegan: there are more that we could lose 08/05/2008 09:47:03 AM from Jen Deegan: I mean really not releasing them, not just taking out of the layout. 08/05/2008 09:47:13 AM from Jen Deegan: we want this to be a quality piece of software. 08/05/2008 09:47:32 AM from Nomi Harris: I agree that it would be better to have fewer features but all working well. 08/05/2008 09:47:39 AM from Nomi Harris: We can include the Graph Editor with a big disclaimer. 08/05/2008 09:47:50 AM from Karen: I really like the Graph Editor though. It really makes OE2 for me. 08/05/2008 09:47:59 AM from Chris: we've been through this before. people want the GE available, but we cannot wait for the GE to be perfect. 08/05/2008 09:47:59 AM from Nomi Harris: Yes, it's way cool, but it's also way buggy and slow. 08/05/2008 09:48:06 AM from Jen Deegan: but you are using the beta version anyway so you lose nothing if we release without 08/05/2008 09:48:26 AM from midori: Releasing with a caveat about GE is ok with me. But there's a lot of other stuff that's flaky. 08/05/2008 09:48:28 AM from Nomi Harris: Making the OE not respond to big selection events will be a big win. 08/05/2008 09:48:28 AM from Jen Deegan: we need to think about curators elsewhere who will be stuck with the release version for years 08/05/2008 09:48:46 AM from Jen Deegan: what else could we shelve? 08/05/2008 09:48:55 AM from Nomi Harris: The Parent Editor? 08/05/2008 09:48:56 AM from Jen Deegan: to cut down bug fixing and testing time? 08/05/2008 09:49:10 AM from Jen Deegan: what about the tree viewer? 08/05/2008 09:49:12 AM from Chris: Jen: that's a reasonable suggestion but I think we still want to make the beta GE an option for people using the release version. 08/05/2008 09:49:25 AM from midori: nooooooo! I need the parent editor. 08/05/2008 09:49:27 AM from Jen Deegan: why? 08/05/2008 09:49:36 AM from Jen Deegan: that was to Chris. 08/05/2008 09:49:54 AM from Chris: Remember, some sys admins won't allow folk to use the non-release version 08/05/2008 09:50:05 AM from Jen Deegan: yes but if it's needed it should be working 08/05/2008 09:50:12 AM from Chris: Can we have an end to this cyclic discussion.. it seems to always come up 08/05/2008 09:50:12 AM from Jen Deegan: why do people need a broken tool? 08/05/2008 09:50:40 AM from Jen Deegan: we were discussing what else we could shelve for the next release. 08/05/2008 09:51:14 AM from Jen Deegan: Midori needs the parent editor if we can't fix keyboard shortcuts. 08/05/2008 09:51:19 AM from Nomi Harris: Hey, the OE bug tracker has had 574 bug reports, but only 108 are still open, so we've fixed >80%! 08/05/2008 09:51:27 AM from Jen Deegan: Yay! 08/05/2008 09:51:28 AM from midori: Returning to an earlier topic ... I've given Karen and a few others bug tracker permissions that I think will let them set priorities. Karen - can you try one? 08/05/2008 09:51:29 AM from Jen Deegan: well done 08/05/2008 09:51:44 AM from Jen Deegan: what about the tree viewer? 08/05/2008 09:51:52 AM from midori: Re parent editor: it's not just me; lots of people will find it useful (even if they don't know it yet ;) ) 08/05/2008 09:52:02 AM from Jen Deegan: great! 08/05/2008 09:52:03 AM from Nomi Harris: Have you tried the parent editor in b43? 08/05/2008 09:52:08 AM from Nomi Harris: I did fix some of the major issues with it. 08/05/2008 09:52:17 AM from midori: I'd rather have it than not, but if I'm forced to choose, I'll take the parent editor. 08/05/2008 09:52:24 AM from Jen Deegan: good to know. 08/05/2008 09:52:26 AM from Nomi Harris: It's still mega-slow for terms that have a lot of parents. 08/05/2008 09:52:31 AM from Jen Deegan: so are keyboard shortcuts off the list? 08/05/2008 09:52:49 AM from Karen: Midori, yes I'll try to change a priority in the bug tracker. Maybe I should get permissions for the feature tracker too... 08/05/2008 09:53:04 AM from Nomi Harris: Definitely, Karen. 08/05/2008 09:53:14 AM from Nomi Harris: I took a look at keyboard shortcuts and am not sure what's wrong. 08/05/2008 09:53:15 AM from midori: Nomi - I've done a little bit with the b43 parent editor, but I'm really waiting for the fix/alternate handling of cycles. 08/05/2008 09:53:32 AM from Nomi Harris: I can revisit keyboard shortcuts. I've been focusing on speed issues this week. 08/05/2008 09:53:43 AM from Jen Deegan: I think that maybe I could do without the tree viewer if selection in the graphviz viewer was working. 08/05/2008 09:53:55 AM from midori: Keyboard shortcuts - there's one clear bug: the 'merge' shortcut flat-out does not work. 08/05/2008 09:54:09 AM from Nomi Harris: midori, if you like the alternate coloring of cyclical relations (could be gray instead of red, that was just an example), the cycle thing will be fixed. 08/05/2008 09:54:29 AM from midori: Otherwise, it's more that the new system doesn't match the OE1 system for ease of use. There's probably not a lot we can do about that. 08/05/2008 09:54:51 AM from midori: Yes, please! on the cycle thing. Then I'll give the parent editor a good old workout. 08/05/2008 09:54:59 AM from Nomi Harris: Great. 08/05/2008 09:55:14 AM from Nomi Harris: I can do another release today if you like. You don't update from svn and build, do you? 08/05/2008 09:55:41 AM from Jen Deegan: I do. 08/05/2008 09:55:51 AM from Jen Deegan: I could show Midori the ropes if that would help. 08/05/2008 09:55:52 AM from Nomi Harris: I know you do, Jen, I was wondering about midori. 08/05/2008 09:56:11 AM from Nomi Harris: It's up to you guys. I can easily make another release if that's easier for you. 08/05/2008 09:56:22 AM from Nomi Harris: Might be best for midori not to have a moving target, since I check in changes frequently. 08/05/2008 09:56:33 AM from midori: I never have built to date, but suppose I could if there's a good reason. 08/05/2008 09:57:25 AM from Jen Deegan: Slight downside is that there are often code problems to get over. 08/05/2008 09:57:32 AM from Nomi Harris: Not often! occasionally! 08/05/2008 09:57:48 AM from Jen Deegan: :-) 08/05/2008 09:57:52 AM from midori: Hmm. I'd rather be insulated from that. Someone's gotta represent the Clueless User perspective ;) 08/05/2008 09:58:42 AM from Nomi Harris: I was talking to Chris this morning about hiding disjoint_from in the Graph Editor (and possibly the OTE?) 08/05/2008 09:58:53 AM from Nomi Harris: The obvious way to do this is with a global filter; the problem is that that is prohibitively slow. 08/05/2008 09:59:15 AM from Nomi Harris: We need a way to do it on a more basic level. 08/05/2008 10:00:21 AM from Jen Deegan: Chris, would it be possible for you to go through and edit out the menu items for the cross product components that are not meant to be included? That would save us time testing stuff that is not meant to work. 08/05/2008 10:01:53 AM from Jen Deegan: I think we could shelve the ID Fixer untill the next release (sorry to butt in, I'm just putting this down for the record in case anyone wants to comment.) 08/05/2008 10:02:21 AM from Nomi Harris: Karen, you just changed the priority of "google-like Graph Editor nav disappears when GE is undocked" to 6--do you consider that bug a release-stopper? 08/05/2008 10:02:33 AM from midori: I still don't even know what the ID Fixer does, so I wouldn't miss it. 08/05/2008 10:03:02 AM from Jen Deegan: I have a perl script that does what it does and I'm happy to keep using that. 08/05/2008 10:04:08 AM from midori: Some of the bugs I've reported don't really affect my day-to-day editing, but getting them fixed would be good for the user guide. 08/05/2008 10:04:13 AM from Nomi Harris: Should I comment out the menu item for the ID fixer, then? 08/05/2008 10:04:13 AM from Karen: When the size control disappears, it makes the GE unusable, since I can't see the part I need to see, but I haven't been editing for a while, so I'm a little fuzzy on details. 08/05/2008 10:04:28 AM from Nomi Harris: Yeah, but you can always redock it... 08/05/2008 10:04:29 AM from Jen Deegan: yes you could get rid of the ID Fixer. 08/05/2008 10:05:00 AM from Jen Deegan: Chris, which of the XP components was it that you said shouldn't be there? 08/05/2008 10:05:30 AM from David OS: By size control, so you mean magnification control? I find this can usually be fixed by right clicking. 08/05/2008 10:05:58 AM from Jen Deegan: David, does the graph editor completely work for you? 08/05/2008 10:05:59 AM from Karen: yes the magnification control, I'll try right clicking 08/05/2008 10:06:12 AM from Jen Deegan: if so then what OS are you on? 08/05/2008 10:06:27 AM from midori: For me the biggest problem is the gradual slowdown that happens over the course of an editing session -- mainly because it's often not so gradual, and may not take many edits. 08/05/2008 10:06:29 AM from Chris: Jen: the XP matrix editor is clunky and non-intuitive at this time 08/05/2008 10:06:38 AM from Chris: That's because I wrote it.. 08/05/2008 10:06:48 AM from Jen Deegan: shall we comment out the XP matrix editor and save it for next release then? 08/05/2008 10:06:55 AM from Jen Deegan: :-) modesty. 08/05/2008 10:07:11 AM from David OS: Yep. Graph Editor works pretty well for me. system = red hat linux (desktop) or Ubuntu (slow - laptop) 08/05/2008 10:07:19 AM from Jen Deegan: good to know. 08/05/2008 10:07:24 AM from Jen Deegan: I will try it on linux then. 08/05/2008 10:08:26 AM from Jen Deegan: So I have the following: 08/05/2008 10:08:28 AM from Jen Deegan: Needed for this release:parent editor - yeskeyboard shortcuts - notree viewer - no (if selection in graphviz viewer working)xp matric editor - no 08/05/2008 10:08:58 AM from Jen Deegan: the other major issues are to do with slowness aren't they? 08/05/2008 10:09:12 AM from Jen Deegan: actually I think the tree viewer one is too. 08/05/2008 10:09:14 AM from Chris: Jen: we can comment out the XP matrix editor for the release 08/05/2008 10:09:17 AM from midori: Re tree viewer - I'm a bit leery of losing something that's working in OE1. 08/05/2008 10:09:25 AM from Jen Deegan: yes me too. 08/05/2008 10:09:41 AM from Jen Deegan: maybe once the slowness problems are solved it will come right. 08/05/2008 10:09:44 AM from Nomi Harris: I haven't worked much on the Tree Viewer. 08/05/2008 10:10:05 AM from Jen Deegan: I only use it for getting to as specific instance of a term in the OTE. 08/05/2008 10:10:24 AM from Jen Deegan: currently selection in the graphviz viewer is not so good and that is the other way of doing it. 08/05/2008 10:10:24 AM from Chris: Midori: I agree in principle but I thought no one used the tree viewer? The whole denormalized tree paradigm just doesn't scale with the current GO 08/05/2008 10:10:43 AM from Karen: which one is the tree viewer? 08/05/2008 10:10:52 AM from Jen Deegan: DAG View of old. 08/05/2008 10:11:01 AM from midori: Do we really have any idea who uses which viewers, outside this little group? 08/05/2008 10:11:08 AM from Jen Deegan: not really 08/05/2008 10:11:09 AM from David OS: Never use tree viewer. Definitely doesn't scale for are AO. More important to me is getting filtering fixed in OTE. 08/05/2008 10:11:19 AM from Nomi Harris: Filtered save, you mean? 08/05/2008 10:11:33 AM from David OS: That'd be good too. 08/05/2008 10:11:57 AM from Amina: David are there any other filtering issues? 08/05/2008 10:11:59 AM from Nomi Harris: I fixed some filtering issues in the OTE, but I'm not working with the reasoner--did you mean reasoner-related filtering issues? 08/05/2008 10:12:17 AM from David OS: But no - I'm talking abour filters applied to the OTE. This issue came up a couple of weeks ago. I've added some more details to the ticket... 08/05/2008 10:12:22 AM from Jen Deegan: is the filter button that you use to apply the search criteria to the OTE that he means I think. 08/05/2008 10:12:35 AM from Jen Deegan: the one that was lost from OBO-Edit1 08/05/2008 10:12:52 AM from Jen Deegan: would you like a demo? 08/05/2008 10:13:02 AM from Nomi Harris: You mean, "The one that was implemented in OE1 that was never implemented in OE2" 08/05/2008 10:13:07 AM from Jen Deegan: yes 08/05/2008 10:13:07 AM from Nomi Harris: Sure, I'd like a demo. 08/05/2008 10:13:32 AM from David OS: Clicking the spanner allows you to choose various filtering and rendering in OTE and in graph editor. But broken in OTE (or perhaps now fixed?) 08/05/2008 10:13:33 AM from Jen Deegan: I'll get it ready. David is that what you meant.? 08/05/2008 10:13:55 AM from David OS: Having the apply filter button back from OTE1 would do the same thing. 08/05/2008 10:14:07 AM from Jen Deegan: I'll show that button in action. 08/05/2008 10:14:33 AM from David OS: Ideally it would work for filters requiring reasoner. 08/05/2008 10:14:50 AM from David OS: I think this already works for such filters in graph editor. 08/05/2008 10:15:04 AM from Nomi Harris: I will check it today. I think I fixed that. 08/05/2008 10:15:16 AM from David OS: OK. Cool. 08/05/2008 10:15:23 AM from midori: Filtering in OTE - I think I might have noticed something, but will have to investigate further to remember what was going on (and it may be fixed now anyway). 08/05/2008 10:15:38 AM from Nomi Harris: Test in b43. I just made changes in filtering. 08/05/2008 10:16:00 AM from midori: ok 08/05/2008 10:16:02 AM from Jen Deegan: I have a demo ready, Shall I do it at the end or now. 08/05/2008 10:16:13 AM from Nomi Harris: I think we're done with the chat now, aren't we? 08/05/2008 10:16:17 AM from David OS: Now's good for me 08/05/2008 10:16:23 AM from Nomi Harris: Everyone will look at their bug reports and adjust the priorities appropriately. 08/05/2008 10:16:36 AM from midori: I can be done with the chat 08/05/2008 10:16:43 AM from Nomi Harris: Did you have anything else to discuss, midori? 08/05/2008 10:16:49 AM from Nomi Harris: You were going to show me your dbxref problem. 08/05/2008 10:17:02 AM from midori: Nomi - it might not hurt to email the list about bug priorities, to catch any submitters who aren't here. 08/05/2008 10:17:14 AM from Nomi Harris: Will do. 08/05/2008 10:17:17 AM from Amina: Nomi I updated the bug report for the dbxref issue last week 08/05/2008 10:17:30 AM from midori: Demo - OK, but if Jen wants to go first that's fine 08/05/2008 10:17:42 AM from Jen Deegan: shall I? 08/05/2008 10:18:23 AM from Jen Deegan: Okay, I'm going to set up a search, but then apply it as a filter instead on the OTE. 08/05/2008 10:18:23 AM from midori: please do - when you're done, maybe this computer will be done with its backup, and capable of doing a demo! 08/05/2008 10:18:31 AM from Nomi Harris: Amina, which one? I'm talking about http://sourceforge.net/tracker/index.php?func=detail&aid=2025804&group_id=36855&atid=418257 08/05/2008 10:18:31 AM from Jen Deegan: just in case the chat disappears. 08/05/2008 10:19:53 AM from Jen Deegan: did that make sense? 08/05/2008 10:19:57 AM from Nomi Harris: Yes 08/05/2008 10:20:01 AM from Jen Deegan: oh good. 08/05/2008 10:20:03 AM from Nomi Harris: I will see what I can do. 08/05/2008 10:20:07 AM from Jen Deegan: brilliant. 08/05/2008 10:20:12 AM from Nomi Harris: But first I'm going to spend some more time investigating slowness and CPU spikes. 08/05/2008 10:20:18 AM from Jen Deegan: and we will prioritize. 08/05/2008 10:20:22 AM from Jen Deegan: thanks. 08/05/2008 10:20:38 AM from Nomi Harris: Midori, can you show your dbxref bug now? Or is your computer still backing up? 08/05/2008 10:20:53 AM from Nomi Harris: Can you go to the little turning wheel on the top of the screen and right-mouse and ask it to stop the backup? 08/05/2008 10:21:01 AM from Amina: There was another dbxref bug report I updated and put in an example for - this demo should be useful 08/05/2008 10:21:09 AM from midori: I'll try ... just loading GO; worst that can happen is it'll be slow 08/05/2008 10:21:14 AM from midori: what turning wheel? 08/05/2008 10:21:41 AM from Nomi Harris: At the top right of my screen, near the battery indicator 08/05/2008 10:21:43 AM from Jen Deegan: my dbxref bug is fixed now. 08/05/2008 10:21:50 AM from midori: I don't have that wheel. 08/05/2008 10:22:03 AM from Nomi Harris: Oh. I guess I have different backup software. 08/05/2008 10:22:26 AM from midori: this is Tim's homebrew rsync backup 08/05/2008 10:22:42 AM from midori: ready any time, tho 08/05/2008 10:22:46 AM from Nomi Harris: I'm ready 08/05/2008 10:23:42 AM from midori: ok, here goes ... 08/05/2008 10:25:00 AM from Jen Deegan: That's a crazy-go-nuts bug 08/05/2008 10:25:07 AM from midori: was that clear? 08/05/2008 10:25:28 AM from midori: It's basically the same as what I originally reported. 08/05/2008 10:25:28 AM from Jen Deegan: was it serial appearance and disappearance of dbxrefs? 08/05/2008 10:26:22 AM from midori: I can use the dbxref library to add up to two dbxrefs (total, counting any that were already there). Then, when I try to add a third, nothing happens, and trynig a fourth makes one disappear. 08/05/2008 10:26:28 AM from Jen Deegan: I think maybe Nomi can't see the chat while you demo. 08/05/2008 10:26:36 AM from midori: (and yes, I am going nuts) 08/05/2008 10:26:40 AM from Nomi Harris: Sorry, right, I couldn't see the chat. 08/05/2008 10:26:47 AM from midori: is it all there now? 08/05/2008 10:27:00 AM from Nomi Harris: So weird, that's the same bug I fixed, though I was suspicious of my fix because I don't understand why it fixed it. 08/05/2008 10:27:13 AM from Nomi Harris: So apparently my fix worked for me (on Mac) and Jen (on Windows) but not for midori (on Mac)? 08/05/2008 10:27:14 AM from Jen Deegan: I had this or similar but it is fixed now. 08/05/2008 10:27:27 AM from Nomi Harris: I will take another look at it, midori. 08/05/2008 10:27:38 AM from Nomi Harris: I don't understand the bug at all. It's possible it's a Java bug. 08/05/2008 10:27:40 AM from midori: Well, I can confirm the "not fixed for midori on Mac" part. 08/05/2008 10:27:40 AM from Jen Deegan: mine was not as mad as Midori's 08/05/2008 10:27:59 AM from midori: yay, I'm the maddest! 08/05/2008 10:28:07 AM from Jen Deegan: your dbxrefs were almost flashing midori. 08/05/2008 10:28:11 AM from Jen Deegan: is that what you see? 08/05/2008 10:28:25 AM from Nomi Harris: It looked flashy to me but I thought that might be WebEx/network redraw slowness. 08/05/2008 10:28:28 AM from midori: flashing? lemme look again ... 08/05/2008 10:28:46 AM from Jen Deegan: they were appearing and disappearing really quite quickly. 08/05/2008 10:28:49 AM from Nomi Harris: Yeah, the flashing probably made Jen seasick! 08/05/2008 10:29:08 AM from Jen Deegan: oi! 08/05/2008 10:29:11 AM from Tanya: I saw lots of flashing. 08/05/2008 10:29:23 AM from Tanya: (on the screen) 08/05/2008 10:29:27 AM from Tanya: :) 08/05/2008 10:29:31 AM from Jen Deegan: were you doing anything to cause it? Ididn't see you doing anything to cause the flasshing. 08/05/2008 10:29:32 AM from Nomi Harris: Anyway, whether or not it flashed, midori couldn't add a third dbxref. 08/05/2008 10:29:38 AM from Nomi Harris: so let's not worry about the flashing. 08/05/2008 10:29:44 AM from Jen Deegan: ok 08/05/2008 10:29:51 AM from Nomi Harris: Are we done for today? 08/05/2008 10:29:56 AM from midori: interesting ... might be a webex thing, 'cos I don't think it's flashing. 08/05/2008 10:30:00 AM from Jen Deegan: Midori,have you tried clicking the + button ? 08/05/2008 10:30:06 AM from Jen Deegan: that helped with me. 08/05/2008 10:30:30 AM from Tanya: catch you later 08/05/2008 10:30:39 AM from Nomi Harris: Thanks, all. 08/05/2008 10:30:41 AM from Nomi Harris: Bye 08/05/2008 10:30:45 AM from Jen Deegan: when all my dbxrefs disappear I can bring them back one at a time by clicking the +button 08/05/2008 10:30:47 AM from Jen Deegan: bye 08/05/2008 10:30:51 AM from Nomi Harris: Oh, interesting. 08/05/2008 10:31:08 AM from Jen Deegan: and if I add one from the dbxref library then they all disappear again. 08/05/2008 10:31:12 AM from midori: which + button? in dbxrefs? 08/05/2008 10:31:13 AM from Jen Deegan: but it's fixed for me now. 08/05/2008 10:31:16 AM from Jen Deegan: yes 08/05/2008 10:31:37 AM from midori: will try, but the bug remains a bug 08/05/2008 10:31:41 AM from Jen Deegan: yes ture 08/05/2008 10:31:52 AM from Jen Deegan: just interested to characterize it further. 08/05/2008 10:31:57 AM from Jen Deegan: shall we be off now? 08/05/2008 10:31:59 AM from midori: ah, + does make them show up. 08/05/2008 10:32:03 AM from Jen Deegan: cool! 08/05/2008 10:32:09 AM from Nomi Harris: So at least there's a workaround for the bug 08/05/2008 10:32:21 AM from Jen Deegan: yes 08/05/2008 10:32:25 AM from Nomi Harris: Bye? 08/05/2008 10:32:28 AM from Jen Deegan: bye! 08/05/2008 10:32:29 AM from midori: ok, bye