OE Webex 1Jul08
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07/01/2008 09:31:14 AM from Amina: Hi everyone 07/01/2008 09:31:34 AM from Jen Deegan: Hi 07/01/2008 09:31:34 AM from Nomi Harris: Hi 07/01/2008 09:31:43 AM from Jen Deegan: sorry, was just answering your mails. 07/01/2008 09:31:56 AM from Nomi Harris: No problem! 07/01/2008 09:32:17 AM from Jen Deegan: How's it going? 07/01/2008 09:32:23 AM from melissaH: Hi! long time since I've been around. 07/01/2008 09:32:24 AM from Nomi Harris: Thanks for all the user guide updating you've already done, Jen. 07/01/2008 09:32:31 AM from Nomi Harris: Nice to see you back, Melissa! 07/01/2008 09:32:37 AM from Jen Deegan: You're welcome! I was trying hard to rattle through it. 07/01/2008 09:32:57 AM from melissaH: Its nice to be back! 07/01/2008 09:33:00 AM from midori: Hi Melissa" 07/01/2008 09:33:03 AM from Jen Deegan: Where were you? 07/01/2008 09:33:19 AM from midori: (apparently your return hasn't improved my typing) 07/01/2008 09:33:25 AM from Jen Deegan: :-) 07/01/2008 09:33:26 AM from melissaH: too many trips, too many grant obligations, no onotlogy editing or OE testing. 07/01/2008 09:33:38 AM from Jen Deegan: Ah! sounds like all kinds of fun. 07/01/2008 09:33:40 AM from Amina: Hi Melissa and Jen 07/01/2008 09:33:43 AM from Jen Deegan: Hi Amina. 07/01/2008 09:33:45 AM from melissaH: Hi Amina! 07/01/2008 09:34:01 AM from Nomi Harris: Melissa, are you going to have a bit of time this week to help test and document? 07/01/2008 09:34:14 AM from melissaH: yep! why I am here. hoping to make up for lost time. 07/01/2008 09:34:20 AM from Nomi Harris: Great! 07/01/2008 09:34:29 AM from Nomi Harris: Which aspect of OE do you want to focus on? 07/01/2008 09:34:49 AM from melissaH: and I am a bit naive since I've been out of the loop. so help assign me something? 07/01/2008 09:35:12 AM from Nomi Harris: I'm not sure what your normal usage pattern is. What do you typically do in OE? 07/01/2008 09:35:16 AM from melissaH: I tend to use the tree editor a lot, and also the parent editor. 07/01/2008 09:35:28 AM from Jen Deegan: There are lots of really normal boring pages that just need read through and updated. 07/01/2008 09:35:33 AM from melissaH: and I have non- transitive relations and need global filtering 07/01/2008 09:35:57 AM from Amina: Melissa would you be interested in working on the Viewing Ontologies section then 07/01/2008 09:36:06 AM from melissaH: so have you all been saving in OE2 yet? 07/01/2008 09:36:12 AM from melissaH: sure 07/01/2008 09:36:16 AM from Nomi Harris: And Amina said she'd work on the filtering pages, but it would be great to have you read them over too. 07/01/2008 09:36:31 AM from Nomi Harris: Yes, saving should work, but that would definitely be a good thing to test! 07/01/2008 09:36:39 AM from Jen Deegan: I have done the first half of the first page of viewing ontologies but am very happy to hand it over. 07/01/2008 09:36:41 AM from Amina: oh yea I could definately use some help for the filtering examples 07/01/2008 09:36:46 AM from melissaH: k 07/01/2008 09:36:46 AM from Nomi Harris: Any bugs you find where saving isn't working right are definitely high priority. 07/01/2008 09:36:54 AM from midori: I've done a few saves, with no mishaps ( fingers crossed) 07/01/2008 09:37:10 AM from Amina: Jen I didnt know you were working on it - I'm sorry 07/01/2008 09:37:16 AM from Jen Deegan: I found a save bug but I will put it in SF. 07/01/2008 09:37:22 AM from Jen Deegan: not that's fine! 07/01/2008 09:37:33 AM from Nomi Harris: Melissa, I don't know what your level of technical ability is. Are you comfortable editing html? What about committing your changes? 07/01/2008 09:37:33 AM from melissaH: my biggest problem in the past is that testing has been hard because I haven't really been editing in OE2. 07/01/2008 09:38:03 AM from midori: Same here! 07/01/2008 09:38:05 AM from melissaH: not really. I can use svn fine. 07/01/2008 09:38:21 AM from Nomi Harris: Was "not really" about the html? 07/01/2008 09:38:28 AM from melissaH: so its been hard to find time to do both. (and lately I haven't even been editing in OE1) 07/01/2008 09:38:49 AM from Nomi Harris: For the most part, if you just need to make changes to the text, you won't need to do much in the way of html. 07/01/2008 09:39:03 AM from Nomi Harris: You'll see where the text is, and just substitute new text (or update the images). 07/01/2008 09:39:04 AM from David OS: Sorry I'm late. Problems getting webex to fire up. 07/01/2008 09:39:12 AM from Nomi Harris: Hi, David, glad you could join us. 07/01/2008 09:39:22 AM from Amina: Hi David 07/01/2008 09:39:25 AM from melissaH: yeah- i had the same prob. didn't like two instances. 07/01/2008 09:39:29 AM from Nomi Harris: By the way, if anyone updates images in the web pages, please note that a lot of images have height and width tags. 07/01/2008 09:39:35 AM from melissaH: I'll give it a go. 07/01/2008 09:39:41 AM from Nomi Harris: If you change the image, you may need to update or remove the height/width tags. 07/01/2008 09:39:43 AM from midori: oh yeah, that bit me a while back. 07/01/2008 09:39:49 AM from Nomi Harris: Otherwise, your new image will show up somewhat warped looking. 07/01/2008 09:40:18 AM from midori: wasn't hard to fix, but was bo-o-o-o-ring 07/01/2008 09:40:18 AM from Jen Deegan: I have a general question for the working group. 07/01/2008 09:40:50 AM from Jen Deegan: As I am working through documenting components that are previously undocumented 07/01/2008 09:41:01 AM from Jen Deegan: I have been finding e.g. config settings that just don't do anything 07/01/2008 09:41:05 AM from Nomi Harris: (Midori, I usually just remove the height/width tags, because that's the simplest.) 07/01/2008 09:41:24 AM from Jen Deegan: sometimes I have no idea why we wanted them in the first place or what they are meant to do 07/01/2008 09:41:29 AM from Nomi Harris: Jen, those should be logged as bug reports (with sub-5 priority). 07/01/2008 09:41:29 AM from midori: Yep, that's what I've been doing since about the second one. 07/01/2008 09:41:36 AM from Amina: Jen are these settings that should ideally be doing something? 07/01/2008 09:41:48 AM from Jen Deegan: I was wondering what is the best medium for asking the working group whether they would miss a given feature if it was just removed. 07/01/2008 09:41:49 AM from Nomi Harris: You can note whether that's a wanted feature or whether it's just a useless option that should be removed. 07/01/2008 09:41:55 AM from Jen Deegan: that's what we need to find out really. 07/01/2008 09:42:00 AM from Nomi Harris: Right, sorry for interrupting. 07/01/2008 09:42:05 AM from Jen Deegan: no problem. 07/01/2008 09:42:08 AM from Nomi Harris: What about just using the mailing list? 07/01/2008 09:42:17 AM from Jen Deegan: there tend to be a lot of them. 07/01/2008 09:42:18 AM from Nomi Harris: Maybe you can assemble a list so you don't send too many little messages about it. 07/01/2008 09:42:25 AM from Jen Deegan: maybe on a wiki page? 07/01/2008 09:42:30 AM from Jen Deegan: then send the link? 07/01/2008 09:42:36 AM from Amina: yeah that would work too 07/01/2008 09:42:44 AM from Jen Deegan: I thought rather than millions of bug reports. 07/01/2008 09:42:50 AM from Jen Deegan: what do the others think? 07/01/2008 09:42:56 AM from Jen Deegan: would you have time to look? 07/01/2008 09:43:11 AM from Nomi Harris: I would look at it (but might then forget to look back at it in the future). 07/01/2008 09:43:15 AM from melissaH: maybe send a reminder that its on the wiki. 07/01/2008 09:43:21 AM from Nomi Harris: How about a wiki page, and a single bug report that points to the wiki page? 07/01/2008 09:43:28 AM from Jen Deegan: I could put a date e.g. day if you want this kept by two weeks from now... 07/01/2008 09:43:29 AM from midori: either mailing list or wiki would be fine with me. 07/01/2008 09:43:40 AM from Jen Deegan: great 07/01/2008 09:43:45 AM from Nomi Harris: Wiki might be good so we can remove the ones that are fixed. 07/01/2008 09:43:49 AM from Jen Deegan: I'll start doing that and see what happens. 07/01/2008 09:43:52 AM from Jen Deegan: true 07/01/2008 09:44:06 AM from Jen Deegan: they could be removed to the list of features that are half implemented if that exists. 07/01/2008 09:44:13 AM from Jen Deegan: I'm done, thanks. 07/01/2008 09:44:21 AM from Nomi Harris: Ok 07/01/2008 09:44:42 AM from Nomi Harris: So we still don't have a Windows box that I can use to see why some of the OE config files appear to be empty. 07/01/2008 09:45:06 AM from Nomi Harris: But the configuration is all working on Windows, right? It's just a mystery about why the files are empty? Was there some reason you needed to look at them? 07/01/2008 09:45:08 AM from Jen Deegan: thanks for the update on that. 07/01/2008 09:45:12 AM from melissaH: I didn't reply to your email about that, but I am windows. can I help? 07/01/2008 09:45:14 AM from Jen Deegan: yes it works 07/01/2008 09:45:18 AM from Nomi Harris: (Amina said our Windows testing box should be ready today!) 07/01/2008 09:45:30 AM from Jen Deegan: no I think it needs to be Nomi or Amina. 07/01/2008 09:45:32 AM from Nomi Harris: Jen, so it's not actually a bug, just a puzzling thing? 07/01/2008 09:45:32 AM from Jen Deegan: thanks though 07/01/2008 09:45:40 AM from Jen Deegan: It is a bug 07/01/2008 09:45:54 AM from Jen Deegan: then think is that I am trying to upgrade the graphviz configuration to the new system 07/01/2008 09:46:10 AM from Jen Deegan: and it's a bit tricky to figure out how the new system works, since it kind of doesn't 07/01/2008 09:46:18 AM from Nomi Harris: What do you mean "new system"? 07/01/2008 09:46:23 AM from Nomi Harris: New directory for config files? 07/01/2008 09:46:32 AM from Jen Deegan: well before you arrived John did this huge code rewrite 07/01/2008 09:46:44 AM from Jen Deegan: no to the wrench icon for configuration files. 07/01/2008 09:46:47 AM from Nomi Harris: Oh. 07/01/2008 09:46:57 AM from Jen Deegan: and the graphviz plugin is still on the old system 07/01/2008 09:47:07 AM from Jen Deegan: and I tried to move it to the new system with the wrench 07/01/2008 09:47:17 AM from Jen Deegan: and it's hard because I can't track down how the new system works 07/01/2008 09:47:23 AM from Nomi Harris: So one thing that's a bit of a gotcha is that the config files only get saved when you quit OBO-Edit. 07/01/2008 09:47:26 AM from Jen Deegan: and in the process I realised that that is becauase it doesn't 07/01/2008 09:47:36 AM from Nomi Harris: So you can do wrench stuff and look at the config files and they won't appear to have changed. 07/01/2008 09:47:38 AM from Jen Deegan: yes I understand that part. 07/01/2008 09:47:40 AM from Nomi Harris: Ok. 07/01/2008 09:47:46 AM from Nomi Harris: So what doesn't work? 07/01/2008 09:47:50 AM from Jen Deegan: but in windows they really aren't saved 07/01/2008 09:47:57 AM from Jen Deegan: the files are there but are totally empty 07/01/2008 09:48:06 AM from Nomi Harris: I see, so on Mac you can change configurations with the wrench and they get saved, 07/01/2008 09:48:09 AM from Jen Deegan: and the config details can't be found at all on my hard drive 07/01/2008 09:48:15 AM from Jen Deegan: yes that's right 07/01/2008 09:48:19 AM from Jen Deegan: clear as day. 07/01/2008 09:48:21 AM from Nomi Harris: but on Windows, when you do the same thing, they are not saved, and when you restart OE on Windows it forgets your configuration? 07/01/2008 09:48:30 AM from Jen Deegan: I can read the details right there in the files. 07/01/2008 09:48:46 AM from Nomi Harris: But leaving the files aside, what about the OE behavior? 07/01/2008 09:48:48 AM from Jen Deegan: it remembers my configuration, that's the creepy thing. 07/01/2008 09:49:01 AM from Jen Deegan: OE behaves beautifully. 07/01/2008 09:49:09 AM from Jen Deegan: so this is a developer chat thing really. 07/01/2008 09:49:15 AM from Jen Deegan: I shouldn't take up everyone's time on it. 07/01/2008 09:49:32 AM from Jen Deegan: erm, I guess so yes. 07/01/2008 09:49:38 AM from Nomi Harris: Ok. 07/01/2008 09:49:46 AM from Amina: Jen I should point out - I was looking into the windows config dir issues a while back for a different bug and windows decides to make that dir invisible to the user for \ some mysterious reason 07/01/2008 09:49:47 AM from Nomi Harris: I will look into it when we get the Windows test box up. 07/01/2008 09:50:10 AM from Jen Deegan: It's okay I did find it. 07/01/2008 09:50:15 AM from Amina: so it could be that the files are present and saved 07/01/2008 09:50:17 AM from Jen Deegan: It's jus the files inside are empty. 07/01/2008 09:50:30 AM from Nomi Harris: If you copy them to another directory, can you see the contents? 07/01/2008 09:50:38 AM from Jen Deegan: I will try that. 07/01/2008 09:50:39 AM from Amina: I'll send you an email about where you can look for them thru the terminal 07/01/2008 09:50:39 AM from Jen Deegan: thanks. 07/01/2008 09:50:40 AM from Nomi Harris: Maybe we should take this offline, since it doesn't really affect the other OEWG people? 07/01/2008 09:50:43 AM from Nomi Harris: Thanks, Amina. 07/01/2008 09:50:53 AM from Jen Deegan: yes that would be good to go offline. 07/01/2008 09:50:58 AM from Nomi Harris: We can also add a note to the user guide in case other power users are puzzled. 07/01/2008 09:51:12 AM from Jen Deegan: I shouldn't think they will be 07/01/2008 09:51:28 AM from Amina: yeah this needs to be in the user guide for windows users 07/01/2008 09:51:32 AM from Nomi Harris: Jen reminded me and Amina this morning about the need to focus on the really crucial features of OE2 in order to get it ready for public relase. 07/01/2008 09:51:35 AM from Nomi Harris: (release) 07/01/2008 09:51:58 AM from Nomi Harris: Of course, we are already trying to do this (with occasional diversions to fix little easily-fixable-though-not-critical issues) 07/01/2008 09:52:05 AM from Nomi Harris: but we welcome feedback about what to focus on. 07/01/2008 09:52:13 AM from Jen Deegan: I would really wlecome that from others too. 07/01/2008 09:52:17 AM from Jen Deegan: so I know what to test. 07/01/2008 09:52:27 AM from midori: test everything! 07/01/2008 09:52:34 AM from Nomi Harris: Amina is trying to fix the filtered save 07/01/2008 09:52:34 AM from Jen Deegan: I was wondering though 07/01/2008 09:52:49 AM from Nomi Harris: I and others have been looking at reasoner performance 07/01/2008 09:53:02 AM from Jen Deegan: whether it makes sense to have some of the really just nice-to-have features hold back the next release. 07/01/2008 09:53:11 AM from midori: For me, the memory and CPU issues are top priority, because it's so difficult to test anything else when OE's CPU usage spikes and stalls the whole app. 07/01/2008 09:53:12 AM from David OS: "Amina is trying to fix the filtered save" Ahhh - thought she had. Am really itching to use this. 07/01/2008 09:53:23 AM from Amina: David I'm still testing it 07/01/2008 09:53:35 AM from David OS: OK cool. 07/01/2008 09:53:42 AM from Nomi Harris: Yes, I spent several days last week using YourKit (a profiling tool) to try to track down memory and CPU issues. 07/01/2008 09:53:43 AM from Amina: there are some link filter bugs too that I'm hoping are interconnected with the term filter 07/01/2008 09:54:00 AM from Jen Deegan: If I made a list of the features that I think are just nice-to-have and that could be left over to the next release then could we all look at it and figure out what we wo\ uld not miss? 07/01/2008 09:54:08 AM from Nomi Harris: I was hoping to find some obvious places for improvement, but sadly, there is nothing obvious. 07/01/2008 09:54:15 AM from midori: Drat! 07/01/2008 09:54:16 AM from Amina: and hopefully also give some insight into the global filter bugs 07/01/2008 09:54:34 AM from Nomi Harris: I will continue the research, but this week I'm trying to focus on documenting. 07/01/2008 09:55:04 AM from midori: Fair enough. I'll try to do what testing I can, if OE will behave. 07/01/2008 09:55:08 AM from Nomi Harris: I have concluded, though, that the new reasoner (LinkPile) may be unworkable because it is exponential in its running time 07/01/2008 09:55:21 AM from Nomi Harris: so even if we make some improvements in it, it's going to blow up on big ontologies. 07/01/2008 09:55:23 AM from Amina: David do you think you would have some time for user documentation this week? 07/01/2008 09:55:44 AM from Nomi Harris: midori, since I started profiling, I haven't seen any CPU spikes that don't involve the reasoner. 07/01/2008 09:56:04 AM from Nomi Harris: And I'm completely mystified by Jen's slow text commits. For me, text commits are fast unless I have the reasoner on. 07/01/2008 09:56:27 AM from Amina: The windows box might help with those issues 07/01/2008 09:56:29 AM from Nomi Harris: Jen, you might try wiping out your config (you can move it elsewhere temporarily) and see if commits return to being fast. 07/01/2008 09:56:33 AM from David OS: I may be able to write something on the graph editor. But can't promise I'll have time to do anything like a complete job I'm afraid. 07/01/2008 09:56:49 AM from Nomi Harris: I think Jen already updated the Graph Editor page, but it would be great if you could take a look at it 07/01/2008 09:56:49 AM from Jen Deegan: I'll try that 07/01/2008 09:56:53 AM from Nomi Harris: and see if there's anything you want to add. 07/01/2008 09:56:59 AM from midori: I'll keep trying, then, but I've had the reasoner off for all of the CPU spikes I reported (in fact, that's what made me put in a bug report - no reasoner, but lousy perf\ ormance anyway). 07/01/2008 09:57:04 AM from Jen Deegan: I think that page needs more work. 07/01/2008 09:57:06 AM from Amina: sounds good David 07/01/2008 09:57:14 AM from Nomi Harris: Are text commits reliably slow for you, Jen? Every time you open OE and edit a term, it takes 13 seconds? 07/01/2008 09:57:31 AM from Jen Deegan: yes they do seem to be. 07/01/2008 09:57:36 AM from Jen Deegan: I think 07/01/2008 09:57:41 AM from Jen Deegan: I am doubting myself now. 07/01/2008 09:57:44 AM from Nomi Harris: David, before you edit the Graph Editor man page, just make sure you're updated to the latest version--Jen changed it after the last release, but she committed to svn. 07/01/2008 09:57:46 AM from Jen Deegan: I will double triple check 07/01/2008 09:57:55 AM from midori: I think I've seen slow commits too, so I'll test again. 07/01/2008 09:58:24 AM from Nomi Harris: If anyone doesn't want to deal with editing html pages or with svn commits, please feel free to send me your updates to the help pages and I'll commit them. 07/01/2008 09:58:25 AM from Jen Deegan: is the standard config now not to do verification checks on text commit? 07/01/2008 09:58:54 AM from Jen Deegan: I know that was one pitfall and I wondered if it might come back if people nuke their config directory. 07/01/2008 09:59:17 AM from Nomi Harris: It looks like it still is configured to do verification checks on text commit. 07/01/2008 09:59:21 AM from Nomi Harris: Should we turn that off, maybe? 07/01/2008 09:59:41 AM from Jen Deegan: that might be good 07/01/2008 09:59:57 AM from Nomi Harris: Ok. 07/01/2008 10:00:17 AM from Jen Deegan: for speed checks you could jave have things set to run on manual until we iron out these problems. 07/01/2008 10:00:27 AM from Jen Deegan: does that seem reasonable? 07/01/2008 10:00:29 AM from Nomi Harris: Why is there even a checkbox for "on manual"? 07/01/2008 10:00:41 AM from Jen Deegan: yes on the verification checker configuration 07/01/2008 10:00:49 AM from Jen Deegan: you can set it only to run when you tell it to 07/01/2008 10:00:58 AM from Jen Deegan: that means fewer mysterious things happening automatically. 07/01/2008 10:01:02 AM from Nomi Harris: If you unchecked "on manual" , then if you clicked "Run manual check now", would it do nothing? 07/01/2008 10:01:09 AM from midori: correct 07/01/2008 10:01:13 AM from Jen Deegan: good point! 07/01/2008 10:01:17 AM from Jen Deegan: I hadn't thought of that. 07/01/2008 10:01:19 AM from midori: (I assume, but I haven't actually tried!) 07/01/2008 10:01:19 AM from Nomi Harris: That would be silly, wouldn't it? 07/01/2008 10:01:24 AM from Nomi Harris: Should I take that checkbox off? 07/01/2008 10:01:26 AM from Jen Deegan: it would 07/01/2008 10:01:28 AM from Jen Deegan: :-) 07/01/2008 10:01:35 AM from midori: Which checkbox? 07/01/2008 10:01:43 AM from Jen Deegan: the on manual one 07/01/2008 10:01:44 AM from Nomi Harris: The "on manual" checkbox in the verification manager 07/01/2008 10:01:50 AM from Nomi Harris: Maybe it's there as a reminder 07/01/2008 10:01:53 AM from Jen Deegan: to be honest it works 07/01/2008 10:01:56 AM from Nomi Harris: that you can do verification checks manually 07/01/2008 10:02:00 AM from Jen Deegan: and it reminds me that it's an option. 07/01/2008 10:02:03 AM from Nomi Harris: Right. 07/01/2008 10:02:06 AM from midori: There are a whole bunch of checks, and each one has an "on manual" option. 07/01/2008 10:02:11 AM from Nomi Harris: Ok, I guess it's harmless enough... 07/01/2008 10:02:28 AM from Jen Deegan: is the spell checker tha one that causes havoc for the text commit. 07/01/2008 10:02:32 AM from Jen Deegan: that was a problem before. 07/01/2008 10:02:39 AM from Jen Deegan: I wonder if it's sneaked back on somehow. 07/01/2008 10:02:50 AM from midori: So you can set it up so that some checks, but not others, run when you hit 'run manual check now.' 07/01/2008 10:03:00 AM from Nomi Harris: Right, sorry 07/01/2008 10:03:09 AM from Nomi Harris: I just realized I hadn't expanded the panel enough 07/01/2008 10:03:16 AM from midori: ... So I tihnk the 'on manual' checkboxes should stay. Unless I'm not thinking of the same thing you are ... 07/01/2008 10:03:21 AM from Nomi Harris: to see the text that says "Show warnings" 07/01/2008 10:03:27 AM from Jen Deegan: I would be keen to keep them too. 07/01/2008 10:03:32 AM from Nomi Harris: I thought it was referring to whether it runs the verification checks, but I was wrong. 07/01/2008 10:03:37 AM from Nomi Harris: Sorry for the confusion. 07/01/2008 10:03:50 AM from midori: no prob! 07/01/2008 10:04:22 AM from Nomi Harris: Is the spelling check in "Definition checks"? 07/01/2008 10:04:33 AM from Jen Deegan: yes 07/01/2008 10:04:39 AM from Jen Deegan: an other places I thnk 07/01/2008 10:04:40 AM from Nomi Harris: There are several checks that are turned on for text edit, including that one. 07/01/2008 10:04:59 AM from Nomi Harris: Which checks should be on for text edit? Should they all be off? 07/01/2008 10:05:20 AM from Jen Deegan: it depends 07/01/2008 10:05:27 AM from Jen Deegan: maybe for speed tests at first they should 07/01/2008 10:05:27 AM from David OS: Name checks should be on by default 07/01/2008 10:05:41 AM from David OS: Cycle check too I think 07/01/2008 10:06:00 AM from Jen Deegan: ideally many should be on, but if we are really dtruggling for speed could we test with them off then work up? 07/01/2008 10:06:22 AM from Nomi Harris: Yes 07/01/2008 10:06:34 AM from Nomi Harris: Have you changed your verification checks, Jen, or are you using the default settings? 07/01/2008 10:06:39 AM from David OS: But best to set this manually before testing then futz with the defaults? 07/01/2008 10:06:50 AM from David OS: Or am I getting my wires crossed here... 07/01/2008 10:06:52 AM from midori: Aside on commit speed: based on two minutes of slapdash testing, it looks like commit time is correlated with ontology size. Just a second or two to commit a text change \ in a tiny test ontology, but about 10 sec for an equivalent edit in GO. 07/01/2008 10:07:10 AM from Jen Deegan: I just worry that people will forget after deleting the config folder then report bug problems that we know about. 07/01/2008 10:07:24 AM from Nomi Harris: I tend to test on smaller ontologies unless I'm specifically testing an issue reported with GO 07/01/2008 10:07:28 AM from Jen Deegan: that would explain it 07/01/2008 10:07:38 AM from Nomi Harris: but I'm pretty sure I tested with GO when you reported that commit slowness, Jen. 07/01/2008 10:07:38 AM from Jen Deegan: thought is is quick on windows and slow on mac as far as I can tell. 07/01/2008 10:07:42 AM from Nomi Harris: I'll look at it again today. 07/01/2008 10:07:52 AM from Jen Deegan: I'll look again tomorrow as well. 07/01/2008 10:08:01 AM from midori: I don't think repeat bug reports are that big a deal -- we can use the SF tracker 'duplicate' setting 07/01/2008 10:08:08 AM from Jen Deegan: yes it is fast on my winXP machine 07/01/2008 10:08:17 AM from midori: my correlation with ontology size is on a Mac 07/01/2008 10:08:48 AM from Nomi Harris: I will look into this. 07/01/2008 10:08:51 AM from Jen Deegan: thanks. 07/01/2008 10:09:03 AM from Nomi Harris: So, midori, which parts of the user guide are you going ot work on? 07/01/2008 10:09:08 AM from Jen Deegan: would it make sense for me to send you my config directory? 07/01/2008 10:09:19 AM from David OS: Fast on my linux box too - just tested on GO. 07/01/2008 10:09:31 AM from midori: good question ... a lot of the sutff I do regularly is claimed. 07/01/2008 10:09:44 AM from Jen Deegan: is amina really doing all of filtering? 07/01/2008 10:09:53 AM from Jen Deegan: we could do bits if it helped. 07/01/2008 10:09:58 AM from Amina: I could use some help with the examples 07/01/2008 10:10:01 AM from midori: I can do the slog through existing docs looking for what needs updating. 07/01/2008 10:10:04 AM from Jen Deegan: sure 07/01/2008 10:10:09 AM from Amina: or eeven look into documenting other sections 07/01/2008 10:10:12 AM from Amina: like the reasoner 07/01/2008 10:10:22 AM from Nomi Harris: So, David, when you did text edits in GO on your linux box, they were fast? I just want to make sure I got what you were saying. 07/01/2008 10:10:32 AM from Nomi Harris: Midori, that would be great. 07/01/2008 10:10:36 AM from Jen Deegan: it would be great if people could be really specific about which page they are doing so we know what not to do. 07/01/2008 10:10:41 AM from David OS: I'm happy to look over filtering once you have a draft and edit / suggest examples. 07/01/2008 10:10:48 AM from Amina: we have some considerable changes to mention in the reasoner section 07/01/2008 10:10:52 AM from Nomi Harris: And everyone should do frequent commits and updates to make sure we stay in synch. 07/01/2008 10:11:04 AM from Nomi Harris: Amina, do you want to tackle the reasoner section? 07/01/2008 10:11:27 AM from Amina: yes I'll work on that and have Chris review it once hes back 07/01/2008 10:11:31 AM from Jen Deegan: I could do filtering if you want to do the reasoner 07/01/2008 10:11:39 AM from Amina: sounds good Jen 07/01/2008 10:11:44 AM from Jen Deegan: great, thanks. 07/01/2008 10:11:58 AM from Jen Deegan: I left cross products as I don't ahve enough information 07/01/2008 10:12:24 AM from Amina: Karen E said she would look into the cross products setion 07/01/2008 10:12:33 AM from Jen Deegan: brilliant 07/01/2008 10:12:41 AM from David OS to All Attendees: Can someone send me the address of the svn. (sorry if I missed this) 07/01/2008 10:12:49 AM from Nomi Harris: I'll send her a reminder. 07/01/2008 10:12:59 AM from Amina: Jen are you also doing GraphViz Plugin under Plugins then? 07/01/2008 10:13:09 AM from Nomi Harris: She already did. 07/01/2008 10:13:20 AM from Nomi Harris: By the way, Jen, you noted that GraphViz and dbxref could move to components, 07/01/2008 10:13:22 AM from Amina: ic great! 07/01/2008 10:13:27 AM from Nomi Harris: but then where should the page on how to install plugins go? 07/01/2008 10:13:53 AM from Jen Deegan: I'm not sure, I think they are sort of developer docs 07/01/2008 10:13:57 AM from Jen Deegan: the plugin bit. 07/01/2008 10:14:01 AM from Jen Deegan: http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code for david. 07/01/2008 10:14:18 AM from David OS to All Attendees: Cheers 07/01/2008 10:14:24 AM from Jen Deegan: we used to call all the components plugins but now we don't 07/01/2008 10:14:35 AM from Jen Deegan: so that section is not really needed any longer 07/01/2008 10:14:35 AM from Nomi Harris: Well, most of them aren't plugins anymore, 07/01/2008 10:14:39 AM from Nomi Harris: but GraphViz still is, isn't it? 07/01/2008 10:14:47 AM from Jen Deegan: I'm not sure 07/01/2008 10:14:52 AM from Jen Deegan: the component is part of the code 07/01/2008 10:14:53 AM from Nomi Harris: You have to get the GraphViz jar from somewhere external. 07/01/2008 10:14:56 AM from Nomi Harris: Don't you? 07/01/2008 10:14:59 AM from Jen Deegan: yes 07/01/2008 10:15:04 AM from Jen Deegan: does that make it a plugin? 07/01/2008 10:15:10 AM from Jen Deegan: I wasn't sure 07/01/2008 10:15:37 AM from Nomi Harris: Well, possibly it isn't a plugin per-se but it is still qualitatively different from components that just work without your having to do any additional setup 07/01/2008 10:15:45 AM from Jen Deegan: true 07/01/2008 10:15:48 AM from Jen Deegan: I don't mind at all 07/01/2008 10:15:58 AM from Nomi Harris: The Term Image component used to be a plugin, and now it isn't. 07/01/2008 10:16:03 AM from Jen Deegan: yes 07/01/2008 10:16:10 AM from Jen Deegan: we don't ahve any other plugins yet do we? 07/01/2008 10:16:35 AM from Jen Deegan: it doesn't matter though, we can keep a space for them 07/01/2008 10:16:39 AM from Nomi Harris: That definition-helper one the German company is working on 07/01/2008 10:16:48 AM from Jen Deegan: oh yes 07/01/2008 10:16:52 AM from Nomi Harris: Remember that? I should ping them again. 07/01/2008 10:16:53 AM from David OS to All Attendees: Jen - have you been working on the graph editor or the graph viewer. Am looking at latest svn version and can only see changed to latter. 07/01/2008 10:16:55 AM from melissaH: yeah, whatever happened with that? that was terrific 07/01/2008 10:17:05 AM from Jen Deegan: I didn't work on the graph viewer 07/01/2008 10:17:06 AM from Nomi Harris: I wanted them to commit it (or at least the changes they had to make in the OE classes to make the plugin work) 07/01/2008 10:17:13 AM from Jen Deegan: sorry graph editor 07/01/2008 10:17:17 AM from Nomi Harris: Well, it had a lot of issues, but it was still cool. 07/01/2008 10:17:18 AM from Jen Deegan: d'oh 07/01/2008 10:17:36 AM from Jen Deegan: I did the graph viewer completely 07/01/2008 10:17:52 AM from Nomi Harris: Graph Viewer or GraphViz viewer? 07/01/2008 10:17:56 AM from David OS to All Attendees: OK - so will work on graph editor then. I rarely use the graph viewer. Damn panels are too small... 07/01/2008 10:17:58 AM from Jen Deegan: both 07/01/2008 10:18:08 AM from Nomi Harris: You're talking about the help pages? 07/01/2008 10:18:12 AM from Nomi Harris: I'm a little confused. 07/01/2008 10:18:17 AM from Jen Deegan: me? 07/01/2008 10:18:22 AM from David OS to All Attendees: help pages. Yep 07/01/2008 10:18:28 AM from Nomi Harris: Yes, when you said "I did the graph viewer completely," what did you mean? 07/01/2008 10:18:33 AM from Jen Deegan: I did all of the graphviz and graph viewer. I didn't do anything to the graph editor. 07/01/2008 10:18:42 AM from Jen Deegan: the help pages. 07/01/2008 10:18:46 AM from Nomi Harris: Ok. 07/01/2008 10:18:53 AM from Jen Deegan: oh good. (phew) 07/01/2008 10:19:03 AM from Nomi Harris: So, everyone, keep checking the wiki page 07/01/2008 10:19:14 AM from Nomi Harris: http://wiki.geneontology.org/index.php/OBO-Edit:_Documentation_Week 07/01/2008 10:19:19 AM from Jen Deegan: can people mark really clearly what page they are doing at any given time? 07/01/2008 10:19:28 AM from Nomi Harris: Yes, I was just going to say that (again) 07/01/2008 10:19:29 AM from Jen Deegan: so if we are at a loose end we know what's free. 07/01/2008 10:19:47 AM from Jen Deegan: thanks. 07/01/2008 10:19:54 AM from midori: I'll mark ones I think are OK (and others are free to disagree). 07/01/2008 10:20:02 AM from Nomi Harris: Great. 07/01/2008 10:20:04 AM from Jen Deegan: that would be great 07/01/2008 10:20:08 AM from Jen Deegan: me too 07/01/2008 10:20:15 AM from Nomi Harris: Remember that Friday is a holiday in the US, so this is a short week for us. 07/01/2008 10:20:31 AM from midori: us expats get to work along with the locals. 07/01/2008 10:20:32 AM from Jen Deegan: I am away 4th to 14th 07/01/2008 10:20:36 AM from Nomi Harris: I am not planning to do a new OE beta release this week unless there's particular demand. 07/01/2008 10:20:43 AM from Nomi Harris: Oh! We'll miss you, Jen. 07/01/2008 10:20:46 AM from David OS to All Attendees: Think I need a login - as the wiki is GO. Presumably will also need to get my SF acc to allow svn commit for GO? 07/01/2008 10:20:50 AM from Jen Deegan: thanks :-) 07/01/2008 10:20:58 AM from Nomi Harris: I'll be away July 10-11. 07/01/2008 10:21:07 AM from Jen Deegan: yes that's right david. 07/01/2008 10:21:08 AM from Nomi Harris: Amina is going to be away for a few days around the 18th. 07/01/2008 10:21:19 AM from Jen Deegan: Good to know, thanks. 07/01/2008 10:21:19 AM from Nomi Harris: Wait, is David saying stuff that I'm missing again?? 07/01/2008 10:21:24 AM from Jen Deegan: yes 07/01/2008 10:21:25 AM from David OS: ? 07/01/2008 10:21:31 AM from Jen Deegan: you are on all attendees 07/01/2008 10:21:33 AM from midori: David - wiki login should be straightforward; just create an account. 07/01/2008 10:21:44 AM from Jen Deegan: likewise SF 07/01/2008 10:21:47 AM from Nomi Harris: But I just heard David's "?" 07/01/2008 10:21:48 AM from midori: (and holler if anything goes awry). 07/01/2008 10:21:56 AM from Nomi Harris: Why am I hearing some of what he says but missing other things? 07/01/2008 10:22:05 AM from Jen Deegan: weird software 07/01/2008 10:22:07 AM from Nomi Harris: David, stop talking behind my back! :-) 07/01/2008 10:22:09 AM from Jen Deegan: I did report it last week 07/01/2008 10:22:12 AM from Jen Deegan: :-) 07/01/2008 10:22:17 AM from David OS: Sorry Nomi 07/01/2008 10:22:24 AM from Nomi Harris: Hmph! 07/01/2008 10:22:33 AM from Jen Deegan: that must be quite weird 07/01/2008 10:22:39 AM from midori: I think I can also give David GO SF svn access. 07/01/2008 10:22:41 AM from Jen Deegan: like we're hearing voices 07/01/2008 10:22:43 AM from Nomi Harris: Can someone else save the chat today so we will have all of David's behind-my-back comments on record? 07/01/2008 10:22:52 AM from Amina: I'll do it 07/01/2008 10:22:56 AM from Nomi Harris: IThanks 07/01/2008 10:23:05 AM from Nomi Harris: Wow, I'm typing really badly today, sorry. 07/01/2008 10:23:05 AM from Jen Deegan: it's the regular SF login 07/01/2008 10:24:00 AM from David OS: OK - have one of those - just thought I might need write permission set. 07/01/2008 10:24:00 AM from Jen Deegan: shall we shuffle off then? 07/01/2008 10:24:03 AM from midori: David - SF knows you as djs93, right? 07/01/2008 10:24:07 AM from David OS: yep 07/01/2008 10:24:17 AM from Jen Deegan: I don't think they needed to give me special rights. 07/01/2008 10:24:45 AM from midori: Jen - you already had the requisite permissions. I'm just setting them for David now. 07/01/2008 10:24:49 AM from Jen Deegan: ah! 07/01/2008 10:24:55 AM from David OS: Cheers 07/01/2008 10:24:56 AM from Jen Deegan: I was already special. :-) 07/01/2008 10:25:03 AM from Nomi Harris: Thanks, midori. 07/01/2008 10:25:11 AM from Nomi Harris: So, are we pretty much done with this chat? 07/01/2008 10:25:15 AM from Jen Deegan: yep 07/01/2008 10:25:38 AM from Nomi Harris: Ok, bye all. 07/01/2008 10:25:41 AM from Jen Deegan: byeeeeeeeeeeee 07/01/2008 10:25:44 AM from midori: OK, David, you should be in now. 07/01/2008 10:25:46 AM from Nomi Harris: Thanks for your help with testing and documentation. 07/01/2008 10:25:49 AM from Nomi Harris: Bye! 07/01/2008 10:25:50 AM from David OS: Bye 07/01/2008 10:25:51 AM from midori: bye all 07/01/2008 10:25:59 AM from Amina: bye all 07/01/2008 10:26:11 AM from melissaH: bye 07/01/2008 10:26:26 AM from Jen Deegan: Amina did you want to hang around or shall we talk another time?