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?