OE Webex 29Jul08

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07/29/2008    09:31:13 AM    from Nomi Harris:  Hello!
07/29/2008    09:31:33 AM    from midori:       hi Nomi
07/29/2008    09:31:34 AM    from Nomi Harris:  Since I was not the first to join, please make sure your "Send to" pulldown menu is set to "All participants"
07/29/2008    09:31:42 AM    from Nomi Harris:  Otherwise, everyone but me will see what you're saying.
07/29/2008    09:36:00 AM    from Nomi Harris:  So, I still haven't been able to find out from John where the mysterious 1.101 source is.
07/29/2008    09:36:14 AM    from Jen Deegan:   That is really quite mysterious isn't it?
07/29/2008    09:36:23 AM    from Nomi Harris:  But it's sounding like it doesn't make lots of sense to try to do a lot of work on 1.101 anyway.
07/29/2008    09:36:31 AM    from Jen Deegan:   yes that's sounds right
07/29/2008    09:36:38 AM    from midori:       I did find an email from John saying that there's only one line that differs between 1.100 and 1.101. I'll forward it ...
07/29/2008    09:36:49 AM    from Nomi Harris:  That seems wrong, though, given all the differences I found.
07/29/2008    09:36:52 AM    from midori:       ... but I agree that focusing on OE2 is better.
07/29/2008    09:37:31 AM    from Nomi Harris:  One of the topics today is filtered save, but we'll have to wait for Amina to talk about that.
07/29/2008    09:37:42 AM    from Nomi Harris:  She and Chris discussed some solution for that.  Chris is away this week.
07/29/2008    09:38:17 AM    from Nomi Harris:  I have been working on getting the components (particularly OTE) to reload when needed but to avoid unnecessary reloading.
07/29/2008    09:38:41 AM    from Nomi Harris:  Yesterday I was fixing the problem I just introduced where committing a text edit would make the OTE close up all the terms, which was annoying.
07/29/2008    09:39:04 AM    from midori:       yikes! I'm glad I didn't see that!!!
07/29/2008    09:39:14 AM    from Nomi Harris:  Yes, it would have made your head explode.
07/29/2008    09:39:19 AM    from Jen Deegan:   cuttin down on reloading sounds good
07/29/2008    09:39:30 AM    from Nomi Harris:  Oh, I also (I think) fixed the quick filtering ("f" button).
07/29/2008    09:39:48 AM    from Jen Deegan:   that's to filter by relationship isn't it?
07/29/2008    09:39:48 AM    from Amina:        Hi everyone.. sorry I'm late
07/29/2008    09:39:53 AM    from Jen Deegan:   Hi Amina
07/29/2008    09:39:58 AM    from Nomi Harris:  Yes, filter by relationship.
07/29/2008    09:40:06 AM    from Jen Deegan:   great
07/29/2008    09:40:34 AM    from Nomi Harris:  I think I have somewhat reduced the number of unnecessary reloads in the OTE and Graph Editor, which I hope will speed things up a bit.
07/29/2008    09:40:49 AM    from Nomi Harris:  I still have not seen the slowdowns that have been reported in long editing sessions.
07/29/2008    09:40:54 AM    from midori:       I've just found a small rendering bug (at least, the consequences for users are small)
07/29/2008    09:41:01 AM    from Nomi Harris:  Yes, midori?
07/29/2008    09:41:12 AM    from Jen Deegan:   did you try the big singel edits that I suggested?
07/29/2008    09:41:15 AM    from midori:       Re slowdowns -- I'm still getting them, and it's worse at home than at work.
07/29/2008    09:41:33 AM    from Nomi Harris:  Jen, I did, but didn't see a slowdown.
07/29/2008    09:41:36 AM    from Jen Deegan:   werid
07/29/2008    09:41:40 AM    from Jen Deegan:   weird I mean
07/29/2008    09:41:45 AM    from midori:       My home computer isn't as powerful as the one at work, but the home-work performance difference is much more pronounced than for OE1.
07/29/2008    09:41:59 AM    from Nomi Harris:  I am planning to make the editing operations print log messages so I will be able to look at your log files and see what edits you did.
07/29/2008    09:42:21 AM    from midori:       Re rendering - noticed the bug just before the meeting started; I'll put a report in SF shortly.
07/29/2008    09:42:25 AM    from Nomi Harris:  Ok.
07/29/2008    09:42:44 AM    from Nomi Harris:  Amina, do you want to talk about the proposal for fixing filtered save that you and Chris came up with?
07/29/2008    09:42:58 AM    from midori:       Briefly, the "blending" feature doesn't seem to be worknig.
07/29/2008    09:43:12 AM    from Nomi Harris:  I don't think I've tried blending.
07/29/2008    09:43:49 AM    from midori:       I just did today, and nothing happened.
07/29/2008    09:44:13 AM    from Jen Deegan:   that was very new when john left, maybe it's not finished
07/29/2008    09:44:15 AM    from Harold:       what is it suppose to do?
07/29/2008    09:45:22 AM    from Amina:        sorry for the delay - my work machine wasn't responding - I can go ahead and talk about the search proposal
07/29/2008    09:46:39 AM    from Amina:        so in context to the searches which require the reasoner (yeild incorrect answeres with the reasoner off) - these will automatically not be allowed with the reasoner off
07/29/2008    09:47:06 AM    from midori:       sounds good
07/29/2008    09:47:07 AM    from Jen Deegan:   like 'find redundant links'?
07/29/2008    09:48:00 AM    from Amina:        the option to do an advanced search with relationships will br provided only for "Self" by default and "Root" "Ancestor" etc with the Reasoner on
07/29/2008    09:48:36 AM    from Jen Deegan:   so when we turn on the reasoner these options mysteriously appear?
07/29/2008    09:48:57 AM    from Nomi Harris:  It's not *that* mysterious!  There are other menu options that do that.
07/29/2008    09:49:02 AM    from Amina:        the link filter can be used to search the implied links with the reasoner on
07/29/2008    09:49:19 AM    from Amina:        Jen - I was going to propose graying the options
07/29/2008    09:49:28 AM    from Jen Deegan:   that sounds excellent!
07/29/2008    09:49:34 AM    from Amina:        they would all appear - just be inactive
07/29/2008    09:49:37 AM    from Jen Deegan:   that way we will be reminded that they exist.
07/29/2008    09:49:56 AM    from Nomi Harris:  Right.
07/29/2008    09:50:03 AM    from midori:       still sounds good
07/29/2008    09:50:05 AM    from Jen Deegan:   sounds great to me
07/29/2008    09:50:15 AM    from Amina:        great
07/29/2008    09:50:26 AM    from Amina:        I'll have this done soon
07/29/2008    09:50:34 AM    from Jen Deegan:   double excellent
07/29/2008    09:51:00 AM    from Nomi Harris:  There are some right-menu options in the Graph Editor that are grayed out when the reasoner is off, but others that are enabled and yet seem to rely on the reasoner and t\
hrow an exception if the reasoner is off.
07/29/2008    09:51:28 AM    from Nomi Harris:  I was looking into this yesterday.
07/29/2008    09:51:45 AM    from Nomi Harris:  Show -> Show ancestors/descendants
07/29/2008    09:52:12 AM    from Nomi Harris:  I'm not sure why they should require the reasoner, but that's how the code is implemented.
07/29/2008    09:52:45 AM    from Amina:        It is quiet odd since showing ancestors does not require the reasoner
07/29/2008    09:53:02 AM    from Nomi Harris:  Maybe we can look at it together later, Amina.
07/29/2008    09:53:13 AM    from Jen Deegan:   I have noticed that I need to start the reasoner or the roots don't all work out right.
07/29/2008    09:53:15 AM    from Amina:        yeah sounds good
07/29/2008    09:53:30 AM    from Jen Deegan:   if that could work without the reasoner it would be very helpful
07/29/2008    09:53:45 AM    from Nomi Harris:  BTW, I made "change relationship" work for multiple terms.
07/29/2008    09:53:47 AM    from Amina:        sure Jen
07/29/2008    09:53:58 AM    from Jen Deegan:   brilliant, thanks.
07/29/2008    09:54:08 AM    from Jen Deegan:   Nomi, did you have any luck with graphviz?
07/29/2008    09:54:13 AM    from Nomi Harris:  Not yet.
07/29/2008    09:54:21 AM    from Jen Deegan:   are you using the pixelglow one?
07/29/2008    09:54:49 AM    from Nomi Harris:  I was using the one from graphviz.org, which I assumed would be the official version, but maybe not...
07/29/2008    09:54:58 AM    from Jen Deegan:   for the mac you need the pixelglow one
07/29/2008    09:55:02 AM    from Nomi Harris:  Ah.
07/29/2008    09:55:09 AM    from Nomi Harris:  graphviz.org has a mac version
07/29/2008    09:55:09 AM    from Jen Deegan:   the graphviz.org one never worked for us
07/29/2008    09:55:12 AM    from Nomi Harris:  but I guess it's defective.
07/29/2008    09:55:12 AM    from Jen Deegan:   I think.
07/29/2008    09:55:18 AM    from Jen Deegan:   yes I think that might be right
07/29/2008    09:55:22 AM    from Nomi Harris:  Ok.  I will try pixelglow and will be sure to document that in the help page.
07/29/2008    09:55:29 AM    from Jen Deegan:   I think it's in there.
07/29/2008    09:55:37 AM    from Harold:       yes, from what I've heard, the one on graphviz.org is really a beta
07/29/2008    09:55:40 AM    from Nomi Harris:  I think it had an URL that wasn't graphviz.org,
07/29/2008    09:55:41 AM    from midori:       T he one that comes with fink works, but it's ugly. Pixelglow al the way!
07/29/2008    09:55:46 AM    from Nomi Harris:  but I assumed that was out-of-date.
07/29/2008    09:55:48 AM    from Jen Deegan:   yes
07/29/2008    09:55:56 AM    from Nomi Harris:  There wasn't an explicit "don't use graphviz.org!" warning.
07/29/2008    09:55:59 AM    from Jen Deegan:   oh no, it's pretty solid still
07/29/2008    09:56:24 AM    from Nomi Harris:  graphviz.org offers betas; I downloaded the so-called "stable" version.
07/29/2008    09:56:24 AM    from Jen Deegan:   GraphViz is an independent, external application available from http://www.graphviz.org/ (the MacOS version is at http://www.pixelglow.com/graphviz/). 
07/29/2008    09:56:36 AM    from Alexander Diehl:      It still works for me on both versions of OE.
07/29/2008    09:56:39 AM    from Nomi Harris:  Ok.  I guess I need to RTFM better next time. :-)
07/29/2008    09:56:41 AM    from Jen Deegan:   that's good
07/29/2008    09:56:48 AM    from Jen Deegan:   no worries
07/29/2008    09:56:57 AM    from Jen Deegan:   I'll check through the doc again
07/29/2008    09:57:06 AM    from Jen Deegan:   I didn't check that bit as I assumed it was all fine
07/29/2008    09:57:10 AM    from midori:       Those of you who are curious about the rendering bug can now read all about it on SourceForge:
07/29/2008    09:57:17 AM    from Nomi Harris:  So, other than the vexing slowdowns, which bugs are driving you nuts this week?
07/29/2008    09:57:21 AM    from midori:       https://sourceforge.net/tracker/index.php?func=detail&aid=2031660&group_id=36855&atid=418257
07/29/2008    09:57:27 AM    from Nomi Harris:  Oh, before I forget:  I will be out this Thurs-Fri, so it's a short week for me.
07/29/2008    09:57:30 AM    from Jen Deegan:   that was fast typing!
07/29/2008    09:57:44 AM    from midori:       The CPU usage, which I suppose is closely related to the slowdowns;
07/29/2008    09:58:00 AM    from Jen Deegan:   I think slowdowns are the main thing for me.
07/29/2008    09:58:04 AM    from Jen Deegan:   it's pretty sound otherwise.
07/29/2008    09:58:27 AM    from Nomi Harris:  Can you tell me a bit about your typical pattern of use?  I've never gotten the opportunity to watch someone using OE for more than a single operation.
07/29/2008    09:58:29 AM    from midori:       the OTE redraw weirdness when I delete a parent via the parent editor (SF 2026858)
07/29/2008    09:58:37 AM    from Nomi Harris:  Do you do a lot of structural edits, or mostly text?
07/29/2008    09:58:47 AM    from Jen Deegan:   I do a lot of stuctural edits just now
07/29/2008    09:58:55 AM    from midori:       I do a lot of both.
07/29/2008    09:59:11 AM    from Jen Deegan:   I got a huge slowdown by making 1000 relationships in one shot.
07/29/2008    09:59:14 AM    from Jen Deegan:   three times
07/29/2008    09:59:18 AM    from Nomi Harris:  What do you mean by "making"?
07/29/2008    09:59:35 AM    from Jen Deegan:   you know when you drag a term over another and then say add is_a child
07/29/2008    09:59:41 AM    from Nomi Harris:  Ok
07/29/2008    09:59:42 AM    from midori:       Structural edits in the OTE were easier in OE1, so I've been trying out the parent editor (because I miss the OE1 hotkey system).
07/29/2008    09:59:48 AM    from Jen Deegan:   I selected 1000 and then did add is_a child
07/29/2008    09:59:58 AM    from Nomi Harris:  How do you select 1000?  Hold the mouse down and scroll?
07/29/2008    10:00:17 AM    from Jen Deegan:   I do a search that gets a lot of results and do click-shift-click
07/29/2008    10:00:29 AM    from Nomi Harris:  midori, I can revisit the hotkeys.  I did take a look and couldn't figure out why they weren't working.  (It's especially mysterious why they'd work at first and then sto\
p working.)
07/29/2008    10:00:35 AM    from Jen Deegan:   I can actually comfortably copy up to 1600 terms
07/29/2008    10:00:43 AM    from Nomi Harris:  You're selecting in the search results window?
07/29/2008    10:00:48 AM    from Jen Deegan:   yes that's right
07/29/2008    10:00:53 AM    from Nomi Harris:  What do you mean "copy"?
07/29/2008    10:00:54 AM    from Jen Deegan:   I have to turn off global select
07/29/2008    10:01:09 AM    from Nomi Harris:  You click the globe icon in the OTE, you mean?
07/29/2008    10:01:12 AM    from Jen Deegan:   just adding another relationship
07/29/2008    10:01:16 AM    from Jen Deegan:   yes that's right
07/29/2008    10:01:17 AM    from midori:       The other thing about hotkeys, though, is that for some reason John couldn't make the OE1 system work for OE2, and the new system is more cumbersome.
07/29/2008    10:01:28 AM    from Jen Deegan:   bizarre!
07/29/2008    10:01:38 AM    from Jen Deegan:   java is very mysterious
07/29/2008    10:01:46 AM    from Jen Deegan:   or computers maybe
07/29/2008    10:01:59 AM    from Nomi Harris:  Or John's software architectures. :-)
07/29/2008    10:02:04 AM    from Jen Deegan:   :-)
07/29/2008    10:02:10 AM    from Jen Deegan:   Did you want to see my copying?
07/29/2008    10:02:18 AM    from midori:       None of those are mutually exclusive ... ;)
07/29/2008    10:02:21 AM    from Jen Deegan:   it's a consistent slowdown I get
07/29/2008    10:02:24 AM    from Nomi Harris:  Yes, maybe when we're done with the meeting, I can watch you do it.
07/29/2008    10:02:29 AM    from Jen Deegan:   great
07/29/2008    10:02:32 AM    from Amina:        I think a demo would really help
07/29/2008    10:02:32 AM    from Jen Deegan:   I'll get it ready
07/29/2008    10:02:43 AM    from midori:       same here -- a succession of small edits will do the same thing
07/29/2008    10:03:10 AM    from Nomi Harris:  So, back to the issue of disjoint relationships in OE1, would it be possible for users to add a global filter to hide them?
07/29/2008    10:03:11 AM    from Jen Deegan:   The first sign for me is that the def dbxrefs go very weird
07/29/2008    10:03:17 AM    from Nomi Harris:  (Without requiring any changes to the code)?
07/29/2008    10:03:27 AM    from Jen Deegan:   sorry?
07/29/2008    10:03:41 AM    from Nomi Harris:  Could OE1 users add a global filter to hide disjoint_from?
07/29/2008    10:03:45 AM    from midori:       Yes, I think we could build such a filter.
07/29/2008    10:03:54 AM    from Nomi Harris:  Would that be a good temporary solution?
07/29/2008    10:04:08 AM    from Jen Deegan:   I think the root thing was going to be complex
07/29/2008    10:04:12 AM    from Nomi Harris:  Yes.
07/29/2008    10:04:30 AM    from Jen Deegan:   is that what you mean?
07/29/2008    10:04:43 AM    from midori:       I didn't want to comment on the root thread, because I only just barely understand root selection anyway (an dthat may be optimistic).
07/29/2008    10:04:45 AM    from Nomi Harris:  No, I don't have any ideas about the root thing.
07/29/2008    10:05:05 AM    from Jen Deegan:   I think the good solution for that just now is to have jane on OBO-Edit2
07/29/2008    10:05:20 AM    from Jen Deegan:   Jane explained the root thing to me
07/29/2008    10:05:26 AM    from Jen Deegan:   it doesn't look very fixable.
07/29/2008    10:05:38 AM    from Jen Deegan:   it doesn't even quite work in OBO-edit 2 yet
07/29/2008    10:06:39 AM    from Nomi Harris:  Hmm
07/29/2008    10:07:07 AM    from Jen Deegan:   is there anything that we can do to help track down commit slowdowns?
07/29/2008    10:07:22 AM    from midori:       It seems like a link filter for "Type" that "don't have" "ID" "equals" "disjoint_from" ought to do the  trick.
07/29/2008    10:07:36 AM    from Nomi Harris:  Maybe you can try it out
07/29/2008    10:07:42 AM    from midori:       For me it's not just commit slowdowns; it's performing-any-operation slowdowns.
07/29/2008    10:07:42 AM    from Nomi Harris:  and if it works, you can suggest it to the mailing list
07/29/2008    10:07:56 AM    from Jen Deegan:   isn't it the root problem that is stopping people though and that wouldnt' solve that I thought.
07/29/2008    10:08:05 AM    from Nomi Harris:  I'm not getting the slowdowns--you guys must have a different usage pattern.
07/29/2008    10:08:20 AM    from Jen Deegan:   Is there anything that we can do to help you replicate it?
07/29/2008    10:08:35 AM    from Nomi Harris:  When we're done here, let me watch you do some editing that causes the slowdowns.
07/29/2008    10:08:41 AM    from Jen Deegan:   great
07/29/2008    10:08:45 AM    from Jen Deegan:   thanks
07/29/2008    10:08:48 AM    from Nomi Harris:  Are we done?
07/29/2008    10:08:56 AM    from Jen Deegan:   yes Iam
07/29/2008    10:09:19 AM    from Nomi Harris:  Ok, bye, everyone except Jen (and Amina, if you want to watch)
07/29/2008    10:09:28 AM    from Jen Deegan:   bye everyone else
07/29/2008    10:09:32 AM    from Alexander Diehl:      bye
07/29/2008    10:09:42 AM    from Nomi Harris:  Go ahead, Jen