From GO Public
08/19/2008 09:26:16 AM from Nomi Harris: Good morning.
08/19/2008 09:26:21 AM from Jen Deegan: morning!
08/19/2008 09:26:31 AM from Nomi Harris: You guys are all so prompt!
08/19/2008 09:26:36 AM from Jen Deegan: :-)
08/19/2008 09:26:52 AM from Jen Deegan: Midori is on leave today.
08/19/2008 09:27:10 AM from Nomi Harris: Oh, right.
08/19/2008 09:27:11 AM from Karen: I have an alarm on my calendar so I don't forget ;)
08/19/2008 09:27:21 AM from Jen Deegan: good plan
08/19/2008 09:27:29 AM from Nomi Harris: Jen, I haven't had a chance to look at your config from when you ran out of memory, but I will soon.
08/19/2008 09:27:40 AM from Jen Deegan: okay, thanks. No rush
08/19/2008 09:27:58 AM from Nomi Harris: I was wondering what exactly you did to make the 'created link' history items.
08/19/2008 09:28:01 AM from Nomi Harris: Was it merges?
08/19/2008 09:28:26 AM from Jen Deegan: no I just selected a large number of terms, then dragged them over another term, then dropped them and did 'add child'.
08/19/2008 09:28:45 AM from Nomi Harris: Ah. Ok. There are several operations that create links.
08/19/2008 09:28:53 AM from Nomi Harris: I have never tried doing that. I will try that.
08/19/2008 09:28:55 AM from Jen Deegan: good point
08/19/2008 09:29:05 AM from Jen Deegan: I always just use the one, so I don't think to specify.
08/19/2008 09:29:14 AM from Nomi Harris: Let's give everyone another 3 minutes and then start the meeting, ok?
08/19/2008 09:29:18 AM from Jen Deegan: ok
08/19/2008 09:29:49 AM from Jen Deegan: Amina, I have noticed that some of my logger statements show on the console. Is that meant to happen?
08/19/2008 09:30:03 AM from Amina: yes
08/19/2008 09:30:07 AM from Jen Deegan: oh good
08/19/2008 09:30:29 AM from Jen Deegan: I have put an awful lot of them in. Will they get in the way?
08/19/2008 09:30:35 AM from Amina: You'll notice they're in a different format compared to the log file
08/19/2008 09:30:52 AM from Amina: No they wont
08/19/2008 09:30:55 AM from Jen Deegan: oh good
08/19/2008 09:31:06 AM from Jen Deegan: they are very good for keeping track of what's going on.
08/19/2008 09:31:10 AM from Amina: are you using - logger.INFO or logger.DEBUG
08/19/2008 09:31:17 AM from Jen Deegan: logger.info
08/19/2008 09:31:24 AM from Jen Deegan: is that good? I can change them.
08/19/2008 09:31:32 AM from Amina: so while debugging the best thing to do is use debug
08/19/2008 09:31:43 AM from Jen Deegan: ok
08/19/2008 09:31:44 AM from Amina: that way we can just comment those out before a release
08/19/2008 09:31:51 AM from Jen Deegan: oh I see
08/19/2008 09:32:16 AM from Jen Deegan: so I should maybe just have logger.info for ones that announce that a component has been started?
08/19/2008 09:32:19 AM from Amina: INFO should be used for something you want to display or leave in there
08/19/2008 09:32:34 AM from Jen Deegan: things that would help you debug later maybe?
08/19/2008 09:32:50 AM from Amina: yeah
08/19/2008 09:32:54 AM from Jen Deegan: oh great
08/19/2008 09:32:58 AM from Jen Deegan: I will chagne that then
08/19/2008 09:33:04 AM from Amina: that would be great
08/19/2008 09:33:06 AM from Jen Deegan: mine should nearly all be debug.
08/19/2008 09:33:09 AM from Jen Deegan: thanks.
08/19/2008 09:33:14 AM from Nomi Harris: I usually use logger.debug for stuff I just need while testing, and then I delete it or comment it out before committing.
08/19/2008 09:33:15 AM from Amina: Let me know if you'd like me to change them
08/19/2008 09:33:45 AM from Jen Deegan: Thanks Nomi, that's a good idea. I'll just change them over myself Amina, but thanks. It's just a few files.
08/19/2008 09:33:49 AM from Amina: Yeah we can do that for all debug statements before commenting
08/19/2008 09:33:54 AM from Jen Deegan: good plan.
08/19/2008 09:33:58 AM from Amina: sorry i mean commiting
08/19/2008 09:34:04 AM from Nomi Harris: Hi, Tanya!
08/19/2008 09:34:06 AM from Tanya: found you!
08/19/2008 09:34:17 AM from Nomi Harris: Before we officially start, I'd like to mention
08/19/2008 09:34:19 AM from Amina: (was talking to Nomi and typing)
08/19/2008 09:34:23 AM from Amina: Hi Tanya
08/19/2008 09:34:31 AM from Nomi Harris: that Amina and I will both be splitting our time between OBO-Edit and Phenote.
08/19/2008 09:34:48 AM from Nomi Harris: This week, we have collaborators from NESCENT visiting to talk to us about Phenote, so we will be focusing on Phenote this week.
08/19/2008 09:34:55 AM from melissaH: hey thats terrific!
08/19/2008 09:35:08 AM from David OS: Excellent!
08/19/2008 09:35:16 AM from Nomi Harris: After that, Amina will be spending probably ~50% of her time on Phenote and I will spend maybe 25% of my time (which, remember, is only 60% time total).
08/19/2008 09:35:30 AM from Nomi Harris: The good thing is that Phenote and OBO-Edit share a lot of code,
08/19/2008 09:35:38 AM from Nomi Harris: so fixing things in one often helps the other as well.
08/19/2008 09:35:46 AM from Jen Deegan: That sounds good.
08/19/2008 09:35:50 AM from Amina: Have most of you worked with Phenote too?
08/19/2008 09:35:55 AM from Jen Deegan: I haven't
08/19/2008 09:36:12 AM from melissaH: We use it a lot at ZFIN
08/19/2008 09:36:13 AM from Karen: I haven't used Phenote either
08/19/2008 09:36:31 AM from Tanya: I haven't
08/19/2008 09:36:34 AM from Amina: We will be having Phenote User Group meetings regularly now - once a month
08/19/2008 09:37:05 AM from Tanya: one of our TAIR curators will attend that - Debbie - she's cool
08/19/2008 09:37:22 AM from Jen Deegan: Will you be with us for a while then Nomi? I thought you were just here for a few months.
08/19/2008 09:37:36 AM from Nomi Harris: Well, in the original plan, I would have already left by now
08/19/2008 09:37:45 AM from Nomi Harris: but Suzi was able to shuffle some funds around so I could stay longer.
08/19/2008 09:37:50 AM from Jen Deegan: Bonus!
08/19/2008 09:38:09 AM from Nomi Harris: Funds are still tight, but some new grants will be coming in soon.
08/19/2008 09:38:17 AM from Jen Deegan: that sounds good then.
08/19/2008 09:38:23 AM from Nomi Harris: (BTW, Amina is on the phone, she'll be back in a minute...)
08/19/2008 09:38:34 AM from David OS: I think this makes alot of sense. I've been very keen to get some of the search tools from oboedit into phenote in some form. I think that this stuff wasn't touched before because it was too dependent on oboedit code and it was often not clear whether to work through oweg or phenote user group to get such features implemented.
08/19/2008 09:38:50 AM from Nomi Harris: Now you'll know who to ask!
08/19/2008 09:39:14 AM from Amina: (Sorry - back)
08/19/2008 09:39:31 AM from Nomi Harris: Our first focus will be the high-priority Phenote bugs that have been reported, but we'd definitely like to do things like what you're suggesting, David, in the future.
08/19/2008 09:39:57 AM from Nomi Harris: Right now, the main goal is to maintain continuity and support for Phenote now that Mark Gibson (the main developer) is gone.
08/19/2008 09:40:06 AM from David OS: I've used phenote extensively - but it still needs quite a bit of work to make it usable for curation at FB - particularly, it needs a better output format.
08/19/2008 09:40:15 AM from Amina: David - that great
08/19/2008 09:40:20 AM from Nomi Harris: Have you logged a feature request for that, David?
08/19/2008 09:40:59 AM from David OS: Think so. Mark was meant to be working on it before he left - so some stuff may be in e-mails. WIll check the tracker.
08/19/2008 09:41:01 AM from Amina: Also when we're done with this topic - Let me know if any of you guys had a change to test the filtered save - in Save As -> Advanced
08/19/2008 09:41:35 AM from Tanya: Where'd Mark go?
08/19/2008 09:41:37 AM from David OS: Quick test of filtered save suggests working fine. Will let you know if I encounter bugs.
08/19/2008 09:41:57 AM from Amina: Mark had to leave Tanya
08/19/2008 09:42:13 AM from Amina: I think he works at NYU now
08/19/2008 09:42:22 AM from Amina: I'm not sure
08/19/2008 09:42:22 AM from Tanya: (ah, and that sentence just looked really strange because my husband's name is Mark :) )
08/19/2008 09:42:33 AM from Jen Deegan: That's what I was thinking.
08/19/2008 09:42:33 AM from Amina: :)
08/19/2008 09:43:48 AM from Amina: David - Is filtered save working well for you
08/19/2008 09:45:01 AM from David OS: Just got back from vacation today so only done a quick test. But so far looks perfect.
08/19/2008 09:45:15 AM from Amina: oh ok
08/19/2008 09:45:16 AM from Nomi Harris: Yay! Glad to hear that, David.
08/19/2008 09:45:24 AM from Amina: Great!
08/19/2008 09:45:40 AM from Nomi Harris: Are you guys finding OE2 faster these days?
08/19/2008 09:45:46 AM from Amina: You might notice that the ids have a different order
08/19/2008 09:45:46 AM from melissaH: yes!
08/19/2008 09:45:58 AM from Amina: in the saved results compared to the search panel
08/19/2008 09:46:00 AM from Jen Deegan: yes much faster
08/19/2008 09:46:03 AM from Nomi Harris: Great!
08/19/2008 09:46:19 AM from Amina: They're all in there though - just different logic
08/19/2008 09:46:23 AM from Nomi Harris: I'm hoping to get the memory use down as well.
08/19/2008 09:46:29 AM from David OS: Don't care about order in file. Shouldn't have any semantic content anyway.
08/19/2008 09:46:37 AM from Amina: Right
08/19/2008 09:46:47 AM from melissaH: (deleting my config file also made a lot of other things work better- thanks nomi)
08/19/2008 09:47:30 AM from David OS: speed looks good. Have been leaving the new reasoner on while browsing - which could never do before.
08/19/2008 09:47:38 AM from Jen Deegan: Thanks for the new batch dbxref adding too. It's brilliant.
08/19/2008 09:47:39 AM from David OS: at least not for long
08/19/2008 09:47:45 AM from Nomi Harris: Yeah, sorry about having to delete your config directory, but it often does fix things!
08/19/2008 09:47:52 AM from Nomi Harris: You know you can do it through the Configuration Manager, right?
08/19/2008 09:48:02 AM from Nomi Harris: And it leaves some things alone, e.g. your autosaved files and your dictionary.
08/19/2008 09:48:06 AM from melissaH: really- no didin't realize
08/19/2008 09:48:12 AM from Nomi Harris: It only deletes the files that could be a problem.
08/19/2008 09:48:20 AM from melissaH: i always forget to try that when things go south
08/19/2008 09:48:20 AM from Tanya: I didn't realize that - that's awesome!
08/19/2008 09:48:26 AM from Jen Deegan: I blitz mine regularly. It's not that much of a problem.
08/19/2008 09:48:27 AM from Nomi Harris: Jen, glad you like the dbxref batch add. I felt sorry for you having to add them one-by-one!
08/19/2008 09:48:28 AM from Tanya: I hate having to reconstruct my file paths.
08/19/2008 09:48:32 AM from Jen Deegan: :-)
08/19/2008 09:49:00 AM from Jen Deegan: tanya, why don't you make an import file?
08/19/2008 09:49:20 AM from Nomi Harris: You mean, a save profile?
08/19/2008 09:49:31 AM from Nomi Harris: Or you mean for loading a bunch of ontology files together?
08/19/2008 09:49:31 AM from Tanya: Nomi - yes.
08/19/2008 09:49:34 AM from Jen Deegan: no I mean the kind of file that Chris has that lists all the file to load.
08/19/2008 09:49:40 AM from Nomi Harris: Right, good idea.
08/19/2008 09:49:58 AM from Jen Deegan: would mean that Nomi could ask us to delete the config file without having to worry about it.
08/19/2008 09:50:16 AM from Jen Deegan: at least while we are in test phase
08/19/2008 09:50:23 AM from Nomi Harris: One thing I am going to try to do is to narrow down which config files tend to be problematic, and see if there are more that can be left alone safely.
08/19/2008 09:50:50 AM from Nomi Harris: I still don't understand why there are weird problems (e.g. text editor not committing) that are fixed by blowing away your config.
08/19/2008 09:50:55 AM from Amina: Multiple files can also be loaded by Ctrl- Select with File -> Open
08/19/2008 09:51:24 AM from Nomi Harris: Next time you have a weird problem that is fixed by resetting your config directory, melissa, can you tar up your bad config directory (minus the autosave files, which can be big) and send it to me so I can do some forensics on it?
08/19/2008 09:51:54 AM from melissaH: you bet
08/19/2008 09:52:20 AM from Nomi Harris: Thanks.
08/19/2008 09:53:20 AM from Nomi Harris: Oh, before I forget, I wanted to remind you all that I will be away next week.
08/19/2008 09:53:32 AM from Jen Deegan: Have a good time away.
08/19/2008 09:53:39 AM from Nomi Harris: And then Monday, Sept 1 is Labor Day (a US holiday).
08/19/2008 09:53:55 AM from Nomi Harris: So, what with focusing on Phenote this week and being away next week, I won't be doing much on OE the next two weeks.
08/19/2008 09:54:14 AM from Jen Deegan: We'll just keep testing in the meantime.
08/19/2008 09:54:17 AM from David OS: Quick question
08/19/2008 09:54:20 AM from Nomi Harris: Yes, David?
08/19/2008 09:55:11 AM from David OS: Do you know what the default filter is for in the OTE - the one you can see i you click the spanner ant then choose term filtering?
08/19/2008 09:55:32 AM from David OS: It seems to hang around by default - but it's a real pain to construct filters around.
08/19/2008 09:56:09 AM from Nomi Harris: I know what you mean.
08/19/2008 09:56:33 AM from Nomi Harris: I have wondered about that too.
08/19/2008 09:56:53 AM from Nomi Harris: (You mean the default global term filters, right?)
08/19/2008 09:56:54 AM from David OS: Does this come from the global filter settings?
08/19/2008 09:57:01 AM from Nomi Harris: It's hardcoded.
08/19/2008 09:57:21 AM from Nomi Harris: You can remove them, and that will be saved in your config, but if you wipe your config, they will come back.
08/19/2008 09:57:42 AM from Nomi Harris: I will look into whether we really need those default filters and talk to Chris about it.
08/19/2008 09:57:49 AM from David OS: But I need to remove that from the global filter and not the OTE filter?
08/19/2008 09:58:10 AM from Nomi Harris: The OTE filter goes on top of the global filter.
08/19/2008 09:58:21 AM from Nomi Harris: I don't see those default filters in the OTE filter.
08/19/2008 09:59:41 AM from David OS: Perhaps another case of having to delete config files? They are there by default in my installation and come back if I try to delete them
08/19/2008 10:00:01 AM from Nomi Harris: Hmm, you mean you see those when you click the wrench in the OTE?
08/19/2008 10:00:12 AM from David OS: Yep
08/19/2008 10:00:28 AM from Nomi Harris: I will look into that.
08/19/2008 10:00:38 AM from Nomi Harris: Can you add a bug report so I don't forget?
08/19/2008 10:01:03 AM from melissaH: I don't see them in the OTE either
08/19/2008 10:01:10 AM from David OS: OK. Didn't realise it was a bug.... Any idea which config file(s) I could try deleting?
08/19/2008 10:01:52 AM from David OS: I certainly didn't add them by hand. They're gibberish to me.
08/19/2008 10:02:00 AM from Nomi Harris: component_prefs/ONTOLOGY_TREE_EDITOR:main
08/19/2008 10:02:22 AM from Nomi Harris: and/or filter_prefs.xml (in your top-level config directory)
08/19/2008 10:02:28 AM from David OS: OK - will try now.
08/19/2008 10:02:41 AM from Nomi Harris: And then try restarting.
08/19/2008 10:02:58 AM from Nomi Harris: I'm not sure whether this is a bug or just a difference in your configuration and mine...
08/19/2008 10:04:40 AM from Amina: Any more agenda items for today?
08/19/2008 10:04:50 AM from Jen Deegan: none from me.
08/19/2008 10:05:04 AM from Nomi Harris: Can we skip next week's meeting, since I'll be away, or do you guys want to meet anyway?
08/19/2008 10:05:21 AM from Jen Deegan: I don't mind skipping it.
08/19/2008 10:05:50 AM from Amina: Yeah if there are any issues o topics we can schedule one
08/19/2008 10:05:55 AM from Amina: or*
08/19/2008 10:06:02 AM from David OS: deleting filter prefs seems to have done it. Cheers.
08/19/2008 10:06:30 AM from Nomi Harris: Did you try quitting and restarting, then?
08/19/2008 10:06:38 AM from Nomi Harris: To make sure the unwanted filters didn't creep back in?
08/19/2008 10:07:04 AM from David OS: quit, then deleted, then restarted.
08/19/2008 10:07:14 AM from Nomi Harris: Great.
08/19/2008 10:07:24 AM from Nomi Harris: Blowing away one's config directory is the fix for many things.
08/19/2008 10:07:34 AM from Nomi Harris: As melissa can attest.
08/19/2008 10:07:36 AM from Nomi Harris: (And Jen.)
08/19/2008 10:07:39 AM from Jen Deegan: yes
08/19/2008 10:07:47 AM from Nomi Harris: So, "see" you all in two weeks?
08/19/2008 10:07:57 AM from Jen Deegan: Maybe if we all blow them away at once it will solve all problems permenantly.
08/19/2008 10:08:01 AM from Jen Deegan: yes
08/19/2008 10:08:08 AM from Nomi Harris: Jen, if only...
08/19/2008 10:08:08 AM from Amina: Bye everyone
08/19/2008 10:08:11 AM from Jen Deegan: :-)
08/19/2008 10:08:14 AM from Nomi Harris: Bye, all, thanks for coming.
08/19/2008 10:08:14 AM from Jen Deegan: See you then.
08/19/2008 10:08:17 AM from David OS: ANd filtering now works without triple nested queries. .... See ya
08/19/2008 10:08:26 AM from Jen Deegan: byee