midori: hi again!
Alex_MGI has joined the channel
5:30 PM
hjd has joined the channel
hjd is now called hjd_mgi
tberardi has joined the channel
tberardi: Whew! Made it!
jrichter has joined the channel
jrichter: Hello, all.
Alex_MGI: Hi
melissaH has joined the channel
melissaH: Hiya, long time no chat.
kchris has joined the channel
jrichter: The whole family's here. It's a Christmas miracle!
melissaH: ho ho ho.
jrichter: <|8-{)>
jrichter: That's my Santa emoticon I just made up.
5:35 PM
jrichter: --{>
tberardi: V. cool.
jrichter: That's his failing renal system!
jrichter: Anyway.
jrichter: Is everyone here?
Alex_MGI: Jane is not.
hjd_mgi: yup
midori: I'm not ... (just kidding)
jrichter: While we wait a few minutes for Jane, all you multitaskers out there should download and try out the Question Plugin I posted last night.
jrichter: I'm interested to know if people think it's worth additional energy.
tberardi: Yessir.
j-lo has joined the channel
midori: I"m waiting for my glacial download ...
jrichter: Now that Jane's here, let's go.
Alex_MGI: What do you do with the plugin?
jrichter: Drop the jar file into your extensions/ directory, and restart OBO-Edit.
jrichter: "Question Plugin" will now appear at the end of your plugins menu.
Alex_MGI: It didn't.
jrichter: Huh.
jrichter: Don't unzip the jar file. That's a common mistake.
Alex_MGI: Restarting again.
5:40 PM
Alex_MGI: Stlll not there. I think the file came unzipped. At least it appeared on my desktop with a .jar extension.
jclark: do we maybe need to add .jar on windows?
j-lo: (sorry I was late - what's the question plugin?
midori: exactly the same symptoms as Alex here ...
Alex_MGI: We're not there yet, Jane.
melissaH: (sorry, my home computer is acting up today, I'll have to try later)
jrichter: Alex & Midori - Can you send me the end of your stderr files? There may be a stack track that can help me figure out what's going wrong.
jclark: I have noe question plugin listed either.
jrichter: I'll try to figure this out while we chat about something else.
jrichter: Does anyone have any outstanding bug reports I haven't addressed?
Alex_MGI: Where do I find the sterr file?
midori: stderr on the way by email
jrichter: (Midori - I never received an email from you with your stderr file re: a NullPointerException bug)
jrichter: (don't worry about it Alex, Midori's file should be enough)
hjd_mgi: I'm still installing 13; I don't seem to be getting notices when a new beta is out
kchris: I didn't get a notice either and the formatting of the SF site is really messed up and annoying
tberardi: I'm not getting those either.
hjd_mgi: I missed the transition ffrom 11 to 12 and 12 to
tberardi: I'm trying to install 13 but it's taking FOREVER to uninstall the old version.
hjd_mgi: I just trash the old version directly on the mac
midori: #(*&%^% ... I'll try again.
j-lo: Happily, all my bugs are now fixed
Alex_MGI: DId you sign up for monitoring on SourceForge, Harold?
jrichter: I'll start sending email announcements again. I think we resolved 2 weeks ago that I would stop sending those if everyone signed up for the automatic sourceforge update messages.
kchris: Did Mike Cherry give the all OK on the obo2obo stuff?
5:45 PM
tberardi: Missed that resolution, John. Sorry.
j-lo: yep
hjd_mgi: I get a "java.lang.NullPointerException" error window poping up, but the program still runs
melissaH: I have a few outstandinding bugs but have been too swamped to test on b13.
midori: John -- I just re-sent the NullPointerException stderr.
Alex_MGI: Harold, restart and see if you get the message again.
jclark: do we need to do the thing where we replace the oboedit jar file that we did for obomerge?
hjd_mgi: After putting the plugin in the extensions directory and restarting, I do not see a question plugin; I see an explantion plugin
jrichter: I figured out the question plugin problem. I'll issue a re-released fix in 5 minutes.
midori: Also re obomerge: will it be included in the platform-independent version?
jrichter: Is it not there now?
hjd_mgi: yes the message comes up again; cllicking "OK" allows the program to comtinue
midori: John - nope. it's in the mac installer version, but not platform-indy
tberardi: easy question: How does one sign up for the automatic SF update messages?
Alex_MGI: I stopped getting it after several restarts, but then it stopped appearing.
jrichter: Well that's a bug. Could you put it on sourceforge?
tberardi: Is it that Monitor button?
midori: John - who're you replying to??
midori: Tanya - yep, that's the beast.
jrichter: Midori - I was replying to you. The missing obomerge script is a bug.
5:50 PM
midori: OK; bug report coming up.
tberardi: Midori - Thanks.
jrichter: Midori - I still haven't gotten your stderr email. I think someone along the way is silently dropping the message because of size.
jrichter: Can you place it on an ftp server?
jrichter: Or, just send me the stack trace for the latest null pointer exception.
hjd_mgi: Is there a way to enlarge the term filter window when compound filtering is selected? I can't see what I"m doing;. It has a scroll bar, but it doesn't do anything.. stays collapsed so there is really no room to move it up or down
midori: It's under 500K! but yes, I"ll put 'em up.
jrichter: Harold - that depends on your screen layout. The easiest way to make things bigger is to make your OBO-Edit window as large and possible, and shrink the main ontology panel.
jrichter: (as large AS possible)
hjd_mgi: That just makes it longer; but it doesn't get wider so I can see my ANDs, etc.
5:55 PM
jclark: you could use my layout
jclark: its in the help guide
Alex_MGI: John, I just sent my stderr file to you (I zipped it first).
hjd_mgi: The scroll bar only works in one direction; when I use it to scroll down to see my filters, I can't scroll back up.
hjd_mgi: : the bottom arrow on the scroll bar is not there, only the top arrow
jrichter: Use Jen's layout. You need to have your search control in a splitpane.
jrichter: You only have the top arrow because the available space is so small.
jrichter: BTW: a variation of Jen's layout will be the default in the next release.
jclark: yippee!
tberardi: Goody.
hjd_mgi: I'd rather still use my layout; but I'd just like the scroll bar to work
Alex_MGI: Will Jen get royalties?
tberardi: No, but we may address her as Queen Jen.
jclark: I'll get an absurd sense of personal pride
jrichter: Jen will get 100% of all the nothing we get paid from this program.
jclark:
jrichter: Harold - send Jen your layout. She'll be able to fix it up with a splitpane so quick it'll make your head spin.
jclark: true
6:00 PM
jclark: fun fun fun
midori: John - stderr files now available from the ebi file exchange site: go to http://www.ebi.ac.uk/systems-srv/mp/file-exchange/ ; right now they're the first two files up there.
tberardi ducking out for other meeting, am leaving chat window open to read discussion that follows
kchris: So with all these layout files available, will there be multiple layout options coming with the next version of obo-edit?
jclark: I think that would be awfully handy
melissaH: me too
jrichter: Karen - no, because it won't be necessary once we move to the new system.
jrichter: Remember the thing with the dockable panels we tested?
kchris: why will it not be necessary?
jclark: I remember
jclark: it looked good
jrichter: That's how OBO-Edit 2.0 will work. If you get a "layout" you like, you can save it, but those layouts are called "Perspectives" in the dockable panel vernacular.
melissaH: yeah, that was great, but still for advanced users.
kchris: how far away are we from that?
jrichter: It's the first thing I'm going to put into 2.0-beta1
jrichter: But it's probably a few months away.
kchris: then perhaps since these layout files are small, you could include the current one, as well as Jen's one, so that if I happen to prefer my old layout, I can go back to it without learning XML, which seems unlikely with current priorities for my time
melissaH: seems like something we should have on the wiki.
jrichter: In the next beta release the documentation contains an "examplelayouts" folder with everyone's favorite layouts.
jrichter: Just like the examplescripts folder we talked about last time.
melissaH: ok. same thing.
6:05 PM
jrichter: I've replaced the questionplugin.jar on sourceforge with a repaired version.
jrichter: This new one should work for you.
j-lo: it's not showing up in the plugins menu still
jclark: funky layout harold.
midori: same here - no new plugin
jrichter: <groan>
jrichter: Forget it. I'll try to do a new release later today.
hjd_mgi: no see new plugin either
midori: (of course, I'm not sure how fast the European mirrors update ...)
jrichter: So there are no outstanding bugs from any working group members besides the NullPointerException
jrichter: Midori - I'm actually sure that's the problem, but I've just discovered that beta14 is required for this plugin anyway.
melissaH: I'll work on checking mine in b13 later today. sorry.
melissaH: b14.
midori: I'd like to confirm fixes, but John says everything I reported from beta12 is fixed.
melissaH: I get a grey screen once in a while, anybody else get this?
6:10 PM
Alex_MGI: no
melissaH: e.g. oboedit window with nothing in it.
jrichter: Does it eventually resolve itself, Melissa?
melissaH: If I restart oboedit
melissaH: it can happen during a session, too.
jrichter: Hmm.... Melissa, send me your stderr file (zipped!). This sounds like a lockup.
melissaH: ok, later from my work computer.
jrichter: Java windows will sometimes go gray if Java is locked up, or working and working so hard that there's no time to update the screen.
hjd_mgi: BTW, from a couple betas back, the program always starts up with the ontology browser window collapsed; when I open it, it's automatically two screens, with the bottom screen active. Is this how it is working for everyone else?
jrichter: What do you mean "collapsed"?
hjd_mgi: Fully closed; I have to pull the bar it to the right to open it. It's not a big deal, but it didn't used to start up that way.
jrichter: Huh. Harold, send me a copy of your layout too, and I'll see what I can do.
6:15 PM
jrichter: Does anyone have any other business? Otherwise, I'll get to work on releasing beta14 with new docs by tonight.
kchris: Did Mike Cherry give you an OK on obo2obo?
midori: Did you or Chris send a response to the paper reviews?
jrichter: According to an email from 12/4, Mike was able to get obo2obo running without a problem, and Jane okayed the result.
jrichter: As far as I know, neither Chris nor I have responded to the paper reviews. I'll send him an email right now.
jrichter: Email sent.
jrichter: Here are my action items for the WG members then:
jrichter: 1) Make sure you're signed up to monitor OBO-Edit betas on sourceforge, so I don't send redundant emails
jrichter: 2) Keep an eye out for beta14 and the Question Plugin tonight. I'm very interested to get feedback on the plugin.
jrichter: That's it for me.
6:20 PM
j-lo: what's the SF mailing list called?
midori: no mailing list ... click 'monitor' on the downloads page
Alex_MGI: It's not exactly a mailing list.
j-lo: i can't see a monitor button on that page - where is it?
j-lo: oh, got it now
midori: sorry, I wasn't very specific .... https://sourceforge.net/project/showfiles.php?group_id=36855
kchris: The formatting of the SF site is completely messed up for me, instead of the dropdown menus, all the contents are in big huge lists that take up a ton of space, can't find anything there
jrichter: What browser are you using? You should probably send SF itself a bug report.
kchris: OmniWeb, the same browser I always use for SF
jrichter: Yeah, they probably need a bug report. They're probably only testing with IE and Mozilla.
Alex_MGI: Sounds like a CSS problem.
jrichter: (and maybe Safari)
Alex_MGI: It works fine on Safari.
kchris: where would I find where to send them a bug report?
jrichter: Hold on...
midori: It's OK in Safari and FIrefox
6:25 PM
jrichter: http://sourceforge.net/tracker/?func=add&group_id=1&atid=200001
jrichter: You can't submit bug reports, only "support requests"
jrichter: But that should be good enough.
jrichter: Are we done, then?
midori: I don't have anything else.
hjd_mgi: Next meeting next thursday?
midori: There's going to be a content webconf sometime next week, most likely Thursday.
jrichter: What do people think? Two weeks from now would be right after Christmas.
Alex_MGI: Okay for me in two weeks, but probably not for others.
midori: I'll be in North Yorkshire then.
j-lo: are we going to try and get this released before xmas?
jrichter: Please god...
Alex_MGI: All I want for Christmas ...
melissaH: sounds like a week from now then.
jrichter: Okay. Same time next week?
kchris: Stanford will be on winter closure that week, so I won't be working the week after Xmas
Alex_MGI: Okay
melissaH: ok here.
j-lo: yeah - lets do it next week
hjd_mgi: Stanford has "winter"???
kchris: The have winter closure regardless of the weather
midori: I'll try to sign off (barring new bugs) before Thurs; anyone who's not on the is_a-complete party can chat.
jrichter: Anyone who wants to can leave, I had a thing for Midori.
midori: I"ll also try to remember to send the reminder email ...
j-lo: so are we all aiming to sign off before thurs then?
jrichter: Midori - Did you get my email about how to specify which file wins in the case of an obomerge conflict?
midori: yes, and replied (did that get lost too???)
jrichter: Hell yes! Sign off as soon as possible. Before Thursday.
6:30 PM
Alex_MGI: Will do, Thanks, Bye.
j-lo: okay. Good night!
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hjd_mgi: ttfn
jrichter: Midori - I haven't gotten an email from you since the reminder for this chat.
midori: aaaaaaaaaaarrrrrrgghhhh.
melissaH: ok, see ya.
jrichter: Try sending email directly to jrichter@fruitfly.org, and see if that helps
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midori: ok
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kchris: Before I go, John, what is the best email address for you. Mike C mentioned that you were not responding to his messages when I was talking to him about obo2obo a few weeks ago.
6:35 PM
jrichter: Karen - try jrichter@berkeleybop.org or jrichter@fruitfly.org. It seems my yale alumnus address is screwing up.
kchris: OK, thanks John.