OE IRC 14Dec06

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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.


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!

j-lo has left the channel

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

melissaH has quit the server saying: Quit: melissaH

hjd_mgi has left the channel

midori: ok

Alex_MGI has quit the server saying: Quit: Quitting!

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.