https://wiki.geneontology.org/index.php?title=OE_IRC_14Dec06&feed=atom&action=historyOE IRC 14Dec06 - Revision history2024-03-28T18:14:45ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OE_IRC_14Dec06&diff=52712&oldid=prevGail at 22:03, 30 June 20142014-06-30T22:03:52Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>midori: hi again!</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>midori: hi again!</div></td></tr>
</table>Gailhttps://wiki.geneontology.org/index.php?title=OE_IRC_14Dec06&diff=14583&oldid=prevMidori: New page: <pre> 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! jrichte...2008-08-01T15:20:15Z<p>New page: <pre> 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! jrichte...</p>
<p><b>New page</b></p><div><pre><br />
midori: hi again!<br />
<br />
Alex_MGI has joined the channel<br />
<br />
5:30 PM<br />
<br />
hjd has joined the channel<br />
<br />
hjd is now called hjd_mgi<br />
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tberardi has joined the channel<br />
<br />
tberardi: Whew! Made it!<br />
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jrichter has joined the channel<br />
<br />
jrichter: Hello, all.<br />
<br />
Alex_MGI: Hi<br />
<br />
melissaH has joined the channel<br />
<br />
melissaH: Hiya, long time no chat.<br />
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kchris has joined the channel<br />
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jrichter: The whole family's here. It's a Christmas miracle!<br />
<br />
melissaH: ho ho ho.<br />
<br />
jrichter: <|8-{)><br />
<br />
jrichter: That's my Santa emoticon I just made up.<br />
<br />
5:35 PM<br />
<br />
jrichter: --{><br />
<br />
tberardi: V. cool.<br />
<br />
jrichter: That's his failing renal system!<br />
<br />
jrichter: Anyway.<br />
<br />
jrichter: Is everyone here?<br />
<br />
Alex_MGI: Jane is not.<br />
<br />
hjd_mgi: yup<br />
<br />
midori: I'm not ... (just kidding)<br />
<br />
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.<br />
<br />
jrichter: I'm interested to know if people think it's worth additional energy.<br />
<br />
tberardi: Yessir.<br />
<br />
j-lo has joined the channel<br />
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midori: I"m waiting for my glacial download ...<br />
<br />
jrichter: Now that Jane's here, let's go.<br />
<br />
Alex_MGI: What do you do with the plugin?<br />
<br />
jrichter: Drop the jar file into your extensions/ directory, and restart OBO-Edit.<br />
<br />
jrichter: "Question Plugin" will now appear at the end of your plugins menu.<br />
<br />
Alex_MGI: It didn't.<br />
<br />
jrichter: Huh.<br />
<br />
jrichter: Don't unzip the jar file. That's a common mistake.<br />
<br />
Alex_MGI: Restarting again.<br />
<br />
5:40 PM<br />
<br />
Alex_MGI: Stlll not there. I think the file came unzipped. At least it appeared on my desktop with a .jar extension.<br />
<br />
jclark: do we maybe need to add .jar on windows?<br />
<br />
j-lo: (sorry I was late - what's the question plugin?<br />
<br />
midori: exactly the same symptoms as Alex here ...<br />
<br />
Alex_MGI: We're not there yet, Jane.<br />
<br />
melissaH: (sorry, my home computer is acting up today, I'll have to try later)<br />
<br />
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.<br />
<br />
jclark: I have noe question plugin listed either.<br />
<br />
jrichter: I'll try to figure this out while we chat about something else.<br />
<br />
jrichter: Does anyone have any outstanding bug reports I haven't addressed?<br />
<br />
Alex_MGI: Where do I find the sterr file?<br />
<br />
midori: stderr on the way by email<br />
<br />
jrichter: (Midori - I never received an email from you with your stderr file re: a NullPointerException bug)<br />
<br />
jrichter: (don't worry about it Alex, Midori's file should be enough)<br />
<br />
hjd_mgi: I'm still installing 13; I don't seem to be getting notices when a new beta is out<br />
<br />
kchris: I didn't get a notice either and the formatting of the SF site is really messed up and annoying <br />
<br />
tberardi: I'm not getting those either.<br />
<br />
hjd_mgi: I missed the transition ffrom 11 to 12 and 12 to <br />
<br />
tberardi: I'm trying to install 13 but it's taking FOREVER to uninstall the old version.<br />
<br />
hjd_mgi: I just trash the old version directly on the mac<br />
<br />
midori: #(*&%^% ... I'll try again.<br />
<br />
j-lo: Happily, all my bugs are now fixed<br />
<br />
Alex_MGI: DId you sign up for monitoring on SourceForge, Harold?<br />
<br />
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.<br />
<br />
kchris: Did Mike Cherry give the all OK on the obo2obo stuff?<br />
<br />
5:45 PM<br />
<br />
tberardi: Missed that resolution, John. Sorry.<br />
<br />
j-lo: yep<br />
<br />
hjd_mgi: I get a "java.lang.NullPointerException" error window poping up, but the program still runs<br />
<br />
melissaH: I have a few outstandinding bugs but have been too swamped to test on b13.<br />
<br />
midori: John -- I just re-sent the NullPointerException stderr. <br />
<br />
Alex_MGI: Harold, restart and see if you get the message again.<br />
<br />
jclark: do we need to do the thing where we replace the oboedit jar file that we did for obomerge?<br />
<br />
hjd_mgi: After putting the plugin in the extensions directory and restarting, I do not see a question plugin; I see an explantion plugin<br />
<br />
jrichter: I figured out the question plugin problem. I'll issue a re-released fix in 5 minutes.<br />
<br />
midori: Also re obomerge: will it be included in the platform-independent version?<br />
<br />
jrichter: Is it not there now?<br />
<br />
hjd_mgi: yes the message comes up again; cllicking "OK" allows the program to comtinue<br />
<br />
midori: John - nope. it's in the mac installer version, but not platform-indy<br />
<br />
tberardi: easy question: How does one sign up for the automatic SF update messages?<br />
<br />
Alex_MGI: I stopped getting it after several restarts, but then it stopped appearing.<br />
<br />
jrichter: Well that's a bug. Could you put it on sourceforge?<br />
<br />
tberardi: Is it that Monitor button?<br />
<br />
midori: John - who're you replying to??<br />
<br />
midori: Tanya - yep, that's the beast.<br />
<br />
jrichter: Midori - I was replying to you. The missing obomerge script is a bug.<br />
<br />
5:50 PM<br />
<br />
midori: OK; bug report coming up.<br />
<br />
tberardi: Midori - Thanks.<br />
<br />
jrichter: Midori - I still haven't gotten your stderr email. I think someone along the way is silently dropping the message because of size.<br />
<br />
jrichter: Can you place it on an ftp server?<br />
<br />
jrichter: Or, just send me the stack trace for the latest null pointer exception.<br />
<br />
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<br />
<br />
midori: It's under 500K! but yes, I"ll put 'em up.<br />
<br />
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.<br />
<br />
jrichter: (as large AS possible)<br />
<br />
hjd_mgi: That just makes it longer; but it doesn't get wider so I can see my ANDs, etc. <br />
<br />
5:55 PM<br />
<br />
jclark: you could use my layout<br />
<br />
jclark: its in the help guide<br />
<br />
Alex_MGI: John, I just sent my stderr file to you (I zipped it first).<br />
<br />
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.<br />
<br />
hjd_mgi: : the bottom arrow on the scroll bar is not there, only the top arrow<br />
<br />
jrichter: Use Jen's layout. You need to have your search control in a splitpane.<br />
<br />
jrichter: You only have the top arrow because the available space is so small.<br />
<br />
jrichter: BTW: a variation of Jen's layout will be the default in the next release.<br />
<br />
jclark: yippee!<br />
<br />
tberardi: Goody.<br />
<br />
hjd_mgi: I'd rather still use my layout; but I'd just like the scroll bar to work<br />
<br />
Alex_MGI: Will Jen get royalties?<br />
<br />
tberardi: No, but we may address her as Queen Jen.<br />
<br />
jclark: I'll get an absurd sense of personal pride<br />
<br />
jrichter: Jen will get 100% of all the nothing we get paid from this program.<br />
<br />
jclark: <br />
<br />
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.<br />
<br />
jclark: true <br />
<br />
6:00 PM<br />
<br />
jclark: fun fun fun<br />
<br />
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.<br />
<br />
tberardi ducking out for other meeting, am leaving chat window open to read discussion that follows<br />
<br />
kchris: So with all these layout files available, will there be multiple layout options coming with the next version of obo-edit?<br />
<br />
jclark: I think that would be awfully handy<br />
<br />
melissaH: me too<br />
<br />
jrichter: Karen - no, because it won't be necessary once we move to the new system.<br />
<br />
jrichter: Remember the thing with the dockable panels we tested?<br />
<br />
kchris: why will it not be necessary?<br />
<br />
jclark: I remember<br />
<br />
jclark: it looked good<br />
<br />
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.<br />
<br />
melissaH: yeah, that was great, but still for advanced users.<br />
<br />
kchris: how far away are we from that?<br />
<br />
jrichter: It's the first thing I'm going to put into 2.0-beta1<br />
<br />
jrichter: But it's probably a few months away.<br />
<br />
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<br />
<br />
melissaH: seems like something we should have on the wiki.<br />
<br />
jrichter: In the next beta release the documentation contains an "examplelayouts" folder with everyone's favorite layouts.<br />
<br />
jrichter: Just like the examplescripts folder we talked about last time.<br />
<br />
melissaH: ok. same thing.<br />
<br />
6:05 PM<br />
<br />
jrichter: I've replaced the questionplugin.jar on sourceforge with a repaired version.<br />
<br />
jrichter: This new one should work for you.<br />
<br />
j-lo: it's not showing up in the plugins menu still<br />
<br />
jclark: funky layout harold. <br />
<br />
midori: same here - no new plugin<br />
<br />
jrichter: <groan><br />
<br />
jrichter: Forget it. I'll try to do a new release later today.<br />
<br />
hjd_mgi: no see new plugin either<br />
<br />
midori: (of course, I'm not sure how fast the European mirrors update ...)<br />
<br />
jrichter: So there are no outstanding bugs from any working group members besides the NullPointerException<br />
<br />
jrichter: Midori - I'm actually sure that's the problem, but I've just discovered that beta14 is required for this plugin anyway.<br />
<br />
melissaH: I'll work on checking mine in b13 later today. sorry.<br />
<br />
melissaH: b14.<br />
<br />
midori: I'd like to confirm fixes, but John says everything I reported from beta12 is fixed.<br />
<br />
melissaH: I get a grey screen once in a while, anybody else get this?<br />
<br />
6:10 PM<br />
<br />
Alex_MGI: no<br />
<br />
melissaH: e.g. oboedit window with nothing in it.<br />
<br />
jrichter: Does it eventually resolve itself, Melissa?<br />
<br />
melissaH: If I restart oboedit<br />
<br />
melissaH: it can happen during a session, too.<br />
<br />
jrichter: Hmm.... Melissa, send me your stderr file (zipped!). This sounds like a lockup.<br />
<br />
melissaH: ok, later from my work computer.<br />
<br />
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.<br />
<br />
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?<br />
<br />
jrichter: What do you mean "collapsed"?<br />
<br />
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.<br />
<br />
jrichter: Huh. Harold, send me a copy of your layout too, and I'll see what I can do.<br />
<br />
6:15 PM<br />
<br />
jrichter: Does anyone have any other business? Otherwise, I'll get to work on releasing beta14 with new docs by tonight.<br />
<br />
kchris: Did Mike Cherry give you an OK on obo2obo?<br />
<br />
midori: Did you or Chris send a response to the paper reviews?<br />
<br />
jrichter: According to an email from 12/4, Mike was able to get obo2obo running without a problem, and Jane okayed the result.<br />
<br />
jrichter: As far as I know, neither Chris nor I have responded to the paper reviews. I'll send him an email right now.<br />
<br />
jrichter: Email sent.<br />
<br />
jrichter: Here are my action items for the WG members then:<br />
<br />
jrichter: 1) Make sure you're signed up to monitor OBO-Edit betas on sourceforge, so I don't send redundant emails<br />
<br />
jrichter: 2) Keep an eye out for beta14 and the Question Plugin tonight. I'm very interested to get feedback on the plugin.<br />
<br />
jrichter: That's it for me.<br />
<br />
6:20 PM<br />
<br />
j-lo: what's the SF mailing list called? <br />
<br />
midori: no mailing list ... click 'monitor' on the downloads page<br />
<br />
Alex_MGI: It's not exactly a mailing list.<br />
<br />
j-lo: i can't see a monitor button on that page - where is it?<br />
<br />
j-lo: oh, got it now<br />
<br />
midori: sorry, I wasn't very specific .... https://sourceforge.net/project/showfiles.php?group_id=36855<br />
<br />
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 <br />
<br />
jrichter: What browser are you using? You should probably send SF itself a bug report.<br />
<br />
kchris: OmniWeb, the same browser I always use for SF<br />
<br />
jrichter: Yeah, they probably need a bug report. They're probably only testing with IE and Mozilla.<br />
<br />
Alex_MGI: Sounds like a CSS problem.<br />
<br />
jrichter: (and maybe Safari)<br />
<br />
Alex_MGI: It works fine on Safari.<br />
<br />
kchris: where would I find where to send them a bug report?<br />
<br />
jrichter: Hold on...<br />
<br />
midori: It's OK in Safari and FIrefox<br />
<br />
6:25 PM<br />
<br />
jrichter: http://sourceforge.net/tracker/?func=add&group_id=1&atid=200001<br />
<br />
jrichter: You can't submit bug reports, only "support requests"<br />
<br />
jrichter: But that should be good enough.<br />
<br />
jrichter: Are we done, then?<br />
<br />
midori: I don't have anything else.<br />
<br />
hjd_mgi: Next meeting next thursday?<br />
<br />
midori: There's going to be a content webconf sometime next week, most likely Thursday.<br />
<br />
jrichter: What do people think? Two weeks from now would be right after Christmas.<br />
<br />
Alex_MGI: Okay for me in two weeks, but probably not for others.<br />
<br />
midori: I'll be in North Yorkshire then.<br />
<br />
j-lo: are we going to try and get this released before xmas?<br />
<br />
jrichter: Please god...<br />
<br />
Alex_MGI: All I want for Christmas ...<br />
<br />
melissaH: sounds like a week from now then.<br />
<br />
jrichter: Okay. Same time next week?<br />
<br />
kchris: Stanford will be on winter closure that week, so I won't be working the week after Xmas<br />
<br />
Alex_MGI: Okay<br />
<br />
melissaH: ok here.<br />
<br />
j-lo: yeah - lets do it next week<br />
<br />
hjd_mgi: Stanford has "winter"???<br />
<br />
kchris: The have winter closure regardless of the weather <br />
<br />
midori: I'll try to sign off (barring new bugs) before Thurs; anyone who's not on the is_a-complete party can chat.<br />
<br />
jrichter: Anyone who wants to can leave, I had a thing for Midori.<br />
<br />
midori: I"ll also try to remember to send the reminder email ...<br />
<br />
j-lo: so are we all aiming to sign off before thurs then?<br />
<br />
jrichter: Midori - Did you get my email about how to specify which file wins in the case of an obomerge conflict?<br />
<br />
midori: yes, and replied (did that get lost too???)<br />
<br />
jrichter: Hell yes! Sign off as soon as possible. Before Thursday.<br />
<br />
6:30 PM<br />
<br />
Alex_MGI: Will do, Thanks, Bye.<br />
<br />
j-lo: okay. Good night!<br />
<br />
j-lo has left the channel<br />
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hjd_mgi: ttfn<br />
<br />
jrichter: Midori - I haven't gotten an email from you since the reminder for this chat.<br />
<br />
midori: aaaaaaaaaaarrrrrrgghhhh.<br />
<br />
melissaH: ok, see ya.<br />
<br />
jrichter: Try sending email directly to jrichter@fruitfly.org, and see if that helps<br />
<br />
melissaH has quit the server saying: Quit: melissaH<br />
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hjd_mgi has left the channel<br />
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midori: ok<br />
<br />
Alex_MGI has quit the server saying: Quit: Quitting!<br />
<br />
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.<br />
<br />
6:35 PM<br />
<br />
jrichter: Karen - try jrichter@berkeleybop.org or jrichter@fruitfly.org. It seems my yale alumnus address is screwing up.<br />
<br />
kchris: OK, thanks John.<br />
<br />
</pre></div>Midori