OE IRC 19Oct06

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gwg has joined the channel
j-lo: Midori's on holiday, so I'm afraid we don't have an agenda
jclark has joined the channel
jrichter: That's okay. I've got one.
jrichter: Item 1: The OBO-Edit 2.0 email
gwg: trust John to have his own agenda..
jrichter: Were there any thoughts on that?
9:35 AM
j-lo: Well, it all sounds like good stuff
j-lo: My only concern is the obol integration stuff 
Alex_MGI: Agree, it sounds like redoing OBO-Edit the way it needs to be done.
kchris: Sorry, I'm just back from vacation, could you give the synopsis of the OBO-Edit 2.0 email?
j-lo: will be even further away, and we're getting kind of desperate!
jrichter: Jane - I can add obol integration to the OBO-Edit 2.0 plan, then.
j-lo: Does that not make it into too big a plan?
jrichter: Maybe we can break it into 3 pieces:
Alex_MGI: Making it a 2.0 release implies it will be a big release and take longer.
jrichter: * GUI/Scripting
jrichter: * Developer improvements
jrichter: * Reasoner/OBOL/OWL
jrichter: I'd want to do GUI/Scripting first, then the reasoner/obol/owl stuff, and then developer improvements.
j-lo: The thing is, we just need something we can use to look for obol missing relations etc - it doesn't have to be formally released
jrichter: I can prioritize OBOL then, and release a beta with those capabilities.
j-lo: what do others think?
jrichter: I need to do the proposed plugin improvements anyway so we can have a decent OBOL plugin.
gwg: that would be v. useful!
j-lo: sounds like a plan then John
jrichter: Did everyone get a chance to look at the new layout system I'm proposing? If not, maybe we should check out https://flexdock.dev.java.net/webstart/flexdockdemo.jnlp right now.
9:40 AM
Alex_MGI: I'm there right now with the menu in front of me of the demos.
jrichter: (click perspective demo)
tberardi: still loading..
MelissaH: got it.
tberardi: got it
jrichter: See all the little tabs in the bottom right corner (or wherever they are). Drag them around the screen.
jrichter: A little outline will appear showing where you can place the component in the layout.
hjd: still loading
MelissaH: I just have three tabs that say samples 1-3
jrichter: Drag it out of the window and let it go to create a new floating window.
tberardi: not doing it
jrichter: Choose "Perspective 2" from the Perspective menu.
kchris: I can't drag the "Sample1", etc tabs anywhere
tberardi: aha, john, that did it
jrichter: Not the sample tabs. You should have some tabs UNDERNEATH various components.
jrichter: The sample thing is fixed. (This demo is trying to show that you can embed fixed components in with your movable ones)
Alex_MGI: I'm just getting a blank window with "show View" and "Perspective" menus at the top.  No tabs or other interface elements are present.
jrichter: Choose a perspective from the perspective menu. You should get a screen layout.
Alex_MGI: Nothing happens at all.
MelissaH: ok, I have a bird view, message log, console, from perspective 2.
tberardi: I picked perspective 2 and that gave me a view where I could move panels around.
jrichter: Try "view demo" if you aren't getting any love from Perspective Demo.
kchris: OK, once you've taken those tabs/buttons and dragged them somewhere, can you reduce them back to tabs?
Alex_MGI: Yes that window has things in it.
jrichter: Yeah. Drag the panel to the middle of the panel where you want to place it as a tab.
jrichter: Let me say that a different way.
hjd: Alex, that's all I see also
9:45 AM
j-lo: aha - I see how it works now
jclark: I got it. That looks good.
jrichter: To make "Bird view" a tab of "Problems", drag "Bird View" to the center of the "Problems" panel.
jclark: is the current beta meant to do this or is it a future thing?
jrichter: This is a OBO-Edit 2.0 thing.
MelissaH: I just get different boxes, no tabs.
jclark: cool
tberardi: cool
Alex_MGI: I can see the possibilities here.
jrichter: We'd still have XML layouts, but now they'll control the contents of the sub panels.
jclark: Will we be able to get the graph weditor window as a separet window all on its own?
jrichter: Yup. Or you can drag the window back into your interface.
jclark: magic!
jclark: That would be fantastic
jrichter: Another cool thing:
tberardi: Oh wow, I just made it appear as a side tab that pops out when you mouse over it.
jrichter: Once you've laid out the screen the way you like, you can save that layout as a "Perspective". You can have a bunch of editing perspectives that you can choose from a dropdown menu.
tberardi: (Clicked the little pushpin like icon on the top)
Alex_MGI: I just dragged a panel completely out of the window!
jclark: can we export the layout so others can have the same?
jrichter: Yes. I'm not sure how that works yet, but I know it's possible.
jclark: great
Alex_MGI: I can't get the panel back in the window, though
jclark: in content meetings we really need everyone to have the same layout
jrichter: Alex: There's a way to do it, but I think it isn't enabled for this demo.
jrichter: Okay, that was item 1 on my agenda.
MelissaH: we like.
jrichter: Here's item 2...
jclark: a lot
tberardi: (Alex, click and hold on the tab and drag that back into the window.)
9:50 AM
kchris: this is great, I never did get the hang of the xml layouts
tberardi: yes, very nice.
Alex_MGI: (not doing it for me)
jrichter: We need to assign testing tasks for OBO-Edit 1.1, and come up with completion criteria.
Alex_MGI: (but that's okay for now)
tberardi: Want to spit out the to-do list and we can volunteer?
jrichter: Yup!
jrichter: DAG Viewer Improvements (I suggest Melissa)
MelissaH: ok, twist my arm...
jrichter: This task includes making sure that path selection works the way you wanted.
hjd: Graphviz plugin
jrichter: Does the graphviz plugin have unresolved problems?
jclark: there are feature requests but not bugs
hjd: not that I see; it appears to work fine; also the thing about the path getting lost when switching between beta and 1.002 no longer occurs 
jrichter: Before we assign any more tasks:
jclark: mine loses the path on every restart
jrichter: Are there new features we need to add before OBO-Edit 1.1 is releasable? Or is it all bug fixes, testing and docs.
jclark: but I reported that
j-lo: there was a really minor request about changing the button colours that would be nice
j-lo: but not urgent
9:55 AM
jrichter: Jane - what buttons are you talking about here? That one all the way on the left with the circle?
j-lo: yep - those
tberardi apologizes for the interruption but has to run to another meeting in 5 mins and needs a testing task
j-lo: just to make them in more contrasting colours
MelissaH: I would like to see the feature where we can have the same viewing options in our Graph view as our DAG view.
j-lo: shall we give tanya a job quickly?
MelissaH: I would like to have the same options for the graph view as we have for the dag view.
MelissaH: soory for the spam
gwg: can /me have a job too as I have to go out in 4 mins time
jrichter: Tanya - would you like to test the improvements to the Find panel?
tberardi: Sure.
tberardi: OK, I'm really lame, but where is the Find panel?
Alex_MGI: Not to be difficult, but perhaps we need an enumerated list of testing tasks.
tberardi: (I can take the reply offline.)
jrichter: The "Root" search aspect and the is_a complete features, in particular.
jrichter: Amelia - Could you handle testing of the text editor panel? This includes autocommit and manual commit modes, and the various warning messages that can be configured in the Text Editing tab of the configuration plugin.
jrichter: It's the thing with the big "Search" button in it.
jrichter: In some layouts it's in its own tab.
jrichter: I agree, Alex. I'm just trying to get the rushed people out the door.
gwg: yup, ok, will do. See yas next time!
Alex_MGI: I understand
gwg has quit the server saying: Quit: Goodbye cruel world!
tberardi thanks John and everyone else for their patience
jrichter: Here's what's left:
jrichter: * obomerge
jrichter: * obodiff
tberardi has quit the server saying: Quit: 
10:00 AM
jrichter: * new layouts AND scripting (big task, but it needs a single tester)
jrichter: * verification system
jrichter: * reasoned prefilters (interface)
jclark: is new layouts AND scripting  something I could do?
jrichter: * new save options, including reasoner-based options
jrichter: (Jen, I'd really like you to do that one)
jclark: yippee!
jrichter: obo2obo
jrichter: * Graphviz plugin save formats
hjd: I;ll thake that one
jrichter: * Adapter load/save profile management
Alex_MGI: I'll do that.
hjd: I can do that one too (I actually use it a lot)
kchris: Are there specific things Mike Cherry will need to use?
jrichter: * Launchers/installers
jrichter: Karen - obo2obo and obodiff are the ones Mike is going to need
jrichter: That's it. Let the bidding begin!
j-lo: John - shall I take the verification system?
kchris: I could take those 2 that Mike will need then, so that I can check with him to make sure we test that it does what he needs.
jrichter: Yes. I'd like that. You'll need to make sure that all the configuration options work, and the different tests run when they're supposed to.
jrichter: You should also create some custom tests.
jrichter: Great!
kchris: Which 'you' should create some custom tests?
j-lo: we've found it quite hard to test obomerge
jrichter: Jane should create custom tests.
jrichter: Jane - why?
j-lo: because it depends on you knowing what the output should be
j-lo: which we don't (that's why we used the script)
jrichter: Jane, why don't you and someone else test obomerge.
10:05 AM
jrichter: Here's how to do it:
jrichter: You come up with a script of edits for each of you to do (maybe 10 edits each) with at least one overlap (ie the first term each of you create is named "cabbage").
jrichter: Set your id generation rule to exactly the same thing before you do the edits.
jrichter: Then you save your results, and try to merge the changes.
j-lo: okay - Jen, shall we give that a go?
jclark: yes
jclark: cabbage sounds good
jclark: I have a problem
j-lo: !
jclark: related to obo-edit
jrichter: ?
jclark: I started it and the font is huge
jclark: it's so huge that I can't make the font window big enough to change the font
j-lo: LOL
jrichter: Hold on while I figure out a fix...
jclark: the button is below the bottom of the window
jclark: sorry
jrichter: One fix is to delete your config file. Doing that would probably solve your graphviz problem too.
jclark: I solved it
jclark: I clicked a load of tabs and the window resized
jrichter: If it happens again, look for the line <object class="java.awt.Font"> in ~/.oboedit/config.xml
jrichter: Change the font size number to something smaller and restart oboedit.
jrichter: Anyway.
jclark: taa
j-lo: what tasks are still left?
10:10 AM
jrichter: We need someone on reasoned prefilters
jrichter: Also the new save options
jrichter: and installers/launchers.
jrichter: Installers/launchers should either be parceled out to several people on different platforms, or done by one person with access to a bunch of different types of machines.
jrichter: Melissa - I think you'd be a good fit for reasoned prefilters.
Alex_MGI: (By the way the "obomerge" documentation is missing from the documentation accessible from OBO-Edit (calls up "obo2obo" instead).)
jclark: it launches fine on XP
jrichter: Thanks for the tip. I'll fix that today.
j-lo: the installers/launchers have probably already been tested on most platforms - I've done MacOSX
MelissaH: ok, I think so too, but I am ignorant and will likely need some hand holding.
jrichter: There's a specific test I want done on the launchers:
jrichter: I need the memory to be set really low, like 32M, so that OBO-Edit will crash when the GO is loaded.
jrichter: Then, I need the memory set back to the normal level.
jrichter: It's possible that the launchers aren't reading the memory settings correctly on every platform.
jrichter: That's the point of this test.
j-lo: should we put all these tests on a wiki?
jclark: just doing that now
jclark: I mean the test
jrichter: Does the WG have a wiki?
j-lo: i think it has a page on the go wiki...
jrichter: Okay, I'll post these assignments on the WG wiki.
jclark: would it nt be better on the obo-edit wiki?
jrichter: Okay, I'll post these assignments on the OBO-Edit wiki.
jclark: when oboedit crashes do I just quit?
10:15 AM
jrichter: Yeah.
j-lo: yep, it's here: http://gocwiki.geneontology.org/index.php/CategoryBO-Edit_working_group
j-lo: (we've moved to gocwiki now btw)
hjd: john, what program do I need to load xdot files? Graphviz doesn't like them
jrichter: Also - I'm adding a feature before the official release where OBO-Edit will show a popup message if it runs out of memory.
jclark: oboedit wont quit
jrichter: Graphviz should like them fine. If graphviz won't use 'em, we might have a bug.
jrichter: Let's parcel out these tasks before we report back on the bug tests...
hjd: well, we have one then
jrichter: Who uses Windows?
j-lo: i do sometimes
jrichter: Jane has too many jobs already. Who else?
MelissaH: me
jrichter: Melissa - can you test the OBO-Edit launcher's memory settings in Windows?
MelissaH: sure.
jrichter: Linux users?
jclark: I am doing xp just now
jclark: it is fine
jrichter: Looks like I'm the only linux/unix person, so I'll do this one and you'll have to trust me.
jrichter: Who wants to test the Mac OS launcher?
10:20 AM
jrichter: I nominate Alex!
Alex_MGI: okay
jrichter: I also nominate Alex for the new OBO save features. Is that okay?
jrichter: Actually, scratch that.
jrichter: I'm going to get Karen Eilbeck to test those, because SO uses more of the relevant OBO features than GO.
jrichter: Okay, I think that's everything.
jrichter: Here's the job list:
jclark: I have a question
jrichter: Yes?
jclark: how will I know how the layout and scripting works to test it?
jrichter: You will use the slowly emerging documentation. You can't test what isn't documented.
jclark: ah, right
jclark: so I wait 'till it emerges
jrichter: (Although you can make some astute deductions by looking at the new default layout)
jclark: true
jrichter: There's a lot to work with now.
jclark: its all xml based isn't it?
jrichter: Yup.
jclark: cool
jrichter: The scripting language now looks a lot like JavaScript.
hjd: need to go to another meeting; will work out the xdot thing etc.
hjd: bye
jrichter: Bye.
hjd has left the channel
jrichter: Okay, here's the job list:
jrichter: Tanya: Search panel
jrichter: Melissa: DAG Viewer, Selection Paths, Reasoned Prefilters, Windows launcher
jrichter: Amelia: Text editor
jrichter: Jane: obomerge, Verification System
10:25 AM
jrichter: Jen: obomerge, layouts, scripting, script editor
jrichter: Harold: GraphViz & load/save profiles
jrichter: John: Linux/Unix launchers
jrichter: Alex: mac launcher
jrichter: Karen E: obo save features
Alex_MGI: The OBO-Edit laucher in OSX appears to read in the reset memory values.
jrichter: That's it.
Alex_MGI: I just tested it.
j-lo: what's our deadline for testing, John?
MelissaH: testing the launcher on windows and have a problem.
kchris: and Karen C: obo2obo and obodiff
jrichter: Right. Thanks.
jrichter: Remember: testing includes checking the accuracy and completeness of the related documentation
MelissaH: get a java heap once I try to load GO, can't get the config panel to come up.  restarting OBOedit gives me a blank window.
jrichter: If you're using a command-line tool, you also need to check the documentation that appears when you run the tool with no arguments
jrichter: Melissa - let's work on that once everyone else takes off.
MelissaH: okay.
jrichter: In terms of testing deadlines: It's going to take me at least a week to get the documentation into shape. Let's aim for a release in 2 weeks.
Alex_MGI: Okay, maybe not, it seems the configuration plugin reports the reset memory value correctly (set back to 512M from 32M), but the GO will not load.
jrichter: Remember, memory settings don't take effect until you restart.
Alex_MGI: Have done several restarts too.
MelissaH: got mine going again and the same thing happened-reset to 512
MelissaH: restart oboedit or my computer? 
jrichter: Restart oboedit.
MelissaH: ok then, its not remembering.
10:30 AM
jrichter: If you're testing memory use, stick around after the meeting if you can.
Alex_MGI: Are my prefs wreaked then?
jrichter: Otherwise, are there any questions/additional issues?
jclark: just one
jrichter: (Alex - we can fix it)
jrichter: Go ahead, Jen.
jclark: if you are completely replacing the  layout system next time round then I just need to check this current one works do I?
jclark: There's no sense getting to attached to it?
jrichter: No. The layout system will still be in place for laying out the sub-components. And the new scripting system stays the same. So all this documentation and testing remains very useful.
jclark: ah right.
jclark: I'll give it a good going over then
jrichter: Okay, if you aren't testing memory usage right now, bye bye!
j-lo: bye
jclark: can someone keep the transcript?
Alex_MGI: Still here.
j-lo has quit the server saying: Quit: 
Alex_MGI: I can.
jrichter: Jen, can you save a transcript now and send it out? The next part will be mind-numbing and useless, so it doesn't need to be recorded.
jclark: kI don't have the button
jclark: karen might
jrichter: Let's give the job to Alex.
jclark: I think she has wandered off
jclark: ok bye 
jrichter: Bye.
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