OE IRC 30Nov06

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Alex_MGI has joined the channel

5:30 PM

tberardi has joined the channel

Alex_MGI: Hi Midori, don't do the peptidylglucan SF entry yet as I am preparing another couple of terms.  Thanks.

midori: OK; the next thing I OE_IRCget to will be the interleukin production stuff anyway.

jrichter has joined the channel

jrichter: Hello, fellow travelers!

midori: greetings

tberardi: Hi, are you in CA yet?

Alex_MGI: Hi

jrichter: I leave for California tonight. Funny story:

jrichter: Our travel reservation person lost the email I sent requesting tickets. When I resent the email a few days later, she somehow didn't receive the line that specified the dates of travel, but received the rest of the email.

jrichter: We finally straightened it out on Wednesday, which was her last day, so she didn't buy the tickets.

5:35 PM

jrichter: She passed the request up to her supervisor, who is out of town.

jrichter: As is the person who is covering for her supervisor.

jrichter: I ended up buying the plane tickets myself.

tberardi: (So you're taking Greyhound?)

tberardi: Ah.

midori: So the travel reservation person adds what, exactly, to your business travel experience?

jrichter: That essential ingredient to all academic pursuits: beauracracy.

jrichter: (if that was mispelled, I did it on purpose. Otherwise I'm a genius)

jrichter: misspelled

jrichter: Kill me.

tberardi: I'll be seeing you tomorrow so watch out!

Alex_MGI: Not until after 1.1

j-lo has joined the channel

jrichter: Tanya: when am I seeing you? And why? I thought PATO wasn't until the weekend...

midori ain't killin' anyone 'til she gets some keyboard shortcuts

tberardi: It's tomorrow (Friday) and Saturday. 

tberardi: Unless you weren't planning on coming to any of the Friday talks.

tberardi takes a reality check to make sure it's Thursday

jrichter: No. I think Suzi just double-booked me. I'm supposed to be giving a BBOP group meeting tomorrow too. I'm happy to cancel it.

jrichter: Anyway, this is probably about everyone who's going to show up.

jrichter: Anybody have any business?

midori: OK; what's on the agenda?

midori: I suggested testing updates and the paper; Chris says he'll try to join the chat later to comment on the paper reviews.

jrichter: Here's my report:

5:40 PM

jrichter: as far as I know, all the pending OBO-Edit bugs are fixed. As soon as the testing and docs are done, we're ready to release.

midori: (I also think I thought of something else early this morning, but it was too early and I can't remember what it was.)

tberardi: Did you get help for doc updating?

jrichter: That idea was roundly urinated upon.


midori: Strictly speaking, it was the idea of having to PAY someone that was urinated upon.

jrichter: Granted.

kchris has joined the channel

j-lo: Looks like we'll have to do it ourselves

kchris: Apologies I'm late, traffic was horrendous 

midori: Anyway ... I've just got beta12. The platform-independent version starts up and loads GO just fine; I haven't had it long enough to test anything else.

jrichter: Note that your graphical glitches have been fixed, including that bug where you couldn't see the "Del" button on list editors.

jrichter: It took a mere 3 years to fix that baby.

midori rejoices

jrichter: Shall we move on to paper update issues?

j-lo: any progress on obomerge John?

jrichter: I thought I fixed it.

jrichter: Is it still broken?

j-lo: oh, haven't tested it yet!

kchris: John, I have a question: where do I report issues like the help for obo2obo being insufficient for a novice to use the script?

jrichter: Good question...

jrichter: I think that has to go on the bug tracker.

5:45 PM

jrichter: What's not making sense?

kchris: Insufficient information about things like names of scripts to call

jrichter: Oh. There aren't any built-in scripts. They're script files.

jrichter: I've usually attached them to emails I've sent around.

kchris: Whatever they are, there isn't enough info in the help to know how to write the command

jrichter: Is the problem that the documentation on the scripting language isn't complete, or that the discussion of how scripts work in obo2obo is lacking?

kchris: I'm not completely sure how to answer that question, so I'll give you a little detail about what I did

j-lo: (if you run the command without any arguments it'll give you a set of instructions btw)

kchris: I tried to test running obo2obo to convert 1.2 to 1.0. The syntax for the command lists something about a script/scriptfile. Nowhere in the help is the name of the script file mentioned. I had to get it from Mike Cherry's email

kchris: I also did try to use the command without arguments and it provides no additional info from that in the help

5:50 PM

jrichter: The scripts are optional; they can perform various analyses or transformations on the ontology before it is saved.

jrichter: There's no mention of script names in the documentation because scripts are provided by users (in theory).

kchris: It might be worth having a specific example for how to write a command that will perform the obo1.2 to obo1.0

jrichter: Yeah; I think something like that should go in the How To or FAQ section, along with a copy of the script that Mike is using.

kchris: IT might be worth documenting all the scripts that you are providing with obo-edit, even if users can provide their own

midori: The fact that scripts are optional is indicated only by the square brackets in the usage lines at the top. That's all well and good for seasoned command-line geeks, but it's terribly easy for novices to overlook.

jrichter: That's the point; I'm providing no command-line scripts.

kchris: I actually did understand that it was optional, but I still couldn't completely figure out how to write a command that worked, so I used Mike's email about the obo2obo bug

j-lo: is it working now Karen?

kchris: obo2obo is not working in beta11, haven't tested 12 yet

jrichter: Yeah, it sounds like we need a How To. That sounds like the best solution to me.

jrichter: obo2obo is fixed in beta12 (at least the bug report Mike submitted)

jrichter: The bug page currently has a single item on it, and that bug hasn't been addressed because I can't understand what the problem is.

kchris: I haven't talked to Mike yet today, yesterday beta12 was not yet available

midori: Ah ... I see one source of confusion: when we say "script" we often mean obo2obo and other utilities (that's what they're called in the user's guide), not necessarily the more restricted meaning that John seems to be using.

jrichter: Oh. Good point. How were we using the word "script"?

jrichter: I call obo2obo, obomerge, etc "command-line utilities"

5:55 PM

jrichter: I call files in the OSL scripting languages "scripts"

kchris: The help for using obo2obo gives this as part of the syntax: -script <scriptname> 

midori: I'm pretty sure that in Karen's comments obo2obo was a "script" ... we haven't quite caught up with the brave new OSL scripting world :P

j-lo: oh this is the extra script Karen?

j-lo: There's no documentation for that

kchris: But nowhere in the help does it mention the particular option that Mike Cherry is using (Mike made this comment too)

jrichter: Okay, let's back up here.

jrichter: The scripts are not mentioned in the documentation because they're external to OBO-Edit. They aren't in the user's guide for the same reason that the macromedia flash plugin isn't documented in the Mozilla docs.

jrichter: I think I should create a "commonly used scripts" section on the OBO-Edit Wiki to document these.

kchris: What are these scripts part of then?

jrichter: The scripts are just independent, stand-alone components. But I'll put a bunch of useful ones up on the Wiki, and I'll create a link from the obo2obo docs and the scripting docs to the Wiki page.

kchris: components of what?

6:00 PM

j-lo: (it's just one script Karen, called strip_replacement_tags.osl - John wrote it for interconverting the GO edit and non-edit files)

tberardi has to run to other meeting now, will keep chat window open so I can read the discussion when I get back

jrichter: They are text files in the OSL scripting language that can be written by any user. There are a bunch of scripts floating around already.

j-lo: (it's like an add-in for obo2obo)

midori: John - I get it about why no specific scripts are documented. But I think the fact that OSL scripts are (a) optional and (b) external/not included/to-be-written-by-the-user is hard to ferret out from the existing documentation (the info is not necessarily absent, but neither is it obvious).

kchris: If they're really only useful for obo-edit, or things like obo2obo that are packaged with obo-edit, why not document it here

kchris: I agree with Midori's comment too

jrichter: I'll try to clarify the documentation on this point, and add some links to the Wiki. Would that work?

Alex_MGI: If there are a set of truly useful, basic scripts, why not include them?

kchris: I agree

jrichter: Okay. I'll add an examplescripts/ folder with some example scripts to the next OBO-Edit release.

kchris: cool 

jrichter: And I'll document all of them in the User's Guide.

kchris: very cool 

Alex_MGI: great!

jrichter: Can we move on to the paper?

midori: One more thing before we leave  the command-line stuff ... this is more of a feature request: can there be (much) shorter aliases for the options? I'm too lazy to type '- formatversion' every #@% time.

6:05 PM

jrichter: Sure. That's easy. Maybe email your suggestions for aliases to the list.

jrichter: ?

jrichter: (The hard part, of course, is documenting them)

midori: OK, tho I don't have strong feelings about what they should be, only that they should be short so I can type less 

j-lo: (by the way, Karen, I spent ages faffing around with obo2obo, so if you need a hand setting it all up just let me know)

jrichter: Midori - I'll see what I can come up with.

midori: thanks! 

midori: on to the paper, then ...

kchris: Mike was helping me yesterday, the weird thing is that I still get out of memory errors, even though I'm on a machine nearly identical to Mike's. Mike said we'd figure out what the problem with my set up is after we have one that's working

jrichter: Remember:

jrichter: The scripts have independent memory settings from OBO-Edit.

jrichter: You need to configure the memory settings for your scripts or you'll always run out of memory.

kchris: even after issuing the unlimit command that Mike says he has to use

jrichter: unlimit command?

kchris: unix command line: unlimit

jrichter: I don't know what he means by that.

kchris: Mike did give me some more info about checking what my memory settings were, but we haven't played with that yet

jrichter: That's not the preferred, cross-platform method.

jrichter: See the User's Guide section... (looking it up)

kchris: maybe the preferred, cross-platform method of controlling script memory settings should be mentioned/linked to in the obo2obo help

midori: Java Options on the Command LIne

jrichter: "The Command Line" -> "Java Options on the Command Line"

6:10 PM

kchris: We can move on. I'll ask Jane or Mike for more help, but we can use my novice eyes to help make sure the documentation will help newbies

midori: Oh, one more random non-paper thing -- I didn't get the usual email saying that beta12 was released, and I don't remember seeing one for beta 11.

jrichter: Huh. I sent one last night.

midori: crud.

jrichter: Our email server must be hosed yet again.

Alex_MGI: I didn't get one either.

midori can't improve on her previous comment

jrichter: It's in my sent-mail folder. You'll probably get it in a few weeks. <sigh>

jrichter: A better way of getting announcements:

jrichter: There's a way to tell sourceforge to automatically notify you when a package has a new release. That's the best way.

midori: Yeah, I used to do that but stopped because it was redundant with your emails ... in the happy days when the latter arrived reliably. At least I thought to look on the downloads page when I saw the bug-fix tracker posts.

jrichter: (To do it, Click "Download Gene Ontology" from the front page of the GO sourceforge site, and then click the "Monitor" link for OBO-Edit betas)

jrichter: If we all use the sourceforge package monitor, I won't send those redundant emails anymore.

midori: okey-dokey

jrichter: So, that thar paper...

kchris: should we also make sure that we set it up so that SourceForge is also sending the automatic notification to go-friends

6:15 PM

kchris: ?

jrichter: Should we? I stopped telling go-friends about betas. I'm only announcing official release there.

midori: that makes sense to me

Alex_MGI: I think John's is the correct policy.

kchris: just official releases to go-friends sounds good to me too

jrichter: Here's what I think about the paper updates:

jrichter: I think we have no choice but to ignore the suggestions that come down to "write a different, longer paper justifying your existence"

Alex_MGI: agreed

jrichter: The only suggestion we can really act on regards OWL support in OBO-Edit. Chris suggested that we address this by mentioning the OBO-to-OWL mapping, and referring to the upcoming paper "in prep"

midori: Chris said yesterday that he would draft a response to the editors about the things we can't address in the paper (too bad he hasn't turned up).

jrichter: It's okay; I'll see him tomorrow.

6:20 PM

jrichter: Does that sound good?

midori: yup

jrichter: Okay. Next item?

Alex_MGI: Are we doing sign-off now for B12?

jrichter: Absolutely. In theory, we have been for weeks.

Alex_MGI: True, but I've been otherwise occupied.

jrichter: By sign-off, I mean checking one's assigned testing areas and updating the testing wiki when things check out.

jrichter: Oh!

jrichter: I've moved the OBO-Edit Wiki to the GO Consortium Wiki site!

jrichter: Follow the link from www.oboedit.org

jrichter: I did this because we decided that OBO-Edit didn't belong on the BBOP project Wiki, since it's a GO consortium project.

Alex_MGI: Now the immunology pages are not all by themseleves!

6:25 PM

jrichter: Did we have any other business? Time's almost up...

midori: As I said earlier, I can't remember the other thing ...

jrichter: Well then,

midori: ... so if we're ready to wrap up, fine

jrichter: Now it's time to say goodbye, to all our company

j-lo: are we meeting next week?

jrichter: I don't think it's necessary.

jrichter: (Although it is fun to pretend I have friends...)

Alex_MGI: Is there a signoff date, per se?  I can't remember.

jrichter: Let's say 2 weeks from now.

jrichter: Sound good?

kchris: OK

Alex_MGI: Fine with me.

midori: Well, it was tomorrow, before I found some tricksy bugs ... two weeks is fine, and coincides with our next chat.

jrichter: Resolved!

6:30 PM

j-lo: (quick q John - the arguments for clash-on-id for obomerge have changed - what's value 1 etc mean?)

jrichter: Karen - could you post a bug report regarding the script documentation, so I can remember to shore things up?

jrichter: Jane - hold on, I'll look it up.

kchris: will do

j-lo: oh maybe it hasn't changed - ignore me!

jrichter: You can optionally specify multiple -ignore-clash-on-id tags. The value of each tag is an id to ignore.

j-lo: yep - gottit

jrichter: Consider yourself ignored!

jrichter: Goodbye then, everyone!

j-lo: bye!

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kchris: bye!

Alex_MGI: bye

kchris has quit the server saying: Quit: I'll be back!

Alex_MGI has quit the server saying: Quit: Quitting!