OE Webex 4Nov08

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11/04/2008 09:30:38 AM from midori: Hi again
11/04/2008 09:30:50 AM from Jen Deegan: Hi again
11/04/2008 09:30:59 AM from Amina Abdulla: Hi Jen
11/04/2008 09:31:16 AM from Jen Deegan: Hi Amina
11/04/2008 09:31:39 AM from Amina Abdulla: Thanks for joining again - there was a small webex glitch
11/04/2008 09:32:15 AM from Jen Deegan: We get that sometimes. Usually it's just one attendee, but if it's the person running the meeting then it all goes down.
11/04/2008 09:32:30 AM from Nomi Harris: Hello
11/04/2008 09:32:31 AM from David OS: Hiya
11/04/2008 09:32:37 AM from Jen Deegan: Hi David
11/04/2008 09:32:44 AM from Amina Abdulla: Hi David
11/04/2008 09:33:09 AM from Amina Abdulla: Thanks for posting the follow ups on your bugs
11/04/2008 09:33:32 AM from David OS: Sorry for not posting earlier.
11/04/2008 09:34:11 AM from Amina Abdulla: At the GO meeting we briefly discussed how we could make our working group meeting more effective and thought it would be useful to have an agenda sent out before the meeting
11/04/2008 09:34:19 AM from midori: I must admit, I'm still behind on bug updates.
11/04/2008 09:34:51 AM from Jen Deegan: I got behind after my last holiday too. There are a lot to keep on top of.
11/04/2008 09:34:59 AM from Jen Deegan: I think an agenda sounds good.
11/04/2008 09:35:16 AM from David OS: Agenda sounds like a good idea. Perhaps it should automatically include bugs that have been commented on in the past week.
11/04/2008 09:35:27 AM from Amina Abdulla: Thats alright Midori
11/04/2008 09:35:31 AM from midori: yup; we used to have them, but lapsed
11/04/2008 09:35:36 AM from Jen Deegan: I think it might be better to keep quite focussed.
11/04/2008 09:35:51 AM from midori: (thanks, Amina ... jet lag is receding, but slowly)
11/04/2008 09:35:53 AM from Amina Abdulla: Yeah that would help everyone get an idea about whats going on
11/04/2008 09:35:56 AM from Jen Deegan: for example we need to make some plans about how to get to the release as fast as possible.
11/04/2008 09:36:26 AM from Jen Deegan: on some meetings we've found if there are automatic agenda items then the important things get squeezed out.
11/04/2008 09:37:03 AM from midori: I agree -- we should do an agenda for each meeting, and as a general rule avoid "rolling" items.
11/04/2008 09:37:04 AM from Amina Abdulla: Yes I was going to suggest having a wiki page with components and testing priorities
11/04/2008 09:37:28 AM from Jen Deegan: good idea
11/04/2008 09:37:31 AM from midori: Amina -- good idea, and one we've used before, with pretty good results
11/04/2008 09:38:10 AM from David OS: A wiki page on XP related issues could be very useful - diffiucult to get a sense of how issues interact from a scattered set of tickets.
11/04/2008 09:38:25 AM from Amina Abdulla: Yeah that way we can start checking off items as ready for release
11/04/2008 09:38:29 AM from Jen Deegan: are you monitoring those david?
11/04/2008 09:38:38 AM from Jen Deegan: perhaps you could compile that list?
11/04/2008 09:38:52 AM from Amina Abdulla: David I agree - A lot of users are confused as to how xps would work in OE2
11/04/2008 09:38:55 AM from midori: an xp page might also help those of us who haven't really used xps in earnest yet, but will have to soon
11/04/2008 09:39:13 AM from Amina Abdulla: I have to admit David - I haven't looked into xps a lot too
11/04/2008 09:39:24 AM from Jen Deegan: yes I really would be interested to get more of a feel for what we will want to do with OE2 and cross products post-release.
11/04/2008 09:40:08 AM from David OS: Happy to write the page as I already have a bunch of notes - and am struggling with these beasties every day.
11/04/2008 09:40:11 AM from Amina Abdulla: Should we have a xps demo on the agenda for our next WG meeting
11/04/2008 09:40:25 AM from Jen Deegan: that would be great (both), thanks David.
11/04/2008 09:40:45 AM from David OS: I can give an XP bug demo ....
11/04/2008 09:41:02 AM from David OS: In fact, any XP demo would also be an XP bug demo
11/04/2008 09:41:07 AM from Amina Abdulla: yes the commit bug demo would be helpful
11/04/2008 09:41:27 AM from Jen Deegan: We have had a bit of a demo of the actual tool but I would be interested to know which XP file we will be working on first. Would you think it would be cell type?
11/04/2008 09:41:27 AM from Amina Abdulla: well thats true:)
11/04/2008 09:41:59 AM from Jen Deegan: I think that Alex Deihl and Chris must already have a workflow for editing these things and I would be really interested to see that.
11/04/2008 09:42:24 AM from Jen Deegan: I think once we are clear on the work flow we can start to test properly.
11/04/2008 09:42:24 AM from midori: we should try to get them for the demo, if possible
11/04/2008 09:42:25 AM from Amina Abdulla: For the release we would also need the JUnit tests for xps
11/04/2008 09:42:27 AM from Jen Deegan: also have proper demos.
11/04/2008 09:43:09 AM from Jen Deegan: Could I ask a related question that comes back to this?
11/04/2008 09:43:37 AM from Amina Abdulla: Sure Jen
11/04/2008 09:44:45 AM from Jen Deegan: I mentioned last week, but Midori was still away. I wondered if it might be okay for us to start committing the live file from OBO-Edit2 just into the editors' version of the file, as long as we make sure to do a load/save in 1.101 and commit back before the public version is generated.
11/04/2008 09:45:46 AM from Jen Deegan: anyway, that way we could also start practising the XP workflow for real, and just stripping it out before the public file is made.
11/04/2008 09:46:12 AM from Jen Deegan: I think that that way normal testing would be much faster, and we could also start testing XPs in earnest.
11/04/2008 09:46:13 AM from midori: Jen, do you mean use OE2 for editing the live file?
11/04/2008 09:46:18 AM from Jen Deegan: yes
11/04/2008 09:46:33 AM from Karen: Mike Cherry is very adamant that the live file must never be commited with beta software.
11/04/2008 09:47:00 AM from Jen Deegan: surely he means the public file rather than the live file
11/04/2008 09:47:05 AM from midori: Agreed - we must not commit a file that was generated by an OE2 beta.
11/04/2008 09:47:11 AM from Jen Deegan: we have now gone to having a privated version in cvs
11/04/2008 09:47:25 AM from Karen: Yes, he does
11/04/2008 09:47:54 AM from midori: He means whatever file we commit. The editors' file is NOT hidden from the public. even though we recommend that people use other copies.
11/04/2008 09:48:03 AM from Karen: However, I'm not sure he'd be keen on your proposal to commite the editors file with beta software unless there is some absolute way to prevent it from transmitting to the public file
11/04/2008 09:48:20 AM from Jen Deegan: yes I suppose that's the hard part.
11/04/2008 09:48:23 AM from midori: The "public" files are all generated from the editors' file.
11/04/2008 09:48:50 AM from Harold: But how often are they generated per day?
11/04/2008 09:48:53 AM from Jen Deegan: it means we all have to load and save in 1.101 every time though and it would be much quicker if just the last person had to load save.
11/04/2008 09:48:59 AM from Jen Deegan: just once
11/04/2008 09:49:22 AM from midori: That said, when OE1.000, 1.100, and 1.101 were approaching release, we did use the load/save approach successfully.
11/04/2008 09:50:01 AM from Jen Deegan: I was thnking that once we are testing XPs the conversion to 1.101 is going to get even longer.
11/04/2008 09:50:03 AM from Karen: It doesn't seem trivial to make sure that you know who the last person will be, and I didn't think it was that much of a problem to just load and resave with the official version of OE
11/04/2008 09:50:26 AM from Jen Deegan: to be honest this doesn't affect me so much, as I mostly work on branch files.
11/04/2008 09:50:32 AM from Jen Deegan: it was for the others I was thinking.
11/04/2008 09:50:45 AM from Harold: It was mentioned before (forgot by whom) that the load/resave sometimes introduced errors also?
11/04/2008 09:50:48 AM from midori: Jen - every commit has to be a file generated by 1.101. No exceptions, for the reasons Karen states (and because we can't stop members of the public from getting the editors' file, tho that's more their problem ...).
11/04/2008 09:51:05 AM from Jen Deegan: okey dokay.
11/04/2008 09:51:10 AM from Jen Deegan: no problem, it was just a though.
11/04/2008 09:51:12 AM from Jen Deegan: t
11/04/2008 09:51:14 AM from Jen Deegan: :-)
11/04/2008 09:51:33 AM from midori: (Note - files in the go/scratch/ directory are exempt from my previous strong statement ;) )
11/04/2008 09:51:42 AM from Jen Deegan: Yay!
11/04/2008 09:51:51 AM from Jen Deegan: That's where I live so I am happy.
11/04/2008 09:52:10 AM from Jen Deegan: back to XPs then?
11/04/2008 09:52:39 AM from Amina Abdulla: Chris brought this up last time - he mentioned how a problem in OE2 is most likely present in OE1 as well
11/04/2008 09:53:05 AM from Jen Deegan: do you remember which? I don't remember the details.
11/04/2008 09:53:31 AM from Amina Abdulla: I don't think we had any specific comments on that
11/04/2008 09:53:46 AM from Jen Deegan: ah
11/04/2008 09:53:49 AM from Amina Abdulla: 10/28/2008 10:29:08 AM from Chris Mungall:
Karen, that's giving you a false sense of security anyway. It's hypothetically possible for a problem introduced in OE2 can be roundtripped via OE1
10/28/2008 10:29:30 AM from Chris Mungall:
The best thing is to be vigilant and check commits using cvs diff
11/04/2008 09:53:58 AM from Karen: He didn't give details on what the problems might be, but from prior experience, resaving in OE1 doesn't strip out extra tags from OE2
11/04/2008 09:54:27 AM from Jen Deegan: yes we need to do that with an extra step, and we will also need to do that with the intersection tags once we get to XPs
11/04/2008 09:55:01 AM from Karen: and doing a CVS diff when what you've done is add new terms doesn't highlight the 'bad' tags separately from the rest of the stuff for the new term
11/04/2008 09:55:38 AM from Jen Deegan: it shows what you've added to the file unintentionally as well as intentionally.
11/04/2008 09:56:18 AM from Karen: There was at one point a suggestion to have a script to remove these new OE2 tags, but I don't think anything has come of that
11/04/2008 09:57:02 AM from midori: I think Chris does have something of the sort, if I understood him correctly.
11/04/2008 09:57:05 AM from Jen Deegan: maybe once we have intersection tags as well it might make sense to have it automated. Currently it's just two search/replaces.
11/04/2008 09:57:23 AM from Jen Deegan: that might be handy to share it round.
11/04/2008 09:57:23 AM from Karen: I agree Jen, but was just commenting that doing a diff isn't necessarily going to help anyone remember to remove these extra tags from new terms.
11/04/2008 09:57:35 AM from Jen Deegan: why wouldn't it?
11/04/2008 09:57:46 AM from David OS: It would be useful to be able to remove created_by tags easily. The version of phenote we use on the Suns chokes on them.
11/04/2008 09:58:32 AM from Jen Deegan: I think it would make sense just to temporarily comment out the code in OE2 that adds them and save ourselves the trouble.:-)
11/04/2008 09:58:44 AM from Jen Deegan: but maybe that's cheating.
11/04/2008 09:58:45 AM from midori: If the diff shows you a whole stanza, you might not realize that some of the tags would cause problems (e.g. created_by)
11/04/2008 09:59:17 AM from Karen: yes, that's exactly what happened to me when I committed some OE2 tags into the file
11/04/2008 09:59:27 AM from Jen Deegan: most of us read all the lines, because the consequences of missing an error would be ghastly.
11/04/2008 09:59:57 AM from Jen Deegan: we used to have to check for missing namespaces by eye if you remember?
11/04/2008 10:00:05 AM from Karen: I did read the lines, but no one had said anything about OE2 adding new types of tags that need to be removed.
11/04/2008 10:00:07 AM from midori: reading them is one thing, spotting which ones will make things break is another ... the latter often learned only by grim experience :P
11/04/2008 10:00:14 AM from Nomi Harris: "It would be useful to be able to remove created_by tags easily.": cat file.obo | grep -v created_by > file-revised.obo
11/04/2008 10:00:17 AM from Jen Deegan: alas yes.
11/04/2008 10:00:28 AM from Karen: My main point is that the way the diff shows the whole stanza, it is actually quite easy to miss these new tags
11/04/2008 10:00:42 AM from Jen Deegan: Nomi's thing is good.
11/04/2008 10:00:47 AM from Jen Deegan: we could set and alias to run that
11/04/2008 10:00:54 AM from Jen Deegan: would save time.
11/04/2008 10:01:07 AM from David OS: Already using grep -v to strip them out...
11/04/2008 10:01:11 AM from midori: you'd also want a step for grep -v creation_date
11/04/2008 10:01:21 AM from Jen Deegan: and later one for intersection.
11/04/2008 10:01:34 AM from Jen Deegan: three aliases would be nice and easy though wouldn't they?
11/04/2008 10:01:34 AM from midori: all that can be put in the regex
11/04/2008 10:01:39 AM from Jen Deegan: great
11/04/2008 10:01:53 AM from David OS: Stripping out intersections sounds dangerous.
11/04/2008 10:01:56 AM from Jen Deegan: shoudl we document this on the wiki then for those who want to test but aren't in this group?
11/04/2008 10:02:21 AM from Karen: sounds like a good idea Jen, to put this on the wiki
11/04/2008 10:03:01 AM from Jen Deegan: I feel that I may be volunteering for that task.
11/04/2008 10:03:25 AM from midori: David - GO will have to be able to provide a file without intersection tags, for legacy users. How to do that without losing or duplicating info is one of the things that's making my head spin (I think Chris has a grip on it).
11/04/2008 10:03:28 AM from Jen Deegan: I have added it to my to do list.
11/04/2008 10:03:34 AM from Amina Abdulla: Thanks Jen
11/04/2008 10:03:38 AM from Jen Deegan: :-)
11/04/2008 10:03:45 AM from Jen Deegan: I agree Midori.
11/04/2008 10:04:08 AM from Jen Deegan: I would like to start getting a grip on the XP workflow very soon, if we are to release in say the next 3 months.
11/04/2008 10:04:22 AM from midori: me too
11/04/2008 10:04:47 AM from Amina Abdulla: Yes - we need to start a OE2 release wiki asap
11/04/2008 10:04:52 AM from Jen Deegan: This is a discussion that just needs Chris added isn't it?
11/04/2008 10:05:09 AM from David OS: Midori: I make all the links hard but leave the intersections in. I guess it wouldn't hurt to strip them out though as they are redundant once links are made hard.
11/04/2008 10:05:16 AM from Amina Abdulla: Jen yes - I will be on the managers call tomorrow with Chris and Suzi
11/04/2008 10:05:29 AM from Jen Deegan: Brilliant! How efficient you are.
11/04/2008 10:05:30 AM from Amina Abdulla: we can discuss this in the OE section
11/04/2008 10:05:37 AM from Jen Deegan: great
11/04/2008 10:05:44 AM from Jen Deegan: We'd better get our questions ready.
11/04/2008 10:06:04 AM from Amina Abdulla: I discussed the post release expectations with Chris briefly
11/04/2008 10:06:11 AM from Jen Deegan: good
11/04/2008 10:06:17 AM from Jen Deegan: any hints?
11/04/2008 10:06:51 AM from Amina Abdulla: Well - there are a lot of components besides the xps that need work
11/04/2008 10:07:02 AM from Jen Deegan: true
11/04/2008 10:07:06 AM from Amina Abdulla: We didn't talk much about the editors perspective on this
11/04/2008 10:07:28 AM from Jen Deegan: If we are just keeping the XP tab that was in 1.101 then at least it should be pretty well tested.
11/04/2008 10:08:01 AM from Amina Abdulla: So Harold had a suggestion yesterday - about changing the Dbxref tab in the Text Editor to Xrefs or Mappings
11/04/2008 10:08:06 AM from Amina Abdulla: https://sourceforge.net/tracker/index.php?func=detail&aid=2219331&group_id=36855&atid=418257
11/04/2008 10:08:06 AM from David OS: I haven't played with the other XP editing components at all. Getting by fine without them for now.
11/04/2008 10:08:34 AM from Jen Deegan: They're all going to be out for the release as I understand it so we can wait to learn those for the next version of OE.
11/04/2008 10:08:44 AM from Jen Deegan: I don't have any preference of the name of the field.
11/04/2008 10:09:04 AM from midori: I didn't have strong feelings about Harold's suggestion either.
11/04/2008 10:09:08 AM from Jen Deegan: Mappings presumeably is the general dbxref field.
11/04/2008 10:09:46 AM from midori: yup
11/04/2008 10:10:26 AM from Amina Abdulla: Ok
11/04/2008 10:10:33 AM from midori: I guess I'd steer clear of "mappings" because the word is also used for the external2go file contents, but "xrefs" or keeping "dbxrefs" would be fine.
11/04/2008 10:11:03 AM from midori: but I'm not gonna howl and gnash my teeth no matter what it's called.
11/04/2008 10:11:25 AM from Amina Abdulla: Ok
11/04/2008 10:11:44 AM from Jen Deegan: what it's trying to say is that one lot are links to exactly analogous things and the other lot are just links to def sources.
11/04/2008 10:12:09 AM from Jen Deegan: it's hard to think of how to make that very clear with variations on xref
11/04/2008 10:12:29 AM from Jen Deegan: maybe exact xref and definition sources?
11/04/2008 10:12:34 AM from Jen Deegan: or something?
11/04/2008 10:13:04 AM from midori: well, in the OE display they're in different places, which helps a lot (I think)
11/04/2008 10:13:11 AM from Jen Deegan: true ;_0
11/04/2008 10:13:13 AM from Jen Deegan: oops
11/04/2008 10:13:24 AM from midori: and the def sources aren't called xrefs or dbxrefs in the .obo file
11/04/2008 10:13:29 AM from Jen Deegan: no
11/04/2008 10:13:41 AM from midori: nor are synonym xrefs ...
11/04/2008 10:14:18 AM from Jen Deegan: if we wanted to be user friendly they could be call analogous categories and definition sources maybe. The question is, do we?
11/04/2008 10:14:35 AM from Jen Deegan: I don't mind at all either way.
11/04/2008 10:15:22 AM from midori: sounds wordy ... and this is the OE interface, not a browser ...
11/04/2008 10:15:26 AM from Jen Deegan: true
11/04/2008 10:15:47 AM from Jen Deegan: don't want the general dbxref tab getting too huge.
11/04/2008 10:16:09 AM from Jen Deegan: Shall we think about it until next week?
11/04/2008 10:16:13 AM from Amina Abdulla: Well should we wait for a concensus on this topic?
11/04/2008 10:16:30 AM from Jen Deegan: yes maybe we'll get an inspiration.
11/04/2008 10:16:38 AM from Jen Deegan: no sense rushing at it.
11/04/2008 10:16:39 AM from midori: I suspect not many people care deeply, but ok.
11/04/2008 10:16:43 AM from Jen Deegan: :-)
11/04/2008 10:16:51 AM from Amina Abdulla: Sounds good Jen- Harold left the meeting early today
11/04/2008 10:17:01 AM from Jen Deegan: anything else to discuss?
11/04/2008 10:17:01 AM from midori: ... Or just change the tab to "xrefs" 'cos that would match the OBO format tag.
11/04/2008 10:17:17 AM from midori: (can you tell I'm one of the ones who doesn't care deeply?)
11/04/2008 10:17:21 AM from Jen Deegan: I think it would be nice to have it more intuitive for new users.
11/04/2008 10:17:30 AM from Amina Abdulla: That sounds reasonable
11/04/2008 10:17:36 AM from Jen Deegan: but I wouldn't get worked up if other disagreed
11/04/2008 10:17:50 AM from midori: One small thing: does someone have the transcripts from the last two meetings?
11/04/2008 10:17:57 AM from Amina Abdulla: I do
11/04/2008 10:18:12 AM from David OS: Would like to see last week's transcript
11/04/2008 10:18:17 AM from Amina Abdulla: the transcripts should be posted to the WG
11/04/2008 10:18:37 AM from midori: If Amina sends them to the wg list I'll put them on the transcript wiki.
11/04/2008 10:18:38 AM from Jen Deegan: shall we send them again if they have missed people?
11/04/2008 10:18:44 AM from Jen Deegan: good idea
11/04/2008 10:18:48 AM from Amina Abdulla: Ok I'll do that
11/04/2008 10:18:48 AM from midori: (I haven't seen them on the list yet)
11/04/2008 10:18:59 AM from Amina Abdulla: I'll send them out again
11/04/2008 10:19:14 AM from Amina Abdulla: Any more items for today?
11/04/2008 10:19:16 AM from midori: thanks
11/04/2008 10:19:34 AM from midori: nothing from me ...
11/04/2008 10:19:39 AM from Jen Deegan: nope me neither.
11/04/2008 10:19:50 AM from David OS: nope
11/04/2008 10:20:19 AM from Jen Deegan: Shall we off then?
11/04/2008 10:20:23 AM from Amina Abdulla: Alright folks - thanks for coming
11/04/2008 10:20:29 AM from Jen Deegan: that was a great meeting Amina, thanks for that.
11/04/2008 10:20:38 AM from Jen Deegan: cheerio then.
11/04/2008 10:20:45 AM from Jen Deegan: see you tomorrow on the call.
11/04/2008 10:20:50 AM from David OS: Bye!
11/04/2008 10:20:53 AM from midori: bye
11/04/2008 10:20:54 AM from Amina Abdulla: Bye everyone
11/04/2008 10:20:55 AM from Karen: bye
11/04/2008 10:20:58 AM from Nomi Harris: Bye