09/23/2008 09:29:41 AM from Nomi Harris to All Participants: Hi
09/23/2008 09:29:48 AM from Jen Deegan to All Participants: Hi
09/23/2008 09:34:16 AM from Amina to All Participants: alright
- I'm done wrestling with webex - this is Amina - Chris is away
09/23/2008 09:34:56 AM from Nomi Harris to All Participants:
So, Amina, I saw you committed a bunch of new icons.
09/23/2008 09:35:01 AM from Amina to All Participants: So I
can't have two instances of webex running
09/23/2008 09:35:19 AM from Amina to All Participants: and
since Chris is the host - I need to be logged in
09/23/2008 09:35:52 AM from Amina to All Participants: away -
Amina: Yeah I'm waiting to get some more from Amelia
09/23/2008 09:35:54 AM from Jen Deegan to All Participants: In
the EBI we solved the name problem by changing it to 'EBI Host'
09/23/2008 09:36:35 AM from midori to All Participants: I
didn't think there was a name problem, actually ... everyone I've met
with has had no trouble grokking the explanation.
09/23/2008 09:36:39 AM from Amina to All Participants: Amina:
Jen I was told your the go to person for a webex account
09/23/2008 09:37:13 AM from Jen Deegan to All Participants:
Yes, but we just get one for the site, so you share Chris's.
09/23/2008 09:37:30 AM from Amina to All Participants: I
tried changing host name for this meeting
09/23/2008 09:37:51 AM from Jen Deegan to All Participants: I
think it has to be done in preferences or something
09/23/2008 09:37:56 AM from Jen Deegan to All Participants:
what did Nomi do?
09/23/2008 09:38:09 AM from midori to All Participants: When I
put the transcript on the wiki, I'll change Chris to Amina in the tags.
09/23/2008 09:38:10 AM from Amina to All Participants: she
used john's account
09/23/2008 09:38:16 AM from Jen Deegan to All Participants: oh
09/23/2008 09:38:19 AM from Jen Deegan to All Participants:
can you do that?
09/23/2008 09:38:31 AM from Amina to All Participants: but
scheduled the meeting as Nomi
09/23/2008 09:38:58 AM from Nomi Harris to All Participants: I
was out yesterday and Amina didn't know John's password.
09/23/2008 09:39:00 AM from Amina to All Participants: Chris
realized he couldn't be here after the meeting was setup
09/23/2008 09:39:04 AM from Jen Deegan to All Participants: ah!
09/23/2008 09:39:05 AM from Jen Deegan to All Participants: I see
09/23/2008 09:39:11 AM from Jen Deegan to All Participants: I
had forgotten that John had one
09/23/2008 09:39:28 AM from Jen Deegan to All Participants: We
should just have one for your whole group as we pay extra for licences.
09/23/2008 09:39:30 AM from Amina to All Participants: Thanks
midori
09/23/2008 09:40:01 AM from midori to All Participants: John
had his own because he wasn't on site; I guess we could change that now.
09/23/2008 09:40:13 AM from Jen Deegan to All Participants:
yes, I was just thinking that.
09/23/2008 09:40:18 AM from Amina to All Participants: yeah
thats a good solution Jen
09/23/2008 09:40:35 AM from Jen Deegan to All Participants:
Would it be a problem for you all just to share Chris's?
09/23/2008 09:40:36 AM from midori to All Participants:
(Totally off-topic: who's got the 5th account?)
09/23/2008 09:40:56 AM from Amina to All Participants: What
about John's account then
09/23/2008 09:41:11 AM from Amina to All Participants: can you
change the name on that one
09/23/2008 09:41:20 AM from Jen Deegan to All Participants:
Actually I think we already have the minimum number of licences so we
don't need to worry.
09/23/2008 09:41:28 AM from Jen Deegan to All Participants:
yes you could could change the username
09/23/2008 09:41:31 AM from Jen Deegan to All Participants:
it's very easy
09/23/2008 09:41:47 AM from Amina to All Participants: I tried
doing that
09/23/2008 09:41:50 AM from midori to All Participants: If we
do need to review who's got accounts, let's do it another time, not in
OEWG meeting.
09/23/2008 09:41:57 AM from Jen Deegan to All Participants: If
you have two licences at your site now it might be good to pass one on
to antoher GO site.
09/23/2008 09:42:05 AM from Jen Deegan to All Participants:
yes we should.
09/23/2008 09:42:11 AM from Jen Deegan to All Participants:
what's next then
09/23/2008 09:42:16 AM from Amina to All Participants: Right -
lets start
09/23/2008 09:42:32 AM from Nomi Harris to All Participants:
So, what did you change in the relationship icons?
09/23/2008 09:43:20 AM from Amina to All Participants: I put
in new icons for is_a and part_of - keeping it consistent with amigo
09/23/2008 09:44:25 AM from Amina to All Participants: also
for new relationships default icon (work in progress) will display the
relationship seperating words by newline instead of _
09/23/2008 09:44:48 AM from Nomi Harris to All Participants:
That should be more readable.
09/23/2008 09:44:49 AM from Amina to All Participants:
vertically instead of horizontally
09/23/2008 09:45:07 AM from Tanya to All Participants:
effectively a space?
09/23/2008 09:45:29 AM from Amina to All Participants: right -
a space in the OTE
09/23/2008 09:45:38 AM from Amina to All Participants: newline
in the Graph Editor
09/23/2008 09:45:47 AM from Tanya to All Participants: got it
09/23/2008 09:46:15 AM from Amina to All Participants: Tanya I
have a workaround for your truncated terms problem
09/23/2008 09:46:25 AM from Tanya to All Participants: cool
09/23/2008 09:46:30 AM from Amina to All Participants: I'll
put up a fix soon
09/23/2008 09:46:32 AM from Tanya to All Participants: was I
misinterpreting your instructions?
09/23/2008 09:47:11 AM from Nomi Harris to All Participants:
It wasn't fixable?
09/23/2008 09:47:16 AM from Amina to All Participants: In the
meantime - if you turn on the semantic parser first and then save
changes (a couple of times) you should get term names back
09/23/2008 09:47:19 AM from midori to All Participants: the
instructions in question came from the real Chris, not the
Amina-playing-Chris-on-webex that we have here
09/23/2008 09:47:34 AM from Tanya to All Participants: OH! Right.
09/23/2008 09:47:45 AM from Amina to All Participants: no you
didn't misinterpret instruction tanya - theres a refresh issue in the OTE
09/23/2008 09:48:06 AM from Tanya to All Participants: Thanks,
Amina.
09/23/2008 09:48:39 AM from Amina to All Participants: I have
a tiny hack for it which doesn't truncate terms - but thats not a fix
and I didn't want to put in patch code
09/23/2008 09:49:08 AM from Amina to All Participants: I'll
post a fix this week
09/23/2008 09:49:42 AM from Amina to All Participants: This is
related to Midori's - OTE redraw oddity bug
09/23/2008 09:49:54 AM from midori to All Participants:
thought it might be, from the symptoms
09/23/2008 09:50:52 AM from Amina to All Participants: So, I
was wondering if anyone else is having problems with autocommit
09/23/2008 09:51:14 AM from midori to All Participants: I
haven't used it much lately, so can't comment cluefully
09/23/2008 09:51:21 AM from Jen Deegan to All Participants: Me
neither
09/23/2008 09:51:32 AM from Jen Deegan to All Participants:
which problem?
09/23/2008 09:51:38 AM from Amina to All Participants: I
couldn't replicate David's bug and it seems like a seious issue
09/23/2008 09:51:55 AM from Karen C to All Participants: I
don't remember what David's bug was
09/23/2008 09:51:58 AM from Nomi Harris to All Participants: I
think I once had a problem with autocommit that was fixed by removing my
config
09/23/2008 09:52:46 AM from midori to All Participants:
Melissa was having some trouble with autocommit a while back; don't
know if she still is.
09/23/2008 09:52:48 AM from Amina to All Participants:
https://sourceforge.net/tracker/index.php?func=detail&aid=2116690&group_id=36855&atid=418257
09/23/2008 09:53:32 AM from Karen C to All Participants: Also,
I don't know if this is something to be concerned about, but yesterday I
accidentally edited the text, and then couldn't undo it. I was forced to
click on another term to let it autocommit, and then manually fixed it.
09/23/2008 09:53:41 AM from Amina to All Participants: I also
don't see:
https://sourceforge.net/tracker/index.php?func=detail&aid=2116702&group_id=36855&atid=418257
09/23/2008 09:53:52 AM from Amina to All Participants: which
is a linux bug
09/23/2008 09:54:07 AM from Nomi Harris to All Participants:
The problem I had that was fixed by removing config was "nag on
autocommit":
http://sourceforge.net/tracker/index.php?func=detail&aid=1881448&group_id=36855&atid=418257
09/23/2008 09:54:15 AM from Amina to All Participants: Ah - I
know why it did that Karen
09/23/2008 09:54:22 AM from Amina to All Participants: Does
that happen a lot?
09/23/2008 09:54:50 AM from midori to All Participants:
accidental text edits are the main reason I do manual commit ...
09/23/2008 09:54:54 AM from Karen C to All Participants: I've
been using OE2 mostly as a browser, not as an editor, lately, so this is
the first time I've seen this.
09/23/2008 09:56:24 AM from Amina to All Participants: ic - I
noticed autocommit slows things down
09/23/2008 09:57:25 AM from Amina to All Participants: Any
more pressing issues
09/23/2008 09:57:49 AM from Amina to All Participants: I'll
look into reproducing the autocommit bug
09/23/2008 09:58:43 AM from Amina to All Participants: We're
less than a month away from the montreal meeting and uber OE 2 beta
09/23/2008 09:58:47 AM from Karen C to All Participants:
Amina, you said you knew why it didn't let me undo my change. Is the
explanation quick enough for this meeting?
09/23/2008 09:59:55 AM from Amina to All Participants: Yeah
since your auto commiting - I think it saves it in realtime and thats
why you had to come back and edit
09/23/2008 10:00:02 AM from Amina to All Participants: I've
seen that before
09/23/2008 10:00:12 AM from Amina to All Participants: Nomi:
is that right?
09/23/2008 10:00:23 AM from Nomi Harris to All Participants: Huh?
09/23/2008 10:00:48 AM from Amina to All Participants: The
explanation for why Karen couldn't edit
09/23/2008 10:01:12 AM from Nomi Harris to All Participants: I
didn't understand the explanation.
09/23/2008 10:01:24 AM from Nomi Harris to All Participants:
Autocommit checks every 0.5 seconds (I think) to see if anything needs
to be committed.
09/23/2008 10:01:34 AM from Nomi Harris to All Participants:
Undo should work.
09/23/2008 10:01:51 AM from Jen Deegan to All Participants: I
thought it just committed when you selected another term. Every half
second sounds better.
09/23/2008 10:02:00 AM from Jen Deegan to All Participants:
That's good to know.
09/23/2008 10:02:05 AM from Nomi Harris to All Participants: I
think that's what it's supposed to do. It could be buggy.
09/23/2008 10:02:05 AM from Amina to All Participants: you've
worked with it more than I have - I've noticed weird behavior though
09/23/2008 10:02:11 AM from Karen C to All Participants: Hmm,
I guess what annoyed me was that I saw what I did before I clicked on
another term and went up to the Edit menu and the 'Undo' option was
grayed out.
09/23/2008 10:02:17 AM from Nomi Harris to All Participants:
You can also force autocommit--I think it was maybe option-return or
something?
09/23/2008 10:02:31 AM from midori to All Participants:
command-return in OE2
09/23/2008 10:02:42 AM from midori to All Participants: works
with autocommit on or off
09/23/2008 10:03:26 AM from Nomi Harris to All Participants:
Karen, maybe you were so quick it hadn't autocommitted yet?
09/23/2008 10:04:57 AM from Karen C to All Participants: hmmm,
not really sure, I'll try to pay more attention to exactly what I did if
it happens again.
09/23/2008 10:05:42 AM from Nomi Harris to All Participants:
Sometimes commit issues seem to be fixed by removing your config
(specifically, edit.idw). I have no idea why that should make a
difference.
09/23/2008 10:07:02 AM from Jen Deegan to All Participants:
Maybe we could do a diff on the file before and after corruption. I
know it's not human readable though, so maybe that wouldn't help so much.
09/23/2008 10:07:21 AM from Karen C to All Participants: OK,
I'll remove that. Also, which file should I remove for my odd behavior
with adding words to the dictionary not turning black immediately?
09/23/2008 10:07:23 AM from Nomi Harris to All Participants:
Right. I tried that. It's different, but I can't tell how.
09/23/2008 10:07:42 AM from Nomi Harris to All Participants: I
don't know, you could try moving your whole config directory out of the
way and seeing if that fixes it.
09/23/2008 10:08:52 AM from Karen C to All Participants: Yea,
I was just hoping not to have to redo all the other settings that are
still fine.
09/23/2008 10:09:10 AM from Nomi Harris to All Participants: I
hear you! That's why I said "move" rather than "remove".
09/23/2008 10:09:18 AM from Nomi Harris to All Participants:
Then you could try putting back bits of it and seeing if that works.
09/23/2008 10:09:26 AM from Nomi Harris to All Participants:
Sorry I can't be more specific.
09/23/2008 10:09:54 AM from Jen Deegan to All Participants:
Could I ask a question about verification checks?
09/23/2008 10:09:55 AM from Karen C to All Participants:
Thanks, I'll try to take the time to fiddle with my config settings to
see if the odd stuff I see goes away.
09/23/2008 10:10:20 AM from Amina to All Participants: Midori:
https://sourceforge.net/tracker/index.php?func=detail&aid=1863271&group_id=36855&atid=418257
09/23/2008 10:10:27 AM from Amina to All Participants: is this
urgent?
09/23/2008 10:11:09 AM from Amina to All Participants: Jen: go
ahead
09/23/2008 10:11:30 AM from midori to All Participants: Not
for editing, since there are other ways to do merges. I'd like to know
what to put in the user guide, though -- it wouldn't be nice to documena
feature that's actually broken.
09/23/2008 10:11:37 AM from Jen Deegan to All Participants: I
have my lists of repeatable words and words that can start lowercase and
those that can contain full stops, but I'm not sure where to put them.
09/23/2008 10:12:19 AM from Jen Deegan to All Participants: I
found the plain dictionary.dict file but there weren't files for the
other ones.
09/23/2008 10:12:29 AM from Nomi Harris to All Participants:
I'll look into that and let you know, Jen.
09/23/2008 10:12:35 AM from Amina to All Participants: midori:
I'll look into it and post a follow-up comment
09/23/2008 10:12:36 AM from Jen Deegan to All Participants:
Thanks, that would be great.
09/23/2008 10:13:23 AM from midori to All Participants: ok. I
don't mind if it ends up that we can't have a merge hotkey, as long as
the documentation is accurate.
09/23/2008 10:13:47 AM from Nomi Harris to All Participants:
If it's not high-priority, we should probably just take the hotkey
description out of the manual
09/23/2008 10:13:56 AM from Nomi Harris to All Participants:
and keep the bug report but bump the priority down.
09/23/2008 10:14:02 AM from Nomi Harris to All Participants:
There are other bugs that seem more important to fix.
09/23/2008 10:14:03 AM from Amina to All Participants: Right
now there are only a handful of priority > 5 bugs
09/23/2008 10:14:20 AM from midori to All Participants: fine
by me; I can update the docs
09/23/2008 10:14:27 AM from Amina to All Participants: yeah
the hotkey is priority 6
09/23/2008 10:14:32 AM from Jen Deegan to All Participants: I
will go back and check my items soon, I have got a bit snowed under
since my holiday.
09/23/2008 10:14:37 AM from Nomi Harris to All Participants:
Have the memory/speed issues been better?
09/23/2008 10:14:39 AM from Amina to All Participants: There
are some imp features to work on though
09/23/2008 10:15:02 AM from midori to All Participants: I'll
probably close the CPU spike bug at the end of the week.
09/23/2008 10:15:08 AM from Jen Deegan to All Participants:
speed is much better.
09/23/2008 10:15:10 AM from Nomi Harris to All Participants: Yay!
09/23/2008 10:15:41 AM from Jen Deegan to All Participants:
the bug that makes the menu appear when I click on the OTE terms is
still weird, but I know that is a very difficult one.
09/23/2008 10:16:07 AM from midori to All Participants: I've
actually been able to use b49 for editing ... couldn't really say that
for previous betas.
09/23/2008 10:16:19 AM from midori to All Participants: What
it needs now:
09/23/2008 10:16:23 AM from Jen Deegan to All Participants:
yes it's sooo much better.
09/23/2008 10:16:31 AM from midori to All Participants: - fix
the bugs other people have been reporting
09/23/2008 10:17:05 AM from midori to All Participants: -
polishing, because there are small non-smooth (and unfortunately
hard-to-describe) things that make it still feel "beta"
09/23/2008 10:17:14 AM from midori to All Participants: -
TESTING!
09/23/2008 10:17:49 AM from Jen Deegan to All Participants: I
have a heap of bugs to submit from our meeting with Chris.
09/23/2008 10:17:58 AM from Jen Deegan to All Participants: -
also documenting.
09/23/2008 10:18:02 AM from Amina to All Participants: Yeah -
the intermittent bugs users report are helpful - those are loop holes
you wouldn't necessarily notice
09/23/2008 10:18:40 AM from Amina to All Participants: Chris
was telling me about the discussion you all had about a "Save links
only" feature
09/23/2008 10:18:55 AM from Amina to All Participants: I think
that would be a neat feature
09/23/2008 10:19:54 AM from Amina to All Participants: A new
logo for OE2 would be cool too
09/23/2008 10:19:55 AM from midori to All Participants: Jen -
did you want to bring up the idea for the feature tracker?
09/23/2008 10:20:01 AM from Jen Deegan to All Participants: Oh
yes!
09/23/2008 10:20:11 AM from Jen Deegan to All Participants: I
had that in mind literally 2 minutes ago.
09/23/2008 10:20:28 AM from Jen Deegan to All Participants: I
wondered if you would mind if I added an OBO-Edit 3 menu item on the
feature request tracker?
09/23/2008 10:20:42 AM from midori to All Participants: I'm
surprised that I remembered it before, rather than immediately after,
the meeting ended :P
09/23/2008 10:20:43 AM from Jen Deegan to All Participants: so
if I have a feature request that I would like added for OBO-Edit3 then I
can specify that.
09/23/2008 10:20:49 AM from Jen Deegan to All Participants: :-)
09/23/2008 10:21:04 AM from Amina to All Participants: sounds
good to me
09/23/2008 10:21:06 AM from Nomi Harris to All Participants:
Sounds like a good idea.
09/23/2008 10:21:07 AM from midori to All Participants: the
idea is to make it clear when we're not expecting a feature to be ready
in OE2
09/23/2008 10:21:07 AM from Jen Deegan to All Participants: great
09/23/2008 10:21:14 AM from Jen Deegan to All Participants:
yes exactly.
09/23/2008 10:21:21 AM from midori to All Participants:
category or group?
09/23/2008 10:21:38 AM from Nomi Harris to All Participants:
Group
09/23/2008 10:21:52 AM from Jen Deegan to All Participants:
yes Group, I thought.
09/23/2008 10:21:54 AM from Amina to All Participants: I was
thinking category
09/23/2008 10:21:57 AM from Jen Deegan to All Participants: oh
:-)
09/23/2008 10:22:01 AM from Nomi Harris to All Participants:
Category is still OBO-Edit.
09/23/2008 10:22:10 AM from Amina to All Participants: oh Right
09/23/2008 10:22:17 AM from midori to All Participants: you
guys arm-wrestle among yourselves ...
09/23/2008 10:22:49 AM from Jen Deegan to All Participants:
Shall I do it? I think I got admin rights when I started being a
developer but I've never done any of that stuff.
09/23/2008 10:22:56 AM from Nomi Harris to All Participants: Sure
09/23/2008 10:22:57 AM from Amina to All Participants: just
checked - group
09/23/2008 10:23:02 AM from Jen Deegan to All Participants:
great, will do.
09/23/2008 10:24:03 AM from Nomi Harris to All Participants:
Jen, are you sure OE2 can use a list of allowed repeated words?
09/23/2008 10:24:21 AM from Tanya to All Participants: Midori
and/or Jen- when you edit in OE2 are there any special steps beyond
opening the saved file in OE1 again then committing that version to cvs
that need to be done for the live gene_ontology_write.obo?
09/23/2008 10:24:27 AM from Jen Deegan to All Participants:
yes the verification checker produces one and puts it in the config
directory.
09/23/2008 10:24:33 AM from Nomi Harris to All Participants:
Ah. Ok.
09/23/2008 10:24:52 AM from Jen Deegan to All Participants:
yes we have to remove the creation date and created by tags.
09/23/2008 10:25:22 AM from Jen Deegan to All Participants:
it's not clear whether we want to switch to having those tags after
release.
09/23/2008 10:25:25 AM from Tanya to All Participants: By script?
09/23/2008 10:25:29 AM from Tanya to All Participants: Or
manually?
09/23/2008 10:25:34 AM from Jen Deegan to All Participants: I
just do a search and replace.
09/23/2008 10:25:35 AM from midori to All Participants: I also
delete the duplicate transitive_over tags from the regulates
relationships, but that's not actually necessary.
09/23/2008 10:25:46 AM from Jen Deegan to All Participants: Gosh!
09/23/2008 10:25:46 AM from midori to All Participants: emacs
macro
09/23/2008 10:26:06 AM from midori to All Participants:
(there's a very-low-priority bug report on it)
09/23/2008 10:26:25 AM from Jen Deegan to All Participants: If
they're not wanted after release it wouldn't be too hard to stop
OBO-Edit producing them though would it?
09/23/2008 10:26:38 AM from midori to All Participants: I
think we will keep them after release.
09/23/2008 10:26:44 AM from Jen Deegan to All Participants:
oh, that's easy then
09/23/2008 10:27:17 AM from Jen Deegan to All Participants:
There was some plan to retrofit them to old terms by mining cvs but I'm
not sure that will happen will it?
09/23/2008 10:27:20 AM from Tanya to All Participants: thanks
09/23/2008 10:27:49 AM from Jen Deegan to All Participants:
that may be one for the ontology-developer list though.
09/23/2008 10:27:52 AM from midori to All Participants: sounds
low priority, but probably not ruled out
09/23/2008 10:28:16 AM from Jen Deegan to All Participants:
Are we about done?
09/23/2008 10:28:46 AM from Tanya to All Participants: stick a
fork in us
09/23/2008 10:28:53 AM from Jen Deegan to All Participants: :-)
09/23/2008 10:30:13 AM from Tanya to All Participants: bye then!
09/23/2008 10:30:20 AM from Jen Deegan to All Participants: Bye!
09/23/2008 10:30:22 AM from Amina to All Participants: Alright
- bye everyone
09/23/2008 10:30:29 AM from Nomi Harris to All Participants: Bye!
09/23/2008 10:30:30 AM from Karen C to All Participants: bye
09/23/2008 10:30:33 AM from Jen Deegan to All Participants:
Good meeting, Amina!
09/23/2008 10:30:36 AM from midori to All Participants: bye
09/23/2008 10:30:37 AM from Jen Deegan to All Participants:
cheerio.