OE IRC 5Oct06: Difference between revisions
Jump to navigation
Jump to search
(New page: <pre> area51.slashnet.org has activated the following mode : No External Message area51.slashnet.org has activated the following mode : Only Operator Change Topic 5:25 PM kchris has joi...) |
No edit summary |
||
Line 1: | Line 1: | ||
[[Category:OBO-Edit working group]] | |||
<pre> | <pre> | ||
area51.slashnet.org has activated the following mode : No External Message | area51.slashnet.org has activated the following mode : No External Message |
Latest revision as of 18:07, 30 June 2014
area51.slashnet.org has activated the following mode : No External Message area51.slashnet.org has activated the following mode : Only Operator Change Topic 5:25 PM kchris has joined the channel 5:30 PM jclark has joined the channel j-lo has joined the channel j-lo: hello jrichter has joined the channel jrichter: Hey, folks. tberardi has joined the channel kchris: Hello tberardi: Hi, sorry I'm late. jclark: hello jclark: Midori said to tell you that she's going to be a bit late but is leaving her chat window open to get the transcript. jrichter: Okay. jclark: shall we start? jrichter: Sure. Are you in charge, Jen? jclark: sort of jclark: I don't have the agenda though jrichter: Ahh... then I'll do my items first, and then Midori can add on any when she arrives. jclark: good-oh 5:35 PM jrichter: Item 1: John's status report: jrichter: a) The paper jrichter: It looks like we've finally got it ready to go. Once I integrate Jane's edit, it's ready to submit. Unless there are objections from those assembled, I'm going to submit it today. Is that okay? kchris: good with me jclark: yes jrichter: b) OBO-Edit Documentation jrichter: It turns out that the new features in OBO-Edit require a LOT of new documentation. I'm going to have to rewrite the entire "Customizing OBO-Edit Section", and the documentation will require extensive proofreading and testing to make sure its comprehensible. I'm thinking I've got at least 2 weeks of work here. jclark: That was my section wasn't it? jclark: I'll take a look jrichter: Excellent! jrichter: I'd like people to send me their favorite OBO-Edit layout. It would be nice to have a bunch of example layouts for users to try. jclark: is the plan that you write it and I read it and see if I can make all the stuff work? tberardi: I like and use Jen's layout. jrichter: That's right, Jen. jclark: I'll make an improved one with the new gadgetry jrichter: Excellent! I think you'll be impressed. jclark: I checked and I am already jrichter: Since we have 2 weeks, does anyone have a tutorial they'd like to add to the documentation (maybe based on an email you wrote or something)... jrichter: ? 5:40 PM kchris: I still use the default, but would really be happier if I found the instructions Midori gave me for using a layout that allowed resizing the query results window hjd has joined the channel tberardi: Is there something in the documentation now about finding is_a orphans? tberardi: If not, that would be handy. kchris: For tutorials, we did talk about the idea of providing instructions for doing a query where you limit to one ontology, e.g. only function, I still can't remember how to write that query jrichter: Hmm... maybe a better way to do this is to solicit the working group list for "Frequently Asked Questions" like "How do you limit a search to a single ontology" jrichter: People on the list can compose answers, and I'll pick up the slack on any remaining unanswered questions. jrichter: Does that sound good? j-lo: yep jrichter: Moving on to c) OBO-Edit 1.1 Last Minute Features jrichter: As I was writing some documentation for the layout customization section, I was stunned by how hard it was to use the layout editor. It's highly intolerant of errors, and it's impossible to tell where your mistake is if there's a problem with the layout.. jrichter: The worst part is, all that error information exists, it's just not being displayed. jclark: funky 5:45 PM midori: Hi guys ... finally here for real. jclark: how's the cat? midori: do you really wanna know? :P jrichter: I'd like permission to update that part of the Configuration Plugin to display line numbers in the layout editor, and I'd like to add a panel that will show you any errors (with the associate line number) if you try to enter a bad layout. jclark: yes jclark: good idea midori: permission? nay, I grant encouragement! jrichter: (BTW: I've already dropped in a new editor component that does syntax highlighting and automatic tabbing) jrichter: Cool! jrichter: Two more things on my agenda: jrichter: 2) The install4j installers: jrichter: I know the popup messages are annoying, but did the new installer system work well for everyone? midori: I haven't tested it yet ... kchris: nor I hjd: I had no problem with beta 5 install jclark: it works for windows jrichter: And no memory problems? midori: the platform-independent beta5 opens & loads GO nicely ... hjd: I've loaded up to 5 ontologies simulataineously, and it seems to work ok jclark: oh, actually now you mention it I used the platform independent version hjd: I'm using the mac installer version jrichter: It sounds like Harold's the only one who uses the installers. Please give the installers a try on your platform; I think the problems have been solved. If everything works well, I can get money to buy the program. 5:50 PM jclark: okay midori: downloading now ... jrichter: The main problem to look for would be OutOfMemory issues. jrichter: Last thing from me... 3) Webex status report? jclark: we tried it on monday jrichter: How's that going, Jen/Tanya? jclark: it worked for me but not for jane or david jclark: nto sure why tberardi: We did three locations on Friday. tberardi: Denver, Hinxton and Palo Alto. tberardi: Prices: tberardi: $38.50/month tberardi: Voice options tberardi: VoIP: 2 cents/min/person jrichter: ! tberardi: 800 number: 20 cents/min/person hjd: I've had a Webex with one person down in Boston (boston - bar harbor); Didn't know it does voice; does it do video too? tberardi: 650 number (local for Palo ALto): 5 cents/min/person tberardi: Yes, it does video with max 5 locations. tberardi: the voice component is extra. tberardi: VoIP is cheap but only 2 people max can talk at one time. tberardi: Others have to wait for the host to pass the 'mike' tberardi: the phone numbers let everyone talk at once tberardi: but are more expensive tberardi: For VoIP and for web meeting, max number of attendees is 200. tberardi: Think that's enough info? jclark: yes jrichter: When are we getting an account? jclark: the pricing seems problematic tberardi: I do want to test VoIP with at least three locations. tberardi: I have an account we can use now at Carnegie. hjd: I just got a mike, so I'm game jclark: Do you think if we paid more per month then the voice would be free? tberardi: Do we need approval to get another one for GO purposes? tberardi: I think this is the negotiated contract with Stanford as a whole. tberardi: And we can't mess with it. jclark: is that able to be opened up to the whole consortium? 5:55 PM tberardi: I could get it here at Carnegie or Mike C. could get it at the Dept. of Genetics. tberardi: Well, technically, no. tberardi: The account goes to one person. jclark: I think if we have to have a stanford person on every call then it will nto work jrichter: No, it will nto. tberardi: Right. tberardi: It will not work. jclark: should we find out the cost of a non stanford account? tberardi: webex.com jrichter: I know: $300/month. tberardi: !!! jrichter: That's why I was pushing convoq.com jclark: and VoIP? jrichter: VoIP is always pay per play, I think. jclark: oh right tberardi: We didn't have too much luck with convoq, though. tberardi: (Jen, David and I tried.) jclark: we need to write down all these costs so I can take them to the menagement call tberardi: I believe I sent an email to you, Jen and John. jclark: I think it has to be the $300 one so we can all use it kchris: I've missed something, why do we need this? tberardi: Did that disappear into cybervoid? tberardi: Want to take that, John? jclark: no actually, I have it, but we need to add on the requirements doc that john is writing jrichter: It would be helpful for: jclark: I hadn't managed to type that yet jrichter: 1) These meetings jrichter: 2) Webinars jclark: online content meetings jrichter: 3) Remote trainings of all kinds jclark: management calls tberardi: Harold: I'll email you separately to set up a test. j-lo: and we want it for content meetings too j-lo: quite urgently jrichter: $300/month is WAY too much. There are cheaper solutions. jrichter: I'm looking up a price breakdown now... jclark: but do they work? jrichter: megameeting does tberardi: Would you like to try having a webex meeting for our next OBO-Edit meeting? jclark: ok right jrichter: http://www.megameeting.com/web-conferencing-chart.html jclark: we need to test options but it doesn't have to be this meeting jclark: yes hjd: was that $300 per one site, or each one? if one site is needed for starting, and everyone else connects in, that's $3600 per year, but what would it be saving in terms of travel costs? jclark: john should we test that next? tberardi: No, the cost is only associated to the host. tberardi: Attending is free. jrichter: That page I posted shows a comparison of the major products. jclark: cool jclark: John can we talk about this in a separate meeting? we need to get details 6:00 PM jrichter: Okay, let's take this offline. jclark: we also need to do more testing jclark: cool jclark: what's next? jrichter: Any other agenda items? j-lo: John - following the content meeting we had with David earlier this week, we have an urgent feature request jrichter: ! j-lo: it's to prevent us re-using ids j-lo: when we're editing a section of the ontology midori: I don't remember any feature requests that I'd characterize as 'urgent'.... j-lo: parallel to the live ontology midori: (we have a social workaround for the ID problem) jclark: yes hjd: ? j-lo: well, that hasn't worked so far jclark: what did you think oboedit was going to do jane? jclark: true j-lo: not sure jclark: that's the tricky part j-lo: perhaps assign temporary ids? tberardi: What's the problem? jclark: because it's when we merge files that the problem arises jclark: it's when we edit two files in parallel jclark: and use the same id twice jrichter: Okay, here are the possible solutions: jrichter: 1) Assign temporary ids that are scoped per-file. When a user does some kind of "sync" operation, all the temporary ids are resolved to real, global identifiers. jrichter: Advantages: Easy to write, doesn't require network access jrichter: Disadvantages: All the problems of id clashes have been shunted to the "sync" operation. If two people sync without communicating, we're still screwed. jclark: I think we have to assume that we're oblivious of the id clash 6:05 PM jrichter: 2) Create a simple ID server on geneontology.org. When a user requests an id, the server never, EVER gives out that id again. jclark: that would be good jrichter: Advantages: Works every time, no possibility for problems jrichter: Disadvantages: We'd rapidly waste our id space, it would require network access to create terms midori: I wouldn't bother with (1) then, because if communication works, we don't need it, and if communication fails it won't help. jrichter: We may need some combination of 1 & 2, actually. The temporary ids could be used until the user can communicate with the id server. j-lo: yes - sometimes it's useful to be able to edit offline jclark: true midori: What we thought of was to have obomerge cough up a warning if terms in the changed files share an ID but not the term name. jclark: that seems more straightforward to me jrichter: That won't work. jclark: oh jrichter: OBO-Edit won't be able to tell if its an id clash or a name change. hjd: wouldn't it be possible to just assign ranges, much like we do for entire Mods, but maybe split them per curator (mods's take care of assignment)? midori: We'd get some "false positives" when we really just change term names, but I could live with that. jclark: sometimes curators aren't bright enough to remember that they're editing two fiels concurrently jclark: files jrichter: Okay, it sounds like there are 2 proposals on the table: jrichter: 1) Warnings for obomerge (easy) midori: Harold - that's essentially what we decided to do pending any technical solution; we'd assign a range per meeting as well. jrichter: 2) ID Server System (quite tricky) midori: (for "we" read: Midori & David will be ID Range Czars) jrichter: I can sneak 1) into the current release, but I think that 2) needs to wait OBO-Edit 1.2, if we can. Otherwise we're going to have delays. kchris: To me, the fact that the ID server system is tricky means that it is probably not a good use of our time currently j-lo: can we just do 1 then? 6:10 PM jclark: I think 1 is best j-lo: every big content change we've done has had this id problem, it's a huge time waster jrichter: Sure. I think the ID server idea is good, though. It deserves a place on the feature request tracker. Suzi has been begging for something like this for about 2 years. midori: We need the non-technological aspects of ID management anyway, so I'd make 1 the priority ... maybe not even do 2 if we turn out to get on OK wit 1 plus aggressive ID range management by humans. kchris: I completely agree with Midori jclark: me too jrichter: So voted. I'll add name warnings into obomerge. midori: (fine to do 2 somewhere along the line if we or other O-E users need it later, but I don't feel the need right now) j-lo: is that equivalent to the sync function john? tberardi: (BTW, I just tried the Windows installer and it worked well. OBO-Edit opened and I was able to open the ontology without a problem. The pop-ups were a little annoying though so I ended up just clicking on 'Yes to all.') jrichter: Jane - no. This would just tell you if two files you're trying to merge reuse an id with a different name. midori: I've tested the Mac installer -- fine for installing, starting up, and loading GO. jrichter: Should I go ahead with the temporary id feature too? jrichter: Or was that voted down? j-lo: I'd prefer the sync idea - I thought that was the vote jclark: I don't think we need that j-lo: I do because the obomerge method will still require hand assigning ids when things go wrong midori: I agree with Jen. I think we've had problems in the past because we didn't manage ID ranges well. kchris: couldn't you effectively create a temporary ID anyway, just by changing the name space? 6:15 PM jclark: if obomerge shows duplicate ids we have easy ways to deal with that jrichter: No! Namespaces don't effect ids! midori: Karen - we can and do, but ... what John said. jclark: eh? j-lo: they're not that easy Jen! kchris: sorry, I meant the prefix that is part of the ID jclark: I have fixed one before jclark: I have a script from Midori midori: we'd like to be able to just do find/replace to convert temporary prefixes to GO: jrichter: You know, now that I think about it, I may be able to get a more sophisticated behavior out of obomerge if I'm very, very tricky. jrichter: Jane - would it be okay if obomerge just reassigns clashing ids? j-lo: yes jclark: yes that would be good midori: reassigns them to what? jclark: it could ask for a new range tberardi: Midori, does anyone still fill in the go_numbers file? midori: ... and we would need to be able to tell obomerge which file keeps its IDs jclark: I do j-lo: what about name changes though, John? j-lo: won't it give them new ids? kchris: automatic reassignment seems possibly problematic to me, based on the fact that someone, Midori?, already mentioned cases where it is just a name change midori: Tanya - Jen does, and one of my action items from this week is to bring the rest of it up to date. jclark: true jrichter: Now that I think about it more, there's a way I can tell the difference between name changes and new term creation. jclark: wouldn't it just be better if obomerge just listed the problematic ids and names? jrichter: Best of obomerge could fix them too, optionally. Then we solve everyone's problem. tberardi: That would certainly be a useful first step. (What Jen said.) j-lo: I'd like it automatic midori: could we try it with just step 1 first? midori: automatic worries me more, actually ... jclark: me too kchris: automatic worries me a lot 6:20 PM j-lo: doesn't worry me at all! jrichter: It's equally easy to write either version, I think. Detecting the problem is a lot harder than fixing it. jrichter: How 'bout I write the full featured version, with automatic reassignment, but we leave the reassignment features undocumented. j-lo: okay jrichter: A task force will go about the task of seeing whether the reassignment features are useful and safe. jclark: sure jclark: good idea kchris: instead of automatic reassignment, could it bring them up with some sort of yes/no checkboxes midori begins to suspect that j-lo is just angling to be relieved of file-merging duty ... jclark: file merging does suck quite a lot midori: agree with j, j, & k tberardi: I was wondering about that. jrichter: Karen - it probably couldn't, because obomerge is meant to be a non-interactive script. j-lo: \j-lo never wants to do that again! jclark: It's no fun jrichter: You could run it in "warnings" mode, and then go ahead and do the merge if you aren't bothered by the warnings. jclark: I did it about 16 times for the cns file midori: oooh, I like John's latest suggestion! jclark: there might be quite a lot of warnings jclark: Could it list the terms in those warnings? midori: 'tis the nature of the beast, I'm afraid ... jclark: true tberardi: (A way to get your heart racing while at the computer.) jrichter: Jen - absolutely. midori: good idea to have it show terms jclark: That would be good jclark: Then we'd know where we are jclark: We can manually reassign and then merge j-lo: it's the error-prone human fixing of said warnings that worries me jrichter: Would it be useful to have a little command line utility called "reassignoboid" that would take a file and reassign an id in it? jclark: We have a script that midori wrote j-lo: it's so easy to introduce new problems when you're doing search and replace on the file jclark: the script rocks midori: tell me more, 'cos I suspect the answer (to John) is yes jrichter: Usage: jrichter: reassignoboid <oldid> <newid> <inputfile.obo> -o <outputfile.obo> 6:25 PM midori asks in an aside to Jen - which script is that? I can't remember! jrichter: or, if you're nasty: jrichter: reassignoboid <oldidregexp> <replacementidregexp> <inputfile.obo> -o <outputfile.obo> jclark: it take the obo file and a two column tab delimeted file with old id in first column and new id in second column and replaces jclark: splendid j-lo: would you have to do that for each id you've reused? midori: oh, that one! using it on obo files is your adaptation; I wrote it for something else originally jclark: oh right. jclark: It's fantastic jclark: I like it a lot midori: j-lo - the regexp option would let you do a batch at once jrichter: Jane - obomerge could do it automatically. You'd run this script if you wanted to change a specific id. jrichter: I could write the script so that you could give it an unlimited number of oldid:newid pairs. jclark: that would be good midori: yup jrichter: Should this be done for OBO-Edit 1.1, or wait until 1.2? jrichter: (I think it's < 1 day) midori: we'll use it as soon as it's available, so if it's quick , let's go for 1.1 jrichter: Okay, for OBO-Edit 1.1: obomerge improvements, reassignoboid script! jclark: Yay! midori: yay too jrichter: I've got a fussy baby in my lap. Any other items? jclark: can you tell me the path to the eclipse oboedit file so I can import from cvs? jrichter: I'll post that on the developers wiki today. jclark: ta 6:30 PM jclark: nothing else for me then jrichter: Oh! One more thing for the grammar cops. jrichter: Is it a "User's Guide" or a "Users Guide"? midori: for next time, we should report on 1.1 beta testing (which means I ought to do more testing in the meantime , if possible ...) tberardi: Users' Guide jrichter: (I think 1, on the "Farmer's Almanac Logic tberardi: Well, are you addressing a single person or all users? midori: User's Guide (for one user) or Users' Guide (for plural users) jrichter: I'm addressing "The User" tberardi: Then, 1. jclark: User Guide? midori: in that case, User's Guide jclark: That would be a guide to users I suppose jrichter: Good. Nothing changes then. jrichter: I'm off to write some scripts and so on! kchris: singular User's Guide seems file, it's a guide to the use who is reading it at the time jclark: Good luck tberardi: Keep me in the webmeeting loop. I'm happy to try the VoIP option, if we desire. jclark: ta tberardi: on webex. jclark: yes jrichter: Bye. jclark: bye midori: likewise on the web meeting front tberardi: bye j-lo: see ya jrichter has quit the server saying: Client exited jclark: cheerio tberardi has quit the server saying: Quit: kchris: bye j-lo has quit the server saying: Quit: jclark has quit the server saying: Quit: jclark