Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-22

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:27 josephwb joined #opentreeoflife
01:37 jimallman joined #opentreeoflife
01:53 josephwb joined #opentreeoflife
02:29 josephwb joined #opentreeoflife
11:53 josephwb joined #opentreeoflife
12:09 josephwb joined #opentreeoflife
12:12 PEM joined #opentreeoflife
12:16 josephwb joined #opentreeoflife
13:19 PEM joined #opentreeoflife
13:30 blackrim joined #opentreeoflife
13:30 blackrim left #opentreeoflife
13:34 blackrim joined #opentreeoflife
13:36 josephwb joined #opentreeoflife
14:15 blackrim josephwb: I assume you also aren't updating the newicks with the up to date synth trees?
14:15 blackrim Because of all the taxonomy changes, I haven't been sending things around to the plant folks, but I am going to do that real quick in a bit. I wonder, if you haven't already, whether it would be good to send some things to the animal folks. That way we know where we stand with things
14:16 blackrim If towodo comes on, I will ask about the status of IRMNG. probably not worth an email at this point
14:30 kcranstn joined #opentreeoflife
14:31 kcranstn mornin!
14:31 josephwb yeah, i will send them around
14:31 blackrim kcranstn: morning!
14:31 kcranstn sending email to group about talking this afternoon
14:31 blackrim josephwb: thanks. yeah, also if you mention that any changes to taxonomy (other than the potential additions of fossil info) need to be made nowish
14:32 blackrim kcranstn: sounds good. do you mean the software group?
14:32 kcranstn "nowish" - very precise ;)
14:33 blackrim kcranstn: yeah, well jonathan is working with david so things are still in flux so there is time.
14:33 blackrim that would be the "ish"
14:34 blackrim :-p
14:35 blackrim i am sure there will also be more edits once towodo gets those servers back up for us to upload the taxonomy for laura to see again
14:35 josephwb ack. i didn't have draft 12. i will need to check these again. hopefully nothing has changed much within animals.
14:36 blackrim josephwb: i dont think much has changed there. between the versions 10-12 it was mostly fungi. that said, I am rechecking plants right now
14:42 josephwb good; i'll check regardless.
14:47 kcranstn I've added a short list of concerns with current architecture: https://docs.google.com/document/d/1F6O-RG-anyP_7_U083mJ500LBWq8TrteU89QswwUsho/edit#
14:47 kcranstn in advance of this afternoon's meeting
14:48 kcranstn please add / update at necessary, but let's keep it brief at this point
14:49 blackrim kcranstn: i will be there (just not sending a reply email)
14:51 kcranstn blackrim: figured so
14:52 jimallman joined #opentreeoflife
14:53 blackrim kcranstn: i didn't initiate though, so don't blame me. i'm innocent i tells ya
14:56 kcranstn blackrim: likely story
16:30 blackrim /close
16:30 blackrim left #opentreeoflife
16:31 PEM joined #opentreeoflife
18:19 towodo joined #opentreeoflife
18:24 mtholder joined #opentreeoflife
19:22 PEM joined #opentreeoflife
19:35 blackrim joined #opentreeoflife
19:36 blackrim towodo: database should be loading now. assuming the rest of the push-db works as expected, it will be up there momentarily.
19:38 towodo I've done push-db before so have no reason to think it won't work.  But you read the instructions I hope, about how to create the tarball? https://github.com/OpenTreeOfLife/opentree/blob/master/deploy/README.md
19:38 blackrim i did
19:41 towodo excellent, excellent.
19:41 PEM joined #opentreeoflife
19:42 blackrim there are definitely still some funny taxonomy things in plants that i am working out. so i will let you know what i find in a couple secs
19:44 towodo blackrim, fossils are ready to go, except for 900 NCBI genera that are marked fossil but probably shouldn't be. Hoping to hear from Tony overnight with a solution.  I hope addition of IRMNG is not too disruptive - I'm merging in its taxonomy, not just the extinct flags, because it places a bunch of incertae sedis things
19:45 blackrim towodo: that sounds good.
19:45 blackrim josephwb: did your loading just stop? wondering if it is a taxonomy server down?
19:47 josephwb let me check one with incomplete mapping.
19:48 blackrim josephwb: it was definitely working this morning so it would just be something recent
19:48 blackrim I get one of these "failed to get the names from server fixNamesFromTrees 3
19:48 josephwb running one now
19:49 josephwb nope; worked for me
19:50 josephwb that was ambiguous. nope: i did not have a problem. it worked for me.
19:50 blackrim ok, that is wierd. investigating what is up
19:52 blackrim josephwb: stupid mistake on my part. got it
19:59 josephwb good
20:01 blackrim towodo: you want taxonomic issue I found here? or you want an email? I would rather here, but if you want email , that is fine
20:01 towodo here is ok
20:01 blackrim ok, species Coscinium blumeanum with id 706277 has the right ncbi id (goes to palms) but then points to id  genus then points
20:02 blackrim sorry, points to id 688894 and a genus in amoebozoa
20:02 blackrim this is the offending genus line 688894|1037479|Coscinium|genus|if:12055,ncbi:483231
20:10 towodo amoebozoa is not in a 'division'… so things can drift in and out… actually I changed it recently, I thought, so that things can't drift out of plants and into basal euks, let me look at the code.  oops incoming call
20:14 PEM joined #opentreeoflife
20:14 blackrim towodo: investigating another one that seems to be protozoa. will see if it is a similar thing
20:16 blackrim yep, same thing with this one 1033741|4925663|Perezia carthamoides|species|ncbi:516731
20:16 blackrim it is a plant going to protozoa because of IF presumably (looking at the parent).
20:20 towodo ah, no, I didn't put in that hack. currently motion is prohibited only when source & dest are in divisions (different ones)
20:20 towodo it really really wants names to match up
20:26 towodo sorry, i'm on a call...
20:36 blackrim no problem, just exploring some others
20:57 blackrim towodo: no other problems that i see. so those two are mine and seem to be something with the if and ncbi.
20:59 towodo i can always special case them
21:02 towodo call starting
21:02 mtholder left #opentreeoflife
21:03 blackrim left #opentreeoflife
22:00 josephwb joined #opentreeoflife

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary