Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-17

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

All times shown according to UTC.

Time Nick Message
00:20 miranda joined #opentreeoflife
00:44 josephwb joined #opentreeoflife
01:26 towodo joined #opentreeoflife
01:31 josephwb joined #opentreeoflife
01:37 miranda joined #opentreeoflife
01:51 ilbot3 joined #opentreeoflife
01:51 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
01:54 towodo joined #opentreeoflife
01:57 josephwb hi towodo
01:57 towodo hi
01:57 josephwb Finally got a chance to look at inclusion tests (hackathon delays), but I want to make sure I understand it.
01:57 josephwb The README says:
01:57 josephwb "Inclusion" can be indirect, i.e. it doesn't refer to taxon parent/child relationships but rather logical inclusion, as if the taxa were sets of individual organisms or samples.
01:58 josephwb But we are still talking about ancestor -> descendant relationships, right?
01:59 josephwb Just that the ancestor might be X nodes above the descendant
01:59 josephwb where X might be 10 or whatever
01:59 towodo yes, that’s all
02:00 josephwb ok, thanks. the "as if the taxa were sets of individual organisms or samples" is what confused me
02:00 towodo my bad habit of talking like a mathematician
02:01 josephwb this is my bad, not yours
02:01 towodo the test is called ‘inclusion’ taking the view that taxa are sets
02:01 josephwb now, what if one (or both) nodes do not happen to be in the synthetic tree?
02:02 towodo uh, I’m not sure. I think that situation should be flagged and analyzed, so that either the test or the tree can be fixed.
02:02 josephwb ok, thanks again
02:03 towodo I guess I should push out that study id representation change
02:04 josephwb which one is that?
02:04 josephwb oh, what i did?
02:04 towodo yes
02:05 juliemallen joined #opentreeoflife
02:05 josephwb hopefully we can get the treemachine DB on production soon (for the sake of the hackathon).
02:05 josephwb responses are *slightly* different against prod and dev
02:06 josephwb are the inclusion tests holding this back?
02:06 towodo did someone decide that the new DB passes muster and should go to production? I don’t really know who’s responsible for that decision; I’d rather not be since then I’d have to face Dail & Laura
02:07 josephwb me neither
02:07 josephwb i mean, i do not know who decides
02:07 towodo it’s a hot potato. nobody wants the responsibility.
02:07 josephwb i am happy to take the heat. but i don't have the authority.
02:08 josephwb let's blame jimallman
02:08 towodo ha.
02:08 jimallman i heard that.
02:08 josephwb (hehe)
02:08 * jimallman is catching up now...
02:08 josephwb jimallman: nothing to do with you
02:08 towodo in any case I’m not doing it tonight… maybe we can touch base in the a.m.
02:09 josephwb fair enough. i will have distributed the inclusion tests by then.
02:09 towodo no, I think the inclusion tests are nice, but I just mentioned them because you explicitly asked if there any other checks to be done
02:10 josephwb yes, i understand, i just mean that they may add more weight to the replacement argument.
02:12 josephwb i guess we need people to weigh in on whether the dev tree is better than the current prod tree.
02:12 josephwb stephen and i believe it is.
02:12 jimallman are the reported microbe issues in the prod or dev tree?
02:12 jimallman or both?
02:13 towodo dev, I assume, since Dail was responding to Stephen’s request for people to review the dev tree
02:13 josephwb right.
02:13 towodo pushing out https://github.com/OpenTreeOfLife/treemachine/pull/120 to production now…
02:13 josephwb but the prod tree has problems dating back to, well, almost the last ms submission
02:14 towodo to early April I believe
02:14 josephwb that seems right
02:15 towodo ok treemachine is updated… josephwb, if you could do a test I’d appreciate it, I need to get to sleep
02:15 josephwb will do. thanks. see you tomorrow.
02:15 davidwinter joined #opentreeoflife
02:16 josephwb BTW, i hope to get the induced_tree bug fixed early tomorrow. might want to fasttrack that to deployment. sure to get lots of test at the hackathon!
02:16 josephwb issue here: https://github.com/OpenTreeOfLife/treemachine/issues/121
02:17 jimallman hi davidwinter! i see you found my #treeforall channel. i grabbed that just in case anyone (else) mistook the hashtag for an IRC channel name.
02:23 davidwinter Hi, jimallman, yup I'm that easily confused :) Soon worked out the right channel though!
02:23 jimallman a hackathon is a blizzard of different tools, channels, apps…
02:24 towodo joined #opentreeoflife
02:28 josephwb hey davidwinter. nice to work with you and Francois today. you two are far better R wizards than i will ever be. nice to have you guys closer than a Twitter radius.
02:33 davidwinter Same to you Joeseph, was ++useful for us to have an OT dev "on tap"
02:33 davidwinter (and francois is light years ahead of me -- the man's a machine :)
02:42 josephwb i've been away from R for a while now, and when I was in it, it was dealing with ML optimization. interesting/phun to learn about API wrapping from guys.
02:56 davidwinter joined #opentreeoflife
03:14 josephwb joined #opentreeoflife
03:28 davidwinter joined #opentreeoflife
04:38 josephwb joined #opentreeoflife
04:44 mtholder joined #opentreeoflife
06:32 mtholder joined #opentreeoflife
06:44 mtholder joined #opentreeoflife
07:31 mtholder joined #opentreeoflife
10:48 josephwb joined #opentreeoflife
11:06 josephwb morning tree dorks.
11:25 mtholder joined #opentreeoflife
12:09 kcranstn joined #opentreeoflife
12:24 arlins joined #opentreeoflife
12:37 mtholder joined #opentreeoflife
12:54 kcranstn joined #opentreeoflife
12:55 kcranstn mornin!
13:00 mtholder good morning/afternoon
13:02 mjwhy joined #opentreeoflife
13:03 mjwhy hey Karen- note we have different boardrooms now on floor 6
13:05 mjwhy rooms 1 and 2, API camping in room 2
13:06 gaurav_enwp joined #opentreeoflife
13:11 towodo joined #opentreeoflife
13:12 davidwinter joined #opentreeoflife
13:13 kcranstn joined #opentreeoflife
13:16 josephwb joined #opentreeoflife
13:16 codiferous joined #opentreeoflife
13:20 blackrim joined #opentreeoflife
13:27 lcoghill joined #opentreeoflife
13:30 miranda joined #opentreeoflife
13:32 blackrim left #opentreeoflife
13:35 davidwinter Hey OT people -- have filed an issue with the return values of an API at the main OT repo: https://github.com/OpenTreeOfLife/opentree/issues/440
13:35 davidwinter let me know if there is a more appropriate place to put it
13:35 kcranstn that works
13:36 blackrim joined #opentreeoflife
13:38 PEM joined #opentreeoflife
13:47 drycafe joined #opentreeoflife
13:48 guest|46966 joined #opentreeoflife
13:49 hlapp left #opentreeoflife
13:51 codiferous i
13:52 blackrim me
13:52 codiferous i'll work on prototype program stuff and couchdb research, etc
13:52 codiferous you
13:52 blackrim i will work on specifier types and sample set of annotations
13:54 josephwb kcranstn and towodo: treemachine service issue that could use your thoughts: https://github.com/OpenTreeOfLife/treemachine/issues/124
13:57 mjwhy hey support team
13:57 mjwhy possible to get a projector in room 2
13:57 mjwhy ?
13:57 josephwb codiferous ^
13:57 kcranstn no projector on the ceiling?
13:58 josephwb nope
13:58 kcranstn you can ask at the desk downstairs
13:58 kcranstn if they don’t have one, let us know and we can get one from EEB
14:05 jhill1 joined #opentreeoflife
14:09 mjwhy Karen- why no WORMS in the taxonomy pipeline?
14:13 mtholder towodo ^
14:14 towodo haven’t gotten around to it yet, too busy. it’s logically in the pipeline, just not very far down it
14:15 kcranstn initially, there were IP concerns, but we can get the data we need through the API without needing to go through a DUA
14:15 towodo we got the taxonomy already via their API (took 2 weeks)
14:15 towodo I have to add new ranks to the ranks list, then do some surgery because different parts of WORMS have different priority relative to NCBI
14:17 jhill1 Cool, didn't realise WORMS has the API up
14:32 hlapp joined #opentreeoflife
14:32 hlapp http://www.w3.org/TR/prov-o/#description
14:34 kcranstn https://github.com/OpenTreeOfLife/phylesystem-api/wiki/Annotations-in-NexSON
14:42 kcranstn is this what we should be developing against? https://code.google.com/p/annotation-ontology/
14:44 kcranstn ^hlapp?
14:47 jhill1 https://github.com/kevin1024/vcrpy
15:03 hlapp @kcranstn1 yes, also here: http://www.openannotation.org/spec/core/core.html
15:09 mwestneat joined #opentreeoflife
15:12 codiferous https://github.com/OpenTreeOfLife/phylesystem-api/wiki/Annotations-in-NexSON#2-primary-annotation-objects
15:18 hlapp http://www.openannotation.org/spec/core/appendices.html#ProvMapping
15:19 towodo joined #opentreeoflife
15:26 josephwb Y'All: for testing graph/* or tree_of_life/* services, please query against the devapi (not api)
15:28 gaurav_enwp joined #opentreeoflife
15:59 codiferous joined #opentreeoflife
16:13 temi joined #opentreeoflife
16:16 hlapp left #opentreeoflife
16:20 karolisr joined #opentreeoflife
16:24 jeet-api joined #opentreeoflife
16:24 jeet-api Hi Mark, I am getting an error trying to pull trees in NeXML format from the study/tree REST service
16:24 jeet-api [python:master:cddbbf7:+M+U]$ curl http://devapi.opentreeoflife.org/v2/study/pg_1144/tree/tree2324.nexml
16:24 jeet-api {"description": "Cannot convert from 1.2.1 to NeXML", "error": 1}
16:24 jeet-api [python:master:cddbbf7:+M+U]$ curl http://api.opentreeoflife.org/v2/study/pg_1144/tree/tree2324.nexml
16:24 jeet-api {"description": "Cannot convert from 1.2.1 to NeXML", "error": 1}
16:25 jeet-api On the other hand, other formats come across fine: curl http://devapi.opentreeoflife.org/v2/study/pg_1144/tree/tree2324.tre
17:00 lcoghill joined #opentreeoflife
17:00 josephwb joined #opentreeoflife
17:00 mjwhy joined #opentreeoflife
17:03 jimallman joined #opentreeoflife
17:03 scrollback joined #opentreeoflife
17:03 Guest87702 joined #opentreeoflife
17:03 jhill1 joined #opentreeoflife
17:03 karolisr joined #opentreeoflife
17:03 jeet-api joined #opentreeoflife
17:03 lcoghill joined #opentreeoflife
17:03 josephwb joined #opentreeoflife
17:03 mjwhy joined #opentreeoflife
17:15 kcranstn joined #opentreeoflife
17:16 mtholder joined #opentreeoflife
17:16 towodo joined #opentreeoflife
17:18 temi joined #opentreeoflife
17:22 codiferous joined #opentreeoflife
17:33 jeet-api joined #opentreeoflife
17:33 jeet-api mtholder, hello
17:33 jeet-api @mtholder, hi
17:34 josephwb hey karolisr
17:34 kcranstn getting ready for daily reports, for folks who are upstairs
17:34 kcranstn so come on down
17:35 josephwb hey karolisr (again)
17:35 josephwb hey karolisr (again *2)
17:35 josephwb *done testing IRC*
17:35 karolisr thanks it works
17:36 mtholder left #opentreeoflife
17:36 mtholder joined #opentreeoflife
17:38 mjwhy joined #opentreeoflife
17:40 mtholder re: previous nexml bug report. Sorry that is a horrid message. Bottom line, it does not support returning bits of the resource in nexml - you can get the whole study or nothing in nexml. So the URL should be http://api.opentreeoflife.org/v2/study/pg_1144.nexml
17:40 mtholder (and I should return a better error message for http://api.opentreeoflife.org/v2/study/pg_1144/tree/tree2324.nexml )
17:41 josephwb joined #opentreeoflife
17:43 blackrim joined #opentreeoflife
17:50 kcranstn mtholder?
17:54 josefuyeda joined #opentreeoflife
18:23 miranda joined #opentreeoflife
18:28 lcoghill joined #opentreeoflife
18:37 jeet-api joined #opentreeoflife
18:38 jeet-api ok, thanks. Should have read the docs better: "NexSON supports fine-grained access to parts of the study (see below). NeXML can only be returned for the study. Newick and NEXUS formats can only return the full study, trees or subtrees"
18:38 jeet-api Sorry
18:38 josephwb joined #opentreeoflife
18:42 davidwinter joined #opentreeoflife
18:43 gaurav_enwp joined #opentreeoflife
18:58 towodo joined #opentreeoflife
18:59 kcranstn joined #opentreeoflife
19:13 kcranstn joined #opentreeoflife
19:20 towodo joined #opentreeoflife
19:49 towodo joined #opentreeoflife
19:50 towodo joined #opentreeoflife
19:50 josephwb you there mtholder?
19:51 mtholder yes
19:51 mtholder josephwb^
19:51 josephwb jeet will be bugging you soon
19:51 mtholder ok
19:51 towodo joined #opentreeoflife
19:52 josephwb mtholder regards phylesystem calls
19:53 josephwb that was a hint of what jeet is concerned about, not an observation of mtholder
19:53 jeet-o-saurus joined #opentreeoflife
19:53 mtholder got it. Though I do regard those calls
19:54 josephwb *mtholder regards phylesystem calls*
19:56 jeet-o-saurus hi mtholder, do you have some examples for get_study_otu and get_study_otus that get results? I keep getting 404's, but that's because maybe I don't know any organism names anymore
19:56 jeet-o-saurus Speaking of organism names, what is the etymology of "muriqui"?
19:58 francoism joined #opentreeoflife
20:00 gaurav_enwp when we download a study from e.g. http://tree.opentreeoflife.org/curator/study/view/pg_2854/?tab=metadata, does anybody know what license we get them under? We're wondering if we can reupload them to Github without violating their licensing terms.
20:01 kcranstn the licensing is not consistent
20:01 kcranstn some are cc0
20:01 kcranstn some have no license (e.g. the ones from treebase)
20:01 mtholder http://api.opentreeoflife.org/v2/study/ot_42/otu/otu210
20:01 mtholder call http://api.opentreeoflife.org/v2/study/ot_42/otus first to get the otus object (that is what I do at least)
20:01 mtholder jeet-o-saurus
20:02 kcranstn anyone who gave me a passport or PR card can come pick them up now
20:02 kcranstn I don’t want to keep them overnight
20:05 daisie joined #opentreeoflife
20:06 jeet-o-saurus ok, thanks
20:06 gaurav_enwp kcranstn: thanks on both counts!
20:16 josephwb is there coffee down there?
20:16 kcranstn yes
20:17 kcranstn and tea-flavoured coffee
20:17 kcranstn oops
20:17 kcranstn coffee-flavoured tea
20:17 josephwb sweet. i am on my way.
20:25 josephwb *not enough coffee-flavoured tea left*
20:32 jeet-o-saurus joined #opentreeoflife
20:34 gaurav_enwp joined #opentreeoflife
20:49 Dilrini joined #opentreeoflife
20:57 gaurav_enwp joined #opentreeoflife
20:58 juliema joined #opentreeoflife
21:09 gaurav_enwp joined #opentreeoflife
21:49 josephwb joined #opentreeoflife
23:15 josephwb joined #opentreeoflife
23:35 mjwhy joined #opentreeoflife

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