Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-08-19

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Time Nick Message
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01:48 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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15:58 kcranstn mtholder - thanks for that API doc
15:58 mtholder sure.
16:24 jar286 joined #opentreeoflife
16:53 kcranstn welcome back, jar286! (although you never disappeared from irc...)
16:54 jar286 I left the laptop on when I went away
16:54 kcranstn it was like you never left us
16:54 18VAAIDCK joined #opentreeoflife
16:55 jar286 like those parked police cars with life-size officer-dummies
16:56 jar286 if I’m late to the 1:00 hangout it’s because I’m having trouble finding a room to take it in (left my key at home when I went to MIT… argh)
16:58 jar286 joined #opentreeoflife
16:59 josephwb i will be late. mac is stuck on update, and need to install new browser on debian machine
18:08 jar286 joined #opentreeoflife
18:13 josephwb pmidford2 if it is easier for you, i can edit the DB. i had to edit it before to add all of the git SHAs, so it is not too hard
18:14 josephwb i.e. git SHAs are not part of loading
18:17 pmidford2 <josephwb> It doesn't much matter to me, I think jimallman  was going to fix it on his end.  Also kcranstn seemed a bit nervous about more db changes.   If you the db, it will be picked it up when the job runs, but I'll pass whatever I get on to jim.
18:17 josephwb ok. not a big deal, i think. i can do it, and put it on dev.
18:18 kcranstn whatever is easy with low probability of downtream mess
18:18 josephwb i'll see what i can do, but hardcoding it at this point is fine, i think
18:23 jar286 kcranstn, just reviewed all open PRs and they look fine to me (except for stats, as discussed)
18:23 kcranstn ok, thnaks
18:23 kcranstn thanks
18:24 kcranstn am hoping to have a documentation PR for tomorrow (but only modifying help text throughout)
18:24 kcranstn so probability of damage is low
18:26 pmidford2 Question about the API call for number of tips - should I be calling /v2/tree_of_life  or /v2/graph  - the documentation shows them returning the same value, but are they the same?
18:31 josephwb they should be the same
18:32 josephwb pmidford2 ^
18:32 pmidford2 <josephwb> Thanks
18:32 josephwb the second call is if they are lots of trees in the *graph* but only some contribute to synthesis
18:32 josephwb at the moment, all trees in the graph go into synthesis
18:33 pmidford2 <josephwb> If the situation where not all the trees went into synthesis would  the first one be more correct?
18:34 pmidford2 If the situation were...
18:44 josephwb pmidfor2 yes. the first gives the number contributing to synth, the second if the total of all trees in the graph
18:45 pmidford2 <josephwb> thanks got it.
18:51 josephwb study: published 18 Aug, in OpenTree: 19 August
18:52 josephwb so quick the doi is not recognized yet
18:52 kcranstn !
18:52 josephwb so i am getting ot-validation problems
18:52 kcranstn not much we can do about that until the DOI resolves
18:53 josephwb cannot search for it, either. do i keep it open?
18:53 josephwb ah! i cannot save it! help!
18:53 kcranstn keep it open = ??
18:54 kcranstn ah, so you have done a bunch of curation work but it won’t save?
18:54 josephwb yes
18:54 josephwb ot_314
18:54 kcranstn wonder if we should do check on the metadata tab before allowing people to continue...
18:55 josephwb i saved a bunch, with comments, but the history is empty, and the study is empty on a second computer
18:55 josephwb jimallman ^
18:55 kcranstn sounds like this needs an issue
18:56 josephwb this study has no doi: https://tree.opentreeoflife.org/curator/study/view/ot_301
18:56 josephwb i will try removing it?
18:56 josephwb nope
18:59 josephwb sent you the error jimallman
19:01 * jimallman has been away, catching up now
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19:06 jimallman josephwb: this just looks like a missing publication year (in Metadata). have you tried adding one and saving?
19:06 josephwb yup. erg.
19:06 josephwb thanks
19:13 josephwb pmidford2 i think the source count includes taxonomy (i think)\
19:14 josephwb it is in the list, anyway. checking now
19:15 josephwb yes it is. so: 478 studies in graph + 1 taxonomy
19:15 josephwb 478 trees, that is
19:16 pmidford2 That makes sense, so the other 5 are?
19:16 josephwb "trivial". figuring out which they are now
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22:28 jar286 jimallman, I believe I’ve transferred all OTT information that was in the files repo to the doc/ directory of the reference-taxonomy repo
22:30 jar286 there is an index page, doc/README.md, see https://github.com/OpenTreeOfLife/reference-taxonomy/tree/ott2.7.md/doc
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