Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-01

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All times shown according to UTC.

Time Nick Message
00:57 jimallman joined #opentreeoflife
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19:17 mtholder jimallman: I'm working on https://github.com/OpenTreeOfLife/api.opentreeoflife.org/issues/59
19:17 mtholder that will mean a change in the returned JSON
19:18 mtholder preferences on the structure?
19:18 jimallman mtholder: i'm here, reading this now...
19:18 mtholder {"sha": "e13343535837229ced29d44bdafad2465e1d13d8", "nexson": nexson_obj}
19:19 mtholder or we could call the nexson_obj "data"
19:19 jimallman sure, that works. i think we've used 'nexson' elsewhere, no?
19:19 jimallman (returned from to_nexson, perhaps)
19:20 mtholder I think so. I'll check. it'll mean return['nexson']['nexml'] for access to the toplevel. which is weird, but OK
19:21 jimallman that is weird, but in a way it clarifies that by 'nexml' we really mean 'nexson'  :)
19:22 mtholder I think we use 'data' in to_nexson and merge_otus
19:22 mtholder maybe I'll go with data.
19:22 jimallman as you wish, just shooting for consistency
19:23 mtholder i don't think that we'll pass around anything other than nexson, but I guess we might (in which case we'll need a format specifier).
19:24 jimallman just checked... to_nexson seems to return the Nexson itself, with no wrapper {"ned:nsxml"...}
19:25 jimallman s/ned/nex, stupid auto-correct
19:25 jimallman sure, data is fine too
19:25 mtholder hmm. I'm looking at the code (less reliable than the ws-output), but it looks like data. Maybe it is being altered in a view?...
19:26 mtholder were you getting 'nexson' from 'to_nexson' on ot7?
19:26 jimallman nope, on my local
19:26 jimallman so maybe it's out of date
19:27 mtholder I didn't intentionally change that, but I might have changed it.
19:27 mtholder as I age the proportion of my actions that are intentional declines...
19:27 jimallman and it's still called to_nexml, so maybe i'm badly out of sync
19:28 mtholder I did change the service name intentionally. not entirely senile (yet)...
19:29 jimallman i'll pull the latest and take a look, if these old eyes can find the right keys
19:30 mtholder oops I did change it, when I had to return the uploadid.
19:31 mtholder I updated the README on external-format-to-nexson but I forgot to mention the changed return value to you.
19:31 mtholder in my defense, this was all of 1 week ago, so there is really no way I could have remembered that ;-)
19:32 jimallman no problem. :D
19:34 jimallman hm, i've been working mostly on a different branch 'honeybadgerfish-conversion'... i'll need to merge this one eventually and adapt to it.
19:34 jimallman or i could merge it into honeybadgerfish-conversion now, i guess, but that feels icky
19:35 mtholder not likely to be a problem (despite the icky feeling) because I am just working in two controllers on that branch.
19:36 mtholder if I were a good person, I'd be tweaking the JS code to deal with the changes to the API. That would be the whole point of being on a branch, I suppose. But I'm not a good person...
19:37 mtholder fwiw: i'm done with the external-format-to-nexson branch except for bug fixes...
19:37 mtholder as they are reported. I don't know of outstanding bugs.
19:37 mtholder *in that code
19:39 mtholder nm. I see a conflict...
19:39 jimallman ?
19:39 jimallman attempted merge of these two branches?
19:39 mtholder yeah.
19:40 mtholder I'll see if I can get a merge working and push it. I don't think the conflict is very substantial.
19:41 jimallman OK, or i'm glad to take a look...
19:43 mtholder I'm on it. You just added som messages about the import at the end, and I refactored the last steps. No conflict in the logic, we just hit the same lines with complementary changes....
19:45 jimallman kewl
19:52 jimallman i'm just reading up on git subtrees. holy crap! that's cool.
19:57 mtholder yes. we should probably be using subtrees.
21:03 jimallman towodo, mtholder: i found the leaf-count and added this to the visible properties of a node in the main web app (tree browser). i've label this "Organisms within this clade", but I'm curious to know if there's a better phrase to use here: "Leaf nodes"? "Clade members"? the count is strictly for leaf nodes, not inner nodes.
21:03 jimallman this is live on dev.opentreeoflife.org, but the counts are all zero. it seems the tree data is in a weird state. i can find nodes using the taxon-search tool, but each one seems isolated from all others.
21:04 towodo that's a toughy.
21:04 towodo we can't say 'taxa' because some nodes are from phylogeny
21:05 towodo wait, it's leaf nodes only? say 'species'
21:05 jimallman ok, no need for "extant" vs. extinct?
21:05 jimallman "Species within this clade", then
21:10 towodo let's give it a try
21:10 jimallman done
21:17 mtholder joined #opentreeoflife
21:30 towodo jimallman, currently all the extinct species are filtered out
21:31 towodo except for the ones that aren't properly flagged as such
21:32 towodo i.e. should be flagged extinct but aren't.  you know what i mean
22:02 mtholder jimallman: I merged your honeybadgerfish branch into my external-format-to-nexson and did the manual merge.
22:03 mtholder it is pushed to GitHub as external-format-to-nexson. What is on ot7 is the merged version "resolved conflict,..." commit.
22:04 mtholder I looked through the JS a bit to see how it needs to be tweaked, and I got some of the changes in the "Partial migration to the new tree import API" commit.
22:04 mtholder but I haven't debugged that commit at all.
22:05 jimallman towodo: got it, thanks
22:05 mtholder needs the latest pull of peyotl, too. btw.
22:05 jimallman hrm, ok. i'm off to dinner with a friend, will dig in later tonight
22:05 jimallman mtholder: ^
22:07 mtholder sounds good. have fun.

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