Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-03-02

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All times shown according to UTC.

Time Nick Message
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02:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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15:09 kcranstn I was looking for the conversation about why the stats on the curator pages are not up-to-date. Do I remember correctly that this is an oti problem? is there an issue?
15:09 kcranstn https://devtree.opentreeoflife.org/curator/profile/kcranston
15:09 kcranstn “This user has not curated any studies"
15:30 jimallman kcranstn: there’s a ticket for the related oti bug. it only indexes the first listed author, and does the same thing generally for all multi-valued properties.
15:30 kcranstn cool, thanks
15:30 jimallman https://github.com/OpenTreeOfLife/oti/issues/35
15:34 kcranstn “what to do with oti” needs some major discussion after we get through this synthesis update
15:37 jimallman it’s kind of a beast. i went spelunking in the oti code, since it seems like a simple fix (“change from single-valued to multi-valued indexing for these properties”). i got lost in layers of indirection and never did find the definitive mapping of properties to index types.
15:37 kcranstn wheeeeeee
15:45 josephwb i'm sure cody can fix that quickly
15:45 kcranstn not as high priority as the synthesis stuff...
15:45 josephwb right
15:46 josephwb i find his code a little hard to follow, but that's probably just because i don't know what i am doing ;)
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16:49 kcranstn jar286?
16:49 jar286 here
16:50 jar286 kcranstn ^
16:50 kcranstn is there a script to count hte number of descendent taxa in OTT given a taxon?
16:50 jar286 it’s very easy to do using smasher
16:50 kcranstn documentation?
16:51 kcranstn (someone else is asking)
16:51 jar286 hang on
16:51 jar286 well https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/scripting.md  is part of it
16:51 jar286 but what’s missing is a description of count()
16:52 kcranstn could you also use smasher to do similar things with the synthetic tree (reading in the .tre file?)
16:53 jar286 ummm… now that’s terra incognita
16:53 jar286 smasher has a newick reader, but it’s not up to the task of reading the synthetic tree
16:54 kcranstn why? (don’t the taxonomies have siimilar scale?_
16:54 kcranstn )
16:54 jar286 it ought to work, but as I say the newick parser would need some work
16:54 kcranstn the question I got was “Is there a way to get an estimate of the number of microbial eukaryote nodes in Open Tree?"
16:55 jar286 of course you’d need a list of non-microbe eukaryote taxa
16:56 kcranstn or clades that you consider microbial euks
16:56 kcranstn let’s assume the user has a definition
16:56 jar286 you could try reading the synthetic tree in smasher, but I bet you it would crap out due to newick label issues
16:57 jar286 not too hard to fix, but it would have to be done
16:58 kcranstn ok, I am going to reply with “no simple way, but I’ve created an issue..."
17:00 jar286 maybe peyotl or dendropy?
17:02 jar286 I’ll add count() and tipcount() to the documentation
17:03 kcranstn tagged you in the feedback issue
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17:16 travis-ci OpenTreeOfLife/phylesystem-api#692 (sh-issue - 3064221 : Emily Jane McTavish): The build passed.
17:16 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/c92b18856580^...3064221db41c
17:16 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/52770296
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18:01 mtholder i'm late to this, but kcranstn and jar286 ... you can read the synthetic tree easily with otcetera, and prune it. and count tips. no one operation for counting tips in a subtree.
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