Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-06-19

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All times shown according to UTC.

Time Nick Message
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18:24 jimallman jar286: is there an easy way to get the visible-taxa count for each synthesis release? i assume the number of lines in ‘taxonomy.tsv’ is not going to cut it.
18:25 jimallman s/synthesis release/taxonomy release
18:25 jar286 oh yeah, I was going to get this info to you… hang on, it might already be documented
18:25 jimallman thanks. also the date for ott2.9 would be helpful
18:31 jar286 https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/scripting.md
18:32 jar286 sorry I’ve been so useless on opentree, cramming to get nescent closed by end of month
18:32 jar286 jimallman ^
18:32 jimallman no problem at all, i also have a few irons in the fire
18:34 jar286 basically you load the OTT you want to look at, do v = selectVisible to prune it, then do v.count()   [the latter isn’t documented]
18:34 jar286 to get date for 2.9 I’d probably go to ot10 and look at the file write date…
18:42 jimallman thanks!
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21:16 kcranstn jimallman - can you fill out that whenisgood poll for meeting times?
21:17 jimallman done!
21:19 kcranstn thanks
21:27 jimallman kcranstn: do you happen to know if ecat-dev.gbif.org has a new name? i’m trying to build the current ott and this domain is failing..
21:27 jimallman (domain name does not resolve for me)
21:31 kcranstn that sounds like a temporary server gbif might have provided for jar286_
21:32 jar286_ yes, that gbif file now has a new url
21:32 jar286_ I can dig it up, hang on...
21:33 jar286_ gbif.org > Data > Explore Datasets > GBIF backbone >    yields http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
21:40 jimallman :D thanks, i’d JUST found this link.
21:41 jar286_ I should have mentioned you in my message, to get your attention
21:42 jimallman ok, dumb question. how do i get the actual data (.zip)?
21:42 jimallman drat!
21:46 kcranstn The Darwin Core Archive link
21:46 kcranstn is the only zip file I see on the page
21:47 kcranstn is that correct, jar286_ ?
21:47 kcranstn oops, he is gone
21:49 kcranstn not clear to me what format expected by https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/feed/gbif/process_gbif_taxonomy.py
21:49 jimallman yes, that’s why “drat”…. i’m actually looking for something called ‘checklist1.zip’
21:50 kcranstn are you looking for a specific version of gbif?
21:50 jimallman i’ve been trying to build the ott2.9 using the Makefile, but maybe i should just be using make_ott.py?
21:51 kcranstn why are you building the taxonomy?
21:51 jimallman i’m trying to get taxon counts from ott2.9, and jar pointed me to the docs… thought i’d give it a try
21:52 kcranstn shouldn’t have to build (unless 2.9 is not posted anywhere?)
21:52 jimallman by docs, i mean https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/scripting.md
21:53 kcranstn this seems like a waste of time. I don’t see 2.9 posted on http://files.opentreeoflife.org/ott/ but you should be able to get it from jar
21:53 kcranstn no need to bild
21:53 kcranstn build
21:53 jimallman it’s available on ot10, but i don’t know a straightforward way of getting these counts from the raw files… see our prior conversation from 2:24pm today.
21:54 kcranstn you should be able to just load the taxonomy using smasher and then do queries
21:55 jimallman ok, so download and unzip the delimited text files from ot10, put them in the local path for smasher… i’ll give it a go.
21:55 kcranstn for example, look at this https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/counts.py
21:56 kcranstn you create a Taxonomy object for ott (no need to have all of the separate input files)
21:56 * jimallman nods
21:58 kcranstn how are your chickens holding up in the heat?
22:01 jimallman ah, pretty well thanks to all the trees.
22:02 jimallman (they just hang out in the underbrush). we have a few young ones that are living in the silo with careful ventilation.
22:03 kcranstn any attempts to use water as part of the cooling strategy are met with horror over herer
22:04 jimallman it does sound vaguely suspect...
22:04 jimallman oh, you mean neighbors?
22:04 kcranstn no, chickens
22:05 jimallman :)
22:05 kcranstn OMG you are killing us with the hose
22:05 jimallman SNAKE!
22:05 jimallman kill kill
22:20 jimallman kcranstn: so i’m up and running now with ott2.9 (from ot10). i untar’d the zip, since smasher apparently needs to read its .tsv files…
22:21 jimallman so now i’m poking at ott2.9 with the python api, which is need. i can get the ‘count’ and ‘tipCount’, but it’s not clear whether these are for visible taxa, or all. i’m assuming visible, which is all i want at the moment.
22:21 jimallman >>> ott.taxon('Mammalia').tipCount()
22:21 jimallman 21335
22:22 jimallman >>> ott.tipCount()                   ()
22:22 jimallman 3021500
22:22 jimallman hm, this is odd:
22:22 jimallman >>> ott.taxon('Mammalia').isExtinct()
22:22 jimallman True
22:22 jimallman oh, that makes sense.
22:32 jimallman (for the record) this seems to give the desired information:  >>> ott.adHocReport()
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