Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-08-01

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Time Nick Message
00:26 kcranstn joined #opentreeoflife
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03:52 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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16:04 jimallman kcranstn: i’ve fixed all the study download options and added a popup explaining each. this is working now on devtree: http://devtree.opentreeoflife.org/curator/study/edit/pg_2584?tab=metadata
16:06 jimallman i’d like to push to production (this is on master already) but would love a second pair of eyes. Note that you can click each format’s name in the popup to see more background information. These are the best links I could find, but suggestions are welcome.
16:07 kcranstn I’ll take a look at this later this afternoon
16:07 jimallman thanks!
16:16 towodo jimallman, this looks pretty good to me, very glad to see it all working now. should be announced at some point.
16:16 towodo We need to get CC0 information into the NEXUS when it’s available, I assume it’s already there for Nexml…
16:17 towodo which reminds me, there doesn’t seem to be anything about CC0 (presence or absence) on the metadata page. How does a curator retrospectively attach CC0 to a study that has already been entered?  Not that it should be too easy, but there ought to be some way to do it other than frobbing github.
16:30 jimallman ah yes, there’s an open ticket for this (retroactive CC0)
16:30 jimallman i can add this next and push the combination to production later
17:04 towodo not urgent…
17:04 jimallman i’ve realized we don’t show any licenses (in the main curation page) other than CC0, so I’d like to get that done at least.
17:05 towodo we shouldn’t show any licenses.
17:05 towodo CC0 is a waiver and should be the only option other than no marking.
17:05 * jimallman hangs head
17:06 towodo it’s the creed
17:06 jimallman but note that we allow for other waivers (and even some licenses) when creating/importing
17:06 towodo really?
17:06 jimallman i’d need to retrace the conversations to remind myself of why that is, but yes
17:07 jimallman choices are: CC0, CC-BY, Other (specify license name and preferred URL), or “I have no authority”
17:08 towodo oh. hmm. I think I remember, vaguely.
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17:09 jimallman something something existing repositories…
17:09 towodo e.g. if the data were supplementary material for a BMC article, it would be CC-BY, maybe.
17:11 towodo this is annoying because there are many different flavors of CC-BY, and each has its own URL
17:12 towodo to be pedantic you’d want to off CC-BY 4.0, 3.0, 2.5, and 2.0 as separate options
17:12 towodo s/off/offer/
17:12 jimallman hm, i see. i’ll see which we’ve assumed in the code
17:12 jimallman certainly it’s easy to offer options like those above in the dropdown, plus any others we expect
17:15 towodo that should be CC0, not CC-0 — should I edit & commit? also I prefer “applicable waiver or license” to “existing license”
17:17 towodo the distinction between CC-BY 4.0 and previous CC-BYs is significant here (CC 4.0 licenses are evil for data)
17:18 jimallman I can take care of those text tweaks, since I’m already in the neighborhood. thanks for the close look!
17:19 towodo but I’m sort of tempted to flush all of the licenses since there are no data rights that can be licensed… oh well, best not to stir the nest right now
17:21 jimallman as a reminder, all this came together in mid-May (the main study-creation overhaul was committed May 19), and there was a lot of discussion about these options. i seem to recall we decided to “allow” any license. we certainly don’t block of validate their choices. i don’t recall how we planned to respond to a problematic license, or none.
17:22 * jimallman needs to check the weekly meeting notes, having limited luck with email..
17:38 towodo don’t worry about it, I say don’t rock the boat
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20:53 josephwb you there jimallman?
20:53 jimallman hi!
20:54 josephwb i have a simple question: does devtree export nexsons differently than the prod server?
20:54 josephwb i am testing out mapping
20:54 josephwb but the nexson isn't being read correctly
20:54 jimallman ?
20:54 josephwb sorry, too quick
20:55 josephwb i went to devtree to play with mapping
20:55 josephwb i exported the nexson for testing in treemachine
20:55 josephwb it isn't being read in
20:55 jimallman i see, the download button in Metadata tab, you mean?
20:55 josephwb yes
20:55 jimallman gotcha
20:55 josephwb i haven't tried that tab on prod tho
20:56 josephwb *trying now*
20:56 jimallman devtree is the right place! though the NexSON download should be indentical in both
20:56 josephwb not sure what is going on
20:57 jimallman it’s possible that the HBF version is different from what you’re expecting? we download HBF 1.2 (see the download link), but you can also get 1.0 or 1.1
20:57 josephwb will test the prod export
20:57 josephwb HBF?
20:57 jimallman thanks, let me know!
20:57 jimallman HBF = HoneyBadgerFish, our funky conversion standard for NexSON
20:58 jimallman (see the download-formats popup for helpful background links  :)
20:58 josephwb popup?
20:59 jimallman on devtree, it’s a link on the words ‘several formats’
20:59 jimallman (it’s not there on production yet)
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20:59 josephwb oh, i see
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21:00 josephwb why isn't that on prod?
21:00 josephwb popups
21:00 jimallman i haven’t pushed it yet, was hoping to get another couple of fixes done today
21:00 josephwb gotcha
21:00 josephwb exported nexson from prod doesn't work in same way
21:00 josephwb i am going to compare it to what I get from curl
21:01 jimallman agreed. note esp. the query string option ‘output_nexml2json’: http://devapi.opentreeoflife.org/phylesystem/v1/study/pg_2584?output_nexml2json=1.2
21:06 josephwb ok
21:06 josephwb *wrong window*
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21:10 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#579 (master - bb52e65 : Jim Allman): The build passed.
21:10 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/3f4fbdb49b52...bb52e65a777e
21:10 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/31460684
21:10 travis-ci left #opentreeoflife
21:11 josephwb curl nexson is 323 kB; export from curator is 144 kB
21:12 towodo different nexson versions?
21:12 josephwb same study
21:12 josephwb not sure what you mean
21:12 josephwb re: nexson versions
21:12 towodo we went through different versions of the nexson format itself.
21:13 josephwb both were downloaded right now
21:13 josephwb so, should be same?
21:13 towodo right, but peyotl knows how to generate multiple versions of the same file. you have to choose which nexson version is to be generated. i think.
21:14 towodo can you eyeball them and say roughly what is different?
21:14 josephwb hmm. i didn't choose anything
21:14 towodo right, the curator tool did, and I’m suggesting maybe it chose wrong.
21:16 josephwb understood.
21:17 josephwb the curl file (larger) works, export from curator doesn't
21:19 josephwb is the version in the nexson?
21:21 jimallman it’s in the URL (see my note above)… what URL did you use from curl?
21:21 josephwb api.opentreeoflife.org/phyle...
21:22 jimallman https://github.com/OpenTreeOfLife/phylesystem-api/tree/master/docs#get-arguments
21:23 jimallman this describes the different values for “NexSON mapping” used (what we mean by “version”)
21:24 jimallman ah, it looks like the default is 0.0.0 (“vanilla” badgerfish JSON), while the curation app uses 1.2 (our preferred mapping)
21:24 josephwb i am using this for curl: https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#return-a-single-study
21:25 jimallman ok, so it looks like you’re getting the default 0.0.0 mapping.
21:25 josephwb ok. so that works.
21:26 josephwb that is how we are getting all of the studies for synthesis. Is that wrong?
21:26 jimallman i see how this is confusing, if you’re not interested in the details of our evolving format. maybe we can change the default maping to 1.2..?
21:27 jimallman the actual data should be identical, it’s just a question of how the JSON is structured. i think you’re fine.
21:27 josephwb ok
21:27 josephwb i must have missed the version discussion
21:27 jimallman (the curation app actually still uses 1.0.0)
21:27 josephwb treemachine apparently does not like the newer version
21:28 jimallman yeah, i’m not surprised
21:28 josephwb but we are supporting both formats?
21:30 jimallman yes, peyotl should produce all of three (0.0.0, 1.0.0, 1.2.x) with full data
21:31 josephwb good
21:33 josephwb ok, i can get what works by just curling the dev server
21:34 josephwb *phew*
21:57 jimallman glad to hear it! note that the download URLs on devtree are all just GET calls to the API, so most formats are done by file extension (.tre, .nex, …)
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22:43 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#580 (master - 7c25107 : Jim Allman): The build passed.
22:43 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/bb52e65a777e...7c25107e59e5
22:43 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/31466624
22:43 travis-ci left #opentreeoflife

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