Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-27

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Time Nick Message
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15:06 josephwb you there jimallman?
15:06 jimallman josephwb: howdy!
15:06 josephwb ran into something
15:07 josephwb i uploaded a tree with a bad label (missing actually: NA)
15:07 josephwb so I deleted the tree
15:07 josephwb but all of the taxa from that original tree (including NA) remain in the OTU mapping
15:07 josephwb even with no trees associated with the record
15:08 josephwb can i get rid of them?
15:08 jimallman hmm. yes, we don’t currently sweep for “orphaned” OTUs in this case.
15:08 josephwb ok, so just ignore?
15:08 jimallman in fact, if you re-import a tree (make a second copy), it will get a new ID and a whole slew of duplicate OTUs will be created.
15:08 josephwb oh, crap
15:09 jimallman yeah, we’ve taken a very conservative approach to merging or cleaning up unique elements.
15:09 josephwb shold i just trash the study then?
15:09 jimallman i’m not the right person to ask. i rather think they’re just harmless clutter.
15:09 jimallman since they’re not used in any tree, synthesis should be unaffected, right?
15:10 josephwb yeah. but: aesthetics, man!
15:10 josephwb i will throw it out
15:10 towodo they'll show up in searches
15:10 jimallman i hear you! we could talk to mtholder about adding logic to clean this up on save, or when removing a tree.
15:10 jimallman we already pass new trees to the server for appropriate merging.
15:11 jimallman shall i do this (raise the question with Mark) in the form of a ticket?
15:11 josephwb oh, i don't see how to delete a study anymore
15:12 josephwb http://devtree.opentreeoflife.org/curator/study/view/ot_40
15:12 jimallman Login to Edit, then the Delete button will appear..
15:13 jimallman big, red button (i had to check myself)
15:13 josephwb yup, thanks
15:17 josephwb jimallman minor thing: when mapping, if I reject a mapping before the entire list is done, it seems to add the name back into the queue
15:17 jimallman yes, i try to keep the party going.
15:18 jimallman i guess it would make sense to give you a chance to try some modifications/hinting. think i should pause mapping when something gets rejected?
15:19 josephwb nah, just an observation. not a big deal.
15:19 josephwb and another thing (tho probably a taxomachine thing?): "Genus sp." taxa are getting mapped to "Genus sp. random suffix". These should instead be mapped to "Genus"
15:20 josephwb *random emoticon*
15:26 josephwb jimallman ^
15:27 jimallman hm… that makes sense. i’ll start tracking this (planning to move some TNRS code today)…
15:27 josephwb jimallman (sorry to keep bugging you): what is the ordering criterion for studies in the curator e.g. http://devtree.opentreeoflife.org/curator
15:27 * jimallman does a thing
15:27 josephwb it is not by name, or upload date
15:27 josephwb or curator
15:28 jimallman see the active filter… looks like the default is sort by publication date, newest first
15:28 josephwb is it pubdate + something esle?
15:29 jimallman josephwb: ^^
15:29 jimallman pub date, newest first
15:29 josephwb it somehow finds out when different 2014 papers come out?
15:29 towodo (then random if date is same?)
15:29 josephwb ok
15:30 jimallman right, there’s no secondary sort if dates are close.. it’s Javascript sorting, so the previous order will linger
15:31 jimallman regarding date sorting, i think it’s just the year. which is kind of clunky
15:34 josephwb i think year/name is most intuitive
15:35 josephwb fyi: the different aliases thing seems back e.g. "Joseph Brown", "Joseph W. Brown"
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16:01 jimallman josephwb: i had guessed the changing author name reflected a change in your GitHub profile. did you change your name there?
16:01 jimallman or is one of these names possibly “inherited” from phylografter?
16:03 josephwb phylografter, i guess
16:04 josephwb i don't care. it was just raised as an issue before (and fixed, i thought)
16:14 jimallman josephwb: nah, once the curator name is added to a study, i don’t see how we can detect that it’s actually a similar-but-not-quite-the-same name. but i’m surprised that we’re not seeing studies with both names..
16:15 jimallman josephwb: yes, as predicted… self-collaboration!  http://devtree.opentreeoflife.org/curator/study/view/pg_2851
16:16 josephwb wee!
16:16 jimallman maximum impact!
16:16 josephwb those guys work great together
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19:22 josephwb towodo: i put the file up on ot10, updated the index.html page (https://github.com/OpenTreeOfLife/opentree/blob/master/deploy/files.opentreeoflife.org/trees/index.html), and did the "push -c …" deploy command
19:22 towodo did you say "push.sh … files" only I hope?
19:22 josephwb you mention in your email do do it independently on the "live site". what/where is that?
19:23 josephwb i did "http://push.sh/ … opentree"
19:23 towodo nope.
19:23 towodo the index doesn't go live unless you either copy it manually to ot10, or use 'push.sh -x ot10.confg files'
19:24 towodo it's not part of the opentree component
19:24 towodo I can see why it's confusing.
19:24 josephwb ok
19:24 towodo because it's in the opentree repo.   maybe I should move it.
19:24 towodo and you're using the config file from deployed-systems, right?
19:25 josephwb yes
19:26 towodo ok.  files.opentreeoflife.org = ot10, so if the file is under that files.etc directory on ot10, it will be 'live'
19:26 josephwb oh, there it is
19:26 josephwb did you do that, oe me?
19:26 josephwb or me
19:26 towodo the push.sh … files command pushes the little files from the files dir in the opentree repo out to that directory
19:26 towodo I didn't do anything
19:27 josephwb all i did was push -c … opentree
19:27 josephwb a delay, i guess
19:28 josephwb index page needs a line break, but I need to go pick up daughter
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