Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-08-18

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All times shown according to UTC.

Time Nick Message
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16:07 josephwb did my first ever treebase import.
16:07 kcranstn yay!
16:07 josephwb brought in a bunch of taxa that do not appear in *any* trees
16:08 kcranstn which study?
16:08 josephwb curator says: "this is not expected". indeed
16:08 josephwb ronquist hymenoptera tip-dating paper
16:08 kcranstn in insects, I don’t know how unexpected that really is
16:08 josephwb maybe the taxa are in some data matrices, but not tres?!?
16:09 josephwb trees
16:10 josephwb kcranstn: i think you misunderstand: i imported a bunch of trees. with it came a list of taxa. a bunhc of those taxa are not in any of the study trees.
16:10 josephwb i didn't mean "new taxa to synthesis"
16:11 kcranstn ah, taxa in the treebase XML file that aren’t in any of the trees in the file
16:11 josephwb now the otu-mapping page is clogged with taxa that do not appear in any trees
16:11 josephwb yes
16:11 kcranstn argh
16:11 josephwb any you cannot remove these orphaned names, as far as i know
16:12 kcranstn we should be double-checking treebase studies for NJ trees that don’t appear in the paper
16:12 kcranstn (that has nothing to do with your current work, just a reminder to myself)
16:12 josephwb +1
16:12 josephwb hard to map tree files to figures, tho
16:13 josephwb most people do a *horrible* job labelling trees
16:21 josephwb jimallman: i created a new study on devtree this morning, got a bunch of "duplicate study" hits, but none turned out to be genuine
16:22 jimallman josephwb: yes, i have an open ticket to Cody about this. we have a cool duplicate-checking service now, but it’s kind of frisky and reports many false positives.
16:23 josephwb ok, i only report this cuz it looked like you closed the issue
16:23 josephwb but i see: not your problem
16:23 josephwb (oti)
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16:31 jimallman here’s the ticket: https://github.com/OpenTreeOfLife/oti/issues/19
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19:55 josephwb1 just ran into an instance where a custom context would help
19:55 josephwb1 2 taxa with same name *within* insects
19:56 josephwb1 curator returns one of them (with no explanation)
19:56 josephwb1 happens to be the wrong one (Dipteran, rather than Hymenopteran)
19:56 josephwb1 *very* hard to track down these problems
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20:16 josephwb1 ack! prod curator is returning names that are *not* valid synonyms.
20:16 josephwb1 looks like fuzzy matches
20:16 josephwb1 BAD
20:24 josephwb1 email sent to jimallman, cody, and kcranstn. this is an urgent problem.
20:28 kcranstn don’t see jimallman online...
20:28 josephwb1 i know…
20:29 kcranstn when was it last working properly?
20:29 josephwb1 not sure
20:30 josephwb1 had weird synonym hits earlier today
20:30 josephwb1 but the situation was odd (synonyms *within* insects)
20:31 josephwb1 so, i don't know
20:35 kcranstn I think we need tighter controls on production
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20:41 josephwb yeah, curator is currently unusable
20:42 kcranstn but we aren’t sure if the problem is curator or taxomachine
20:42 josephwb true
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21:40 kcranstn I can confirm that the mappings don’t correspond to entries in synonyms.tsv
21:43 towodo I think Cody & Jim will have to figure it out. If I speculate too great a chance of figuring wrong.
21:43 towodo sorry
21:44 kcranstn ok
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