Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-30

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All times shown according to UTC.

Time Nick Message
00:32 josephwb joined #opentreeoflife
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11:48 josephwb morning ilbot3
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12:48 josephwb you there jimallman?
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14:53 jimallman howdy, just catching up on email now..
14:53 jimallman josephwb: ^
14:59 josephwb hey jimallman. it was nothing. i wasn't up-to-date on emails myself, missed on of yours (answered my question)
15:03 jimallman i see. yeah, clearly the context list should be dynamic everywhere it’s used.
15:05 jimallman josephwb: i see that the list is pretty long these days. Would it be helpful to make it a nested list, with (inactive) parent items for FUNGI, ANIMALS, PLANTS, etc. and the real choices indented beneath?
15:05 josephwb maybe
15:06 josephwb it is plants that are the most blown out
15:06 jimallman i’ll try it here, and send some screenshots for general discussion
15:06 josephwb yes, general discussion would be good
15:07 josephwb the list is rather long, even as it stands on the curator
15:08 josephwb it is those pesky nonmonophyletic microbes which would make a nested list ugly
15:09 josephwb *done expressing opinion*
15:16 kcranstn joined #opentreeoflife
15:17 kcranstn if that list of contexts is getting too long, perhaps we can think about a text box entry instead?
15:18 kcranstn also, having one or more negative contexts would be helpful for Dail’s case (not in plants, not in animals)
15:18 josephwb +1 for -
15:19 kcranstn that probably needs a new service, not just UI
15:19 josephwb yeah…
15:20 josephwb i think this be some work for cody. should make sure it would be useful (i.e. relative to just more finely grained contexts)
15:23 josephwb excluding a context, or combining multiple contexts (e.g. Bacteria + Archaea) are not part of taxomachine.
15:40 jimallman i see that joseph has already found the mockup of a complete, indented list: https://github.com/OpenTreeOfLife/opentree/issues/396#issuecomment-50632119
15:41 jimallman kcranstn: my concern with a text box entry (assuming you mean autocomplete, too) is that it becomes a guessing game instead of a simple choice.
15:43 jimallman i think the boolean/exclusion idea is very interesting
15:45 kcranstn guessing game because not all names can be used as contexts?
15:45 josephwb right
15:45 * jimallman nods
15:45 josephwb https://github.com/OpenTreeOfLife/taxomachine/blob/master/src/main/java/org/opentree/taxonomy/contexts/ContextDescription.java#L23-72
15:46 josephwb those are the ones currently implemented.
15:46 kcranstn got it
15:46 jimallman hm, so is that an arbitrary list? i mean, *could* the search context be any clade?
15:46 josephwb have to be built by taxomachine upon building the graph, so can't do one the fly
15:47 josephwb i'm asking Dail whether anything is missing from the list
15:47 jimallman ok, i surmised as much from one of Jonathan’s comments
15:59 kcranstn is that pull request deployed on dev, @jimallman?
15:59 jimallman kcranstn: not yet, but i’ve tested it on my local server… pushing it to dev now...
16:03 jimallman it’s on dev now and working as expected :)
16:06 kcranstn so that list is coming from taxomachine now?
16:06 kcranstn doesn’t seem to match for me
16:06 kcranstn taxomachine out of sync?
16:08 jimallman or you might need to clear browser cache (old JS)… what’s missing vs. production?
16:08 jimallman (you should definitely see “SAR group”, for instance)
16:09 josephwb taxomachine has had the same contexts for… well, a long time
16:10 josephwb maybe only since 5 June
16:11 kcranstn nope - I see the same list in dev and production
16:11 kcranstn cache cleared
16:13 jimallman odd. at the risk of stating the obvious, we’re talking about the OTU Mapping list, right? the others (in tree browser and Metadata) were already dynamic.
16:13 kcranstn yes
16:13 kcranstn no SAR in my list
16:13 josephwb what are you looking at kcranstn? i can check too
16:14 josephwb on prod I see the same list as before
16:14 kcranstn and on dev?
16:15 josephwb new list
16:15 josephwb on dev
16:15 jimallman same here, and i’ve shut down my local server to be sure. no funny stuff in /etc/hosts, either.
16:15 josephwb but not with the unclickable categories
16:16 kcranstn ah, got
16:16 kcranstn it
16:16 jimallman right, categories were an in-browser mockup, still under discussion
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