Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-08-19

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01:48 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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03:07 josephwb jimallman: apologies for raising the klaxon alarm today
03:10 jimallman josephwb: no problem! i’m reviewing emails now.
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11:22 josephwb morning ilbot3.
11:22 josephwb all is well?
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20:29 josephwb hey jimallman
20:29 jimallman josephwb: howdy. testing a quick fix for OTU mapping now…
20:29 josephwb cody and i have been talking about the missing taxon issue that was raised on the call
20:30 josephwb making a service that will return 1) whether is in the graph, 2) whether it is in the synthetic tree
20:30 kcranstn nice!
20:30 josephwb should be helpful?
20:30 josephwb so, if not in graph, you know to look at flags
20:31 josephwb if in graph, but not in synth tree, tell them it is not monophyletic
20:31 kcranstn although, don’t we know that already? (i.e. we are able to display error messages in the curator for each of these instances)
20:32 josephwb this seems like it would be more streamlined(?)
20:33 josephwb we could add that if it is not in the synth tree, return the nearest ancestor that *is* in the tree
20:33 josephwb i.e. for the Laura's out there
20:33 josephwb (Stephen's example)
20:34 kcranstn that would be helpful
20:35 kcranstn returning the nearest ancestor
20:35 jimallman OK, that sounds better than building links to all ancestors and saying “Go fish!”
20:35 jimallman (since currently, these links would not be guaranteed)
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20:41 josephwb1 i have disconnected, apparently
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21:33 jimallman kcranstn: As requested, i’ve added a pull request (incl. screenshots) for the “phase 1” messages for missing/isolated taxa. If accepted, this will merge to ‘master’ instead of Cavia, so we’d still need to decide what goes to production (Cavia). If you want just these changes on production, we’ll need to cherry-pick to a new branch and PR.
21:34 jimallman https://github.com/OpenTreeOfLife/opentree/pull/404
21:55 kcranstn thanks, jimallman!
21:58 kcranstn I think the messages might be reversed
21:58 kcranstn the disconnected node = in taxamachine but not monophyletic in synthetic tree
21:59 jimallman argh! that’s what i had before.
22:00 kcranstn :0
22:00 jimallman reversed these based on yesterday’s call. science is hard.
22:00 kcranstn :)
22:00 kcranstn science IS hard
22:00 kcranstn I also have suggestions for the text. Will add to the PR
22:00 jimallman thanks. mind if i revert the message-switch first?
22:01 kcranstn sure
22:01 jimallman one sec
22:04 jimallman OK, reverted in the PR. want new screenshots?
22:04 kcranstn no, that’s fine
22:04 jimallman ok.
22:13 kcranstn done
22:15 jimallman kcranstn: singular form of taxa is taxon? or is either taxon or taxa OK?
22:16 kcranstn argh. yes, singular = taxon
22:16 kcranstn brain fart
22:16 kcranstn fixed
22:16 jimallman ok. and are you asking me to remove links to Home and “show details” (admittedly these is usually gobbledegook)
22:17 kcranstn the home link is fine. not sure what is under the Show Details
22:18 jimallman it’s the server-side error or exception, usually TaxonNotFound JSON:
22:18 jimallman { "exception" : "TaxonNotFoundException", "fullname" : "opentree.exceptions.TaxonNotFoundException", "stacktrace" : [ "opentree.GraphBase.findGraphTaxNodeByUID(GraphBase.java:125)", "opentree.plugins.GoLS.getNodeIDForottId(GoLS.java:682)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
22:18 jimallman { "exception" : "TaxonNotFoundException", "fullname" : "opentree.exceptions.TaxonNotFoundException", "stacktrace" : [ "opentree.GraphBase.findGraphTaxNodeByUID(GraphBase.java:125)", "opentree.plugins.GoLS.getNodeIDForottId(GoLS.java:682)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)",
22:18 kcranstn argh
22:18 kcranstn yes, let’s not show that. It doesn’t really help
22:19 jimallman agreed. once in a blue moon, there will be a different error (API outage)… but I’m checking for the TaxonNotFound error before telling them the taxon is not in the system.
22:19 jimallman so if it’s a different error, i’ll keep the ugly details (as we do elsewhere) to help troubleshoot problems
22:19 kcranstn that makes sense (when the errors help us). In this case, we know the error
22:36 jimallman ok, ready for review (incl. screenshots)
22:37 kcranstn merged
22:42 kcranstn in completely different news, my chickens are moulting really early this year
22:43 jimallman Pher says end of summer is typical for our birds. Poor itchy birds!
22:44 kcranstn our moulted really late last year (they were cooooold)
22:45 jimallman it’s been interesting to see how parrots are different. no big moult, just occasional feathers dropping. Supposedly it’s symmetrical, they’ll always drop a matched pair (so as not to affect flight), but i’ve seen a couple of big’uns with no match.
22:46 kcranstn yeah, flying is not that important for the chix
22:46 jimallman more of a stunt
22:46 kcranstn assisted running
22:46 jimallman exactly
22:47 jimallman ours get more value from feathers as protection than escape (near-misses where the predator just gets a mouthful of fluff)
22:48 jimallman re: the latest changes, i’m looking over the master branch to see whether we’re OK for a push to Cavia (production). i don’t think there have been major changes in OT taxonomy or other dependencies, so we might be able to push up a lot of good stuff (incl. today’s OTU mapping tweaks).
22:48 jimallman meanwhile, i should push our latest to devtree
22:49 kcranstn ok
22:53 jimallman done, working now on devtree
22:54 jimallman i’ll work on a second PR with the “phase 2” messages (some flag information, but less than before)… should have that tomorrow AM
22:54 kcranstn sorry about the delay in responding to your first request for feedback on this...
22:55 kcranstn let me know if you want to bounce some ideas for messages
22:58 jimallman Thanks, will try some ideas later on devtree (on a separate branch). Off to dinner for awhile…
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