Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-18

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Time Nick Message
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01:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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12:23 josephwb mtholder: I am a bit confused regarding your response on the contextQueryForNames issue
12:23 josephwb you state "the call specified no contextName"
12:23 josephwb but that context is what is to be inferred
12:25 josephwb i don't believe "contextName" is a possible argument for contextQueryForNames
12:25 josephwb it is for "autocompleteBoxQuery", but (I don't think) not "contextQueryForNames"
12:29 josephwb don't think you're here, so put these comments in github issue https://github.com/OpenTreeOfLife/taxomachine/issues/51
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12:34 kcranstn_ contextName is indeed an argument
12:35 mtholder I was thinking of "context" as the echoing of the "contextName" arg.
12:36 mtholder it makes sense if it is inferring it. though then there is still the issue of why it only returns the plant hit (or only the animal for drosophila)
12:37 josephwb kcranstn_: i stand corrected (but don't understand why)
12:37 mtholder some documentation would be nice
12:37 mtholder I'll take a look at the code...
12:38 josephwb the only way i see it making sense is to *narrow* a context
12:38 mtholder yes that would make sense.
12:38 josephwb e.g. with a bunch of plants, specify the context as plants to narrow it to Eudicots
12:39 josephwb or Metazoa to mammals
12:39 josephwb or, I'm an idiot
12:41 mtholder it look like if contextName is null then setAutomaticContextInference(true) is used. So in that case, I think that "context" in the response will be identical to "contextName" in the query
12:41 mtholder but if it is left blank, if finds the narrowest named context (I am guessing)
12:41 mtholder "it is blank" = "contextName is not passed in as an arg"
12:42 mtholder sorry. "it is left blank" = "contextName is not passed in as an arg"
12:43 josephwb sounds right
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13:37 josephwb blackrim: wife is sick, so i need to take my son to swimming lessons this AM
13:38 blackrim josephwb: no problems. hope she feels better!
13:38 josephwb we've all been through it in the last week: 24 hrs of no energy
13:39 josephwb so, not painful
13:40 josephwb running metazoa synth now
13:40 josephwb birds ran successfully yesterday
13:40 josephwb not great, but not horrible either
13:41 blackrim ok, you think there are mapping things or other issues with how things are getting in?
13:41 blackrim or changes to taxonomy?
13:41 josephwb yes?
13:41 josephwb but likely minor things. tree is not too far off from last one
13:41 blackrim presumably, the error you had is fixed and the trees are reflected in synth (and no ______ bits)
13:41 josephwb same studies as before
13:41 josephwb yes, the ___ thing is gone
13:43 josephwb i had made a change to 'cleanName'
13:44 josephwb thinking it was unnecessary
13:44 blackrim I see. I am running plants now but will get Bryan to take a look at taxonomy of plants to make sure things are good.
13:44 josephwb it was necessary
13:46 josephwb hope to get started with dail today in selecting/ordering microbe studies
13:48 josephwb ok, off to swimming
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17:14 jimallman mtholder: i see that the phylesystem-1 shard on devapi is 29 commits ahead its origin. is this expected?
17:14 jimallman https://gist.github.com/jimallman/b908576757905616a3c8
17:14 mtholder nope.
17:14 mtholder i'll look into it.
17:15 jimallman thanks!
17:17 mtholder actually it is not a problem. It is not pulling, but the mirror pulls from the working repo and github.
17:17 mtholder opentree@ashby:~/repo/phylesystem-1_par/mirror/phylesystem-1$ git status
17:17 mtholder # On branch master
17:17 mtholder nothing to commit (working directory clean)
17:17 mtholder It is confusing though. Thanks for pointing it out.
17:17 mtholder I'll create an issue.
17:19 mtholder https://github.com/OpenTreeOfLife/phylesystem-api/issues/95
17:20 mtholder jimallman^
17:21 jimallman mtholder: but doesn’t this mean that we’re holding onto local changes (new/modified/deleted studies) without pushing back to github?
17:21 mtholder no. the working repo doesn't know that it has pushed.
17:22 mtholder 'cuz the mirror pulls from the working dir.
17:22 mtholder the top commit in the working dir and github are the same now.
17:22 mtholder it has been 27 commits since our last pull (to the working repo)
17:22 jimallman ok, that makes sense. i was concerned when i went looking for the new supporting-file information on ot_22, and realized it wasn’t on github. but i see it’s there now.
17:23 mtholder I need to get the pulls working and then this confusing state will go away.
17:23 jimallman not sure what the lag-time is, i was mainly concerned about oti having stale info
17:23 jimallman ok, sorry for the false alarm
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