Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-19

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All times shown according to UTC.

Time Nick Message
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00:54 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#167 (master - 9ed5a96 : Jim Allman): The build passed.
00:54 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/2c40d6181218...9ed5a9674632
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04:54 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#383 (study_import_options - df2290c : Jim Allman): The build passed.
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05:19 mtholder hi jimallman. re your email: I was intending that get_ot_study_info_from_treebase_nexml would wrap get_ot_study_info_from_nexml and would move some of the meta elements around, but I've never implemented that.
05:19 mtholder I think that treebase stores some info that we'd like in meta tags,
05:19 mtholder but not the same tags that we are using.
05:20 mtholder the api should not care what version of nexson you use so long as the "@nexml2json" tag is set correctly to 0.0 or 1.0 or 1.2.1
05:21 jimallman right, i'm seeing 'nex:nsxml', with 'meta' inside as expected... but (as you say) it's different stuff
05:21 mtholder confusingly the @version property is the NeXML version not the nexson.
05:22 jimallman agh, OK. I had '0.9' in my badgerfish template earlier, is that correct?
05:22 mtholder 0.9 is correct
05:22 jimallman cool, will revert.
05:23 jimallman so do i understand correctly, that get_ot_study_info_from_treebase_nexml will make general adjustments like 'nex:nexml'  ==>  'nsxml'  ?
05:23 mtholder I have peyotl looking for nex:nexml or nexml as the root element. I hope there is not a lot of other namespaced property decorating
05:23 mtholder I can make it do that.
05:23 mtholder are you seeing lots of other properties with namespaces?
05:23 jimallman i'll take  look and see. i can of course teach the curation JS to be more tolerant, too, but that's going to touch a LOT of code.
05:24 mtholder I think that would be unwise.
05:24 mtholder js doesn't have namespaces, so we shouldn't expect that of clients
05:24 jimallman other prefixes I'm seeing: dc: prism: skis: tb: ...
05:25 mtholder perhaps I'll make get_ot_study_info_from_treebase_nexml do the trimming. we can probably trash a fair number of those to get to lean and mean ot studies...
05:26 jimallman seems sensible.. should we be tracking the original import source in the NexSON we save?
05:26 mtholder Emily and I are trying to get the local (peyotl) and local-dep (API) branches working. Hopefully tomorrow on that...
05:26 mtholder yeah, that seems wise.
05:27 mtholder could datadeposit be used for that?
05:27 jimallman my latest work is also still on branches, opentree/add-new-study and api/study_import_options
05:28 mtholder after we get the newer api stuff deployed, I can take a stab at cleaning these attributes in treebase studies.
05:28 jimallman re: datadeposit, yes, that makes sense to me. we'd point back to TreeBASE for the datadeposit and block (or allow additions to?) the supporting files there.
05:29 mtholder it is so much easier to test for deadlocks and odd scenarios if we move a lot of the git workflows to peyotl and call those from the api. So that is what EJM and I have mainly been doing today.
05:30 mtholder When we deploy those local branches, the client will have to supply the parent SHA for PUTs
05:30 jimallman sounds great! don't rush the TreeBASE cleanup on my account.. i can work on something else tomorrow (mmm, git hooks...)
05:30 jimallman FYI - the curation is already sending the SHA on PUTs... it's a query-string value... lemme see...
05:31 jimallman "starting_commit_SHA"
05:31 mtholder I'm afraid that the new validation (now deployed on ot7) maybe too stringent, so you might want to see if that service is being to picky.
05:31 mtholder cool on starting_commit_SHA I'll look for that.
05:31 jimallman mm, OK. i'll take a look at new validation in the morning.
05:32 jimallman hey, we got a media shout-out today.. i was just about to post this to the software mailing list:
05:32 jimallman http://billmoyers.com/2014/03/18/science-deniers-are-freaking-out-about-cosmos/
05:32 mtholder We had been inconsistent on booleans being "true" in some contexts and true in others. it is picky about that, but the GET should return clean nexson. on ot7 it is coming from the hbf_phylesystem_test.
05:33 mtholder Karl Gude mentioned that we had a spike of blog followers, probably from Moyers...
05:34 jimallman my wife was suitably impressed :)
05:34 mtholder that is what it is all about ;)
05:36 * jimallman is Done For The Day, talk to you tomorrow...
05:36 mtholder good night.
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