Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-05-05

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All times shown according to UTC.

Time Nick Message
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02:15 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#513 (modified-study-creation - 43cf068 : Jim Allman): The build has errored.
02:15 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/3baacbecb5fe...43cf0685870e
02:15 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24422205
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02:25 jimallman mtholder: quick question… does the to_nexson service capture study metadata (reference, etc) as well as trees? my initial tests are getting all the tree data but nothing else.
02:26 jimallman i’m poking around to see if i’m missing an option or default, but i figured you’d have a quicker answer.
02:56 mtholder jimallman: sorry. I was logged in to IRC, but had the sound down so I did not notice your Q.
02:56 jimallman no prob
02:56 mtholder I thought that metadata came in with treebase imports
02:57 mtholder those are nexml
02:57 mtholder no metadata for nexus or newick.
02:57 mtholder I'll double check the treebase import...
02:58 jimallman you’re right about treebase, i saw that in my test. but pasting in nexml from your test files, no study metadata shows up (and i see a reference string in the nexml).
02:58 jimallman that was file S15515.xml
02:59 mtholder That is unfortunate, but I do understand it. I'll start an issue in the api for this.
02:59 jimallman i tested treebase id http://treebase.org/treebase-web/search/study/summary.html?id=1925
02:59 jimallman ah, ok. i’ll press on for now. there are lots of wrinkles to the different import paths, and i need to put it on the shelf for the next couple of days...
02:59 mtholder basically treebase imports go through get_ot_study_info_from_treebase_nexml in peyotl/external.py
03:00 mtholder because I know what metadata to expect for them
03:00 jimallman yeah, i figured it was happening on a separate path..
03:00 mtholder other nexml is a bit wilder.
03:00 jimallman i’m shocked.
03:01 mtholder I'm sure you are. This must be the only case of sloppy standards compliance in all of bioinformatics
03:01 jimallman hey, bonus question: are you OK with me merging this stuff (new creation UI) to master, deploying on the dev site, and pointing it all to the dummy docstore on ot6? i thought this was implied in your changes to deployed-systems, but there are lots of little tweaks in the different config files to make it work.
03:01 mtholder I just need to make my function more resistant to missing fields, and then call it from other import avenues.
03:01 jimallman ah, got it.
03:02 mtholder sounds good to me (the point at ot6 stuff).
03:02 mtholder I'm trying to get the update-phylesystem-from-phylografter step working.
03:04 jimallman hm, big changes recently?
03:05 mtholder no. I just want it to use the API rather than the git repo. I may abandon that if it looks messy.
03:05 jimallman i see. hey, i had a notion for simplification of the config files…
03:06 mtholder that sounds promising.
03:06 jimallman why not put the server list (mapping of short names like ‘ot7’ to AWS hostnames) in a top-level script? then all the server-config files can at least just say stuff like:
03:06 jimallman OPENTREE_NEO4J_HOST=${OT9}
03:07 mtholder I like that a lot.
03:08 jimallman it’s almost there now, since we have ‘opentree-servers-txt’
03:08 mtholder presumably if each config source the top level one, then there would not need to be any changes to the deploy scripts.
03:08 jimallman right
03:08 jimallman i’ll save what i’m working on now, then try this in a separate commit
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03:31 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#515 (modified-study-creation - 0850dde : Jim Allman): The build has errored.
03:31 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/43cf0685870e...0850dde2d6bf
03:31 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24425235
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03:33 jimallman mtholder: sorry to bother you again, but i’m having trouble with the latest API. it fails the test build in Travis:
03:33 jimallman https://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org
03:36 jimallman but maybe this is expected? it’s been failing with the same error for the last two days at least..
03:40 mtholder I need to add peyotl to the prereqs for travis. What are the failures that you are seeing?
03:41 mtholder (other than travis)?
03:42 mtholder jimallman: ^
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03:42 jimallman nothing but this error in travis:
03:42 jimallman File "/home/travis/virtualenv/python2.7.6/lib/python2.7/site-packages/pkg_resources.py", line 588, in resolve
03:42 jimallman raise DistributionNotFound(req)
03:42 jimallman pkg_resources.DistributionNotFound: peyotl
03:42 jimallman The command "python setup.py develop" failed and exited with 1 during install.
03:42 jimallman Your build has been stopped.
03:43 jimallman mtholder: see for example https://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24422205
03:43 jimallman i’m sort of halfway into these changes, so i’m inclined to press on and merge to master if you think this is a false alarm.
03:44 mtholder I think that it is. but I'll try to satisy travis.
03:47 jimallman no stress. for now, i’m reverting the deployment config back to its prior state and pushing, so we’ll have old-but-stable dev. i’ll be in meetings Monday, but I can try again Mon night.
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03:54 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#517 (master - a559c04 : Mark T. Holder): The build passed.
03:54 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/b993efcece7b...a559c046b88d
03:54 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24425939
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03:55 mtholder I think i fixed it. Thanks for letting me know. It worked fine if you had installed peyotl previously, but clean installs failed.
03:55 mtholder jimallman: ^
03:55 jimallman yes, that makes sense.
03:56 jimallman hm, Travis is still failing on my pull request. thoughts?
03:56 jimallman https://github.com/OpenTreeOfLife/api.opentreeoflife.org/pull/84
03:56 jimallman mtholder: ^
03:57 jimallman should i merge from master to this branch?
03:59 * jimallman is trying that now...
03:59 mtholder i think that if you do something to trigger a rebuild it will work (the problem was with peyotl not api)
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04:00 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#518 (master - 16d2eb1 : Mark T. Holder): The build passed.
04:00 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/a559c046b88d...16d2eb18a253
04:00 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24426007
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04:00 mtholder the changes all look fine. I'll merge.
04:01 mtholder oops. that is what you mean by "is trying now..."
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04:02 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#521 (master - d74c699 : Jim Allman): The build passed.
04:02 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/16d2eb18a253...d74c6991c8f0
04:02 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/24426245
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