Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2013-12-11

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Time Nick Message
06:27 dukeleto joined #otol
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06:57 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#216 (local - acaa98d : Jonathan "Duke" Leto): The build passed.
06:57 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/2f6762a0759b...acaa98dfc9fb
06:57 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/15269172
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07:03 travis-ci [travis-ci] OpenTreeOfLife/treenexus#72 (leto_study_1003 - 8586c26 : Duke Leto): The build passed.
07:03 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/ba60fe2b27b3...8586c2625bc5
07:03 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15269210
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07:03 travis-ci [travis-ci] OpenTreeOfLife/treenexus#71 (leto_study_1003 - ba60fe2 : Duke Leto): The build passed.
07:03 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/8ed82cc625eb...ba60fe2b27b3
07:03 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15269208
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07:19 travis-ci [travis-ci] OpenTreeOfLife/treenexus#73 (leto_study_12 - 0ad49d5 : Duke Leto): The build passed.
07:19 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/commit/0ad49d59a88d
07:19 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15269541
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07:21 travis-ci [travis-ci] OpenTreeOfLife/treenexus#75 (leto_study_o2711 - 46658dd : Duke Leto): The build passed.
07:21 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/183001f6a6f4...46658ddf93d5
07:21 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15269549
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07:22 travis-ci [travis-ci] OpenTreeOfLife/treenexus#74 (leto_study_o2711 - 183001f : Duke Leto): The build passed.
07:22 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/commit/183001f6a6f4
07:22 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15269547
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15:40 jimallman joined #otol
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17:37 dukeleto jimallman: i succeeded in getting the OpenTree API deployed and functioning (read/write/deletion/creation) on ot1 last night
17:38 jimallman sweet! i'll enable deletion ASAP.
17:38 jimallman any word on the creation options (import from TreeBASE, etc?)
17:39 jimallman ...or are we just creating empty "skeleton" Nexson for now?
17:40 dukeleto jimallman: the creation takes the nexson to be created, but the import stuff has not been implemented
17:40 jimallman ah, ok
17:41 jimallman but handles folder and WIP branch(?) creation, i guess.
17:41 jimallman have we got a solid plan for assigning study IDs? i think it's going to come up in today's call...
17:41 dukeleto jimallman: yes, it searches master and WIP branches for the highest study id and then prepends an "o" to the next highest ID
17:42 jimallman got it. will Phylografter also have a prefix ("p###")? i believe Karen at least is still more interested in GUIDs..
17:43 jimallman i have no strong feeling on the matter.
17:43 dukeleto jimallman: here is an example: https://github.com/OpenTreeOfLife/treenexus/commit/4e646d72d5d945a3112e84dc8d4cf9d8557908a4
17:44 jimallman cool.
17:45 dukeleto jimallman: right now, only studies created via the API get the prefix, so new studies from the API don't conflict with new studies from phylografter
17:45 dukeleto jimallman: it seemed that jonathan was not so keen on GUIDs, but I don't have a strong pref
17:46 dukeleto jimallman: GUIDs will likely not feel very friendly to end users, but perhaps they are needed
17:47 jimallman we'll see how the call goes. i don't know whether it matters that phylografter has already generated lots of simple study IDs.
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17:53 travis-ci [travis-ci] OpenTreeOfLife/treenexus#77 (leto_study_o2712 - 7acea5f : Duke Leto): The build passed.
17:53 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/4e646d72d5d9...7acea5fa06e9
17:53 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15297454
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17:55 travis-ci [travis-ci] OpenTreeOfLife/treenexus#76 (leto_study_o2712 - 4e646d7 : Duke Leto): The build passed.
17:55 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/commit/4e646d72d5d9
17:55 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15297452
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17:57 dukeleto jimallman: do you have any concerns with me merging my "local" branch into the API master and my deploy branch into opentree.git ?
17:58 jimallman not that i can think of, no.. am i correct that "local" has tweaks to run in your own development environment, while "deploy" is set up to deploy normally, via push.sh?
17:59 jimallman if so, just make sure that push.sh and other deployment tools know which branch to pull on the remote side..
17:59 dukeleto jimallman: "local" is actually the implementation of committing to git "locally" instead of via the Github API
18:00 jimallman ah, got it. sure, go for it.
18:00 dukeleto jimallman: i have a "deploy_local_git" branch on opentree.git for testing deployment. Currently it tests against the "local" branch but I will change that over to master before merging
18:01 jimallman sounds good to me
18:01 dukeleto jimallman: there is one piece of the puzzle that I had to do manually, which is a one-time-per-new-server thing: copying our deployment SSH keys to ~opentree/.ssh
18:04 dukeleto jimallman: if you have ideas about how to automate that, please let me know
18:05 jimallman ah, good point. i suppose this should be done by whoever/whatever creates to 'opentree' userid
18:09 dukeleto jimallman: do we have documentation anywhere about parts of deployment that are not automated?
18:10 jimallman the readme in /deploy is the documentation
18:10 jimallman ...and yes, it does document this as a manual (preliminary) part of server setup
18:10 jimallman https://github.com/OpenTreeOfLife/opentree/tree/master/deploy
18:11 dukeleto jimallman: ok, i will add stuff there
18:11 jimallman it looks like we upload the .pem file manually, then the script does the rest, including setting up the unprivileged 'opentree' user
18:12 jimallman dukeleto: ^
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19:29 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#217 (local - 75418b0 : Jonathan "Duke" Leto): The build passed.
19:29 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/acaa98dfc9fb...75418b06042e
19:29 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/15302431
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19:40 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#219 (master - 44a536a : Duke Leto): The build passed.
19:40 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/b1eb578de21c...44a536aad086
19:40 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/15302920
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22:24 travis-ci [travis-ci] OpenTreeOfLife/treenexus#78 (jimallman_study_10 - 55d80be : Jim Allman): The build was broken.
22:24 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/70e23e1dbe85...55d80beef817
22:24 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15310798
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22:41 travis-ci [travis-ci] OpenTreeOfLife/treenexus#80 (jimallman_study_10 - 6b4e32e : Jim Allman): The build is still failing.
22:41 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/912e21aaa786...6b4e32ed96c3
22:41 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15311843
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