Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-24

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All times shown according to UTC.

Time Nick Message
00:00 jimallman dammit, i forgot about opentreeapi-test-gh.pem
00:00 jimallman pushing again with that change in place...
00:00 mtholder do you need me to scp that key to the machine?
00:01 jimallman no, i have it, just modified the server-config for ot10 and pushed anew
00:01 jimallman hm, no dice. chasing the error now
00:03 jimallman same error. checking my .pem now...
00:04 jimallman mtholder: it looks like my files for opentreeapi-gh.pem and opentreeapi-test-gh.pem are the same. yes, please scp the proper 'test' version and i'll grab it for my own settings.
00:06 mtholder I just put it in .ssh on ot10
00:06 jimallman danke
00:06 mtholder I put opentree-hbf-test.pem in there too (for hbf_phylesystem_test)
00:10 jimallman i pushed again with the right pem in place this time. same error, though...
00:10 jimallman (as if no user.name, user.email was set in git config)
00:19 mtholder I just ssh'd in and tried interactive mode: No dice but different error:
00:19 mtholder Auto-merging study/9/9.json
00:19 mtholder CONFLICT (content): Merge conflict in study/9/9.json
00:19 mtholder Auto-merging study/10/10.json
00:19 mtholder CONFLICT (content): Merge conflict in study/10/10.json
00:19 mtholder Automatic merge failed; fix conflicts and then commit the result.
00:19 mtholder I've got to run. I'll try to diagnose later. sorry.
00:37 jimallman mtholder: sorry for slow reply, we're cooking dinner here.
00:38 jimallman yes, if I force the username and email into git_env (as describe above), i can get past the "missing name/email" error and see this conflict.
00:38 jimallman mtholder: by force, i meant adding this to the code in API's default controller:
00:38 jimallman git_env    = {"GIT_SSH": git_ssh, "PKEY": pkey, "GIT_COMMITTER_NAME": "OpenTree API", "GIT_COMMITTER_EMAIL": "api@opentreeoflife.org"}
00:38 jimallman this works, but should not be necessary!
00:39 * jimallman will check back again in a few minutes...
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01:11 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#425 (master - 81af84d : Mark T. Holder): The build passed.
01:11 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/4cd5f502f6c6...81af84db3fa1
01:11 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21394625
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01:15 mtholder jimallman, can you try updating the api from master? I just fixed something. I'm not sure it will solve your committer name stuff. But it was necessary for me to get my tests to pass multiple times on ot7
01:16 jimallman yes, will do
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01:20 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#426 (nudge-oti-index - 85fcb6c : Jim Allman): The build passed.
01:20 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/56cf6d4f2cb5...85fcb6cfa600
01:20 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21394937
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01:21 jimallman mtholder: same result.. i'm reading Emily's message for clues...
01:21 mtholder mind if I ssh to ot10 and try something?
01:24 mtholder jimallman: Are you seeing the problems locally and on ot10, or just on ot10
01:24 mtholder ?
01:25 jimallman mtholder: go for it! i'm seeing this on ot10, will try a local test now...
01:30 mtholder hmm. If you have the following in api.opentreeoflife.org/ws-tests/test.conf (on your local machine) the tests run against ot10. Content:
01:30 mtholder [host]
01:30 mtholder apihost = http://ashby.csail.mit.edu/api
01:30 mtholder then if you cd into the ws-tests subdir and run:
01:30 mtholder sh run_tests.sh
01:30 mtholder you test several aspects of the api.
01:30 jimallman ok, hold on.. i was trying it with local api
01:31 mtholder Those are now passing for me on ot10 and one is a study_delete test.
01:32 mtholder you have to have GITHUB_OAUTH_TOKEN in the env of the testing shell
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01:34 jimallman mtholder: i have local.test.conf and global.test.conf. i'm creating a new test.conf
01:34 mtholder yes.
01:35 mtholder I just global.test.conf is trash.
01:36 mtholder i like to keep local.test.conf around so that "cp local.test.conf test.conf" quickly configures me to test locally and "cp ot10.conf test.conf" makes me test against ot10.
01:36 mtholder test.conf is the only one that the scripts use.
01:36 jimallman GITHUB_OAUTH_TOKEN = ~/.ssh/opentree/opentreeapi-test-gh.pem?
01:36 jimallman or opentreeapi-gh.pem?
01:37 mtholder no it is one of those oauth tokens you get from github. looks like a sha
01:37 jimallman ah, for the API. ok...
01:37 jimallman apologies, i'm sleepy tonight
01:38 mtholder no prob. you were up late, i know...
01:40 jimallman mtholder: i created a personal access token on GitHub, but it's not working in my tests ("You have provided an invalid or expired authentication token")
01:40 jimallman lemme check that variable name
01:41 jimallman yep, s/AUTH/OAUTH
01:41 jimallman hmmm... passed 14 out of 14
01:41 jimallman mtholder: ^
01:42 mtholder good. I guess. Maybe.?
01:42 jimallman that's about how i feel about it. but progress! i'm taking a closer look at those tests now..
01:42 mtholder i pushed via ssh from ot10 to see the full error message, but it worked.
01:42 mtholder perhaps one interactive push was enough to get the username stuff working. odd.
01:43 mtholder much of the repetitive guts of the test is in opentreetesting.py in that dir.
01:43 jimallman !
01:43 mtholder so the tests are terse.
01:43 jimallman let me try again from the curation ui...
01:44 * jimallman is boggled
01:44 jimallman mtholder: yes, it's working from the curation tool now.
01:44 mtholder in a good way?
01:44 jimallman wat?
01:44 mtholder not cool.
01:44 mtholder a heisenbug
01:45 jimallman agreed. fwiw, i have done a number of "manual" git operations there, and it never just started working for me... :-
01:45 jimallman :-/
01:45 jimallman what exactly did you push?
01:45 jimallman esp. components?
01:46 jimallman no wait... your reference to "push" above was a git push from command line. never mind.
01:47 jimallman it is odd (to me, at least) that I didn't hang up on a conflict this time. did you untangle that manually, or ...?
01:47 mtholder yes. history lines 277-279 in the bash history on ot10. I also did a git reset --hard, but I think there was no effect of that.
01:47 mtholder perhaps my reset did that. sorry forgot that.
01:47 jimallman right, i tried that a few times (thinking it was a special case) and the conflict always returned.
01:47 jimallman that = git reset --hard
01:47 jimallman so i'm stumped
01:48 mtholder I think that the next system is going to be a lot less brittle. So hopefully we'll get local-dep merged to master soon and this oddness will be a thing of the past.
01:48 jimallman mtholder: dinner's ready here, so i'd like to break for awhile and sleep on this mystery. thanks for your healing touch!
01:49 mtholder bon appetit.
01:49 mtholder later.
01:49 jimallman yeah, i didn't mean to rush y'all on the new code.
01:49 jimallman but this will help us to merge in the delete and index-update stuff, which is great
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03:24 dfcnvt Where is the public user interface that I can interact and learn more about the tree of life? Seem can't find it.
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03:29 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#428 (master - 1261c83 : Mark T. Holder): The build passed.
03:29 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/81af84db3fa1...1261c83b5998
03:29 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21399456
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03:34 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21399601
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14:51 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#430 (caching-validation - 147bdb1 : Mark T. Holder): The build passed.
14:51 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/b86a16b45f06^...147bdb167abc
14:51 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21431115
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16:40 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21439573
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16:42 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#432 (caching-validation - 73588f3 : Mark T. Holder): The build passed.
16:42 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/a64b14a87e43...73588f360b20
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20:06 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#433 (caching-validation - a8dbca0 : Emily Jane McTavish): The build passed.
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20:29 kcranstn I see an action item on the notes about making jimallman an org admin for opentree on github
20:37 kcranstn Is admin sufficient, or does Jim need owner-level permissions: https://help.github.com/articles/what-are-the-different-access-permissions
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21:57 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#434 (local-dep - 451ab8e : Emily Jane McTavish): The build passed.
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