Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-05-05

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All times shown according to UTC.

Time Nick Message
01:45 josephwb joined #opentreeoflife
07:28 mtholder joined #opentreeoflife
10:57 mtholder joined #opentreeoflife
11:42 josephwb joined #opentreeoflife
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14:08 josephwb hey jimallman
14:19 jimallman hi! what’s up?
14:19 josephwb sent an email
14:19 josephwb about seeing "supported by" sources in the web tree browser
14:19 josephwb only "taxonomy" appears at the moment
14:19 josephwb i'm sure you have it in hand
14:20 josephwb mtholder was investigating stuff
14:20 josephwb jimallman ^
14:20 jimallman yes, trying to wrap this up now. hoping to have it ready by our noon meeting
14:20 josephwb gotcha
14:30 jimallman josephwb: i’m hitting a minor snag due to oti indexing some phylografter studies (eg, ‘pg_1234’) as ’1234’, ignoring the pg_ prefix. i’m going to ignore this, since AFAIK all studies in production are prefixed.
14:31 josephwb huh. i have no idea what that is about
14:32 jimallman i think this is a known issue. would be great to replace the data on dev to match our production data (sigh)
14:32 josephwb which data? oti?
14:37 josephwb oh, i see what you mean
14:43 jimallman hm, in fact it seems we now have a mismatch between dev-oti and production data. does that sound right?
14:43 josephwb i don't know about oti
14:44 jimallman in other words, the synthetic tree on devapi uses studies that are not indexed in “dev-oti”, so i’m trying to fetch study info and getting unexpected results. if i run the same fetch on the “production-oti” i get solid hits. this is going to show dumb stuff until we’re on production, which makes for uncomfortable testing.
14:44 josephwb oh, i see
14:45 josephwb is it the gitsha, or the entire study?
14:45 josephwb i know some studies were being deleted by emily
14:45 josephwb dup studies, that is
14:46 josephwb i asked that she make sure not to delete synth input studies
14:47 josephwb or is it just that dev-oti is indexing the dev-curator (with far fewer studies)?
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15:59 jar286 jeez, I leave my house to get away from leafblowers, and arrive at MIT to the sound of concrete drills
16:00 kcranstn :)
16:02 jimallman josephwb: regarding your earlier question, i assume it’s the latter (dev-oti is indexing studies from dev-curator)
16:02 jimallman so lots of duplicates and missing studies. for now, i’m working around this by testing with production-oti.
16:02 josephwb ah
16:02 josephwb that makes sense
16:03 kcranstn you two joining the hangout?
16:03 josephwb isn't it skype?
16:03 jimallman oops, i was on skype :-/
16:03 josephwb doh
16:03 josephwb i was waiting on skype too
16:29 josephwb you there jimallman?
16:29 jimallman no, i’m on skype  :-/
16:29 jimallman sup?
16:29 jimallman josephwb: ^
16:29 josephwb is dev short on space?
16:29 jimallman not sure, but i can check…
16:30 jimallman i assume you mean devapi?
16:30 josephwb i'd like to tar up the older db to grab a copy of it
16:30 josephwb yes ot10
16:31 josephwb i can scp if space is a problem [will just take a while]
16:31 jimallman see df -h output at https://gist.github.com/jimallman/4a6ce4f5ed3f84d57382
16:32 josephwb that looks like enough space
16:32 jimallman yep, root filesystem is almost certainly where you’ll be working. it has 43G available
16:33 josephwb unless a tarred version exists somewhere?
16:34 josephwb should be tarred; it is huge
16:36 jimallman see /home/opentree/downloads, a few .tgz files there
16:36 josephwb seems random what is there
16:37 josephwb anyway, doing the tar sftp delete
16:38 jimallman josephwb: yes, feel free to clobber stuff to make room here
16:41 josephwb didn't know about "df -h". thanks.
17:13 josephwb jimallman it says it will an hour to grab that tarred db!
17:14 jimallman yeah, they’re bigguns
17:14 josephwb i don't think ./push.sh took an hour
17:15 josephwb is there a fatsre tool than sftp?
17:15 jimallman it would be interesting to see how the servers handle a surge in download traffic, though (like when a new taxonomy version is released)
17:16 jimallman i’d start with scp, personally. unless it’s a stable data set, in which case rsync.
17:17 josephwb ok, will try that
17:19 jimallman opinions differ on sftp vs. scp performance, but most agree that scp is usually faster
17:19 jimallman and i’m not seeing any other candidates mentioned
17:20 josephwb scp says 2.5 hours!
17:22 josephwb jimallman is the arguson everything you want it to be?
17:22 jimallman so far, so good!
17:22 josephwb i mean, can i close my treemachine issue? or is there something else to do?
17:22 jimallman oh, lemme see
17:23 josephwb i can add you to the issue
17:23 josephwb and then you can close it when you are happy
17:23 josephwb oh, you are on it
17:23 josephwb no rush; just curious
17:24 josephwb thinking of moving jade over to OpenTree. we are the only ones using it
17:24 jimallman yes, i think we’ve absorbed a few small projects already
17:25 josephwb i don't know if i have the permissions
17:25 josephwb oh, i guess i do
17:25 jimallman surely you’d need to be an admin to *move* a repo. but forking is easy!
17:26 josephwb right
17:26 josephwb just forked it
17:26 josephwb but i can delete it if people do not want it
17:29 jimallman i see that the repo you forked (jar398/jade) is itself a fork. but not apparently a proper git fork, since there’s no link to the upstream repo.
17:29 josephwb i accidentally dleted that. fixing it now
17:29 jar286_ joined #opentreeoflife
17:29 josephwb [meant to delete the OT fork]
17:31 josephwb i meant to delete the fork, but it deleted the original?
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19:18 mtholder jimallman, kcranston: I mentioned this a while back, but now I have an example...
19:18 mtholder look at https://github.com/orgs/OpenTreeOfLife/dashboard
19:18 mtholder it looks like I"ve edited phylesystem-1
19:19 mtholder but if you click on the commits, you see they are correctly ascribed to a curator (not me)
19:19 mtholder https://github.com/OpenTreeOfLife/phylesystem-1/commits/master
19:19 jimallman odd.
19:20 mtholder yeah.
19:20 jimallman any chance you’re sharing a personal GitHub key with devtree?
19:20 mtholder that is from tree.opentre...
19:20 mtholder but... I don't think so...
19:20 jimallman mm, gotcha
19:20 kcranstn weird
19:21 mtholder On the dashboard it says that I "pushed"
19:21 mtholder not merged or committed.
19:21 jimallman there are definitely some wrinkles in how actions can be attributed on GitHub, saw a doc on it recently.
19:21 jimallman right, nor authored
19:21 kcranstn but why Mark?
19:21 mtholder I may have created the key that we use
19:22 mtholder (for the push)
19:23 jimallman a cron job? if it’s the usual deferred push, it has been a per-repo deployment key (see server-config for details)
19:24 jimallman i do not know the origins of that key, but on my machine it’s ~/.ssh/opentree/phylesystem-1.pem
19:25 jimallman starts “MII…”, ends “i0n”
19:26 mtholder yeah that is what it is called on my machine too
19:27 jimallman ah yes, attribution is also based on an associated email (presumably yours)
19:27 jimallman checking git config on ot20 (api.opentreeoflife.org) now…
19:28 jimallman hm, default git config on ot20 is correctly assigned to the OpenTree API user (api@opentreeoflife.org)
19:29 mtholder josephwb, is treemachine run through gcmdr now?
19:31 jimallman … as is the git config in ~/repo/phylesystem-1_par/phylesystem-1
19:31 jimallman and its mirror repo. hmmm.
19:32 jimallman maybe mtholder’s email is in the public key corresponding to  phylesystem-1.pem..?
19:33 mtholder that would make some sense. probably not worth spending too much time on (given that the authorship of the commits seems fine).
19:33 mtholder it makes me look busy, at least.
19:33 josephwb mtholder no
19:33 josephwb gcmdr has not been updated
19:34 kcranstn can you make an issue for that, mtholder? it would be good to figure that out sometime down the road
19:34 mtholder thanks I'm trying to figure out tloaded
19:34 mtholder is in synth.
19:35 jimallman mtholder: possibly caused by unit tests? i think your credentials might be used in some of these.
19:35 mtholder it determines the USING_TAXONOMY bool
19:36 mtholder perhaps, jimallman. But I was trying to be careful not to do anything like that...
19:37 jimallman understandable. i added some write operations (to a test repo) in the unit tests for collections, and i’ve been meaning to ask if there’s a sensible way to handle these.
19:38 mtholder I have peyotl tests that need me to have write permissions to a repo - but I only run those tests locally.
19:38 mtholder and then there are the ws-tests in phylesystem-api.
19:39 mtholder but that should be the normal configuration for deployment to dev...
19:41 mtholder josephwb, what args do you pass to treemachine's loadtrees command?
19:42 josephwb just a sec
19:43 josephwb newfile test.db T subset
19:44 josephwb newfile = newick file
19:46 mtholder thanks.
19:48 josephwb want the bash script i use ti run things?
19:49 mtholder that would be great.
19:49 josephwb sent. let me know is something is not clear
21:48 jimallman josephwb: after chasing down a few wild bugs, the AJAX-loaded supporting information is working now on devtree.
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22:40 josephwb jimallman sweet
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