Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-10

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All times shown according to UTC.

Time Nick Message
00:23 towodo_ joined #opentreeoflife
11:36 towodo joined #opentreeoflife
15:23 towodo joined #opentreeoflife
16:39 jimallman towodo: fyi, i’ve updated Bos to use the latest taxomachine data from ot10, installing and re-indexing oti now…
17:36 towodo jimallman, i will send a message warning people that the system will be offline between 5 and 6.
17:37 jimallman sounds good! i’m working on something more elegant/courteous, but it might not be tested by end of day today (i have a conference call at 2pm, and another minor bug to fix with the NexSON-download features)
17:38 towodo what to you mean something more elegant/courteous?
17:38 towodo s/to/do/
17:39 jimallman new settings in the curator’s config that would notify curators (anyone logging in or editing) of a scheduled outage, then would start blocking edits at the scheduled time
17:39 towodo ah.
17:40 jimallman this would avoid ugly surprises for someone who starts editing before the blackout, then gets stuck with a bunch of work they can’t save.
17:40 jimallman for now, email to a small/known population of testers seems pretty safe.
20:37 jimallman towodo: i’m getting down to the wire with my gentle blocking of study creation and editing. were you thinking we’d just pull the plug on the existing curation tool from 5-6? or should i keep working on this?
20:37 towodo pull the plug.
20:38 towodo you have 22 minutes
20:38 jimallman sounds good. i’ll focus on the final punchlist then.
20:38 towodo ok
20:38 jimallman all tests are passing, so i’m doing the final substitutions in Bos config files.
20:43 jimallman (at this point, the only final change was to move the API server name from ot15.opentreeoflife.org to api.opentreeoflife.org)
20:44 towodo we have to switch both ‘tree’ and ‘api’ to point to the new machines
20:44 towodo I don’t think the order matters
20:45 jimallman right. i’d start with api, just because it’s the most like callee (vs caller)
20:45 towodo first step as i said will be to disable curation on devtree
20:46 jimallman can we just shut down web2py on ot11? ugly, but effective (sorry i didn’t get the nicer block in place)
20:47 jimallman s/can we/shall i
20:47 towodo sure, we can just do apache2ctl stop
20:48 jimallman ok, i’ll wait til 5pm in case someone’s playing chicken..
20:48 towodo yep
20:48 jimallman meanwhile, lemme see if i can remove that redirect on the tree.opentreeoflife.org curator…
20:49 jimallman dev., i mean
20:49 towodo don’t worry about it, it’s in dns
20:49 towodo i mean it’s at namecheap
20:49 towodo i’ll do it
20:52 towodo jimallman, i invited you to a google doc
20:54 jimallman towodo: this is what i was concerned about, but it’ll be clobbered by the next push (rewrites sites-available/opentree):
20:54 jimallman # Bounce to development server via a simple information page
20:54 jimallman RedirectMatch temp ^/curator /opentree/static/bounce-to-devtree-curator.html
20:54 jimallman just temp stuff on ot3
20:55 towodo oh right. let’s figure out where it goes in the google doc
20:58 towodo will we need to refresh the phylesystem-1 local copy from github ?
20:58 jimallman hm, do we expect traffic on dev.opentreeoflife.org ? i’m inclined to shut down this whole domain, or just set apache to redirect all traffic (permanent redirect) to tree.opentreeoflife.org..
20:59 towodo could be traffic in the next 2 minutes.
20:59 jimallman re: refreshing phylesystem.. i’ll bet you’re right about that. just git pull, right?
20:59 towodo let’s keep dev. for now just in case
21:00 jimallman i was wondering about the .tgz database files, actually. aren’t these possibly out of date? or do we update them whenever treemachine and taxomachine are updated?
21:00 jimallman agreed on dev.
21:00 towodo whose .tgz files?
21:00 towodo they are updated manually. not sure of the question
21:00 jimallman the ones we used to install-db for t***machine and oti
21:01 towodo but they’re already installed, right?
21:01 jimallman any chance these are already stale?
21:01 towodo i weent over that in irc earlier in the week i think
21:01 jimallman yes, i was concnerned that there might have been more recent changes in neo4j since these versions of .tgz
21:01 towodo oh, the databases don’t change.
21:02 jimallman ok, just wanted to be sure.
21:02 towodo i see now.
21:02 towodo wanna do the honors of stopping apache or should i?
21:02 jimallman go for it.
21:02 towodo i think i’ll stop both (14 and 15) just for good measure
21:03 jimallman why? nobody should be calling them.
21:03 jimallman just to avoid possible trouble when the DNS changes over?
21:05 towodo ssh -i ~/.ssh/opentree/opentree.pem admin@ot14.opentreeoflife.org "sudo apache2ctl stop"
21:05 towodo thats not what i meant
21:05 towodo i need to stop … lemme see…
21:05 jimallman ot3? ot11?
21:05 towodo dev.
21:06 towodo and devapi.
21:06 jimallman devtree, you mean?
21:06 jimallman (can’t wait to get rid of the confusing dev.)
21:06 towodo no, devapi, where the curator is running now
21:06 jimallman that’s devtree.
21:06 towodo no i mean the back end
21:06 towodo doing this: ssh -i ~/.ssh/opentree/opentree.pem admin@dev.opentreeoflife.org “sudo apache2ctl stop”
21:07 towodo tree. -> dev. = ot3 , right?
21:07 * jimallman nods re: back end
21:07 towodo so it’s stopped enough for me.
21:08 towodo could stop ot11 as well i suppose. but it won’t get very far if anyone tries curator there
21:09 towodo not quite.  need to turn off curation on devapi.
21:09 jimallman and yet i’m still getting responses from devapi.  http://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree
21:09 jimallman sorry, i jumped ahead
21:09 towodo try now.  ssh -i ~/.ssh/opentree/opentree.pem admin@devapi.opentreeoflife.org "sudo apache2ctl stop"
21:10 jimallman dead dead dead. hooray!
21:10 towodo ok what next.  a git pull ?
21:10 towodo should be a no-op
21:11 towodo of phylesystem-1 I think
21:11 towodo what is _par ?
21:12 towodo ‘not a git repository’
21:12 jimallman i think so, i’m looking ot15:~/repo/phylesystem-1_par/mirror
21:13 jimallman and ~/repo/phylesystem-1_par/phylesystem-1
21:13 jimallman seems like we should pull from both…
21:13 towodo this violates my idea of how repo/ works… but there must be a reason
21:13 jimallman yeah, it’s a bit weird. the “local” git repo has a local mirror, it’s about managing traffic with GitHub
21:13 towodo and why is there a phylesystem-0_par ?
21:14 jimallman that’s probably a leftover from when i originally set ot15 up with phylesystem-0
21:14 towodo ok
21:14 jimallman i should probably clobber that.
21:14 towodo yes i think so.
21:14 * jimallman is clobbering…
21:16 towodo looking at install-api.sh
21:16 towodo just wanna redo install-api.sh maybe ?
21:16 jimallman trying to remember if it starts fresh… sounds right…
21:17 towodo no, it does git_refresh, which is the right thing.
21:17 jimallman ah, sounds good
21:17 towodo so I would do push.sh … install-api at this point
21:17 towodo assuming that’s tested….
21:17 towodo which i believe it is (you just used it to set up ot15)
21:17 jimallman yes, but please ‘git pull’ on your deployed-systems…
21:17 towodo ok
21:18 jimallman lest we revert domain names from api. to ot15.
21:19 towodo I wasn’t going to use the deployment system for ot13…
21:19 towodo it’s under someone else’s control
21:19 towodo no matter
21:22 towodo i wasn’t going to be doing any deployment commands, to avoid conflicts like you say
21:22 jimallman gotcha.
21:22 jimallman i was trying to figure out who builds and maintains the “mirror” repos, and it looks like peyotl is responsible for all of that.
21:23 towodo what’s next? are you waiting for me?
21:23 towodo yes.
21:23 jimallman for some reason, i was thinking install-db would take longer. checking the list now…
21:23 jimallman i think we’re ready for DNS changes
21:24 towodo every ‘install-api’ should do a git pull on the master and the mirror, i think.  need to work this out
21:24 towodo it’s git, always fast
21:24 towodo ok, i will do the dns thing
21:26 towodo api currently points to ot12..  changeing now to ot15
21:26 towodo done. TTL is 5 minutes
21:27 jimallman OK, shall i restart apache on ot14 and ot15?
21:27 towodo tree is currently a URL redirect to dev.  changing now to ot14 - blam.
21:28 jimallman ah, good
21:28 towodo it was my mistake to stop them at all.  sure, you can use commands like I put in irc above
21:29 jimallman ssh -i ~/.ssh/opentree/opentree.pem admin@ot14.opentreeoflife.org "sudo apache2ctl graceful"
21:29 jimallman etc
21:30 towodo is github configured properly? i guess you did that already?
21:30 towodo we’ll find out soon enough
21:30 jimallman yes, apps are registered to the tree. domain and we’re using those values in Bos config
21:30 towodo 2 minutes to be sure all old dns entries are gone
21:31 towodo what about api. ?
21:31 jimallman it’s running (ot15) now…
21:31 jimallman i’m still getting old IPs from ping
21:31 jimallman did you set the short TTL earlier? or just now?
21:31 towodo there could be a delay on the namecheap side
21:32 towodo the TTL *was* 300 (= 5 minutes)
21:32 jimallman sweet
21:34 towodo oops!
21:34 towodo i had set tree to point to ot15.
21:34 towodo fixed.
21:34 towodo another 5 minutes
21:34 towodo maybe i should set that smaller
21:35 towodo wish i could paste images into irc
21:36 towodo ok.  maybe you are right that dev. should be redirected somewhere.
21:36 towodo there may be urls wandering about.
21:36 jimallman i think it makes sense to redirect (permanently) to tree.
21:37 towodo yes. for now i will use namecheap to do that.
21:38 jimallman OK. i assume that means i’m looking at ot14, but my browser still says dev.opentreeoflife.org
21:38 towodo need another minute or two
21:38 jimallman i’ll work on an apache rewrite to bump them from dev. to tree. properly (on the same machine)
21:38 towodo just changed dev. to be url redirect to tree.
21:38 jimallman ah, ok
21:39 towodo i’m getting the correct ping from tree. now
21:39 towodo and from api.
21:39 jimallman same here!
21:39 towodo ok, what now?
21:39 jimallman time for some testing, i think
21:39 towodo ‘test curation’
21:40 towodo cool! it works
21:40 * jimallman is clearing my cache aggressively, to knock out my weird test environment...
21:41 jimallman yes, tree viewer and login (for comments) looking good
21:42 towodo ‘Authorize application
21:42 towodo Open Tree of Life - curation tool (tree.opentreeoflife.org) by @jimallman would like permission to access your account ‘
21:42 jimallman taxon search works… footer values look good
21:42 jimallman yes, that’s the initial login for any GH registered app
21:42 jimallman (good reason to change ownership)
21:42 towodo logged in!
21:43 towodo should we go through the tests in an orderly way? is that what you’re doing?
21:43 towodo i’m being random
21:43 jimallman Bibliographic References page is working (that uses a few services, so that’s good) and NexSON download is good
21:43 jimallman semi-random, it won’t take long either way
21:44 jimallman hey, there’s our alphabetic sort in Bib References! did you notice i got the right-click working in the tree viewer, too?
21:44 towodo “Firefox prevented this site from opening a pop-up window.”
21:45 towodo cool.
21:45 jimallman right, no way around that. gotta relax your popup blocker to use it.
21:45 towodo yep
21:45 jimallman subtree (Newick) download works, so it’s on to curation tests
21:45 towodo I’m confident the whole darn thing works.
21:47 jimallman yeah, it’s looking good
21:49 jimallman OTU mapping checks out.. i’m looking for a test study so I can test a trivial change (adding a tag)...
21:49 jimallman here’s one: http://tree.opentreeoflife.org/curator/study/view/pg_2823
21:51 jimallman OK, my change was saved successfully. now just waiting for oti to update (tests GitHub webhook)...
21:52 jimallman hm, and that might take awhile if we’re not pushing back to GitHub right away
21:52 towodo ha
21:53 jimallman otherwise, i’m done with the checklist. i think we’re good on tree. and api.
21:53 towodo I’m sending email to ot-software re current status.
21:53 towodo with pointer to the google doc, the integration tests page, and the irc log
21:53 towodo ok?
21:54 jimallman sounds great!
21:55 jimallman i can get started on devapi (“rebuild devapi oti index”).. so that needs the latest .tgz from ot10, yes?
21:55 jimallman do we need to update taxomachine there, too?
21:55 towodo i don’t think anything has changed, but worth a check
21:56 jimallman waitaminute… devapi *is* ot10, isn’t it?
21:56 towodo yes
21:56 towodo i think so
21:56 jimallman confirmed
21:56 towodo we should now have development = {tree: ot11, api: ot10=ashby}
21:57 jimallman ah, but now devtree should use phylesystem-0, since it’s no longer the real thing… right?
21:57 towodo right.
21:57 towodo so only the four active machines (5 if we include ot13 / splashpage)
21:57 jimallman and we’re going to have to wean our curators away from devtree, when they’re already used to ignoring the DEVELOPMENT banner in the corner. d’oh!
21:57 towodo right.  maybe tweak the banner to say ‘go away’
21:57 jimallman :D
21:57 jimallman this is a job for the <BLINK> tag
22:01 towodo email sent
22:01 towodo I need to go eat. I’m ok with leaving the rest up to you :)
22:01 jimallman You might want to mention the DEVELOPMENT banner in a follow-up message. Remind people that now We Really Mean It, and they shouldn’t work there.
22:01 jimallman OK, bon appetit!
22:01 towodo yes
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23:29 towodo joined #opentreeoflife

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