Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-27

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All times shown according to UTC.

Time Nick Message
11:43 towodo joined #opentreeoflife
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13:47 josephwb joined #opentreeoflife
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20:24 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
20:25 towodo extracting taxomachine database for oti’s use…
20:31 towodo starting oti re-indexing …
20:34 kcranstn joined #opentreeoflife
20:34 kcranstn how long does oti indexing take?
21:27 jimallman joined #opentreeoflife
21:28 jimallman towodo: i’m around (just doing paperwork) if you want to talk or collaborate..
21:29 towodo thanks. oti indexing finished after 36 minutes. (a while ago) on to next step.
21:30 towodo ot18-status passed
21:30 towodo …
21:30 towodo I’m going to forge ahead
21:31 towodo installing new front end software
21:32 towodo Cannot find GITHUB_CLIENT_SECRET file /Users/jar/.ssh/opentree/curation-GITHUB_CLIENT_SECRET-tree.opentreeoflife.org
21:32 towodo need to copy that from ot15 I guess
21:33 towodo no. benign
21:33 jimallman Bos tree is ot14
21:33 towodo ot14 I meant - but we’re already talking about ot14.
21:33 towodo so np
21:34 jimallman oh yeah
21:34 towodo so, new system is in place other than ot18 -> api switcheroo.
21:34 towodo home page ok
21:34 jimallman i see your (earlier) point about this scenario, this should only bark if there’s no such file in the *destination* directory
21:34 jimallman SECRET, i mean
21:36 towodo http://tree.opentreeoflife.org/curator/study/view/pg_2052   is hanging.
21:36 towodo maybe oti is busy or something… checking…
21:37 jimallman nope, looks like there’s something goofy in the NexSON… OTUS_BY_ID (one of our fast lookups) is undefined
21:37 towodo oh. i’ll try another one
21:38 towodo http://tree.opentreeoflife.org/curator/study/view/pg_1821  also hanging
21:38 jimallman hm, the very same error. the plot thickens.
21:38 jimallman chasing these now…
21:38 towodo I see in oti log: Indexing http://ot18.opentreeoflife.org/phylesystem/v1/../ study pg_1821 from http://ot18.opentreeoflife.org/phylesystem/v1/../default/v1/study/pg_1821.json
21:38 towodo Calling "http://127.0.0.1:7478/db/data/ext/IndexServices/graphdb/indexNexsons" with data="{'urls': ['http://ot18.opentreeoflife.org/phylesystem/v1/../default/v1/study/pg_1821.json']}"
21:38 towodo no error.
21:39 towodo conceivable I messed up client pem or something.  copied from ot15
21:40 towodo I have a complete transcript of what I’ve done so far
21:40 jimallman no, i think this is a JS error in curation code.
21:40 towodo ah
21:40 towodo glad you’re here
21:40 jimallman i seem to be trying to evaluate a client-structure that hasn’t been built yet. weird that it’s just now showing up...
21:41 towodo double checked OPENTREE_BRANCH … seems ok, everything from Cavia
21:43 jimallman OK. this is triggered by some recently added code that tries to resolve sibling-only conflicts (identically-mapped OTUs with no taxon exemplar) in incoming study NexSON.
21:43 towodo scanned install log, looks clean
21:44 jimallman i’ll clean this up and pull the changes to Cavia branch. still odd that i haven’t seen this error before. possibly a race condition…
21:53 jimallman nope, these operations are just plain out of order. now i see that the problem is masked for non-candidate trees, which is probably why i hadn’t tripped over this before.
21:58 kcranstn joined #opentreeoflife
21:59 kcranstn hey folks - I am around, too
21:59 towodo hello KC
22:00 kcranstn how was asheville, jimallman?
22:00 jimallman hi! it was pretty, and nice driving weather.
22:01 jimallman i got to see my brother-in-law’s workplace, he does R&D for police-military training. A laid-back, super-fun skunkworks in the middle of farmland.
22:01 kcranstn um… that sounds… interesting
22:03 jimallman more fun than you’d think. remotely triggered smoke and fire effects! portable video networks! dummies with impact sensors! fake bombs for bomb-squad training! lots of on-site 3D fabrication of prototype gadgets.
22:04 jimallman ok, for 8th-grade boy values of fun.
22:05 kcranstn all in the name of military-industrial-complex ;)
22:05 jimallman (yes, our tax dollars at play)
22:05 jimallman and we went to a wholesame gem and metals show. very neat stuff, though we saw some … troubling fossils and turtle shells.
22:09 kcranstn I hauled my horse trailer with my (new to me) Big Ass Truck for the first time
22:12 jimallman ah, the Big Ass Truck! we discussed this.
22:12 jimallman congrats
22:16 kcranstn so, what’s the status of the upgrade?
22:16 jimallman i’m just pushing up a minor JS fix that blocks loading of some studies..
22:17 jimallman otherwise it sounds like we’re ready to switch domain names and do some final testing
22:17 kcranstn excellent
22:18 kcranstn josephwb was asking whether the new MRCA test would be in this deployment
22:20 jimallman yes, the curation app is closely tracking the master branch (all features on devtree)
22:20 jimallman towodo: i have the JS fix in place. do you want to push a fresh opentree, or should i?
22:20 towodo I will
22:20 towodo sorry I was doing something else
22:21 towodo ready now?
22:21 towodo ./push.sh -c ../../deployed-systems/Cavia/tree.config opentree
22:21 jimallman yes, it’s all ready
22:21 towodo ok here goes
22:22 towodo done. testing…
22:23 towodo let’s see… how do I clear the damn firefox cache…
22:25 towodo this works: http://tree.opentreeoflife.org/curator/study/view/pg_41
22:26 towodo jimallman, this hangs: http://tree.opentreeoflife.org/curator/study/view/pg_2052
22:36 kcranstn I am going to step away for a bit
22:41 towodo jimallman, I’m stepping away for a bit too - getting dinner.
22:42 jimallman ok, yes a few distractions here too. i’ll chase down this bug and report soon.
22:43 jimallman re: clearing cache in FF… History menu > Clear Recent History… select Cache, then click Clear Now.
22:44 jimallman alternately, File  > Preferences > Advanced > Network > Cached Web Content, click Clear Now
22:55 kcranstn joined #opentreeoflife
23:16 jimallman fyi - bug fixed and code merged to Cavia. ready for another try…
23:20 towodo ok, updated. tryng again…
23:23 towodo jimallman, looks good to me although I haven’t tried an update
23:25 towodo worked! on to next steps unless you have testing to do.
23:26 towodo *** DNS updated ***
23:26 towodo going to eat now
23:40 jimallman same here, cooking dinnner… i’ll try some light testing in the meantime
23:48 towodo changing ot18 -> api in tree.config
23:51 towodo done… now looking at same change in api.config …
23:54 towodo ‘deploy api’

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