Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-02-20

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All times shown according to UTC.

Time Nick Message
03:11 mtholder joined #opentreeoflife
03:12 towodo joined #opentreeoflife
04:06 mtholder hi jimallman. I was about to send you an email, but (in what is probably a gross violation of irc norms), I'll just slam text at you through irc:
04:06 mtholder Those type-coercion bugs that I mentioned in email have been fixed, and deployed. See
04:06 mtholder http://ec2-54-203-212-107.us-west-2.compute.amazonaws.com/api/v1/study/10?output_nexml2json=1.0.0
04:06 mtholder http://ec2-54-203-212-107.us-west-2.compute.amazonaws.com/api/v1/study/10?output_nexml2json=0.0.0
04:06 mtholder http://ec2-54-203-212-107.us-west-2.compute.amazonaws.com/api/v1/study/10?output_nexml2json=1.2.0
04:06 jimallman no problem here
04:06 mtholder Writing in syntactic variants other than 0.0.0 will probably fail, which I'm sure makes it hard for you to test.
04:06 mtholder 438 does load in 1.2.0 (after a while).
04:06 mtholder i should have some time work on it tomorrow. Let me know if you'd prefer me to work on: (1) porting the nexson validation to the new syntax, or (2) the otus-merging/trees-merging tool to help with import from external formats.
04:08 jimallman i suppose (2) would be more immediately useful, but i have other things I'm working on too.. so feel free to work in whatever order is easiest.
04:09 mtholder OK. I think they are both about the same in terms of ease.
04:09 jimallman do i understand correctly that (1) would allow writing / saving in the newer syntax? that would be somewhat reassuring, since i'm making lots of client-side edits that haven't been subjected to scrutiny by other tools.
04:09 mtholder yup.
04:09 jimallman but yeah, (2) would fit my current "hot list" a little better.
04:10 mtholder Should i move the import-a-tree-from-external-format controller to the api repo?
04:10 jimallman woah, i didn't realize I can GET stuff in 1.2.0.. that also gives me something to work on (digesting that format and using it throughout)
04:10 mtholder that is new.
04:11 mtholder and not very tested.
04:11 jimallman sweet!
04:11 jimallman regarding the proper place for to_nexml (or equivalent), let's hold off on that for now. it probably "belongs" more to the API than the web apps, but i'd like to wait til we have a better understanding of the file-storage side of tree import..
04:12 mtholder OK.
04:13 mtholder I'll probably move to using peyotl as a dependency for that controller (that will unify my nexml to nexson code and help me deal with the lots-o-whitespace in "$" bug).
04:14 mtholder but there is a deploy function for pulling and installing peyotl on deployment.
04:14 mtholder so it should not be too much of a headache.
04:28 jimallman yes, if it's in the common functions.sh then we can call it for either component
04:29 jimallman once we figure out the all-singing, all-dancing static file storage solution, it can probably be made visible to both opentree and api components. at that point the to_nexml method can go wherever it logically belongs.
04:32 mtholder sounds good.
04:34 mtholder i just did some benchmarking with my old (and hideous through-nexml conversion) translating 438 from v0.0 to v1.0 took 2m30sec. now it is 12.6 seconds, and v1.2 to 1.0 takes 9 seconds.
04:35 mtholder file size is 44M for v0.0 and 23M for v1.0 and down to 21M for v1.2.
05:07 jimallman mtholder: nice! even the conversion time is not out of bounds IMO, given the size of the study.
05:08 mtholder yeah. it won't be a fun experience, but that tree is so big it is questionable whether anyone would try to edit it manually.
14:40 ilbot3 joined #opentreeoflife
14:40 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
14:44 towodo joined #opentreeoflife
15:17 kcranstn joined #opentreeoflife
15:17 kcranstn mornin!
15:29 jimallman howdy
15:43 kcranstn joined #opentreeoflife
16:03 jimallman kcranstn: are we having our 11am call today?
16:03 blackrim joined #opentreeoflife
16:10 kcranstn 11 am?
16:11 jimallman hm, maybe my calendar reminder is wrong..
16:11 jimallman (i have a weekly tickler for Fri 11am-noon)
16:12 jimallman sorry for needless panic
16:20 * jimallman has realized the true extent of his confusion (Happy Thursday!)
16:24 kcranstn :)
16:31 jimallman kcranstn: is there an opentree branch with new help/sidebar text? or should i start one?
16:31 jimallman i thought we might volley this branch back and forth, or we could meet at NESCent and work on it together.
16:32 kcranstn I have a local branch called curator_documentation that I haven't pushed yet
16:32 kcranstn and meeting at NESCent sounds fun
16:32 kcranstn tomorrow?
16:36 jimallman sure! after lunch (2pm+) would be best for me.
16:36 kcranstn works for me
16:37 jimallman great, let's do it.
16:52 kcranstn I can't load dev.opentreeoflife.org
17:07 * jimallman is checking this out...
17:08 jimallman curl: (6) Could not resolve host: dev.opentreeoflife.org
17:08 jimallman (DNS outage? expired domain name? not sure yet)
17:12 jimallman whois looks good (opentreeoflife.org is reserved until March 2014), but ping and dig both report "unknown host". perhaps the AWS instance has gone down?
17:14 jimallman scratch that, i'm getting no response from any of the opentreeoflife.org subdomains (dev, www, files, ...)
17:16 jimallman kcranstn: i'm not sure what's going wrong yet, but for now you can use dev.opentreeoflife.org by its AWS hostname: http://ec2-54-202-237-199.us-west-2.compute.amazonaws.com/opentree/
17:17 jimallman or, for the curation tool, http://ec2-54-202-237-199.us-west-2.compute.amazonaws.com/curator
17:23 kcranstn nothing looks strange at namecheap - .com and .org were set to expire mid-march (I just renewed them)
17:28 jimallman i'm getting a SERVFAIL error from DNS lookups (dig)... looking for possible causes now...
17:32 jimallman possible causes: misconfiguration of DNS zone file... DNS propagation failure... authoritative name server is down... the latter two should clear up without our intervention
17:33 kcranstn I think the issue is wordpress
17:33 kcranstn ievobio.org is also giving the same response (and also forwards to wordpress)
17:34 jimallman but files.opentreeoflife.org is also down...
17:37 jimallman based on the output from ping and dig, i think ievobio.org is suffering from the same DNS problems:
17:37 jimallman https://gist.github.com/jimallman/5407f78d2a887338d5f0
17:39 jimallman ah, looks like namecheap is under DDoS attack:
17:39 jimallman https://twitter.com/Namecheap
17:40 jimallman https://news.ycombinator.com/item?id=7271834
17:40 kcranstn wow
17:41 jimallman i'm posting a heads-up to the software group... feel free to forward as appropriate
17:42 jimallman i suppose i'll just add general opentree group as CC
17:42 kcranstn sounds good
17:46 kcranstn it's back
17:48 blackrim joined #opentreeoflife
17:48 blackrim left #opentreeoflife
17:49 kcranstn well, at least that motivated me to renew the domains ;)
17:50 jimallman hm, still out for me... i suppose any fixes will take time to propagate.
17:50 jimallman www, files, dev. none are responding here
18:05 mtholder joined #opentreeoflife
18:33 jimallman i'm looking into FreeDNS (highly recommended) as a possible secondary DNS provider for *.opentreeoflife.org domains: http://freedns.afraid.org/
19:09 towodo joined #opentreeoflife
19:46 kcranstn joined #opentreeoflife
19:56 jimallman joined #opentreeoflife
20:32 kcranstn joined #opentreeoflife
21:05 mtholder joined #opentreeoflife
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22:40 jimallman joined #opentreeoflife
22:54 kcranstn joined #opentreeoflife
22:58 jimallman kcranstn: apologies, Namecheap is restoring service but our domains are still down for some of us. If you like, we can move to their alternate DNS "v1" servers and have everything back up in a few minutes:
22:58 jimallman http://t.co/J4mMgRHQjS
23:00 kcranstn sure, I can do that
23:03 kcranstn "record type ns not supported" with v1 (which we are using in order to have the wordpress-hosted blog have a custom url)

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